2019-01-01 14:04:23 +08:00
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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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2018-10-08 04:52:23 +08:00
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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2016-08-22 23:25:19 +08:00
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#
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2018-10-08 04:52:23 +08:00
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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2016-08-22 23:25:19 +08:00
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from spack import *
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import sys
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2016-08-25 05:07:12 +08:00
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import os
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2016-08-22 23:25:19 +08:00
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class Nwchem(Package):
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"""High-performance computational chemistry software"""
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homepage = "http://www.nwchem-sw.org"
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url = "http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz"
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2018-06-16 01:46:35 +08:00
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tags = ['ecp', 'ecp-apps']
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2019-10-11 13:44:41 +08:00
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version('6.8.1', sha256='fd20f9ca1b410270a815e77e052ec23552f828526cd252709f798f589b2a6431',
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2018-09-04 09:36:49 +08:00
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url='https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.revision-v6.8-133-ge032219-srconly.2018-06-14.tar.bz2')
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2019-10-11 13:44:41 +08:00
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version('6.8', sha256='8401d9f4cce2f653a38639df61260b06be580ff0e1b8d77ed3262da159b372a6',
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2018-05-28 21:11:22 +08:00
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url='https://github.com/nwchemgit/nwchem/archive/v6.8-release.tar.gz')
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2016-08-22 23:25:19 +08:00
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depends_on('blas')
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depends_on('lapack')
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depends_on('mpi')
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2016-08-23 17:55:00 +08:00
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depends_on('scalapack')
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2016-08-22 23:25:19 +08:00
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2018-07-20 01:03:40 +08:00
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depends_on('python@2.7:2.8', type=('build', 'link', 'run'))
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2016-08-22 23:25:19 +08:00
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Patches are hashed with specs, and can be associated with dependencies.
- A package can depend on a special patched version of its dependencies.
- The `Spec` YAML (and therefore the hash) now includes the sha256 of
the patch in the `Spec` YAML, which changes its hash.
- The special patched version will be built separately from a "vanilla"
version of the same package.
- This allows packages to maintain patches on their dependencies
without affecting either the dependency package or its dependents.
This could previously be accomplished with special variants, but
having to add variants means the hash of the dependency changes
frequently when it really doesn't need to. This commit allows the
hash to change *just* for dependencies that need patches.
- Patching dependencies shouldn't be the common case, but some packages
(qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it
makes the code structure mirror maintenance responsibilities.
- Note that this commit means that adding or changing a patch on a
package will change its hash. This is probably what *should* happen,
but we haven't done it so far.
- Only applies to `patch()` directives; `package.py` files (and their
`patch()` functions) are not hashed, but we'd like to do that in the
future.
- The interface looks like this: `depends_on()` can optionally take a
patch directive or a list of them:
depends_on(<spec>,
patches=patch(..., when=<cond>),
when=<cond>)
# or
depends_on(<spec>,
patches=[patch(..., when=<cond>),
patch(..., when=<cond>)],
when=<cond>)
- Previously, the `patch()` directive only took an `md5` parameter. Now
it only takes a `sha256` parameter. We restrict this because we want
to be consistent about which hash is used in the `Spec`.
- A side effect of hashing patches is that *compressed* patches fetched
from URLs now need *two* checksums: one for the downloaded archive and
one for the content of the patch itself. Patches fetched uncompressed
only need a checksum for the patch. Rationale:
- we include the content of the *patch* in the spec hash, as that is
the checksum we can do consistently for patches included in Spack's
source and patches fetched remotely, both compressed and
uncompressed.
- we *still* need the patch of the downloaded archive, because we want
to verify the download *before* handing it off to tar, unzip, or
another decompressor. Not doing so is a security risk and leaves
users exposed to any arbitrary code execution vulnerabilities in
compression tools.
2017-09-24 06:25:33 +08:00
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# first hash is sha256 of the patch (required for URL patches),
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# second is sha256 for the archive.
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2016-08-23 20:51:40 +08:00
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# patches for 6.6-27746:
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2016-10-21 22:32:52 +08:00
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urls_for_patches = {
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'@6.6': [
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Patches are hashed with specs, and can be associated with dependencies.
- A package can depend on a special patched version of its dependencies.
- The `Spec` YAML (and therefore the hash) now includes the sha256 of
the patch in the `Spec` YAML, which changes its hash.
- The special patched version will be built separately from a "vanilla"
version of the same package.
- This allows packages to maintain patches on their dependencies
without affecting either the dependency package or its dependents.
This could previously be accomplished with special variants, but
having to add variants means the hash of the dependency changes
frequently when it really doesn't need to. This commit allows the
hash to change *just* for dependencies that need patches.
- Patching dependencies shouldn't be the common case, but some packages
(qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it
makes the code structure mirror maintenance responsibilities.
- Note that this commit means that adding or changing a patch on a
package will change its hash. This is probably what *should* happen,
but we haven't done it so far.
- Only applies to `patch()` directives; `package.py` files (and their
`patch()` functions) are not hashed, but we'd like to do that in the
future.
- The interface looks like this: `depends_on()` can optionally take a
patch directive or a list of them:
depends_on(<spec>,
patches=patch(..., when=<cond>),
when=<cond>)
# or
depends_on(<spec>,
patches=[patch(..., when=<cond>),
patch(..., when=<cond>)],
when=<cond>)
- Previously, the `patch()` directive only took an `md5` parameter. Now
it only takes a `sha256` parameter. We restrict this because we want
to be consistent about which hash is used in the `Spec`.
- A side effect of hashing patches is that *compressed* patches fetched
from URLs now need *two* checksums: one for the downloaded archive and
one for the content of the patch itself. Patches fetched uncompressed
only need a checksum for the patch. Rationale:
- we include the content of the *patch* in the spec hash, as that is
the checksum we can do consistently for patches included in Spack's
source and patches fetched remotely, both compressed and
uncompressed.
- we *still* need the patch of the downloaded archive, because we want
to verify the download *before* handing it off to tar, unzip, or
another decompressor. Not doing so is a security risk and leaves
users exposed to any arbitrary code execution vulnerabilities in
compression tools.
2017-09-24 06:25:33 +08:00
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('http://www.nwchem-sw.org/images/Tddft_mxvec20.patch.gz', 'ae04d4754c25fc324329dab085d4cc64148c94118ee702a7e14fce6152b4a0c5', 'cdfa8a5ae7d6ee09999407573b171beb91e37e1558a3bfb2d651982a85f0bc8f'),
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('http://www.nwchem-sw.org/images/Tools_lib64.patch.gz', 'ef2eadef89c055c4651ea807079577bd90e1bc99ef6c89f112f1f0e7560ec9b4', '76b8d3e1b77829b683234c8307fde55bc9249b87410914b605a76586c8f32dae'),
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('http://www.nwchem-sw.org/images/Config_libs66.patch.gz', '56f9c4bab362d82fb30d97564469e77819985a38e15ccaf04f647402c1ee248e', 'aa17f03cbb22ad7d883e799e0fddad1b5957f5f30b09f14a1a2caeeb9663cc07'),
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('http://www.nwchem-sw.org/images/Cosmo_meminit.patch.gz', 'f05f09ca235ad222fe47d880bfd05a1b88d0148b990ca8c7437fa231924be04b', '569c5ee528f3922ee60ca831eb20ec6591633a36f80efa76cbbe41cabeb9b624'),
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('http://www.nwchem-sw.org/images/Sym_abelian.patch.gz', 'e3470fb5786ab30bf2eda3bb4acc1e4c48fb5e640a09554abecf7d22b315c8fd', 'aa693e645a98dbafbb990e26145d65b100d6075254933f36326cf00bac3c29e0'),
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('http://www.nwchem-sw.org/images/Xccvs98.patch.gz', '75540e0436c12e193ed0b644cff41f5036d78c101f14141846083f03ad157afa', '1c0b0f1293e3b9b05e9e51e7d5b99977ccf1edb4b072872c8316452f6cea6f13'),
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('http://www.nwchem-sw.org/images/Dplot_tolrho.patch.gz', '8c30f92730d15f923ec8a623e3b311291eb2ba8b9d5a9884716db69a18d14f24', '2ebb1a5575c44eef4139da91f0e1e60057b2eccdba7f57a8fb577e840c326cbb'),
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('http://www.nwchem-sw.org/images/Driver_smalleig.patch.gz', 'a040df6f1d807402ce552ba6d35c9610d5efea7a9d6342bbfbf03c8d380a4058', 'dd65bfbae6b472b94c8ee81d74f6c3ece37c8fc8766ff7a3551d8005d44815b8'),
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('http://www.nwchem-sw.org/images/Ga_argv.patch.gz', '6fcd3920978ab95083483d5ed538cd9a6f2a80c2cafa0c5c7450fa5621f0a314', '8a78cb2af14314b92be9d241b801e9b9fed5527b9cb47a083134c7becdfa7cf1'),
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('http://www.nwchem-sw.org/images/Raman_displ.patch.gz', 'ca4312cd3ed1ceacdc3a7d258bb05b7824c393bf44f44c28a789ebeb29a8dba4', '6a16f0f589a5cbb8d316f68bd2e6a0d46cd47f1c699a4b256a3973130061f6c3'),
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('http://www.nwchem-sw.org/images/Ga_defs.patch.gz', 'f8ac827fbc11f7d2a9d8ec840c6f79d4759ef782bd4d291f2e88ec81b1b230aa', 'c6f1a48338d196e1db22bcfc6087e2b2e6eea50a34d3a2b2d3e90cccf43742a9'),
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('http://www.nwchem-sw.org/images/Zgesvd.patch.gz', 'c333a94ceb2c35a490f24b007485ac6e334e153b03cfc1d093b6037221a03517', '4af592c047dc3e0bc4962376ae2c6ca868eb7a0b40a347ed9b88e887016ad9ed'),
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('http://www.nwchem-sw.org/images/Cosmo_dftprint.patch.gz', '449d59983dc68c23b34e6581370b2fb3d5ea425b05c3182f0973e5b0e1a62651', 'd3b73431a68d6733eb7b669d471e18a83e03fa8e40c48e536fe8edecd99250ff'),
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('http://www.nwchem-sw.org/images/Txs_gcc6.patch.gz', '1dab87f23b210e941c765f7dd7cc2bed06d292a2621419dede73f10ba1ca1bcd', '139692215718cd7414896470c0cc8b7817a73ece1e4ca93bf752cf1081a195af'),
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('http://www.nwchem-sw.org/images/Gcc6_optfix.patch.gz', '8f8a5f8246bc1e42ef0137049acab4448a2e560339f44308703589adf753c148', '15cff43ab0509e0b0e83c49890032a848d6b7116bd6c8e5678e6c933f2d051ab'),
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('http://www.nwchem-sw.org/images/Util_gnumakefile.patch.gz', '173e17206a9099c3512b87e3f42441f5b089db82be1d2b306fe2a0070e5c8fad', '5dd82b9bd55583152295c999a0e4d72dd9d5c6ab7aa91117c2aae57a95a14ba1'),
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('http://www.nwchem-sw.org/images/Util_getppn.patch.gz', 'c4a23592fdcfb1fb6b65bc6c1906ac36f9966eec4899c4329bc8ce12015d2495', '8be418e1f8750778a31056f1fdf2a693fa4a12ea86a531f1ddf6f3620421027e'),
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('http://www.nwchem-sw.org/images/Gcc6_macs_optfix.patch.gz', 'ff33d5f1ccd33385ffbe6ce7a18ec1506d55652be6e7434dc8065af64c879aaa', 'fade16098a1f54983040cdeb807e4e310425d7f66358807554e08392685a7164'),
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('http://www.nwchem-sw.org/images/Notdir_fc.patch.gz', '54c722fa807671d6bf1a056586f0923593319d09c654338e7dd461dcd29ff118', 'a6a233951eb254d8aff5b243ca648def21fa491807a66c442f59c437f040ee69')
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2016-10-21 22:32:52 +08:00
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]
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}
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# Iterate over patches
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2018-03-23 04:41:55 +08:00
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for __condition, __urls in urls_for_patches.items():
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for __url, __sha256, __archive_sha256 in __urls:
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patch(__url, when=__condition, level=0, sha256=__sha256, archive_sha256=__archive_sha256)
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2016-08-23 20:51:40 +08:00
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2016-08-22 23:25:19 +08:00
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def install(self, spec, prefix):
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2017-03-03 02:01:29 +08:00
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scalapack = spec['scalapack'].libs
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lapack = spec['lapack'].libs
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blas = spec['blas'].libs
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2016-08-22 23:25:19 +08:00
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# see http://www.nwchem-sw.org/index.php/Compiling_NWChem
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args = []
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args.extend([
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'NWCHEM_TOP=%s' % self.stage.source_path,
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2016-08-25 05:07:12 +08:00
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# NWCHEM is picky about FC and CC. They should NOT be full path.
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# see http://www.nwchem-sw.org/index.php/Special:AWCforum/sp/id7524
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'CC=%s' % os.path.basename(spack_cc),
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'FC=%s' % os.path.basename(spack_fc),
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2016-08-22 23:25:19 +08:00
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'USE_MPI=y',
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'MPI_LOC=%s' % spec['mpi'].prefix,
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'USE_PYTHONCONFIG=y',
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'PYTHONVERSION=%s' % spec['python'].version.up_to(2),
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Python command, libraries, and headers (#3367)
## Motivation
Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically.
I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers.
Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends.
## Prefix
For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`.
Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things.
To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable.
## Command
In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking:
If the spec is for Python 3, try searching for the `python3` command.
If the spec is for Python 2, try searching for the `python2` command.
If neither are found, try searching for the `python` command.
## Libraries
Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work.
The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing:
```
lib/libpython2.7.dylib
```
For Python 3.6 on CentOS 6, I'm seeing:
```
lib/libpython3.so
lib/libpython3.6m.so.1.0
lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0
```
Notice the `m` after the version number. Yeah, that's a thing.
## Headers
In Python 2.7, I'm seeing:
```
include/python2.7/pyconfig.h
```
In Python 3.6, I'm seeing:
```
include/python3.6m/pyconfig.h
```
It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6
Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.
2017-04-30 08:24:13 +08:00
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'PYTHONHOME=%s' % spec['python'].home,
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2016-09-22 03:27:59 +08:00
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'BLASOPT=%s' % ((lapack + blas).ld_flags),
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'BLAS_LIB=%s' % blas.ld_flags,
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'LAPACK_LIB=%s' % lapack.ld_flags,
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2016-08-23 17:55:00 +08:00
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'USE_SCALAPACK=y',
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2016-09-22 03:27:59 +08:00
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'SCALAPACK=%s' % scalapack.ld_flags,
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2016-08-24 19:40:02 +08:00
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'NWCHEM_MODULES=all python',
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2016-08-22 23:25:19 +08:00
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'NWCHEM_LONG_PATHS=Y' # by default NWCHEM_TOP is 64 char max
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])
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2016-08-23 17:55:00 +08:00
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# TODO: query if blas/lapack/scalapack uses 64bit Ints
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# A flag to distinguish between 32bit and 64bit integers in linear
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# algebra (Blas, Lapack, Scalapack)
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2018-06-28 01:27:03 +08:00
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use_32_bit_lin_alg = True
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2016-08-23 17:55:00 +08:00
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2018-06-28 01:27:03 +08:00
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if use_32_bit_lin_alg:
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2016-08-23 17:55:00 +08:00
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args.extend([
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'USE_64TO32=y',
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'BLAS_SIZE=4',
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2016-08-23 22:46:40 +08:00
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'LAPACK_SIZE=4',
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2016-08-23 17:55:00 +08:00
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'SCALAPACK_SIZE=4'
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])
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else:
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args.extend([
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'BLAS_SIZE=8',
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2016-08-23 22:46:40 +08:00
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'LAPACK_SIZE=8'
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2016-08-23 17:55:00 +08:00
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'SCALAPACK_SIZE=8'
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])
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2016-08-22 23:25:19 +08:00
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if sys.platform == 'darwin':
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target = 'MACX64'
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args.extend([
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'CFLAGS_FORGA=-DMPICH_NO_ATTR_TYPE_TAGS'
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])
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else:
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target = 'LINUX64'
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args.extend(['NWCHEM_TARGET=%s' % target])
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with working_dir('src'):
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make('nwchem_config', *args)
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2018-06-28 01:27:03 +08:00
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if use_32_bit_lin_alg:
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2016-08-23 17:55:00 +08:00
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make('64_to_32', *args)
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2016-08-22 23:25:19 +08:00
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make(*args)
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# need to install by hand. Follow Ubuntu:
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# http://packages.ubuntu.com/trusty/all/nwchem-data/filelist
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# http://packages.ubuntu.com/trusty/amd64/nwchem/filelist
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share_path = join_path(prefix, 'share', 'nwchem')
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mkdirp(prefix.bin)
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install_tree('data', share_path)
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install_tree(join_path('basis', 'libraries'),
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join_path(share_path, 'libraries'))
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install_tree(join_path('nwpw', 'libraryps'),
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join_path(share_path, 'libraryps'))
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b_path = join_path(self.stage.source_path, 'bin',
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target, 'nwchem')
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chmod = which('chmod')
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chmod('+x', b_path)
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install(b_path, prefix.bin)
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# Finally, make user's life easier by creating a .nwchemrc file
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# to point to the required data files.
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nwchemrc = """\
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nwchem_basis_library {data}/libraries/
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nwchem_nwpw_library {data}/libraryps/
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ffield amber
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amber_1 {data}/amber_s/
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amber_2 {data}/amber_q/
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amber_3 {data}/amber_x/
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amber_4 {data}/amber_u/
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spce {data}/solvents/spce.rst
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charmm_s {data}/charmm_s/
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charmm_x {data}/charmm_x/
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""".format(data=share_path)
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|
|
with open(".nwchemrc", 'w') as f:
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f.write(nwchemrc)
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|
|
install(".nwchemrc", share_path)
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