Transferred pending changes from efischer/develop

lib/spack/docs/basic_usage.rst

@@ -1246,6 +1246,82 @@ overrides ``setup_dependent_environment`` in the following way:
 to insert the appropriate ``PYTHONPATH`` modifications in the module
 files of python packages.
 
+
+Recursive Modules
+``````````````````
+
+In some cases, it is desirable to load not just a module, but also all
+the modules it depends on.  This is not required for most modules
+because Spack builds binaries with RPATH support.  However, not all
+packages use RPATH to find their dependencies: this can be true in
+particular for Python extensions, which are currently *not* built with
+RPATH.
+
+Modules may be loaded recursively with the command:
+
+.. code-block:: sh
+
+    $ module load `spack module tcl --dependencies <spec>...
+
+More than one spec may be placed on the command line here.
+
+Module Comamnds for Shell Scripts
+``````````````````````````````````
+
+Although Spack is flexbile, the ``module`` command is much faster.
+This could become an issue when emitting a series of ``spack load``
+commands inside a shell script.  By adding the ``--shell`` flag,
+``spack module find`` may also be used to generate code that can be
+cut-and-pasted into a shell script.  For example:
+
+.. code-block:: sh
+
+    $ spack module find tcl --dependencies --shell py-numpy git
+    # bzip2@1.0.6%gcc@4.9.3=linux-x86_64
+    module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
+    # ncurses@6.0%gcc@4.9.3=linux-x86_64
+    module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
+    # zlib@1.2.8%gcc@4.9.3=linux-x86_64
+    module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
+    # sqlite@3.8.5%gcc@4.9.3=linux-x86_64
+    module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
+    # readline@6.3%gcc@4.9.3=linux-x86_64
+    module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
+    # python@3.5.1%gcc@4.9.3=linux-x86_64
+    module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
+    # py-setuptools@20.5%gcc@4.9.3=linux-x86_64
+    module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
+    # py-nose@1.3.7%gcc@4.9.3=linux-x86_64
+    module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
+    # openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64
+    module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
+    # py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64
+    module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
+    # curl@7.47.1%gcc@4.9.3=linux-x86_64
+    module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
+    # autoconf@2.69%gcc@4.9.3=linux-x86_64
+    module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
+    # cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64
+    module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
+    # expat@2.1.0%gcc@4.9.3=linux-x86_64
+    module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
+    # git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64
+    module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
+
+The script may be further edited by removing unnecessary modules.
+This script may be directly executed in bash via
+
+.. code-block :: sh
+
+    source <( spack module find tcl --dependencies --shell py-numpy git )
+
+
+Regenerating Module files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Module and dotkit files are generated when packages are installed, and
+are placed in the following directories under the Spack root:
+
 Configuration files
 ^^^^^^^^^^^^^^^^^^^
 

lib/spack/docs/getting_started.rst

@@ -35,6 +35,21 @@ For a richer experience, use Spack's `shell support
 
 This automatically adds Spack to your ``PATH``.
 
+Clean Environment
+~~~~~~~~~~~~~~~~~~
+
+Many packages' installs can be broken by changing environment
+variables.  For example, a packge might pick up the wrong build-time
+dependencies (most of them not specified) depending on the setting of
+``PATH``.  ``GCC`` seems to be particularly vulnerable to these issues.
+
+Therefore, it is recommended that Spack users run with a *clean
+environment*, especially for ``PATH``.  Only software that comes with
+the system, or that you know you wish to use with Spack, should be
+included.  This procedure will avoid many strange build errors that no
+one knows how to fix.
+
+
 Installation
 --------------------
 
@@ -53,3 +68,54 @@ This will install a new spack script in ``/my/favorite/prefix/bin``,
 which you can use just like you would the regular spack script.  Each
 copy of spack installs packages into its own ``$PREFIX/opt``
 directory.
+
+Bootstrapping
+--------------
+
+Although Spack itself does not needinstallation, it is 
+
+Install Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to use Spack's generated environment modules, you must have
+installed the *Environment Modules* package.  On many Linux
+distributions, this can be installed from the vendor's repository.
+For example: ```yum install environment-modules``
+(Fedora/RHEL/CentOS).  If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+1. Consider using system tcl.  If so, add to ``packages.yaml``::
+
+    packages:
+        tcl:
+            paths:
+                tcl@8.5: /usr
+            version: [8.5]
+            buildable: False
+2. Install with::
+
+    spack install environment-modules
+
+3. Activate with::
+
+    TMP=`tempfile`
+    echo >$TMP
+    MODULE_HOME=`spack location -i environment-modules`
+    MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
+    ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
+    cp .bashrc $TMP
+    echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
+    cat $TMP >>.bashrc
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  Re-load your .bashrc (or log out and in
+again), and then test that the ``module`` command is found with:
+
+    module avail
+
+
+
+
+
+git
+binutils