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lib/spack/docs/basic_usage.rst
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@ -114,13 +114,13 @@ that the packages is installed:
$ spack install mpileaks $ spack install mpileaks
==> Installing mpileaks ==> Installing mpileaks
==> mpich is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4. ==> mpich is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4.
==> callpath is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318. ==> callpath is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318.
==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da. ==> adept-utils is already installed in /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da.
==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz ==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
######################################################################## 100.0% ######################################################################## 100.0%
==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23/mpileaks-1.0.tar.gz
==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23. ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23.
==> No patches needed for mpileaks. ==> No patches needed for mpileaks.
==> Building mpileaks. ==> Building mpileaks.
@ -128,7 +128,7 @@ that the packages is installed:
==> Successfully installed mpileaks. ==> Successfully installed mpileaks.
Fetch: 2.16s. Build: 9.82s. Total: 11.98s. Fetch: 2.16s. Build: 9.82s. Total: 11.98s.
[+] /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpileaks@1.0-59f6ad23 [+] /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpileaks@1.0-59f6ad23
The last line, with the ``[+]``, indicates where the package is The last line, with the ``[+]``, indicates where the package is
installed. installed.
@ -230,7 +230,7 @@ Running ``spack find`` with no arguments lists installed packages:
$ spack find $ spack find
==> 74 installed packages. ==> 74 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
ImageMagick@6.8.9-10 libdwarf@20130729 py-dateutil@2.4.0 ImageMagick@6.8.9-10 libdwarf@20130729 py-dateutil@2.4.0
adept-utils@1.0 libdwarf@20130729 py-ipython@2.3.1 adept-utils@1.0 libdwarf@20130729 py-ipython@2.3.1
atk@2.14.0 libelf@0.8.12 py-matplotlib@1.4.2 atk@2.14.0 libelf@0.8.12 py-matplotlib@1.4.2
@ -256,7 +256,7 @@ Running ``spack find`` with no arguments lists installed packages:
lcms@2.6 pixman@0.32.6 xz@5.2.0 lcms@2.6 pixman@0.32.6 xz@5.2.0
libdrm@2.4.33 py-dateutil@2.4.0 zlib@1.2.8 libdrm@2.4.33 py-dateutil@2.4.0 zlib@1.2.8
-- chaos_5_x86_64_ib / gcc@4.9.2 -------------------------------- -- linux-debian7-x86_64 / gcc@4.9.2 --------------------------------
libelf@0.8.10 mpich@3.0.4 libelf@0.8.10 mpich@3.0.4
Packages are divided into groups according to their architecture and Packages are divided into groups according to their architecture and
@ -279,7 +279,7 @@ in more detail using ``spack find -d``, and by asking only to show
$ spack find --deps libdwarf $ spack find --deps libdwarf
==> 2 installed packages. ==> 2 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962 libdwarf@20130729-d9b90962
^libelf@0.8.12 ^libelf@0.8.12
libdwarf@20130729-b52fac98 libdwarf@20130729-b52fac98
@ -295,7 +295,7 @@ want to know whether two packages' dependencies differ, you can use
$ spack find -l libdwarf $ spack find -l libdwarf
==> 2 installed packages. ==> 2 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962 libdwarf@20130729-b52fac98 libdwarf@20130729-d9b90962 libdwarf@20130729-b52fac98
Now the ``libwarf`` installs have hashes after their names. These are Now the ``libwarf`` installs have hashes after their names. These are
@ -309,14 +309,14 @@ use ``spack find -p``:
$ spack find -p $ spack find -p
==> 74 installed packages. ==> 74 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
adept-utils@1.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da adept-utils@1.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da
atk@2.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/atk@2.14.0-3d09ac09 atk@2.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/atk@2.14.0-3d09ac09
boost@1.55.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/boost@1.55.0 boost@1.55.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/boost@1.55.0
bzip2@1.0.6 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/bzip2@1.0.6 bzip2@1.0.6 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/bzip2@1.0.6
cairo@1.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/cairo@1.14.0-fcc2ab44 cairo@1.14.0 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/cairo@1.14.0-fcc2ab44
callpath@1.0.2 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318 callpath@1.0.2 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318
... ...
And, finally, you can restrict your search to a particular package And, finally, you can restrict your search to a particular package
@ -325,10 +325,10 @@ by supplying its name:
.. code-block:: sh .. code-block:: sh
$ spack find -p libelf $ spack find -p libelf
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libelf@0.8.11 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11 libelf@0.8.11 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.11
libelf@0.8.12 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12 libelf@0.8.12 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.12
libelf@0.8.13 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13 libelf@0.8.13 /home/gamblin2/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.13
``spack find`` actually does a lot more than this. You can use ``spack find`` actually does a lot more than this. You can use
*specs* to query for specific configurations and builds of each *specs* to query for specific configurations and builds of each
@ -338,7 +338,7 @@ package. If you want to find only libelf versions greater than version
.. code-block:: sh .. code-block:: sh
$ spack find libelf@0.8.12: $ spack find libelf@0.8.12:
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libelf@0.8.12 libelf@0.8.13 libelf@0.8.12 libelf@0.8.13
Finding just the versions of libdwarf built with a particular version Finding just the versions of libdwarf built with a particular version
@ -348,7 +348,7 @@ of libelf would look like this:
$ spack find -l libdwarf ^libelf@0.8.12 $ spack find -l libdwarf ^libelf@0.8.12
==> 1 installed packages. ==> 1 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962 libdwarf@20130729-d9b90962
We can also search for packages that have a certain attribute. For example, We can also search for packages that have a certain attribute. For example,
@ -359,6 +359,7 @@ will find every installed package with a 'debug' compile-time option enabled.
The full spec syntax is discussed in detail in :ref:`sec-specs`. The full spec syntax is discussed in detail in :ref:`sec-specs`.
.. _compiler-config:
Compiler configuration Compiler configuration
----------------------------------- -----------------------------------
@ -445,7 +446,7 @@ If you want to see specifics on a particular compiler, you can run
fc = /usr/local/bin/ifort-15.0.090 fc = /usr/local/bin/ifort-15.0.090
This shows which C, C++, and Fortran compilers were detected by Spack. This shows which C, C++, and Fortran compilers were detected by Spack.
Notice also that we didn't have to be too specific about the Notice also that we didn\'t have to be too specific about the
version. We just said ``intel@15``, and information about the only version. We just said ``intel@15``, and information about the only
matching Intel compiler was displayed. matching Intel compiler was displayed.
@ -460,19 +461,17 @@ editing your ``~/.spack/compilers.yaml`` file. You can do this by running
Each compiler configuration in the file looks like this:: Each compiler configuration in the file looks like this::
... ...
chaos_5_x86_64_ib: compilers:
... - compiler:
intel@15.0.0: modules = []
operating_system: OS
paths:
cc: /usr/local/bin/icc-15.0.024-beta cc: /usr/local/bin/icc-15.0.024-beta
cxx: /usr/local/bin/icpc-15.0.024-beta cxx: /usr/local/bin/icpc-15.0.024-beta
f77: /usr/local/bin/ifort-15.0.024-beta f77: /usr/local/bin/ifort-15.0.024-beta
fc: /usr/local/bin/ifort-15.0.024-beta fc: /usr/local/bin/ifort-15.0.024-beta
...
The chaos_5_x86_64_ib string is an architecture string, and multiple spec: intel@15.0.0:
compilers can be listed underneath an architecture. The architecture
string may be replaced with the string 'all' to signify compilers that
work on all architectures.
For compilers, like ``clang``, that do not support Fortran, put For compilers, like ``clang``, that do not support Fortran, put
``None`` for ``f77`` and ``fc``:: ``None`` for ``f77`` and ``fc``::
@ -488,10 +487,11 @@ list displayed by ``spack compilers``.
You can also add compiler flags to manually configured compilers. The You can also add compiler flags to manually configured compilers. The
valid flags are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, valid flags are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``,
``ldflags``, and ``ldlibs``. For example,:: ``ldflags``, and ``ldlibs``. For example::
... ...
chaos_5_x86_64_ib: compilers:
- compiler:
... ...
intel@15.0.0: intel@15.0.0:
cc: /usr/local/bin/icc-15.0.024-beta cc: /usr/local/bin/icc-15.0.024-beta
@ -518,10 +518,10 @@ Spack, that descriptor is called a *spec*. Spack uses specs to refer
to a particular build configuration (or configurations) of a package. to a particular build configuration (or configurations) of a package.
Specs are more than a package name and a version; you can use them to Specs are more than a package name and a version; you can use them to
specify the compiler, compiler version, architecture, compile options, specify the compiler, compiler version, architecture, compile options,
and dependency options for a build. In this section, we'll go over and dependency options for a build. In this section, we\'ll go over
the full syntax of specs. the full syntax of specs.
Here is an example of a much longer spec than we've seen thus far:: Here is an example of a much longer spec than we\'ve seen thus far::
mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2 mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2
@ -546,8 +546,8 @@ More formally, a spec consists of the following pieces:
boolean variants boolean variants
* ``name=<value>`` Optional compiler flag specifiers. Valid flag names are * ``name=<value>`` Optional compiler flag specifiers. Valid flag names are
``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``. ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
* ``arch=<value>`` Optional architecture specifier (``arch=bgq_os``) * ``target=<value> os=<value>`` Optional architecture specifier
* ``^`` Dependency specs (``^callpath@1.1``) (``target=haswell os=CNL10``) * ``^`` Dependency specs (``^callpath@1.1``)
There are two things to notice here. The first is that specs are There are two things to notice here. The first is that specs are
recursively defined. That is, each dependency after ``^`` is a spec recursively defined. That is, each dependency after ``^`` is a spec
@ -626,7 +626,7 @@ compilers, variants, and architectures just like any other spec.
Specifiers are associated with the nearest package name to their left. Specifiers are associated with the nearest package name to their left.
For example, above, ``@1.1`` and ``%gcc@4.7.2`` associates with the For example, above, ``@1.1`` and ``%gcc@4.7.2`` associates with the
``callpath`` package, while ``@1.2:1.4``, ``%gcc@4.7.5``, ``+debug``, ``callpath`` package, while ``@1.2:1.4``, ``%gcc@4.7.5``, ``+debug``,
``-qt``, and ``arch=bgq_os`` all associate with the ``mpileaks`` package. ``-qt``, and ``target=haswell os=CNL10`` all associate with the ``mpileaks`` package.
In the diagram above, ``mpileaks`` depends on ``mpich`` with an In the diagram above, ``mpileaks`` depends on ``mpich`` with an
unspecified version, but packages can depend on other packages with unspecified version, but packages can depend on other packages with
@ -758,14 +758,18 @@ in gnu autotools. If all flags are set, the order is
Architecture specifiers Architecture specifiers
~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~
.. Note:: The architecture can be specified by using the reserved
words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). You can also
use the triplet form of platform, operating system and processor.
Architecture specifiers are part of specs but are not yet .. code-block:: sh
functional. They will be in Spack version 1.0, due in Q3 2015.
The architecture specifier looks identical to a variant specifier for a spack install libelf arch=cray_xc-CNL10-haswell
non-boolean variant. The architecture can be specified only using the
reserved name ``arch`` (``arch=bgq_os``). Users on non-Cray systems won't have to worry about specifying the architecture.
Spack will autodetect what kind of operating system is on your machine as well
as the processor. For more information on how the architecture can be
used on Cray machines, check here :ref:`spack-cray`
.. _sec-virtual-dependencies: .. _sec-virtual-dependencies:
@ -985,7 +989,7 @@ of installed packages.
$ module avail $ module avail
------- /home/gamblin2/spack/share/spack/modules/chaos_5_x86_64_ib -------- ------- /home/gamblin2/spack/share/spack/modules/linux-debian7-x86_64 --------
adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7 adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7
automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0 automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0
boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5 boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5
@ -1056,7 +1060,7 @@ Spack. For example, this will add the ``mpich`` package built with
$ spack use mpich %gcc@4.4.7 $ spack use mpich %gcc@4.4.7
Prepending: mpich@3.0.4%gcc@4.4.7 (ok) Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
$ which mpicc $ which mpicc
~/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4/bin/mpicc ~/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc
Or, similarly with modules, you could type: Or, similarly with modules, you could type:
@ -1089,8 +1093,8 @@ than one installed package matches it), then Spack will warn you:
$ spack load libelf $ spack load libelf
==> Error: Multiple matches for spec libelf. Choose one: ==> Error: Multiple matches for spec libelf. Choose one:
libelf@0.8.13%gcc@4.4.7 arch=chaos_5_x86_64_ib libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64
libelf@0.8.13%intel@15.0.0 arch=chaos_5_x86_64_ib libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64
You can either type the ``spack load`` command again with a fully You can either type the ``spack load`` command again with a fully
qualified argument, or you can add just enough extra constraints to qualified argument, or you can add just enough extra constraints to
@ -1150,7 +1154,7 @@ Modules may be loaded recursively with the command:
More than one spec may be placed on the command line here. More than one spec may be placed on the command line here.
Module Comamnds for Shell Scripts Module Commands for Shell Scripts
`````````````````````````````````` ``````````````````````````````````
Although Spack is flexbile, the ``module`` command is much faster. Although Spack is flexbile, the ``module`` command is much faster.
@ -1543,7 +1547,7 @@ an *extension*. Suppose you have Python installed like so:
$ spack find python $ spack find python
==> 1 installed packages. ==> 1 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
python@2.7.8 python@2.7.8
.. _spack-extensions: .. _spack-extensions:
@ -1556,7 +1560,7 @@ You can find extensions for your Python installation like this:
.. code-block:: sh .. code-block:: sh
$ spack extensions python $ spack extensions python
==> python@2.7.8%gcc@4.4.7 arch=chaos_5_x86_64_ib-703c7a96 ==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96
==> 36 extensions: ==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six py-basemap py-libxml2 py-pil py-pytz py-six
@ -1568,7 +1572,7 @@ You can find extensions for your Python installation like this:
py-h5py py-numpy py-pyqt py-shiboken py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed: ==> 12 installed:
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2 py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2
py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10 py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10
py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1 py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1
@ -1584,8 +1588,8 @@ prefixes, and you can see this with ``spack find -p``:
$ spack find -p py-numpy $ spack find -p py-numpy
==> 1 installed packages. ==> 1 installed packages.
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/py-numpy@1.9.1-66733244 py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/py-numpy@1.9.1-66733244
However, even though this package is installed, you cannot use it However, even though this package is installed, you cannot use it
directly when you run ``python``: directly when you run ``python``:
@ -1646,9 +1650,9 @@ installation:
.. code-block:: sh .. code-block:: sh
$ spack activate py-numpy $ spack activate py-numpy
==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7. ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=linux-debian7-x86_64-3c74eb69 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7. ==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=linux-debian7-x86_64-5f70f816 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7. ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.
Several things have happened here. The user requested that Several things have happened here. The user requested that
``py-numpy`` be activated in the ``python`` installation it was built ``py-numpy`` be activated in the ``python`` installation it was built
@ -1663,7 +1667,7 @@ packages listed as activated:
.. code-block:: sh .. code-block:: sh
$ spack extensions python $ spack extensions python
==> python@2.7.8%gcc@4.4.7 arch=chaos_5_x86_64_ib-703c7a96 ==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96
==> 36 extensions: ==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six py-basemap py-libxml2 py-pil py-pytz py-six
@ -1675,14 +1679,14 @@ packages listed as activated:
py-h5py py-numpy py-pyqt py-shiboken py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed: ==> 12 installed:
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2 py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2
py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10 py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10
py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1 py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1
py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0 py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0
==> 3 currently activated: ==> 3 currently activated:
-- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- -- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1 py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1
@ -1711,7 +1715,7 @@ dependencies, you can use ``spack activate -f``:
.. code-block:: sh .. code-block:: sh
$ spack activate -f py-numpy $ spack activate -f py-numpy
==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7. ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.
.. _spack-deactivate: .. _spack-deactivate:
@ -1743,7 +1747,7 @@ Spack currently needs to be run from a filesystem that supports
``flock`` locking semantics. Nearly all local filesystems and recent ``flock`` locking semantics. Nearly all local filesystems and recent
versions of NFS support this, but parallel filesystems may be mounted versions of NFS support this, but parallel filesystems may be mounted
without ``flock`` support enabled. You can determine how your without ``flock`` support enabled. You can determine how your
filesystems are mounted with ``mount -p``. The output for a Lustre filesystems are mounted with ``mount -p``. The output for a Lustre
filesystem might look like this: filesystem might look like this:
.. code-block:: sh .. code-block:: sh
@ -1764,7 +1768,7 @@ This issue typically manifests with the error below:
Traceback (most recent call last): Traceback (most recent call last):
File "./spack", line 176, in <module> File "./spack", line 176, in <module>
main() main()
File "./spack", line 154, in main File "./spack", line 154,' in main
return_val = command(parser, args) return_val = command(parser, args)
File "./spack/lib/spack/spack/cmd/find.py", line 170, in find File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
specs = set(spack.installed_db.query(**q_args)) specs = set(spack.installed_db.query(**q_args))
@ -1782,6 +1786,142 @@ This issue typically manifests with the error below:
A nicer error message is TBD in future versions of Spack. A nicer error message is TBD in future versions of Spack.
.. _spack-cray:
Spack on Cray
-----------------------------
Spack differs slightly when used on a Cray system. The architecture spec
can differentiate between the front-end and back-end processor and operating system.
For example, on Edison at NERSC, the back-end target processor
is \"Ivy Bridge\", so you can specify to use the back-end this way:
.. code-block:: sh
spack install zlib target=ivybridge
You can also use the operating system to build against the back-end:
.. code-block:: sh
spack install zlib os=CNL10
Notice that the name includes both the operating system name and the major
version number concatenated together.
Alternatively, if you want to build something for the front-end,
you can specify the front-end target processor. The processor for a login node
on Edison is \"Sandy bridge\" so we specify on the command line like so:
.. code-block:: sh
spack install zlib target=sandybridge
And the front-end operating system is:
.. code-block:: sh
spack install zlib os=SuSE11
Cray compiler detection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Spack can detect compilers using two methods. For the front-end, we treat
everything the same. The difference lies in back-end compiler detection.
Back-end compiler detection is made via the Tcl module avail command.
Once it detects the compiler it writes the appropriate PrgEnv and compiler
module name to compilers.yaml and sets the paths to each compiler with Cray\'s
compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load
the correct PrgEnv and compiler module and will call appropriate wrapper.
The compilers.yaml config file will also differ. There is a
modules section that is filled with the compiler\'s Programming Environment
and module name. On other systems, this field is empty []::
...
- compiler:
modules:
- PrgEnv-intel
- intel/15.0.109
...
As mentioned earlier, the compiler paths will look different on a Cray system.
Since most compilers are invoked using cc, CC and ftn, the paths for each
compiler are replaced with their respective Cray compiler wrapper names::
...
paths:
cc: cc
cxx: CC
f77: ftn
fc: ftn
...
As opposed to an explicit path to the compiler executable. This allows Spack
to call the Cray compiler wrappers during build time.
For more on compiler configuration, check out :ref:`compiler-config`.
Setting defaults and using Cray modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you want to use default compilers for each PrgEnv and also be able
to load cray external modules, you will need to set up a packages.yaml.
Here\'s an example of an external configuration for cray modules:
.. code-block:: yaml
packages:
mpi:
modules:
mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10: cray-mpich
mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10: cray-mpich
This tells Spack that for whatever package that depends on mpi, load the
cray-mpich module into the environment. You can then be able to use whatever
environment variables, libraries, etc, that are brought into the environment
via module load.
You can set the default compiler that Spack can use for each compiler type.
If you want to use the Cray defaults, then set them under *all:* in packages.yaml.
In the compiler field, set the compiler specs in your order of preference.
Whenever you build with that compiler type, Spack will concretize to that version.
Here is an example of a full packages.yaml used at NERSC
.. code-block:: yaml
packages:
mpi:
modules:
mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-mpich
mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge: cray-mpich
buildable: False
netcdf:
modules:
netcdf@4.3.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-netcdf
netcdf@4.3.3.1%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-netcdf
buildable: False
hdf5:
modules:
hdf5@1.8.14%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-hdf5
hdf5@1.8.14%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-hdf5
buildable: False
all:
compiler: [gcc@5.2.0, intel@16.0.0.109]
Here we tell spack that whenever we want to build with gcc use version 5.2.0 or
if we want to build with intel compilers, use version 16.0.0.109. We add a spec
for each compiler type for each cray modules. This ensures that for each
compiler on our system we can use that external module.
For more on external packages check out the section :ref:`sec-external_packages`.
Getting Help Getting Help
----------------------- -----------------------

23
lib/spack/docs/configuration.rst
View File

@ -53,6 +53,7 @@ in the first directory it finds to which it has write access. Add
more elements to the list to indicate where your own site's temporary more elements to the list to indicate where your own site's temporary
directory is. directory is.
.. _sec-external_packages:
External Packages External Packages
---------------------------- ----------------------------
@ -70,20 +71,20 @@ directory. Here's an example of an external configuration:
packages: packages:
openmpi: openmpi:
paths: paths:
openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3 openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
This example lists three installations of OpenMPI, one built with gcc, This example lists three installations of OpenMPI, one built with gcc,
one built with gcc and debug information, and another built with Intel. one built with gcc and debug information, and another built with Intel.
If Spack is asked to build a package that uses one of these MPIs as a If Spack is asked to build a package that uses one of these MPIs as a
dependency, it will use the the pre-installed OpenMPI in dependency, it will use the the pre-installed OpenMPI in
the given directory. the given directory. Packages.yaml can also be used to specify modules
Each ``packages.yaml`` begins with a ``packages:`` token, followed Each ``packages.yaml`` begins with a ``packages:`` token, followed
by a list of package names. To specify externals, add a ``paths`` by a list of package names. To specify externals, add a ``paths`` or ``modules``
token under the package name, which lists externals in a token under the package name, which lists externals in a
``spec : /path`` format. Each spec should be as ``spec: /path`` or ``spec: module-name`` format. Each spec should be as
well-defined as reasonably possible. If a well-defined as reasonably possible. If a
package lacks a spec component, such as missing a compiler or package lacks a spec component, such as missing a compiler or
package version, then Spack will guess the missing component based package version, then Spack will guess the missing component based
@ -108,9 +109,9 @@ be:
packages: packages:
openmpi: openmpi:
paths: paths:
openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3 openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
buildable: False buildable: False
The addition of the ``buildable`` flag tells Spack that it should never build The addition of the ``buildable`` flag tells Spack that it should never build
@ -118,6 +119,9 @@ its own version of OpenMPI, and it will instead always rely on a pre-built
OpenMPI. Similar to ``paths``, ``buildable`` is specified as a property under OpenMPI. Similar to ``paths``, ``buildable`` is specified as a property under
a package name. a package name.
If an external module is specified as not buildable, then Spack will load the
external module into the build environment which can be used for linking.
The ``buildable`` does not need to be paired with external packages. The ``buildable`` does not need to be paired with external packages.
It could also be used alone to forbid packages that may be It could also be used alone to forbid packages that may be
buggy or otherwise undesirable. buggy or otherwise undesirable.
@ -181,7 +185,6 @@ concretization rules. A provider lists a value that packages may
dependency. dependency.
Profiling Profiling
------------------ ------------------

286
lib/spack/docs/packaging_guide.rst
View File

@ -36,10 +36,11 @@ Creating & editing packages
``spack create`` ``spack create``
~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~
The ``spack create`` command generates a boilerplate package template The ``spack create`` command creates a directory with the package name and
from a URL. The URL should point to a tarball or other software generates a ``package.py`` file with a boilerplate package template from a URL.
archive. In most cases, ``spack create`` plus a few modifications is The URL should point to a tarball or other software archive. In most cases,
all you need to get a package working. ``spack create`` plus a few modifications is all you need to get a package
working.
Here's an example: Here's an example:
@ -47,12 +48,16 @@ Here's an example:
$ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz $ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz
Spack examines the tarball URL and tries to figure out the name of the Spack examines the tarball URL and tries to figure out the name of the package
package to be created. It also tries to determine what version strings to be created. Once the name is determined a directory in the appropriate
look like for this package. Using this information, it will try to repository is created with that name. Spack prefers, but does not require, that
find *additional* versions by spidering the package's webpage. If it names be lower case so the directory name will be lower case when ``spack
finds multiple versions, Spack prompts you to tell it how many create`` generates it. In cases where it is desired to have mixed case or upper
versions you want to download and checksum: case simply rename the directory. Spack also tries to determine what version
strings look like for this package. Using this information, it will try to find
*additional* versions by spidering the package's webpage. If it finds multiple
versions, Spack prompts you to tell it how many versions you want to download
and checksum:
.. code-block:: sh .. code-block:: sh
@ -297,9 +302,10 @@ directories or files (like patches) that it needs to build.
Package Names Package Names
~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~
Packages are named after the directory containing ``package.py``. So, Packages are named after the directory containing ``package.py``. It is
``libelf``'s ``package.py`` lives in a directory called ``libelf``. preferred, but not required, that the directory, and thus the package name, are
The ``package.py`` file defines a class called ``Libelf``, which lower case. So, ``libelf``'s ``package.py`` lives in a directory called
``libelf``. The ``package.py`` file defines a class called ``Libelf``, which
extends Spack's ``Package`` class. for example, here is extends Spack's ``Package`` class. for example, here is
``$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py``: ``$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py``:
@ -377,6 +383,8 @@ add a line like this in the package class:
version('8.2.1', '4136d7b4c04df68b686570afa26988ac') version('8.2.1', '4136d7b4c04df68b686570afa26988ac')
... ...
Versions should be listed with the newest version first.
Version URLs Version URLs
~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~
@ -385,8 +393,21 @@ in the package. For example, Spack is smart enough to download
version ``8.2.1.`` of the ``Foo`` package above from version ``8.2.1.`` of the ``Foo`` package above from
``http://example.com/foo-8.2.1.tar.gz``. ``http://example.com/foo-8.2.1.tar.gz``.
If spack *cannot* extrapolate the URL from the ``url`` field, or if If spack *cannot* extrapolate the URL from the ``url`` field by
the package doesn't have a ``url`` field, you can add a URL explicitly default, you can write your own URL generation algorithm in place of
the ``url`` declaration. For example:
.. code-block:: python
:linenos:
class Foo(Package):
def url_for_version(self, version):
return 'http://example.com/version_%s/foo-%s.tar.gz' \
% (version, version)
version('8.2.1', '4136d7b4c04df68b686570afa26988ac')
...
If a URL cannot be derived systematically, you can add an explicit URL
for a particular version: for a particular version:
.. code-block:: python .. code-block:: python
@ -547,7 +568,7 @@ The package author is responsible for coming up with a sensible name
for each version to be fetched from a repository. For example, if for each version to be fetched from a repository. For example, if
you're fetching from a tag like ``v1.0``, you might call that ``1.0``. you're fetching from a tag like ``v1.0``, you might call that ``1.0``.
If you're fetching a nameless git commit or an older subversion If you're fetching a nameless git commit or an older subversion
revision, you might give the commit an intuitive name, like ``dev`` revision, you might give the commit an intuitive name, like ``develop``
for a development version, or ``some-fancy-new-feature`` if you want for a development version, or ``some-fancy-new-feature`` if you want
to be more specific. to be more specific.
@ -557,6 +578,17 @@ branches move forward over time and you aren't guaranteed to get the
same thing every time you fetch a particular version. Life isn't same thing every time you fetch a particular version. Life isn't
always simple, though, so this is not strictly enforced. always simple, though, so this is not strictly enforced.
When fetching from from the branch corresponding to the development version
(often called ``master``,``trunk`` or ``dev``), it is recommended to
call this version ``develop``. Spack has special treatment for this version so
that ``@develop`` will satisfy dependencies like
``depends_on(abc, when="@x.y.z:")``. In other words, ``@develop`` is
greater than any other version. The rationale is that certain features or
options first appear in the development branch. Therefore if a package author
wants to keep the package on the bleeding edge and provide support for new
features, it is advised to use ``develop`` for such a version which will
greatly simplify writing dependencies and version-related conditionals.
In some future release, Spack may support extrapolating repository In some future release, Spack may support extrapolating repository
versions as it does for tarball URLs, but currently this is not versions as it does for tarball URLs, but currently this is not
supported. supported.
@ -582,7 +614,7 @@ Default branch
class Example(Package): class Example(Package):
... ...
version('dev', git='https://github.com/example-project/example.git') version('develop', git='https://github.com/example-project/example.git')
This is not recommended, as the contents of the default branch This is not recommended, as the contents of the default branch
change over time. change over time.
@ -655,7 +687,7 @@ Default
.. code-block:: python .. code-block:: python
version('hg-head', hg='https://jay.grs.rwth-aachen.de/hg/example') version('develop', hg='https://jay.grs.rwth-aachen.de/hg/example')
Note that this is not recommended; try to fetch a particular Note that this is not recommended; try to fetch a particular
revision instead. revision instead.
@ -687,7 +719,7 @@ Fetching the head
.. code-block:: python .. code-block:: python
version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk') version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')
This is not recommended, as the head will move forward over time. This is not recommended, as the head will move forward over time.
@ -697,7 +729,7 @@ Fetching a revision
.. code-block:: python .. code-block:: python
version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk', version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',
revision=128) revision=128)
Subversion branches are handled as part of the directory structure, so Subversion branches are handled as part of the directory structure, so
@ -1346,6 +1378,19 @@ Now, the ``py-numpy`` package can be used as an argument to ``spack
activate``. When it is activated, all the files in its prefix will be activate``. When it is activated, all the files in its prefix will be
symbolically linked into the prefix of the python package. symbolically linked into the prefix of the python package.
Many packages produce Python extensions for *some* variants, but not
others: they should extend ``python`` only if the apropriate
variant(s) are selected. This may be accomplished with conditional
``extends()`` declarations:
.. code-block:: python
class FooLib(Package):
variant('python', default=True, description= \
'Build the Python extension Module')
extends('python', when='+python')
...
Sometimes, certain files in one package will conflict with those in Sometimes, certain files in one package will conflict with those in
another, which means they cannot both be activated (symlinked) at the another, which means they cannot both be activated (symlinked) at the
same time. In this case, you can tell Spack to ignore those files same time. In this case, you can tell Spack to ignore those files
@ -1632,21 +1677,21 @@ the user runs ``spack install`` and the time the ``install()`` method
is called. The concretized version of the spec above might look like is called. The concretized version of the spec above might look like
this:: this::
mpileaks@2.3%gcc@4.7.3 arch=linux-ppc64 mpileaks@2.3%gcc@4.7.3 arch=linux-debian7-x86_64
^callpath@1.0%gcc@4.7.3+debug arch=linux-ppc64 ^callpath@1.0%gcc@4.7.3+debug arch=linux-debian7-x86_64
^dyninst@8.1.2%gcc@4.7.3 arch=linux-ppc64 ^dyninst@8.1.2%gcc@4.7.3 arch=linux-debian7-x86_64
^libdwarf@20130729%gcc@4.7.3 arch=linux-ppc64 ^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64
^libelf@0.8.11%gcc@4.7.3 arch=linux-ppc64 ^libelf@0.8.11%gcc@4.7.3 arch=linux-debian7-x86_64
^mpich@3.0.4%gcc@4.7.3 arch=linux-ppc64 ^mpich@3.0.4%gcc@4.7.3 arch=linux-debian7-x86_64
.. graphviz:: .. graphviz::
digraph { digraph {
"mpileaks@2.3\n%gcc@4.7.3\n arch=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-ppc64" "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
"mpileaks@2.3\n%gcc@4.7.3\n arch=linux-ppc64" -> "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-ppc64" "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-debian7-x86_64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
"callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-ppc64" -> "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-debian7-x86_64" -> "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
"dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" -> "libdwarf@20130729\n%gcc@4.7.3\n arch=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-ppc64" "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libdwarf@20130729\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
"dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-ppc64" "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
} }
Here, all versions, compilers, and platforms are filled in, and there Here, all versions, compilers, and platforms are filled in, and there
@ -1675,9 +1720,9 @@ running ``spack spec``. For example:
^libdwarf ^libdwarf
^libelf ^libelf
dyninst@8.0.1%gcc@4.7.3 arch=linux-ppc64 dyninst@8.0.1%gcc@4.7.3 arch=linux-debian7-x86_64
^libdwarf@20130729%gcc@4.7.3 arch=linux-ppc64 ^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64
^libelf@0.8.13%gcc@4.7.3 arch=linux-ppc64 ^libelf@0.8.13%gcc@4.7.3 arch=linux-debian7-x86_64
This is useful when you want to know exactly what Spack will do when This is useful when you want to know exactly what Spack will do when
you ask for a particular spec. you ask for a particular spec.
@ -1851,7 +1896,7 @@ discover its dependencies.
If you want to see the environment that a package will build with, or If you want to see the environment that a package will build with, or
if you want to run commands in that environment to test them out, you if you want to run commands in that environment to test them out, you
can use the :ref:```spack env`` <spack-env>` command, documented can use the :ref:`spack env <spack-env>` command, documented
below. below.
.. _compiler-wrappers: .. _compiler-wrappers:
@ -2182,12 +2227,12 @@ example:
def install(self, prefix): def install(self, prefix):
# Do default install # Do default install
@when('arch=chaos_5_x86_64_ib') @when('arch=linux-debian7-x86_64')
def install(self, prefix): def install(self, prefix):
# This will be executed instead of the default install if # This will be executed instead of the default install if
# the package's sys_type() is chaos_5_x86_64_ib. # the package's sys_type() is chaos_5_x86_64_ib.
@when('arch=bgqos_0") @when('arch=linux-debian7-x86_64")
def install(self, prefix): def install(self, prefix):
# This will be executed if the package's sys_type is bgqos_0 # This will be executed if the package's sys_type is bgqos_0
@ -2315,7 +2360,7 @@ build system.
.. _sanity-checks: .. _sanity-checks:
Sanity checking an intallation Sanity checking an installation
-------------------------------- --------------------------------
By default, Spack assumes that a build has failed if nothing is By default, Spack assumes that a build has failed if nothing is
@ -2531,6 +2576,59 @@ File functions
.. _package-lifecycle: .. _package-lifecycle:
Coding Style Guidelines
---------------------------
The following guidelines are provided, in the interests of making
Spack packages work in a consistent manner:
Variant Names
~~~~~~~~~~~~~~
Spack packages with variants similar to already-existing Spack
packages should use the same name for their variants. Standard
variant names are:
======= ======== ========================
Name Default Description
------- -------- ------------------------
shared True Build shared libraries
static Build static libraries
mpi Use MPI
python Build Python extension
------- -------- ------------------------
If specified in this table, the corresponding default should be used
when declaring a variant.
Version Lists
~~~~~~~~~~~~~~
Spack packges should list supported versions with the newest first.
Special Versions
~~~~~~~~~~~~~~~~~
The following *special* version names may be used when building a package:
* *@system*: Indicates a hook to the OS-installed version of the
package. This is useful, for example, to tell Spack to use the
OS-installed version in ``packages.yaml``::
openssl:
paths:
openssl@system: /usr
buildable: False
Certain Spack internals look for the *@system* version and do
appropriate things in that case.
* *@local*: Indicates the version was built manually from some source
tree of unknown provenance (see ``spack setup``).
Packaging workflow commands Packaging workflow commands
--------------------------------- ---------------------------------
@ -2782,11 +2880,11 @@ build it:
$ spack stage libelf $ spack stage libelf
==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz
######################################################################## 100.0% ######################################################################## 100.0%
==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64/libelf-0.8.13.tar.gz ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13.tar.gz
==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64. ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64.
$ spack cd libelf $ spack cd libelf
$ pwd $ pwd
/Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64/libelf-0.8.13 /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13
``spack cd`` here changed he current working directory to the ``spack cd`` here changed he current working directory to the
directory containing the expanded ``libelf`` source code. There are a directory containing the expanded ``libelf`` source code. There are a
@ -2851,3 +2949,109 @@ might write:
DWARF_PREFIX = $(spack location -i libdwarf) DWARF_PREFIX = $(spack location -i libdwarf)
CXXFLAGS += -I$DWARF_PREFIX/include CXXFLAGS += -I$DWARF_PREFIX/include
CXXFLAGS += -L$DWARF_PREFIX/lib CXXFLAGS += -L$DWARF_PREFIX/lib
Build System Configuration Support
----------------------------------
Imagine a developer creating a CMake-based (or Autotools) project in a local
directory, which depends on libraries A-Z. Once Spack has installed
those dependencies, one would like to run ``cmake`` with appropriate
command line and environment so CMake can find them. The ``spack
setup`` command does this conveniently, producing a CMake
configuration that is essentially the same as how Spack *would have*
configured the project. This can be demonstrated with a usage
example:
.. code-block:: bash
cd myproject
spack setup myproject@local
mkdir build; cd build
../spconfig.py ..
make
make install
Notes:
* Spack must have ``myproject/package.py`` in its repository for
this to work.
* ``spack setup`` produces the executable script ``spconfig.py`` in
the local directory, and also creates the module file for the
package. ``spconfig.py`` is normally run from the user's
out-of-source build directory.
* The version number given to ``spack setup`` is arbitrary, just
like ``spack diy``. ``myproject/package.py`` does not need to
have any valid downloadable versions listed (typical when a
project is new).
* spconfig.py produces a CMake configuration that *does not* use the
Spack wrappers. Any resulting binaries *will not* use RPATH,
unless the user has enabled it. This is recommended for
development purposes, not production.
* ``spconfig.py`` is human readable, and can serve as a developer
reference of what dependencies are being used.
* ``make install`` installs the package into the Spack repository,
where it may be used by other Spack packages.
* CMake-generated makefiles re-run CMake in some circumstances. Use
of ``spconfig.py`` breaks this behavior, requiring the developer
to manually re-run ``spconfig.py`` when a ``CMakeLists.txt`` file
has changed.
CMakePackage
~~~~~~~~~~~~
In order ot enable ``spack setup`` functionality, the author of
``myproject/package.py`` must subclass from ``CMakePackage`` instead
of the standard ``Package`` superclass. Because CMake is
standardized, the packager does not need to tell Spack how to run
``cmake; make; make install``. Instead the packager only needs to
create (optional) methods ``configure_args()`` and ``configure_env()``, which
provide the arguments (as a list) and extra environment variables (as
a dict) to provide to the ``cmake`` command. Usually, these will
translate variant flags into CMake definitions. For example:
.. code-block:: python
def configure_args(self):
spec = self.spec
return [
'-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),
'-DBUILD_PYTHON=%s' % ('YES' if '+python' in spec else 'NO'),
'-DBUILD_GRIDGEN=%s' % ('YES' if '+gridgen' in spec else 'NO'),
'-DBUILD_COUPLER=%s' % ('YES' if '+coupler' in spec else 'NO'),
'-DUSE_PISM=%s' % ('YES' if '+pism' in spec else 'NO')]
If needed, a packager may also override methods defined in
``StagedPackage`` (see below).
StagedPackage
~~~~~~~~~~~~~
``CMakePackage`` is implemented by subclassing the ``StagedPackage``
superclass, which breaks down the standard ``Package.install()``
method into several sub-stages: ``setup``, ``configure``, ``build``
and ``install``. Details:
* Instead of implementing the standard ``install()`` method, package
authors implement the methods for the sub-stages
``install_setup()``, ``install_configure()``,
``install_build()``, and ``install_install()``.
* The ``spack install`` command runs the sub-stages ``configure``,
``build`` and ``install`` in order. (The ``setup`` stage is
not run by default; see below).
* The ``spack setup`` command runs the sub-stages ``setup``
and a dummy install (to create the module file).
* The sub-stage install methods take no arguments (other than
``self``). The arguments ``spec`` and ``prefix`` to the standard
``install()`` method may be accessed via ``self.spec`` and
``self.prefix``.
GNU Autotools
~~~~~~~~~~~~~
The ``setup`` functionality is currently only available for
CMake-based packages. Extending this functionality to GNU
Autotools-based packages would be easy (and should be done by a
developer who actively uses Autotools). Packages that use
non-standard build systems can gain ``setup`` functionality by
subclassing ``StagedPackage`` directly.

4
lib/spack/spack/__init__.py
View File

@ -176,8 +176,10 @@
# TODO: it's not clear where all the stuff that needs to be included in packages # TODO: it's not clear where all the stuff that needs to be included in packages
# should live. This file is overloaded for spack core vs. for packages. # should live. This file is overloaded for spack core vs. for packages.
# #
__all__ = ['Package', 'Version', 'when', 'ver'] __all__ = ['Package', 'StagedPackage', 'CMakePackage', \
'Version', 'when', 'ver']
from spack.package import Package, ExtensionConflictError from spack.package import Package, ExtensionConflictError
from spack.package import StagedPackage, CMakePackage
from spack.version import Version, ver from spack.version import Version, ver
from spack.multimethod import when from spack.multimethod import when

42
lib/spack/spack/build_environment.py
View File

@ -224,9 +224,12 @@ def set_compiler_environment_variables(pkg, env):
return env return env
def set_build_environment_variables(pkg, env): def set_build_environment_variables(pkg, env, dirty=False):
""" """
This ensures a clean install environment when we build packages This ensures a clean install environment when we build packages.
Arguments:
dirty -- skip unsetting the user's environment settings.
""" """
# Add spack build environment path with compiler wrappers first in # Add spack build environment path with compiler wrappers first in
# the path. We add both spack.env_path, which includes default # the path. We add both spack.env_path, which includes default
@ -262,12 +265,26 @@ def set_build_environment_variables(pkg, env):
# Install root prefix # Install root prefix
env.set(SPACK_INSTALL, spack.install_path) env.set(SPACK_INSTALL, spack.install_path)
# Remove these vars from the environment during build because they # Stuff in here sanitizes the build environemnt to eliminate
# can affect how some packages find libraries. We want to make # anything the user has set that may interfere.
# sure that builds never pull in unintended external dependencies. if not dirty:
env.unset('LD_LIBRARY_PATH') # Remove these vars from the environment during build because they
env.unset('LD_RUN_PATH') # can affect how some packages find libraries. We want to make
env.unset('DYLD_LIBRARY_PATH') # sure that builds never pull in unintended external dependencies.
env.unset('LD_LIBRARY_PATH')
env.unset('LIBRARY_PATH')
env.unset('CPATH')
env.unset('LD_RUN_PATH')
env.unset('DYLD_LIBRARY_PATH')
# Remove any macports installs from the PATH. The macports ld can
# cause conflicts with the built-in linker on el capitan. Solves
# assembler issues, e.g.:
# suffix or operands invalid for `movq'"
path = get_path('PATH')
for p in path:
if '/macports/' in p:
env.remove_path('PATH', p)
# Add bin directories from dependencies to the PATH for the build. # Add bin directories from dependencies to the PATH for the build.
bin_dirs = reversed( bin_dirs = reversed(
@ -405,7 +422,7 @@ def load_external_modules(pkg):
load_module(dep.external_module) load_module(dep.external_module)
def setup_package(pkg): def setup_package(pkg, dirty=False):
"""Execute all environment setup routines.""" """Execute all environment setup routines."""
spack_env = EnvironmentModifications() spack_env = EnvironmentModifications()
run_env = EnvironmentModifications() run_env = EnvironmentModifications()
@ -428,7 +445,7 @@ def setup_package(pkg):
s.package.spec = s s.package.spec = s
set_compiler_environment_variables(pkg, spack_env) set_compiler_environment_variables(pkg, spack_env)
set_build_environment_variables(pkg, spack_env) set_build_environment_variables(pkg, spack_env, dirty)
load_external_modules(pkg) load_external_modules(pkg)
# traverse in postorder so package can use vars from its dependencies # traverse in postorder so package can use vars from its dependencies
spec = pkg.spec spec = pkg.spec
@ -457,7 +474,7 @@ def setup_package(pkg):
spack_env.apply_modifications() spack_env.apply_modifications()
def fork(pkg, function): def fork(pkg, function, dirty=False):
"""Fork a child process to do part of a spack build. """Fork a child process to do part of a spack build.
Arguments: Arguments:
@ -465,6 +482,7 @@ def fork(pkg, function):
pkg -- pkg whose environemnt we should set up the pkg -- pkg whose environemnt we should set up the
forked process for. forked process for.
function -- arg-less function to run in the child process. function -- arg-less function to run in the child process.
dirty -- If True, do NOT clean the environment before building.
Usage: Usage:
def child_fun(): def child_fun():
@ -488,7 +506,7 @@ def child_fun():
if pid == 0: if pid == 0:
# Give the child process the package's build environment. # Give the child process the package's build environment.
setup_package(pkg) setup_package(pkg, dirty=dirty)
try: try:
# call the forked function. # call the forked function.

2
lib/spack/spack/cmd/create.py
View File

@ -325,7 +325,7 @@ def create(parser, args):
# Figure out a name and repo for the package. # Figure out a name and repo for the package.
name, version = guess_name_and_version(url, args) name, version = guess_name_and_version(url, args)
spec = Spec(name) spec = Spec(name)
name = spec.name # factors out namespace, if any name = spec.name.lower() # factors out namespace, if any
repo = find_repository(spec, args) repo = find_repository(spec, args)
tty.msg("This looks like a URL for %s version %s" % (name, version)) tty.msg("This looks like a URL for %s version %s" % (name, version))

2
lib/spack/spack/cmd/diy.py
View File

@ -50,7 +50,7 @@ def setup_parser(subparser):
help="Do not display verbose build output while installing.") help="Do not display verbose build output while installing.")
subparser.add_argument( subparser.add_argument(
'spec', nargs=argparse.REMAINDER, 'spec', nargs=argparse.REMAINDER,
help="specs to use for install. Must contain package AND verison.") help="specs to use for install. Must contain package AND version.")
def diy(self, args): def diy(self, args):

9
lib/spack/spack/cmd/install.py
View File

@ -53,8 +53,15 @@ def setup_parser(subparser):
subparser.add_argument( subparser.add_argument(
'--fake', action='store_true', dest='fake', '--fake', action='store_true', dest='fake',
help="Fake install. Just remove the prefix and touch a fake file in it.") help="Fake install. Just remove the prefix and touch a fake file in it.")
subparser.add_argument(
'--dirty', action='store_true', dest='dirty',
help="Install a package *without* cleaning the environment.")
subparser.add_argument( subparser.add_argument(
'packages', nargs=argparse.REMAINDER, help="specs of packages to install") 'packages', nargs=argparse.REMAINDER, help="specs of packages to install")
subparser.add_argument(
'--run-tests', action='store_true', dest='run_tests',
help="Run tests during installation of a package.")
def install(parser, args): def install(parser, args):
@ -77,6 +84,8 @@ def install(parser, args):
keep_stage=args.keep_stage, keep_stage=args.keep_stage,
ignore_deps=args.ignore_deps, ignore_deps=args.ignore_deps,
make_jobs=args.jobs, make_jobs=args.jobs,
run_tests=args.run_tests,
verbose=args.verbose, verbose=args.verbose,
fake=args.fake, fake=args.fake,
dirty=args.dirty,
explicit=True) explicit=True)

91
lib/spack/spack/cmd/setup.py Normal file
View File

@ -0,0 +1,91 @@
##############################################################################
# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written by Elizabeth Fischer
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License (as published by
# the Free Software Foundation) version 2.1 dated February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import sys
import os
import argparse
import llnl.util.tty as tty
import spack
import spack.cmd
from spack.cmd.edit import edit_package
from spack.stage import DIYStage
description = "Create a configuration script and module, but don't build."
def setup_parser(subparser):
subparser.add_argument(
'-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
help="Do not try to install dependencies of requested packages.")
subparser.add_argument(
'-v', '--verbose', action='store_true', dest='verbose',
help="Display verbose build output while installing.")
subparser.add_argument(
'spec', nargs=argparse.REMAINDER,
help="specs to use for install. Must contain package AND verison.")
def setup(self, args):
if not args.spec:
tty.die("spack setup requires a package spec argument.")
specs = spack.cmd.parse_specs(args.spec)
if len(specs) > 1:
tty.die("spack setup only takes one spec.")
# Take a write lock before checking for existence.
with spack.installed_db.write_transaction():
spec = specs[0]
if not spack.repo.exists(spec.name):
tty.warn("No such package: %s" % spec.name)
create = tty.get_yes_or_no("Create this package?", default=False)
if not create:
tty.msg("Exiting without creating.")
sys.exit(1)
else:
tty.msg("Running 'spack edit -f %s'" % spec.name)
edit_package(spec.name, spack.repo.first_repo(), None, True)
return
if not spec.versions.concrete:
tty.die("spack setup spec must have a single, concrete version. Did you forget a package version number?")
spec.concretize()
package = spack.repo.get(spec)
# It's OK if the package is already installed.
# Forces the build to run out of the current directory.
package.stage = DIYStage(os.getcwd())
# TODO: make this an argument, not a global.
spack.do_checksum = False
package.do_install(
keep_prefix=True, # Don't remove install directory, even if you think you should
ignore_deps=args.ignore_deps,
verbose=args.verbose,
keep_stage=True, # don't remove source dir for SETUP.
install_phases = set(['setup', 'provenance']))

6
lib/spack/spack/concretize.py
View File

@ -166,7 +166,11 @@ def prefer_key(v):
valid_versions.sort(key=prefer_key, reverse=True) valid_versions.sort(key=prefer_key, reverse=True)
if valid_versions: if valid_versions:
spec.versions = ver([valid_versions[0]]) # Disregard @develop and take the next valid version
if ver(valid_versions[0]) == ver('develop') and len(valid_versions) > 1:
spec.versions = ver([valid_versions[1]])
else:
spec.versions = ver([valid_versions[0]])
else: else:
# We don't know of any SAFE versions that match the given # We don't know of any SAFE versions that match the given
# spec. Grab the spec's versions and grab the highest # spec. Grab the spec's versions and grab the highest

3
lib/spack/spack/fetch_strategy.py
View File

@ -307,9 +307,6 @@ def archive(self, destination):
if not self.archive_file: if not self.archive_file:
raise NoArchiveFileError("Cannot call archive() before fetching.") raise NoArchiveFileError("Cannot call archive() before fetching.")
if not extension(destination) == extension(self.archive_file):
raise ValueError("Cannot archive without matching extensions.")
shutil.copy(self.archive_file, destination) shutil.copy(self.archive_file, destination)
@_needs_stage @_needs_stage

222
lib/spack/spack/package.py
View File

@ -37,6 +37,8 @@
import re import re
import textwrap import textwrap
import time import time
import glob
import string
import llnl.util.tty as tty import llnl.util.tty as tty
import spack import spack
@ -50,6 +52,8 @@
import spack.repository import spack.repository
import spack.url import spack.url
import spack.util.web import spack.util.web
from urlparse import urlparse
from StringIO import StringIO from StringIO import StringIO
from llnl.util.filesystem import * from llnl.util.filesystem import *
from llnl.util.lang import * from llnl.util.lang import *
@ -58,9 +62,11 @@
from spack.stage import Stage, ResourceStage, StageComposite from spack.stage import Stage, ResourceStage, StageComposite
from spack.util.compression import allowed_archive from spack.util.compression import allowed_archive
from spack.util.environment import dump_environment from spack.util.environment import dump_environment
from spack.util.executable import ProcessError from spack.util.executable import ProcessError, Executable, which
from spack.version import * from spack.version import *
from spack import directory_layout
from urlparse import urlparse from urlparse import urlparse
"""Allowed URL schemes for spack packages.""" """Allowed URL schemes for spack packages."""
_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"] _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@ -305,6 +311,8 @@ class SomePackage(Package):
parallel = True parallel = True
"""# jobs to use for parallel make. If set, overrides default of ncpus.""" """# jobs to use for parallel make. If set, overrides default of ncpus."""
make_jobs = None make_jobs = None
"""By default do not run tests within package's install()"""
run_tests = False
"""Most packages are NOT extendable. Set to True if you want extensions.""" """Most packages are NOT extendable. Set to True if you want extensions."""
extendable = False extendable = False
"""List of prefix-relative file paths (or a single path). If these do """List of prefix-relative file paths (or a single path). If these do
@ -867,6 +875,7 @@ def _resource_stage(self, resource):
resource_stage_folder = '-'.join(pieces) resource_stage_folder = '-'.join(pieces)
return resource_stage_folder return resource_stage_folder
install_phases = set(['configure', 'build', 'install', 'provenance'])
def do_install(self, def do_install(self,
keep_prefix=False, keep_prefix=False,
keep_stage=False, keep_stage=False,
@ -874,8 +883,11 @@ def do_install(self,
skip_patch=False, skip_patch=False,
verbose=False, verbose=False,
make_jobs=None, make_jobs=None,
run_tests=False,
fake=False, fake=False,
explicit=False): explicit=False,
dirty=False,
install_phases = install_phases):
"""Called by commands to install a package and its dependencies. """Called by commands to install a package and its dependencies.
Package implementations should override install() to describe Package implementations should override install() to describe
@ -891,7 +903,9 @@ def do_install(self,
fake -- Don't really build -- install fake stub files instead. fake -- Don't really build -- install fake stub files instead.
skip_patch -- Skip patch stage of build if True. skip_patch -- Skip patch stage of build if True.
verbose -- Display verbose build output (by default, suppresses it) verbose -- Display verbose build output (by default, suppresses it)
dirty -- Don't clean the build environment before installing.
make_jobs -- Number of make jobs to use for install. Default is ncpus make_jobs -- Number of make jobs to use for install. Default is ncpus
run_tests -- Runn tests within the package's install()
""" """
if not self.spec.concrete: if not self.spec.concrete:
raise ValueError("Can only install concrete packages.") raise ValueError("Can only install concrete packages.")
@ -903,7 +917,7 @@ def do_install(self,
return return
# Ensure package is not already installed # Ensure package is not already installed
if spack.install_layout.check_installed(self.spec): if 'install' in install_phases and spack.install_layout.check_installed(self.spec):
tty.msg("%s is already installed in %s" % (self.name, self.prefix)) tty.msg("%s is already installed in %s" % (self.name, self.prefix))
rec = spack.installed_db.get_record(self.spec) rec = spack.installed_db.get_record(self.spec)
if (not rec.explicit) and explicit: if (not rec.explicit) and explicit:
@ -922,7 +936,11 @@ def do_install(self,
fake=fake, fake=fake,
skip_patch=skip_patch, skip_patch=skip_patch,
verbose=verbose, verbose=verbose,
make_jobs=make_jobs) make_jobs=make_jobs,
run_tests=run_tests)
# Set run_tests flag before starting build.
self.run_tests = run_tests
# Set parallelism before starting build. # Set parallelism before starting build.
self.make_jobs = make_jobs self.make_jobs = make_jobs
@ -942,6 +960,10 @@ def build_process():
tty.msg("Building %s" % self.name) tty.msg("Building %s" % self.name)
self.stage.keep = keep_stage self.stage.keep = keep_stage
self.install_phases = install_phases
self.build_directory = join_path(self.stage.path, 'spack-build')
self.source_directory = self.stage.source_path
with self.stage: with self.stage:
# Run the pre-install hook in the child process after # Run the pre-install hook in the child process after
# the directory is created. # the directory is created.
@ -973,19 +995,29 @@ def build_process():
raise e raise e
# Ensure that something was actually installed. # Ensure that something was actually installed.
self.sanity_check_prefix() if 'install' in self.install_phases:
self.sanity_check_prefix()
# Copy provenance into the install directory on success # Copy provenance into the install directory on success
log_install_path = spack.install_layout.build_log_path( if 'provenance' in self.install_phases:
self.spec) log_install_path = spack.install_layout.build_log_path(
env_install_path = spack.install_layout.build_env_path( self.spec)
self.spec) env_install_path = spack.install_layout.build_env_path(
packages_dir = spack.install_layout.build_packages_path( self.spec)
self.spec) packages_dir = spack.install_layout.build_packages_path(
self.spec)
install(log_path, log_install_path) # Remove first if we're overwriting another build
install(env_path, env_install_path) # (can happen with spack setup)
dump_packages(self.spec, packages_dir) try:
shutil.rmtree(packages_dir) # log_install_path and env_install_path are inside this
except:
pass
install(log_path, log_install_path)
install(env_path, env_install_path)
dump_packages(self.spec, packages_dir)
# Run post install hooks before build stage is removed. # Run post install hooks before build stage is removed.
spack.hooks.post_install(self) spack.hooks.post_install(self)
@ -1003,7 +1035,19 @@ def build_process():
try: try:
# Create the install prefix and fork the build process. # Create the install prefix and fork the build process.
spack.install_layout.create_install_directory(self.spec) spack.install_layout.create_install_directory(self.spec)
spack.build_environment.fork(self, build_process) except directory_layout.InstallDirectoryAlreadyExistsError:
if 'install' in install_phases:
# Abort install if install directory exists.
# But do NOT remove it (you'd be overwriting someon else's stuff)
tty.warn("Keeping existing install prefix in place.")
raise
else:
# We're not installing anyway, so don't worry if someone
# else has already written in the install directory
pass
try:
spack.build_environment.fork(self, build_process, dirty=dirty)
except: except:
# remove the install prefix if anything went wrong during install. # remove the install prefix if anything went wrong during install.
if not keep_prefix: if not keep_prefix:
@ -1013,7 +1057,7 @@ def build_process():
"Spack will think this package is installed. " + "Spack will think this package is installed. " +
"Manually remove this directory to fix:", "Manually remove this directory to fix:",
self.prefix, self.prefix,
wrap=True) wrap=False)
raise raise
# note: PARENT of the build process adds the new package to # note: PARENT of the build process adds the new package to
@ -1485,6 +1529,152 @@ def _hms(seconds):
parts.append("%.2fs" % s) parts.append("%.2fs" % s)
return ' '.join(parts) return ' '.join(parts)
class StagedPackage(Package):
"""A Package subclass where the install() is split up into stages."""
def install_setup(self):
"""Creates an spack_setup.py script to configure the package later if we like."""
raise InstallError("Package %s provides no install_setup() method!" % self.name)
def install_configure(self):
"""Runs the configure process."""
raise InstallError("Package %s provides no install_configure() method!" % self.name)
def install_build(self):
"""Runs the build process."""
raise InstallError("Package %s provides no install_build() method!" % self.name)
def install_install(self):
"""Runs the install process."""
raise InstallError("Package %s provides no install_install() method!" % self.name)
def install(self, spec, prefix):
if 'setup' in self.install_phases:
self.install_setup()
if 'configure' in self.install_phases:
self.install_configure()
if 'build' in self.install_phases:
self.install_build()
if 'install' in self.install_phases:
self.install_install()
else:
# Create a dummy file so the build doesn't fail.
# That way, the module file will also be created.
with open(os.path.join(prefix, 'dummy'), 'w') as fout:
pass
# stackoverflow.com/questions/12791997/how-do-you-do-a-simple-chmod-x-from-within-python
def make_executable(path):
mode = os.stat(path).st_mode
mode |= (mode & 0o444) >> 2 # copy R bits to X
os.chmod(path, mode)
class CMakePackage(StagedPackage):
def make_make(self):
import multiprocessing
# number of jobs spack will to build with.
jobs = multiprocessing.cpu_count()
if not self.parallel:
jobs = 1
elif self.make_jobs:
jobs = self.make_jobs
make = spack.build_environment.MakeExecutable('make', jobs)
return make
def configure_args(self):
"""Returns package-specific arguments to be provided to the configure command."""
return list()
def configure_env(self):
"""Returns package-specific environment under which the configure command should be run."""
return dict()
def spack_transitive_include_path(self):
return ';'.join(
os.path.join(dep, 'include')
for dep in os.environ['SPACK_DEPENDENCIES'].split(os.pathsep)
)
def install_setup(self):
cmd = [str(which('cmake'))] + \
spack.build_environment.get_std_cmake_args(self) + \
['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'],
'-DCMAKE_C_COMPILER=%s' % os.environ['SPACK_CC'],
'-DCMAKE_CXX_COMPILER=%s' % os.environ['SPACK_CXX'],
'-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']] + \
self.configure_args()
env = dict()
env['PATH'] = os.environ['PATH']
env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path()
env['CMAKE_PREFIX_PATH'] = os.environ['CMAKE_PREFIX_PATH']
setup_fname = 'spconfig.py'
with open(setup_fname, 'w') as fout:
fout.write(\
r"""#!%s
#
import sys
import os
import subprocess
def cmdlist(str):
return list(x.strip().replace("'",'') for x in str.split('\n') if x)
env = dict(os.environ)
""" % sys.executable)
env_vars = sorted(list(env.keys()))
for name in env_vars:
val = env[name]
if string.find(name, 'PATH') < 0:
fout.write('env[%s] = %s\n' % (repr(name),repr(val)))
else:
if name == 'SPACK_TRANSITIVE_INCLUDE_PATH':
sep = ';'
else:
sep = ':'
fout.write('env[%s] = "%s".join(cmdlist("""\n' % (repr(name),sep))
for part in string.split(val, sep):
fout.write(' %s\n' % part)
fout.write('"""))\n')
fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = env['SPACK_TRANSITIVE_INCLUDE_PATH'] # Deprecated\n")
fout.write('\ncmd = cmdlist("""\n')
fout.write('%s\n' % cmd[0])
for arg in cmd[1:]:
fout.write(' %s\n' % arg)
fout.write('""") + sys.argv[1:]\n')
fout.write('\nproc = subprocess.Popen(cmd, env=env)\nproc.wait()\n')
make_executable(setup_fname)
def install_configure(self):
cmake = which('cmake')
with working_dir(self.build_directory, create=True):
os.environ.update(self.configure_env())
os.environ['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path()
options = self.configure_args() + spack.build_environment.get_std_cmake_args(self)
cmake(self.source_directory, *options)
def install_build(self):
make = self.make_make()
with working_dir(self.build_directory, create=False):
make()
def install_install(self):
make = self.make_make()
with working_dir(self.build_directory, create=False):
make('install')
class FetchError(spack.error.SpackError): class FetchError(spack.error.SpackError):
"""Raised when something goes wrong during fetch.""" """Raised when something goes wrong during fetch."""

15
lib/spack/spack/platforms/linux.py
View File

@ -1,16 +1,23 @@
import subprocess import subprocess
import platform
from spack.architecture import Platform, Target from spack.architecture import Platform, Target
from spack.operating_systems.linux_distro import LinuxDistro from spack.operating_systems.linux_distro import LinuxDistro
class Linux(Platform): class Linux(Platform):
priority = 90 priority = 90
front_end = 'x86_64'
back_end = 'x86_64'
default = 'x86_64'
def __init__(self): def __init__(self):
super(Linux, self).__init__('linux') super(Linux, self).__init__('linux')
self.add_target(self.default, Target(self.default)) self.add_target('x86_64', Target('x86_64'))
self.add_target('ppc64le', Target('ppc64le'))
self.default = platform.machine()
self.front_end = platform.machine()
self.back_end = platform.machine()
if self.default not in self.targets:
self.add_target(self.default, Target(self.default))
linux_dist = LinuxDistro() linux_dist = LinuxDistro()
self.default_os = str(linux_dist) self.default_os = str(linux_dist)
self.front_os = self.default_os self.front_os = self.default_os

18
lib/spack/spack/test/mock_packages_test.py
View File

@ -82,15 +82,6 @@
f77: None f77: None
fc: None fc: None
modules: 'None' modules: 'None'
- compiler:
spec: clang@3.3
operating_system: redhat6
paths:
cc: /path/to/clang
cxx: /path/to/clang++
f77: None
fc: None
modules: 'None'
- compiler: - compiler:
spec: clang@3.3 spec: clang@3.3
operating_system: yosemite operating_system: yosemite
@ -118,15 +109,6 @@
operating_system: SuSE11 operating_system: SuSE11
spec: gcc@4.5.0 spec: gcc@4.5.0
modules: 'None' modules: 'None'
- compiler:
paths:
cc: /path/to/gcc
cxx: /path/to/g++
f77: /path/to/gfortran
fc: /path/to/gfortran
operating_system: redhat6
spec: gcc@4.5.0
modules: 'None'
- compiler: - compiler:
paths: paths:
cc: /path/to/gcc cc: /path/to/gcc

39
lib/spack/spack/test/versions.py
View File

@ -92,6 +92,9 @@ def test_two_segments(self):
self.assert_ver_eq('1.0', '1.0') self.assert_ver_eq('1.0', '1.0')
self.assert_ver_lt('1.0', '2.0') self.assert_ver_lt('1.0', '2.0')
self.assert_ver_gt('2.0', '1.0') self.assert_ver_gt('2.0', '1.0')
self.assert_ver_eq('develop', 'develop')
self.assert_ver_lt('1.0', 'develop')
self.assert_ver_gt('develop', '1.0')
def test_three_segments(self): def test_three_segments(self):
self.assert_ver_eq('2.0.1', '2.0.1') self.assert_ver_eq('2.0.1', '2.0.1')
@ -389,3 +392,39 @@ def test_formatted_strings(self):
self.assertEqual(v.dotted, '1.2.3') self.assertEqual(v.dotted, '1.2.3')
self.assertEqual(v.dashed, '1-2-3') self.assertEqual(v.dashed, '1-2-3')
self.assertEqual(v.underscored, '1_2_3') self.assertEqual(v.underscored, '1_2_3')
def test_repr_and_str(self):
def check_repr_and_str(vrs):
a = Version(vrs)
self.assertEqual(repr(a), 'Version(\'' + vrs + '\')')
b = eval(repr(a))
self.assertEqual(a, b)
self.assertEqual(str(a), vrs)
self.assertEqual(str(a), str(b))
check_repr_and_str('1.2.3')
check_repr_and_str('R2016a')
check_repr_and_str('R2016a.2-3_4')
def test_get_item(self):
a = Version('0.1_2-3')
self.assertTrue(isinstance(a[1], int))
# Test slicing
b = a[0:2]
self.assertTrue(isinstance(b, Version))
self.assertEqual(b, Version('0.1'))
self.assertEqual(repr(b), 'Version(\'0.1\')')
self.assertEqual(str(b), '0.1')
b = a[0:3]
self.assertTrue(isinstance(b, Version))
self.assertEqual(b, Version('0.1_2'))
self.assertEqual(repr(b), 'Version(\'0.1_2\')')
self.assertEqual(str(b), '0.1_2')
b = a[1:]
self.assertTrue(isinstance(b, Version))
self.assertEqual(b, Version('1_2-3'))
self.assertEqual(repr(b), 'Version(\'1_2-3\')')
self.assertEqual(str(b), '1_2-3')
# Raise TypeError on tuples
self.assertRaises(TypeError, b.__getitem__, 1, 2)

27
lib/spack/spack/version.py
View File

@ -44,6 +44,7 @@
concrete concrete
""" """
import re import re
import numbers
from bisect import bisect_left from bisect import bisect_left
from functools import wraps from functools import wraps
@ -194,10 +195,24 @@ def __iter__(self):
return iter(self.version) return iter(self.version)
def __getitem__(self, idx): def __getitem__(self, idx):
return tuple(self.version[idx]) cls = type(self)
if isinstance(idx, numbers.Integral):
return self.version[idx]
elif isinstance(idx, slice):
# Currently len(self.separators) == len(self.version) - 1
extendend_separators = self.separators + ('',)
string_arg = []
for token, sep in zip(self.version, extendend_separators)[idx]:
string_arg.append(str(token))
string_arg.append(str(sep))
string_arg.pop() # We don't need the last separator
string_arg = ''.join(string_arg)
return cls(string_arg)
message = '{cls.__name__} indices must be integers'
raise TypeError(message.format(cls=cls))
def __repr__(self): def __repr__(self):
return self.string return 'Version(' + repr(self.string) + ')'
def __str__(self): def __str__(self):
return self.string return self.string
@ -221,6 +236,14 @@ def __lt__(self, other):
if self.version == other.version: if self.version == other.version:
return False return False
# dev is __gt__ than anything but itself.
if other.string == 'develop':
return True
# If lhs is dev then it can't be < than anything
if self.string == 'develop':
return False
for a, b in zip(self.version, other.version): for a, b in zip(self.version, other.version):
if a == b: if a == b:
continue continue

24
var/spack/repos/builtin/packages/R/package.py
View File

@ -40,6 +40,7 @@ class R(Package):
extendable = True extendable = True
version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
@ -87,6 +88,29 @@ def install(self, spec, prefix):
make() make()
make('install') make('install')
self.filter_compilers(spec, prefix)
def filter_compilers(self, spec, prefix):
"""Run after install to tell the configuration files and Makefiles
to use the compilers that Spack built the package with.
If this isn't done, they'll have CC and CXX set to Spack's generic
cc and c++. We want them to be bound to whatever compiler
they were built with."""
etcdir = join_path(prefix, 'rlib', 'R', 'etc')
kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
filter_file(env['CC'], self.compiler.cc,
join_path(etcdir, 'Makeconf'), **kwargs)
filter_file(env['CXX'], self.compiler.cxx,
join_path(etcdir, 'Makeconf'), **kwargs)
filter_file(env['F77'], self.compiler.f77,
join_path(etcdir, 'Makeconf'), **kwargs)
filter_file(env['FC'], self.compiler.fc,
join_path(etcdir, 'Makeconf'), **kwargs)
# ======================================================================== # ========================================================================
# Set up environment to make install easy for R extensions. # Set up environment to make install easy for R extensions.
# ======================================================================== # ========================================================================

24
var/spack/repos/builtin/packages/arpack-ng/make_install.patch Normal file
View File

@ -0,0 +1,24 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 607d221..50426c3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -389,3 +389,19 @@ target_link_libraries(bug_1323 arpack ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES})
add_test(bug_1323 Tests/bug_1323)
add_dependencies(check dnsimp_test bug_1315_single bug_1315_double bug_1323)
+
+############################
+# install
+############################
+# 'make install' to the correct location
+install(TARGETS arpack
+ ARCHIVE DESTINATION lib
+ LIBRARY DESTINATION lib
+ RUNTIME DESTINATION bin)
+
+if (MPI)
+ install(TARGETS parpack
+ ARCHIVE DESTINATION lib
+ LIBRARY DESTINATION lib
+ RUNTIME DESTINATION bin)
+endif ()

68
var/spack/repos/builtin/packages/arpack-ng/package.py
View File

@ -27,7 +27,8 @@
class ArpackNg(Package): class ArpackNg(Package):
""" """
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. ARPACK-NG is a collection of Fortran77 subroutines designed to solve large
scale eigenvalue problems.
Important Features: Important Features:
@ -38,43 +39,76 @@ class ArpackNg(Package):
Generalized Problems. Generalized Problems.
* Routines for Banded Matrices - Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems.
* Routines for The Singular Value Decomposition. * Routines for The Singular Value Decomposition.
* Example driver routines that may be used as templates to implement numerous * Example driver routines that may be used as templates to implement
Shift-Invert strategies for all problem types, data types and precision. numerous Shift-Invert strategies for all problem types, data types and
precision.
This project is a joint project between Debian, Octave and Scilab in order to This project is a joint project between Debian, Octave and Scilab in order
provide a common and maintained version of arpack. to provide a common and maintained version of arpack.
Indeed, no single release has been published by Rice university for the last Indeed, no single release has been published by Rice university for the
few years and since many software (Octave, Scilab, R, Matlab...) forked it and last few years and since many software (Octave, Scilab, R, Matlab...)
implemented their own modifications, arpack-ng aims to tackle this by providing forked it and implemented their own modifications, arpack-ng aims to tackle
a common repository and maintained versions. this by providing a common repository and maintained versions.
arpack-ng is replacing arpack almost everywhere. arpack-ng is replacing arpack almost everywhere.
""" """
homepage = 'https://github.com/opencollab/arpack-ng' homepage = 'https://github.com/opencollab/arpack-ng'
url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz' url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
variant('shared', default=True, description='Enables the build of shared libraries') variant('shared', default=True, description='Enables the build of shared libraries')
variant('mpi', default=False, description='Activates MPI support') variant('mpi', default=False, description='Activates MPI support')
# The function pdlamch10 does not set the return variable. This is fixed upstream # The function pdlamch10 does not set the return variable.
# This is fixed upstream
# see https://github.com/opencollab/arpack-ng/issues/34 # see https://github.com/opencollab/arpack-ng/issues/34
patch('pdlamch10.patch', when='@3.3:') patch('pdlamch10.patch', when='@3.3.0')
patch('make_install.patch', when='@3.4.0')
patch('parpack_cmake.patch', when='@3.4.0')
depends_on('blas') depends_on('blas')
depends_on('lapack') depends_on('lapack')
depends_on('automake') depends_on('automake', when='@3.3.0')
depends_on('autoconf') depends_on('autoconf', when='@3.3.0')
depends_on('libtool@2.4.2:') depends_on('libtool@2.4.2:', when='@3.3.0')
depends_on('cmake@2.8.6:', when='@3.4.0:')
depends_on('mpi', when='+mpi') depends_on('mpi', when='+mpi')
@when('@3.4.0:')
def install(self, spec, prefix):
options = ['-DEXAMPLES=ON']
options.extend(std_cmake_args)
options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
# TODO:
# Arpack calls directly find_package(BLAS REQUIRED) and
# find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are
# picked up.
if '+mpi' in spec:
options.append('-DMPI=ON')
# TODO: -DINTERFACE64=ON
if '+shared' in spec:
options.append('-DBUILD_SHARED_LIBS=ON')
cmake('.', *options)
make()
# TODO: make test does not work
# make('test')
make('install')
@when('@3.3.0')
def install(self, spec, prefix): def install(self, spec, prefix):
# Apparently autotools are not bootstrapped # Apparently autotools are not bootstrapped
# TODO: switch to use the CMake build in the next version
# rather than bootstrapping.
which('libtoolize')() which('libtoolize')()
bootstrap = Executable('./bootstrap') bootstrap = Executable('./bootstrap')
@ -83,7 +117,7 @@ def install(self, spec, prefix):
if '+mpi' in spec: if '+mpi' in spec:
options.extend([ options.extend([
'--enable-mpi', '--enable-mpi',
'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names 'F77=%s' % spec['mpi'].mpif77
]) ])
if '~shared' in spec: if '~shared' in spec:

18
var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch Normal file
View File

@ -0,0 +1,18 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 607d221..345b7fc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX})
if (MPI)
# add_library(parpack SHARED
- add_library(parpack
+ add_library(parpack
${parpacksrc_STAT_SRCS}
${parpackutil_STAT_SRCS})
target_link_libraries(parpack ${MPI_Fortran_LIBRARIES})
+ target_link_libraries(parpack arpack)
set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX})
endif ()

1
var/spack/repos/builtin/packages/cereal/package.py
View File

@ -31,6 +31,7 @@ class Cereal(Package):
homepage = "http://uscilab.github.io/cereal/" homepage = "http://uscilab.github.io/cereal/"
url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz" url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz"
version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b')
version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9') version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9')
version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27') version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27')
version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f') version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f')

14
var/spack/repos/builtin/packages/docbook-xml/package.py
View File

@ -23,7 +23,6 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
import os import os
import glob
from spack import * from spack import *
@ -35,9 +34,10 @@ class DocbookXml(Package):
version('4.5', '03083e288e87a7e829e437358da7ef9e') version('4.5', '03083e288e87a7e829e437358da7ef9e')
def install(self, spec, prefix): def install(self, spec, prefix):
cp = which('cp') for item in os.listdir('.'):
src = os.path.abspath(item)
install_args = ['-a', '-t', prefix] dst = os.path.join(prefix, item)
install_args.extend(glob.glob('*')) if os.path.isdir(item):
install_tree(src, dst, symlinks=True)
cp(*install_args) else:
install(src, dst)

46
var/spack/repos/builtin/packages/ibmisc/package.py Normal file
View File

@ -0,0 +1,46 @@
from spack import *
class Ibmisc(CMakePackage):
"""Misc. reusable utilities used by IceBin."""
homepage = "https://github.com/citibeth/ibmisc"
url = "https://github.com/citibeth/ibmisc/tarball/123"
version('0.1.0', '12f2a32432a11db48e00217df18e59fa')
variant('everytrace', default=False, description='Report errors through Everytrace')
variant('proj', default=True, description='Compile utilities for PROJ.4 library')
variant('blitz', default=True, description='Compile utilities for Blitz library')
variant('netcdf', default=True, description='Compile utilities for NetCDF library')
variant('boost', default=True, description='Compile utilities for Boost library')
variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library')
variant('googletest', default=True, description='Compile utilities for Google Test library')
variant('python', default=True, description='Compile utilities for use with Python/Cython')
extends('python')
depends_on('eigen')
depends_on('everytrace', when='+everytrace')
depends_on('proj', when='+proj')
depends_on('blitz', when='+blitz')
depends_on('netcdf-cxx4', when='+netcdf')
depends_on('udunits2', when='+udunits2')
depends_on('googletest', when='+googletest')
depends_on('py-cython', when='+python')
depends_on('py-numpy', when='+python')
depends_on('boost', when='+boost')
# Build dependencies
depends_on('cmake')
depends_on('doxygen')
def configure_args(self):
spec = self.spec
return [
'-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),
'-DUSE_PROJ4=%s' % ('YES' if '+proj' in spec else 'NO'),
'-DUSE_BLITZ=%s' % ('YES' if '+blitz' in spec else 'NO'),
'-DUSE_NETCDF=%s' % ('YES' if '+netcdf' in spec else 'NO'),
'-DUSE_BOOST=%s' % ('YES' if '+boost' in spec else 'NO'),
'-DUSE_UDUNITS2=%s' % ('YES' if '+udunits2' in spec else 'NO'),
'-DUSE_GTEST=%s' % ('YES' if '+googletest' in spec else 'NO')]

2
var/spack/repos/builtin/packages/intel/package.py
View File

@ -73,7 +73,7 @@ def install(self, spec, prefix):
COMPONENTS=%s COMPONENTS=%s
""" % (self.intel_prefix, self.global_license_file, self.intel_components)) """ % (self.intel_prefix, self.global_license_file, self.intel_components))
install_script = which("install.sh") install_script = Executable("./install.sh")
install_script('--silent', silent_config_filename) install_script('--silent', silent_config_filename)

3
var/spack/repos/builtin/packages/libjson-c/package.py
View File

@ -24,6 +24,7 @@
############################################################################## ##############################################################################
from spack import * from spack import *
class LibjsonC(Package): class LibjsonC(Package):
""" A JSON implementation in C """ """ A JSON implementation in C """
homepage = "https://github.com/json-c/json-c/wiki" homepage = "https://github.com/json-c/json-c/wiki"
@ -34,5 +35,5 @@ class LibjsonC(Package):
def install(self, spec, prefix): def install(self, spec, prefix):
configure('--prefix=%s' % prefix) configure('--prefix=%s' % prefix)
make() make(parallel=False)
make("install") make("install")

4
var/spack/repos/builtin/packages/lua/package.py
View File

@ -140,11 +140,11 @@ def setup_environment(self, spack_env, run_env):
@property @property
def lua_lib_dir(self): def lua_lib_dir(self):
return os.path.join('lib', 'lua', '%d.%d' % self.version[:2]) return os.path.join('lib', 'lua', self.version.up_to(2))
@property @property
def lua_share_dir(self): def lua_share_dir(self):
return os.path.join('share', 'lua', '%d.%d' % self.version[:2]) return os.path.join('share', 'lua', self.version.up_to(2))
def setup_dependent_package(self, module, ext_spec): def setup_dependent_package(self, module, ext_spec):
""" """

6
var/spack/repos/builtin/packages/mfem/package.py
View File

@ -31,11 +31,13 @@ class Mfem(Package):
homepage = 'http://www.mfem.org' homepage = 'http://www.mfem.org'
url = 'https://github.com/mfem/mfem' url = 'https://github.com/mfem/mfem'
# version('3.1', git='https://github.com/mfem/mfem.git', version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') url='http://goo.gl/Y9T75B', expand=False, preferred=True)
version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
url='http://goo.gl/xrScXn', expand=False) url='http://goo.gl/xrScXn', expand=False)
# version('3.1', git='https://github.com/mfem/mfem.git',
# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
variant('metis', default=False, description='Activate support for metis') variant('metis', default=False, description='Activate support for metis')
variant('hypre', default=False, description='Activate support for hypre') variant('hypre', default=False, description='Activate support for hypre')

119
var/spack/repos/builtin/packages/mumps/mumps-shared.patch
View File

@ -1,119 +0,0 @@
diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile
--- MUMPS_5.0.1/libseq/Makefile 2015-07-23 19:08:32.000000000 +0200
+++ MUMPS_5.0.1.new/libseq/Makefile 2016-06-07 10:41:16.585179151 +0200
@@ -8,11 +8,15 @@
include ../Makefile.inc
-libmpiseq: libmpiseq$(PLAT)$(LIBEXT)
+libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT)
libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o
$(AR)$@ mpi.o mpic.o elapse.o
$(RANLIB) $@
+
+libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o
+ $(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT)
+
.f.o:
$(FC) $(OPTF) -c $*.f $(OUTF)$*.o
.c.o:
diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile
--- MUMPS_5.0.1/Makefile 2015-07-23 19:08:29.000000000 +0200
+++ MUMPS_5.0.1.new/Makefile 2016-06-07 10:50:21.863281217 +0200
@@ -51,7 +51,7 @@
dexamples: d
(cd examples ; $(MAKE) d)
-requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT)
+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT)
# dummy MPI library (sequential version)
@@ -62,16 +62,25 @@
$(libdir)/libpord$(PLAT)$(LIBEXT):
if [ "$(LPORDDIR)" != "" ] ; then \
cd $(LPORDDIR); \
- $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \
fi;
if [ "$(LPORDDIR)" != "" ] ; then \
cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
fi;
+$(libdir)/libpord$(PLAT)$(SHLIBEXT):
+ if [ "$(LPORDDIR)" != "" ] ; then \
+ cd $(LPORDDIR); \
+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \
+ fi;
+ if [ "$(LPORDDIR)" != "" ] ; then \
+ cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \
+ fi;
+
clean:
(cd src; $(MAKE) clean)
(cd examples; $(MAKE) clean)
- (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT))
+ (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT))
(cd libseq; $(MAKE) clean)
if [ "$(LPORDDIR)" != "" ] ; then \
cd $(LPORDDIR); $(MAKE) realclean; \
diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile
--- MUMPS_5.0.1/PORD/lib/Makefile 2015-07-23 19:08:29.000000000 +0200
+++ MUMPS_5.0.1.new/PORD/lib/Makefile 2016-06-07 10:49:48.889000958 +0200
@@ -13,7 +13,7 @@
OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \
multisector.o gelim.o bucket.o tree.o \
- symbfac.o interface.o sort.o minpriority.o
+ symbfac.o interface.o sort.o minpriority.o
# Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c
# were not direcly used by MUMPS and have been removed from the
@@ -24,12 +24,15 @@
.c.o:
$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
-libpord$(LIBEXT):$(OBJS)
+libpord$(PLAT)$(LIBEXT):$(OBJS)
$(AR)$@ $(OBJS)
$(RANLIB) $@
+libpord$(PLAT)$(SHLIBEXT): $(OBJS)
+ $(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT)
+
clean:
rm -f *.o
realclean:
- rm -f *.o libpord.a
+ rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT)
diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile
--- MUMPS_5.0.1/src/Makefile 2015-07-23 19:08:29.000000000 +0200
+++ MUMPS_5.0.1.new/src/Makefile 2016-06-07 10:40:52.534703722 +0200
@@ -24,7 +24,10 @@
include $(topdir)/Makefile.inc
mumps_lib: $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \
- $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT)
+ $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \
+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \
+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
+
OBJS_COMMON_MOD = \
ana_omp_m.o\
@@ -162,6 +165,13 @@
$(AR)$@ $?
$(RANLIB) $@
+$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT): $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
+ $(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT)
+
+
+$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT): $(OBJS_MOD) $(OBJS_OTHER)
+ $(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
+
# Dependencies between modules:
$(ARITH)mumps_load.o: $(ARITH)mumps_comm_buffer.o \
$(ARITH)mumps_struc_def.o \

160
var/spack/repos/builtin/packages/mumps/package.py
View File

@ -23,10 +23,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
from spack import * from spack import *
import os import os, sys, glob
import sys
import subprocess
class Mumps(Package): class Mumps(Package):
"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@ -47,6 +44,7 @@ class Mumps(Package):
variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
variant('shared', default=True, description='Build shared libraries') variant('shared', default=True, description='Build shared libraries')
depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps', when='~ptscotch+scotch')
depends_on('scotch + esmumps + mpi', when='+ptscotch') depends_on('scotch + esmumps + mpi', when='+ptscotch')
depends_on('metis@5:', when='+metis') depends_on('metis@5:', when='+metis')
@ -56,64 +54,49 @@ class Mumps(Package):
depends_on('scalapack', when='+mpi') depends_on('scalapack', when='+mpi')
depends_on('mpi', when='+mpi') depends_on('mpi', when='+mpi')
patch('mumps-shared.patch', when='+shared')
# this function is not a patch function because in case scalapack # this function is not a patch function because in case scalapack
# is needed it uses self.spec['scalapack'].fc_link set by the # is needed it uses self.spec['scalapack'].fc_link set by the
# setup_dependent_environment in scalapck. This happen after patch # setup_dependent_environment in scalapck. This happen after patch
# end before install # end before install
# def patch(self): # def patch(self):
def write_makefile_inc(self): def write_makefile_inc(self):
if (('+parmetis' in self.spec or if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
'+ptscotch' in self.spec)) and '+mpi' not in self.spec: raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: E501
makefile_conf = [ makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
"LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib
]
orderings = ['-Dpord'] orderings = ['-Dpord']
if '+ptscotch' in self.spec or '+scotch' in self.spec: if '+ptscotch' in self.spec or '+scotch' in self.spec:
join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
makefile_conf.extend([ makefile_conf.extend(
"ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
"LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
join_lib, join_lib,
join_lib.join(['esmumps', join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
'scotch',
'scotcherr']))
])
orderings.append('-Dscotch') orderings.append('-Dscotch')
if '+ptscotch' in self.spec: if '+ptscotch' in self.spec:
orderings.append('-Dptscotch') orderings.append('-Dptscotch')
if '+parmetis' in self.spec and '+metis' in self.spec: if '+parmetis' in self.spec and '+metis' in self.spec:
makefile_conf.extend([ libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
"IMETIS = -I%s" % self.spec['parmetis'].prefix.include, makefile_conf.extend(
"LMETIS = -L%s -l%s -L%s -l%s" % ( ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
self.spec['parmetis'].prefix.lib, 'parmetis', "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
self.spec['metis'].prefix.lib, 'metis')
])
orderings.append('-Dparmetis') orderings.append('-Dparmetis')
elif '+metis' in self.spec: elif '+metis' in self.spec:
makefile_conf.extend([ makefile_conf.extend(
"IMETIS = -I%s" % self.spec['metis'].prefix.include, ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
"LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
'metis')
])
orderings.append('-Dmetis') orderings.append('-Dmetis')
makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
# when building shared libs need -fPIC, otherwise /usr/bin/ld: # when building shared libs need -fPIC, otherwise
# graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
# not be used when making a shared object; recompile with
# -fPIC
fpic = '-fPIC' if '+shared' in self.spec else '' fpic = '-fPIC' if '+shared' in self.spec else ''
# TODO: test this part, it needs a full blas, scalapack and # TODO: test this part, it needs a full blas, scalapack and
# partitionning environment with 64bit integers # partitionning environment with 64bit integers
if '+idx64' in self.spec: if '+idx64' in self.spec:
@ -121,7 +104,7 @@ def write_makefile_inc(self):
# the fortran compilation flags most probably are # the fortran compilation flags most probably are
# working only for intel and gnu compilers this is # working only for intel and gnu compilers this is
# perhaps something the compiler should provide # perhaps something the compiler should provide
['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: E501 ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
'OPTL = %s -O ' % fpic, 'OPTL = %s -O ' % fpic,
'OPTC = %s -O -DINTSIZE64' % fpic]) 'OPTC = %s -O -DINTSIZE64' % fpic])
else: else:
@ -130,47 +113,49 @@ def write_makefile_inc(self):
'OPTL = %s -O ' % fpic, 'OPTL = %s -O ' % fpic,
'OPTC = %s -O ' % fpic]) 'OPTC = %s -O ' % fpic])
if '+mpi' in self.spec: if '+mpi' in self.spec:
makefile_conf.extend( makefile_conf.extend(
["CC = %s" % self.spec['mpi'].mpicc, ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
"FC = %s" % self.spec['mpi'].mpifc, "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
"FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
"SCALAP = %s" % self.spec['scalapack'].fc_link, "SCALAP = %s" % self.spec['scalapack'].fc_link,
"MUMPS_TYPE = par"]) "MUMPS_TYPE = par"])
else: else:
makefile_conf.extend( makefile_conf.extend(
["CC = cc", ["CC = cc",
"FC = fc", "FC = fc",
"FL = fc",
"MUMPS_TYPE = seq"]) "MUMPS_TYPE = seq"])
# TODO: change the value to the correct one according to the # TODO: change the value to the correct one according to the
# compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
makefile_conf.extend([ makefile_conf.append("CDEFS = -DAdd_")
'CDEFS = -DAdd_',
'FL = $(FC)',
])
if '+shared' in self.spec: if '+shared' in self.spec:
makefile_conf.append('SHLIBEXT = .%s' % dso_suffix)
if sys.platform == 'darwin': if sys.platform == 'darwin':
makefile_conf.append( # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg) # NOQA: E501 makefile_conf.extend([
) 'LIBEXT=.dylib',
'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
'RANLIB=echo'
])
else: else:
makefile_conf.append( makefile_conf.extend([
'LDFLAGS = -shared {0}{1}'.format( 'LIBEXT=.so',
self.compiler.fc_rpath_arg, 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
prefix.lib) 'RANLIB=echo'
) ])
else:
makefile_conf.extend([
'LIBEXT = .a',
'AR = ar vr',
'RANLIB = ranlib'
])
makefile_conf.extend([
'LIBEXT = .a',
'AR = ar vr ',
'RANLIB = ranlib'
])
makefile_inc_template = \ makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
join_path(os.path.dirname(self.module.__file__), 'Makefile.inc')
'Makefile.inc')
with open(makefile_inc_template, "r") as fh: with open(makefile_inc_template, "r") as fh:
makefile_conf.extend(fh.read().split('\n')) makefile_conf.extend(fh.read().split('\n'))
@ -179,53 +164,46 @@ def write_makefile_inc(self):
makefile_inc = '\n'.join(makefile_conf) makefile_inc = '\n'.join(makefile_conf)
fh.write(makefile_inc) fh.write(makefile_inc)
def install(self, spec, prefix): def install(self, spec, prefix):
make_libs = [] make_libs = []
# the choice to compile ?examples is to have kind of a sanity # the choice to compile ?examples is to have kind of a sanity
# check on the libraries generated. # check on the libraries generated.
if '+float' in spec: if '+float' in spec:
make_libs.append('s') make_libs.append('sexamples')
if '+complex' in spec: if '+complex' in spec:
make_libs.append('c') make_libs.append('cexamples')
if '+double' in spec: if '+double' in spec:
make_libs.append('d') make_libs.append('dexamples')
if '+complex' in spec: if '+complex' in spec:
make_libs.append('z') make_libs.append('zexamples')
self.write_makefile_inc() self.write_makefile_inc()
make('mumps_lib', parallel=False) # Build fails in parallel
make(*make_libs) make(*make_libs, parallel=False)
install_tree('lib', prefix.lib) install_tree('lib', prefix.lib)
install_tree('include', prefix.include) install_tree('include', prefix.include)
if '~mpi' in spec: if '~mpi' in spec:
install('libseq/libmpiseq.a', prefix.lib) lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
if '+shared' in spec: lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib) install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
install('libseq/mpi.h', prefix.include) for f in glob.glob(join_path('libseq','*.h')):
install('libseq/mpif.h', prefix.include) install(f, prefix.include)
# FIXME: extend the tests to mpirun -np 2 (or alike) when # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
# build with MPI # FIXME: use something like numdiff to compare blessed output with the current
# FIXME: use something like numdiff to compare blessed output with working_dir('examples'):
# with the current if '+float' in spec:
# TODO: test the installed mumps and not the one in stage os.system('./ssimpletest < input_simpletest_real')
if '~mpi' in spec: if '+complex' in spec:
for t in make_libs: os.system('./csimpletest < input_simpletest_real')
make('{0}examples'.format(t)) if '+double' in spec:
os.system('./dsimpletest < input_simpletest_real')
with working_dir('examples'): if '+complex' in spec:
for t in make_libs: os.system('./zsimpletest < input_simpletest_cmplx')
input_file = 'input_simpletest_{0}'.format(
'real' if t in ['s', 'd'] else 'cmplx')
with open(input_file) as input:
test = './{0}simpletest'.format(t)
ret = subprocess.call(test,
stdin=input)
if ret is not 0:
raise RuntimeError(
'The test {0} did not pass'.format(test))

33
var/spack/repos/builtin/packages/oce/package.py
View File

@ -23,20 +23,22 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
from spack import * from spack import *
import platform, sys import platform
class Oce(Package): class Oce(Package):
""" """Open CASCADE Community Edition:
Open CASCADE Community Edition: patches/improvements/experiments contributed by users over the official
patches/improvements/experiments contributed by users over the official Open CASCADE library. Open CASCADE library.
""" """
homepage = "https://github.com/tpaviot/oce" homepage = "https://github.com/tpaviot/oce"
url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz"
version('0.17.2', 'bf2226be4cd192606af677cf178088e5')
version('0.17.1', '36c67b87093c675698b483454258af91') version('0.17.1', '36c67b87093c675698b483454258af91')
version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') version('0.17', 'f1a89395c4b0d199bea3db62b85f818d')
version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') version('0.16', '7a4b4df5a104d75a537e25e7dd387eca')
variant('tbb', default=True, description='Build with Intel Threading Building Blocks') variant('tbb', default=True, description='Build with Intel Threading Building Blocks')
@ -49,8 +51,7 @@ class Oce(Package):
# http://tracker.dev.opencascade.org/view.php?id=26042 # http://tracker.dev.opencascade.org/view.php?id=26042
# https://github.com/tpaviot/oce/issues/605 # https://github.com/tpaviot/oce/issues/605
# https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch
patch('null.patch',when='@0.16:0.17.1') patch('null.patch', when='@0.16:0.17.1')
def install(self, spec, prefix): def install(self, spec, prefix):
options = [] options = []
@ -63,7 +64,8 @@ def install(self, spec, prefix):
'-DOCE_DISABLE_X11:BOOL=ON', '-DOCE_DISABLE_X11:BOOL=ON',
'-DOCE_DRAW:BOOL=OFF', '-DOCE_DRAW:BOOL=OFF',
'-DOCE_MODEL:BOOL=ON', '-DOCE_MODEL:BOOL=ON',
'-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'), '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % (
'TBB' if '+tbb' in spec else 'NONE'),
'-DOCE_OCAF:BOOL=ON', '-DOCE_OCAF:BOOL=ON',
'-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
'-DOCE_VISUALISATION:BOOL=OFF', '-DOCE_VISUALISATION:BOOL=OFF',
@ -77,15 +79,8 @@ def install(self, spec, prefix):
'-DOCE_OSX_USE_COCOA:BOOL=ON', '-DOCE_OSX_USE_COCOA:BOOL=ON',
]) ])
options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
cmake('.', *options) cmake('.', *options)
make("install/strip") make("install/strip")
make("test")
# OCE tests build is brocken at least on Darwin.
# Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib
# see https://github.com/tpaviot/oce/issues/612
# make("test")
# The shared libraries are not installed correctly on Darwin; correct this
if (sys.platform == 'darwin'):
fix_darwin_install_name(prefix.lib)

2
var/spack/repos/builtin/packages/octave/package.py
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@ -61,7 +61,7 @@ class Octave(Package):
variant('qrupdate', default=False) variant('qrupdate', default=False)
variant('qscintilla', default=False) variant('qscintilla', default=False)
variant('qt', default=False) variant('qt', default=False)
variant('suiteparse', default=False) variant('suitesparse', default=False)
variant('zlib', default=False) variant('zlib', default=False)
# Required dependencies # Required dependencies

64
var/spack/repos/builtin/packages/openssl/package.py
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@ -35,7 +35,7 @@ class Openssl(Package):
Transport Layer Security (TLS v1) protocols as well as a Transport Layer Security (TLS v1) protocols as well as a
full-strength general purpose cryptography library.""" full-strength general purpose cryptography library."""
homepage = "http://www.openssl.org" homepage = "http://www.openssl.org"
url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz" url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz"
version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
version('1.0.1r', '1abd905e079542ccae948af37e393d28') version('1.0.1r', '1abd905e079542ccae948af37e393d28')
@ -50,21 +50,25 @@ class Openssl(Package):
parallel = False parallel = False
def url_for_version(self, version): def url_for_version(self, version):
# This URL is computed pinging the place where the latest version is stored. To avoid slowdown # This URL is computed pinging the place where the latest version is
# due to repeated pinging, we store the URL in a private class attribute to do the job only once per version # stored. To avoid slowdown due to repeated pinging, we store the URL
# in a private class attribute to do the job only once per version
openssl_urls = getattr(Openssl, '_openssl_url', {}) openssl_urls = getattr(Openssl, '_openssl_url', {})
openssl_url = openssl_urls.get(version, None) openssl_url = openssl_urls.get(version, None)
# Same idea, but just to avoid issuing the same message multiple times # Same idea, but just to avoid issuing the same message multiple times
warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) warnings_given_to_user = getattr(Openssl, '_warnings_given', {})
if openssl_url is None: if openssl_url is None:
if self.spec.satisfies('@external'): if self.spec.satisfies('@system'):
# The version @external is reserved to system openssl. In that case return a fake url and exit # The version @system is reserved to system openssl. In that
openssl_url = '@external (reserved version for system openssl)' # case return a fake url and exit
openssl_url = '@system (reserved version for system openssl)'
if not warnings_given_to_user.get(version, False): if not warnings_given_to_user.get(version, False):
tty.msg('Using openssl@external : the version @external is reserved for system openssl') tty.msg('Using openssl@system: '
'the version @system is reserved for system openssl')
warnings_given_to_user[version] = True warnings_given_to_user[version] = True
else: else:
openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL openssl_url = self.check_for_outdated_release(
version, warnings_given_to_user) # Store the computed URL
openssl_urls[version] = openssl_url openssl_urls[version] = openssl_url
# Store the updated dictionary of URLS # Store the updated dictionary of URLS
Openssl._openssl_url = openssl_urls Openssl._openssl_url = openssl_urls
@ -75,45 +79,55 @@ def url_for_version(self, version):
def check_for_outdated_release(self, version, warnings_given_to_user): def check_for_outdated_release(self, version, warnings_given_to_user):
latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz' latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz'
older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' # NOQA: ignore=E501
# Try to use the url where the latest tarballs are stored. If the url does not exist (404), then # Try to use the url where the latest tarballs are stored.
# return the url for older format # If the url does not exist (404), then return the url for
# older format
version_number = '.'.join([str(x) for x in version[:-1]]) version_number = '.'.join([str(x) for x in version[:-1]])
try: try:
openssl_url = latest.format(version=version) openssl_url = latest.format(version=version)
urllib.urlopen(openssl_url) urllib.urlopen(openssl_url)
except IOError: except IOError:
openssl_url = older.format(version_number=version_number, version_full=version) openssl_url = older.format(
# Checks if we already warned the user for this particular version of OpenSSL. version_number=version_number, version_full=version)
# If not we display a warning message and mark this version # Checks if we already warned the user for this particular
# version of OpenSSL. If not we display a warning message
# and mark this version
if not warnings_given_to_user.get(version, False): if not warnings_given_to_user.get(version, False):
tty.warn( tty.warn(
'This installation depends on an old version of OpenSSL, which may have known security issues. ') 'This installation depends on an old version of OpenSSL, '
tty.warn('Consider updating to the latest version of this package.') 'which may have known security issues. ')
tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) tty.warn(
'Consider updating to the latest version of this package.')
tty.warn('More details at {homepage}'.format(
homepage=Openssl.homepage))
warnings_given_to_user[version] = True warnings_given_to_user[version] = True
return openssl_url return openssl_url
def install(self, spec, prefix): def install(self, spec, prefix):
# OpenSSL uses a variable APPS in its Makefile. If it happens to be set # OpenSSL uses a variable APPS in its Makefile. If it happens to be set
# in the environment, then this will override what is set in the # in the environment, then this will override what is set in the
# Makefile, leading to build errors. # Makefile, leading to build errors.
env.pop('APPS', None) env.pop('APPS', None)
if spec.satisfies("target=x86_64") or spec.satisfies("target=ppc64"):
if spec.satisfies('target=x86_64') or spec.satisfies('target=ppc64'):
# This needs to be done for all 64-bit architectures (except Linux, # This needs to be done for all 64-bit architectures (except Linux,
# where it happens automatically?) # where it happens automatically?)
env['KERNEL_BITS'] = '64' env['KERNEL_BITS'] = '64'
config = Executable("./config")
config("--prefix=%s" % prefix, options = ['zlib', 'no-krb5', 'shared']
"--openssldir=%s" % join_path(prefix, 'etc', 'openssl'),
"zlib", config = Executable('./config')
"no-krb5", config('--prefix=%s' % prefix,
"shared") '--openssldir=%s' % join_path(prefix, 'etc', 'openssl'),
*options)
# Remove non-standard compiler options if present. These options are # Remove non-standard compiler options if present. These options are
# present e.g. on Darwin. They are non-standard, i.e. most compilers # present e.g. on Darwin. They are non-standard, i.e. most compilers
# (e.g. gcc) will not accept them. # (e.g. gcc) will not accept them.
filter_file(r'-arch x86_64', '', 'Makefile') filter_file(r'-arch x86_64', '', 'Makefile')
make() make()
make("install") make('install')

26
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@ -149,20 +149,22 @@ def install(self, spec, prefix):
make("install") make("install")
# solve Poisson equation in 2D to make sure nothing is broken: # solve Poisson equation in 2D to make sure nothing is broken:
with working_dir('src/ksp/ksp/examples/tutorials'): if ('mpi' in spec) and self.run_tests:
cc = os.environ['CC'] if '~mpi' in self.spec else self.spec['mpi'].mpicc # NOQA: ignore=E501 with working_dir('src/ksp/ksp/examples/tutorials'):
os.system('%s ex50.c -I%s -L%s -lpetsc -o ex50' % ( env['PETSC_DIR'] = self.prefix
cc, prefix.include, prefix.lib)) cc = Executable(spec['mpi'].mpicc)
ex50 = Executable('./ex50') cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib,
ex50('-da_grid_x', '4', '-da_grid_y', '4') '-lpetsc', '-lm', '-o', 'ex50')
if 'superlu-dist' in spec: run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun'))
ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 run('ex50', '-da_grid_x', '4', '-da_grid_y', '4')
if 'superlu-dist' in spec:
run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501
if 'mumps' in spec: if 'mumps' in spec:
ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501
if 'hypre' in spec: if 'hypre' in spec:
ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501
def setup_dependent_environment(self, spack_env, run_env, dependent_spec): def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# set up PETSC_DIR for everyone using PETSc package # set up PETSC_DIR for everyone using PETSc package

4
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@ -43,8 +43,8 @@ class PyH5py(Package):
# Build dependencies # Build dependencies
depends_on('py-cython@0.19:') depends_on('py-cython@0.19:')
depends_on('pkg-config') depends_on('pkg-config')
depends_on('hdf5@1.8.4:+mpi', when='+mpi') depends_on('hdf5@1.8.4:')
depends_on('hdf5@1.8.4:~mpi', when='~mpi') depends_on('hdf5+mpi', when='+mpi')
depends_on('mpi', when='+mpi') depends_on('mpi', when='+mpi')
# Build and runtime dependencies # Build and runtime dependencies

5
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@ -47,6 +47,8 @@ class Python(Package):
extendable = True extendable = True
variant('ucs4', default=False, description='Enable UCS4 unicode strings')
depends_on("openssl") depends_on("openssl")
depends_on("bzip2") depends_on("bzip2")
depends_on("readline") depends_on("readline")
@ -82,6 +84,9 @@ def install(self, spec, prefix):
"LDFLAGS=-L{0}".format(ldflags) "LDFLAGS=-L{0}".format(ldflags)
] ]
if '+ucs4' in spec:
config_args.append('--enable-unicode=ucs4')
if spec.satisfies('@3:'): if spec.satisfies('@3:'):
config_args.append('--without-ensurepip') config_args.append('--without-ensurepip')

54
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@ -0,0 +1,54 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RBh(Package):
"""Boost provides free peer-reviewed portable C++ source libraries. A large
part of Boost is provided as C++ template code which is resolved entirely
at compile-time without linking. This package aims to provide the most
useful subset of Boost libraries for template use among CRAN package. By
placing these libraries in this package, we offer a more efficient
distribution system for CRAN as replication of this code in the sources of
other packages is avoided. As of release 1.60.0-2, the following Boost
libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer'
'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset'
'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion'
'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io'
'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric'
'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit'
'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'."""
homepage = "https://cran.r-project.org/web/packages/BH/index.html"
url = "https://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/BH"
version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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@ -0,0 +1,44 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RColorspace(Package):
"""Carries out mapping between assorted color spaces including RGB, HSV,
HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided."""
homepage = "https://cran.r-project.org/web/packages/colorspace/index.html"
url = "https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace"
version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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@ -0,0 +1,42 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RDichromat(Package):
"""Collapse red-green or green-blue distinctions to simulate the effects of
different types of color-blindness."""
homepage = "https://cran.r-project.org/web/packages/dichromat/index.html"
url = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat"
version('2.0-0', '84e194ac95a69763d740947a7ee346a6')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

54
var/spack/repos/builtin/packages/r-ggplot2/package.py Normal file
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@ -0,0 +1,54 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RGgplot2(Package):
"""An implementation of the grammar of graphics in R. It combines the
advantages of both base and lattice graphics: conditioning and shared axes
are handled automatically, and you can still build up a plot step by step
from multiple data sources. It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map data
to aesthetic attributes. See http://ggplot2.org for more information,
documentation and examples."""
homepage = "http://ggplot2.org/"
url = "https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2"
version('2.1.0', '771928cfb97c649c720423deb3ec7fd3')
extends('R')
depends_on('r-digest')
depends_on('r-gtable')
depends_on('r-mass')
depends_on('r-plyr')
depends_on('r-reshape2')
depends_on('r-scales')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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@ -0,0 +1,44 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RGridextra(Package):
"""Provides a number of user-level functions to work with "grid" graphics,
notably to arrange multiple grid-based plots on a page, and draw tables."""
homepage = "https://github.com/baptiste/gridextra"
url = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtra"
version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2')
extends('R')
depends_on('r-gtable')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

41
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@ -0,0 +1,41 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RGtable(Package):
"""Tools to make it easier to work with "tables" of 'grobs'."""
homepage = "https://cran.r-project.org/web/packages/gtable/index.html"
url = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/gtable"
version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RInline(Package):
"""Functionality to dynamically define R functions and S4 methods with
inlined C, C++ or Fortran code supporting .C and .Call calling
conventions."""
homepage = "https://cran.r-project.org/web/packages/inline/index.html"
url = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/inline"
version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RLabeling(Package):
"""Provides a range of axis labeling algorithms."""
homepage = "https://cran.r-project.org/web/packages/labeling/index.html"
url = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/labeling"
version('0.3', 'ccd7082ec0b211aba8a89d85176bb534')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RLattice(Package):
"""A powerful and elegant high-level data visualization system inspired by
Trellis graphics, with an emphasis on multivariate data. Lattice is
sufficient for typical graphics needs, and is also flexible enough to
handle most nonstandard requirements. See ?Lattice for an introduction."""
homepage = "http://lattice.r-forge.r-project.org/"
url = "https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/lattice"
version('0.20-33', 'd487c94db1bfe00a27270f4c71baf53e')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMagrittr(Package):
"""Provides a mechanism for chaining commands with a new forward-pipe
operator, %>%. This operator will forward a value, or the result of an
expression, into the next function call/expression. There is flexible
support for the type of right-hand side expressions. For more information,
see package vignette."""
homepage = "https://cran.r-project.org/web/packages/magrittr/index.html"
url = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr"
version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMass(Package):
"""Functions and datasets to support Venables and Ripley, "Modern Applied
Statistics with S" (4th edition, 2002)."""
homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
url = "https://cran.r-project.org/src/contrib/MASS_7.3-45.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/MASS"
version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMatrix(Package):
"""Classes and methods for dense and sparse matrices and operations on them
using 'LAPACK' and 'SuiteSparse'."""
homepage = "http://matrix.r-forge.r-project.org/"
url = "https://cran.r-project.org/src/contrib/Matrix_1.2-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix"
version('1.2-6', 'f545307fb1284861e9266c4e9712c55e')
extends('R')
depends_on('r-lattice')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMunsell(Package):
"""Provides easy access to, and manipulation of, the Munsell colours.
Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and
hexadecimal strings suitable for use directly in R graphics. Also provides
utilities to explore slices through the Munsell colour tree, to transform
Munsell colours and display colour palettes."""
homepage = "https://cran.r-project.org/web/packages/munsell/index.html"
url = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/munsell"
version('0.4.3', 'ebd205323dc37c948f499ee08be9c476')
extends('R')
depends_on('r-colorspace')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RPlyr(Package):
"""A set of tools that solves a common set of problems: you need to break a
big problem down into manageable pieces, operate on each piece and then put
all the pieces back together. For example, you might want to fit a model to
each spatial location or time point in your study, summarise data by panels
or collapse high-dimensional arrays to simpler summary statistics. The
development of 'plyr' has been generously supported by 'Becton
Dickinson'."""
homepage = "http://had.co.nz/plyr"
url = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/plyr"
version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b')
extends('R')
depends_on('r-rcpp')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RRcolorbrewer(Package):
"""Provides color schemes for maps (and other graphics) designed by Cynthia
Brewer as described at http://colorbrewer2.org"""
homepage = "http://colorbrewer2.org"
url = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer"
version('1.1-2', '66054d83eade4dff8a43ad4732691182')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RRcpp(Package):
"""The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects
can be mapped back and forth to C++ equivalents which facilitates both
writing of new code as well as easier integration of third-party libraries.
Documentation about 'Rcpp' is provided by several vignettes included in
this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the
paper by Eddelbuettel and Francois (2011, JSS), and the book by
Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these
last two."""
homepage = "http://dirk.eddelbuettel.com/code/rcpp.html"
url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp"
version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RRcppeigen(Package):
"""R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template
library for linear algebra: matrices, vectors, numerical solvers and
related algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices, and
solutions of linear systems. Its performance on many algorithms is
comparable with some of the best implementations based on 'Lapack' and
level-3 'BLAS'. The 'RcppEigen' package includes the header files from the
'Eigen' C++ template library (currently version 3.2.8). Thus users do not
need to install 'Eigen' itself in order to use 'RcppEigen'. Since version
3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2);
earlier version were licensed under the GNU LGPL version 3 or later.
'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'."""
homepage = "http://eigen.tuxfamily.org/"
url = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.8.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen"
version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f')
extends('R')
depends_on('r-matrix')
depends_on('r-rcpp')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RReshape2(Package):
"""Flexibly restructure and aggregate data using just two functions: melt
and dcast (or acast)."""
homepage = "https://github.com/hadley/reshape"
url = "https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2"
version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00')
extends('R')
depends_on('r-plyr')
depends_on('r-stringr')
depends_on('r-rcpp')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RRstan(Package):
"""User-facing R functions are provided to parse, compile, test, estimate,
and analyze Stan models by accessing the header-only Stan library provided
by the 'StanHeaders' package. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference
via Markov Chain Monte Carlo, rough Bayesian inference via variational
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to
quickly and accurately evaluate gradients without burdening the user with
the need to derive the partial derivatives."""
homepage = "http://mc-stan.org/"
url = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/rstan"
version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a')
extends('R')
depends_on('r-ggplot2')
depends_on('r-stanheaders')
depends_on('r-inline')
depends_on('r-gridextra')
depends_on('r-rcpp')
depends_on('r-rcppeigen')
depends_on('r-bh')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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@ -0,0 +1,49 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RScales(Package):
"""Graphical scales map data to aesthetics, and provide methods for
automatically determining breaks and labels for axes and legends."""
homepage = "https://github.com/hadley/scales"
url = "https://cran.r-project.org/src/contrib/scales_0.4.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/scales"
version('0.4.0', '7b5602d9c55595901192248bca25c099')
extends('R')
depends_on('r-rcolorbrewer')
depends_on('r-dichromat')
depends_on('r-plyr')
depends_on('r-munsell')
depends_on('r-labeling')
depends_on('r-rcpp')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

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@ -0,0 +1,55 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RStanheaders(Package):
"""The C++ header files of the Stan project are provided by this package,
but it contains no R code, vignettes, or function documentation. There is a
shared object containing part of the CVODES library, but it is not
accessible from R. StanHeaders is only useful for developers who want to
utilize the LinkingTo directive of their package's DESCRIPTION file to
build on the Stan library without incurring unnecessary dependencies. The
Stan project develops a probabilistic programming language that implements
full or approximate Bayesian statistical inference via Markov Chain Monte
Carlo or variational methods and implements (optionally penalized) maximum
likelihood estimation via optimization. The Stan library includes an
advanced automatic differentiation scheme, templated statistical and linear
algebra functions that can handle the automatically differentiable scalar
types (and doubles, ints, etc.), and a parser for the Stan language. The
'rstan' package provides user-facing R functions to parse, compile, test,
estimate, and analyze Stan models."""
homepage = "http://mc-stan.org/"
url = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders"
version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

51
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@ -0,0 +1,51 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RStringi(Package):
"""Allows for fast, correct, consistent, portable, as well as convenient
character string/text processing in every locale and any native encoding.
Owing to the use of the ICU library, the package provides R users with
platform-independent functions known to Java, Perl, Python, PHP, and Ruby
programmers. Among available features there are: pattern searching (e.g.,
with ICU Java-like regular expressions or the Unicode Collation Algorithm),
random string generation, case mapping, string transliteration,
concatenation, Unicode normalization, date-time formatting and parsing,
etc."""
homepage = "http://www.gagolewski.com/software/stringi/"
url = "https://cran.r-project.org/src/contrib/stringi_1.1.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/stringi"
version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9')
extends('R')
depends_on('icu')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

48
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@ -0,0 +1,48 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RStringr(Package):
"""A consistent, simple and easy to use set of wrappers around the
fantastic 'stringi' package. All function and argument names (and
positions) are consistent, all functions deal with "NA"'s and zero length
vectors in the same way, and the output from one function is easy to feed
into the input of another."""
homepage = "https://cran.r-project.org/web/packages/stringr/index.html"
url = "https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/stringr"
version('1.0.0', '5ca977c90351f78b1b888b379114a7b4')
extends('R')
depends_on('r-stringi')
depends_on('r-magrittr')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

13
var/spack/repos/builtin/packages/ruby/package.py
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@ -35,9 +35,20 @@ class Ruby(Package):
extendable = True extendable = True
version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852') version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852')
depends_on('libffi')
depends_on('zlib')
variant('openssl', default=False, description="Enable OpenSSL support")
depends_on('openssl', when='+openssl')
variant('readline', default=False, description="Enable Readline support")
depends_on('readline', when='+readline')
def install(self, spec, prefix): def install(self, spec, prefix):
configure("--prefix=%s" % prefix) options = ["--prefix=%s" % prefix]
if '+openssl' in spec:
options.append("--with-openssl-dir=%s" % spec['openssl'].prefix)
if '+readline' in spec:
options.append("--with-readline-dir=%s" % spec['readline'].prefix)
configure(*options)
make() make()
make("install") make("install")

32
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@ -0,0 +1,32 @@
From 7489a3f3d569e2fbf5513ac9dcd769017d9f7eb7 Mon Sep 17 00:00:00 2001
From: Lisandro Dalcin <dalcinl@gmail.com>
Date: Thu, 2 Jun 2016 21:57:38 +0300
Subject: [PATCH] OS X: Fix library path in invocation of install_name_tool
---
config/install.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/config/install.py b/config/install.py
index 09acd03..6ce98ae 100755
--- a/config/install.py
+++ b/config/install.py
@@ -25,6 +25,7 @@ class Installer:
def setupDirectories(self):
self.installDir = self.destDir
+ self.archDir = os.path.join(self.rootDir, self.arch)
self.rootIncludeDir = os.path.join(self.rootDir, 'include')
self.archIncludeDir = os.path.join(self.rootDir, self.arch, 'include')
self.rootConfDir = os.path.join(self.rootDir, 'lib','slepc','conf')
@@ -220,7 +221,7 @@ for dir in dirs:
if os.path.splitext(dst)[1] == '.dylib' and os.path.isfile('/usr/bin/install_name_tool'):
(result, output) = commands.getstatusoutput('otool -D '+src)
oldname = output[output.find("\n")+1:]
- installName = oldname.replace(self.destDir, self.installDir)
+ installName = oldname.replace(self.archDir, self.installDir)
(result, output) = commands.getstatusoutput('/usr/bin/install_name_tool -id ' + installName + ' ' + dst)
# preserve the original timestamps - so that the .a vs .so time order is preserved
shutil.copystat(src,dst)
--
2.7.4.1.g5468f9e

15
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@ -28,7 +28,7 @@
class Slepc(Package): class Slepc(Package):
""" """
Scalable Library for Eigenvalue Computations. Scalable Library for Eigenvalue Problem Computations.
""" """
homepage = "http://www.grycap.upv.es/slepc" homepage = "http://www.grycap.upv.es/slepc"
@ -45,9 +45,13 @@ class Slepc(Package):
depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi') depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi')
depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi') depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi')
patch('install_name_371.patch', when='@3.7.1')
def install(self, spec, prefix): def install(self, spec, prefix):
# set SLEPC_DIR for installation # set SLEPC_DIR for installation
os.environ['SLEPC_DIR'] = self.stage.source_path # Note that one should set the current (temporary) directory instead
# its symlink in spack/stage/ !
os.environ['SLEPC_DIR'] = os.getcwd()
options = [] options = []
@ -67,9 +71,10 @@ def install(self, spec, prefix):
configure('--prefix=%s' % prefix, *options) configure('--prefix=%s' % prefix, *options)
make('MAKE_NP=%s' % make_jobs, parallel=False) make('MAKE_NP=%s' % make_jobs, parallel=False)
# FIXME: if self.run_tests:
# make('test') make('test', parallel=False)
make('install')
make('install', parallel=False)
def setup_dependent_environment(self, spack_env, run_env, dependent_spec): def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# set up SLEPC_DIR for everyone using SLEPc package # set up SLEPC_DIR for everyone using SLEPc package

41
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@ -33,6 +33,7 @@ class SuiteSparse(Package):
url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
# FIXME: (see below) # FIXME: (see below)
# variant('tbb', default=True, description='Build with Intel TBB') # variant('tbb', default=True, description='Build with Intel TBB')
@ -40,34 +41,35 @@ class SuiteSparse(Package):
depends_on('blas') depends_on('blas')
depends_on('lapack') depends_on('lapack')
depends_on('metis@5.1.0', when='@4.5.1') depends_on('metis@5.1.0', when='@4.5.1:')
# FIXME: # FIXME:
# in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
# does not seem to be used, which leads to linking errors on Linux. # flags does not seem to be used, which leads to linking errors on Linux.
# Try re-enabling in future versions. # Try re-enabling in future versions.
# depends_on('tbb', when='+tbb') # depends_on('tbb', when='+tbb')
def install(self, spec, prefix): def install(self, spec, prefix):
# The build system of SuiteSparse is quite old-fashioned # The build system of SuiteSparse is quite old-fashioned.
# It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) # It's basically a plain Makefile which include an header
# with a lot of convoluted logic in it. # (SuiteSparse_config/SuiteSparse_config.mk)with a lot of convoluted
# Any kind of customization will need to go through filtering of that file # logic in it. Any kind of customization will need to go through
# filtering of that file
make_args = ['INSTALL=%s' % prefix] make_args = ['INSTALL=%s' % prefix]
# inject Spack compiler wrappers # inject Spack compiler wrappers
make_args.extend([ make_args.extend([
'AUTOCC=no', 'AUTOCC=no',
'CC=cc', 'CC=cc',
'CXX=c++', 'CXX=c++',
'F77=f77', 'F77=f77',
]) ])
# use Spack's metis in CHOLMOD/Partition module, # use Spack's metis in CHOLMOD/Partition module,
# otherwise internal Metis will be compiled # otherwise internal Metis will be compiled
make_args.extend([ make_args.extend([
'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib,
'MY_METIS_INC=%s' % spec['metis'].prefix.include, 'MY_METIS_INC=%s' % spec['metis'].prefix.include,
]) ])
# Intel TBB in SuiteSparseQR # Intel TBB in SuiteSparseQR
@ -78,10 +80,13 @@ def install(self, spec, prefix):
]) ])
# BLAS arguments require path to libraries # BLAS arguments require path to libraries
# FIXME : (blas / lapack always provide libblas and liblapack as aliases) # FIXME: (blas/lapack always provide libblas and liblapack as aliases)
make_args.extend([ if '@4.5.1' in spec:
'BLAS=-lblas', # adding -lstdc++ is clearly an ugly way to do this, but it follows
'LAPACK=-llapack' # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk
]) make_args.extend([
'BLAS=-lblas -lstdc++',
'LAPACK=-llapack'
])
make('install', *make_args) make('install', *make_args)