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Merge pull request #2382 from easybuilders/4.3.x
release EasyBuild v4.3.4
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,13 +18,11 @@ | |
| @author: Kenneth Hoste (Ghent University) | ||
| @author: George Tsouloupas <[email protected]> | ||
| """ | ||
|
|
||
| import os | ||
| import shutil | ||
| from distutils.version import LooseVersion | ||
|
|
||
| from easybuild.easyblocks.generic.configuremake import ConfigureMake | ||
| from easybuild.tools.build_log import EasyBuildError | ||
| from easybuild.tools.filetools import copy_file, mkdir | ||
|
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||
|
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| class EB_BWA(ConfigureMake): | ||
|
|
@@ -35,45 +33,55 @@ class EB_BWA(ConfigureMake): | |
| def __init__(self, *args, **kwargs): | ||
| """Add extra config options specific to BWA.""" | ||
| super(EB_BWA, self).__init__(*args, **kwargs) | ||
| self.files = [] | ||
|
|
||
| def configure_step(self): | ||
| """ | ||
| Empty function as bwa comes with _no_ configure script | ||
| """ | ||
| self.files = ["bwa", "qualfa2fq.pl", "xa2multi.pl"] | ||
| if LooseVersion(self.version) < LooseVersion("0.7.0"): | ||
| self.files = ['bwa', 'qualfa2fq.pl', 'xa2multi.pl'] | ||
| if LooseVersion(self.version) < LooseVersion('0.7.0'): | ||
| # solid2fastq was dropped in recent versions because the same functionality | ||
| # is covered by other tools already | ||
| # cfr. http://osdir.com/ml/general/2010-10/msg26205.html | ||
| self.files.append("solid2fastq.pl") | ||
| self.files.append('solid2fastq.pl') | ||
|
|
||
| def configure_step(self): | ||
| """ | ||
| Empty function as BWA comes with _no_ configure script | ||
| """ | ||
| pass | ||
|
|
||
| def build_step(self): | ||
| """Custom build procedure: pass down compiler command and options as arguments to 'make'.""" | ||
|
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| for env_var in ('CC', 'CFLAGS'): | ||
| if env_var + '=' not in self.cfg['buildopts']: | ||
| self.cfg.update('buildopts', env_var + '="$' + env_var + '"') | ||
|
|
||
| super(EB_BWA, self).build_step() | ||
|
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| def install_step(self): | ||
| """ | ||
| Install by copying files to install dir | ||
| """ | ||
| srcdir = self.cfg['start_dir'] | ||
| destdir = os.path.join(self.installdir, 'bin') | ||
| mandir = os.path.join(self.installdir, 'man') | ||
| manman1dir = os.path.join(self.installdir, 'man/man1') | ||
| mkdir(destdir) | ||
| for filename in self.files: | ||
| srcfile = os.path.join(srcdir, filename) | ||
| copy_file(srcfile, destdir) | ||
|
|
||
| manfile = os.path.join(srcdir, 'bwa.1') | ||
| srcfile = None | ||
| try: | ||
| os.makedirs(destdir) | ||
| os.makedirs(mandir) | ||
| os.makedirs(manman1dir) | ||
| for filename in self.files: | ||
| srcfile = os.path.join(srcdir, filename) | ||
| shutil.copy2(srcfile, destdir) | ||
| shutil.copy2(manfile, manman1dir) | ||
| except OSError as err: | ||
| raise EasyBuildError("Copying %s to installation dir %s failed: %s", srcfile, destdir, err) | ||
| manman1dir = os.path.join(self.installdir, 'man', 'man1') | ||
| mkdir(manman1dir, parents=True) | ||
| copy_file(manfile, manman1dir) | ||
|
|
||
| def sanity_check_step(self): | ||
| """Custom sanity check for BWA.""" | ||
|
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||
| custom_paths = { | ||
| 'files': ["bin/%s" % x for x in self.files], | ||
| 'files': [os.path.join('bin', x) for x in self.files], | ||
| 'dirs': [] | ||
| } | ||
|
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||
| super(EB_BWA, self).sanity_check_step(custom_paths=custom_paths) | ||
| # 'bwa' command doesn't have a --help option, but it does print help-like information to stderr | ||
| # when run without arguments (and exits with exit code 1) | ||
| custom_commands = ["bwa 2>&1 | grep 'index sequences in the FASTA format'"] | ||
|
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||
| super(EB_BWA, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,26 @@ | ||
| ## | ||
| # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild | ||
| # Copyright 2012-2021 Ghent University | ||
| # | ||
| # Copyright:: Copyright 2012-2019 Cyprus Institute / CaSToRC, Uni.Lu, NTUA, Ghent University, | ||
| # Forschungszentrum Juelich GmbH | ||
| # Authors:: George Tsouloupas <[email protected]>, Fotis Georgatos <[email protected]>, Kenneth Hoste, Damian Alvarez | ||
| # License:: MIT/GPL | ||
| # $Id$ | ||
| # This file is part of EasyBuild, | ||
| # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), | ||
| # with support of Ghent University (http://ugent.be/hpc), | ||
| # the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), | ||
| # Flemish Research Foundation (FWO) (http://www.fwo.be/en) | ||
| # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). | ||
| # | ||
| # This work implements a part of the HPCBIOS project and is a component of the policy: | ||
| # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html | ||
| # https://github.com/easybuilders/easybuild | ||
| # | ||
| # EasyBuild 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 v2. | ||
| # | ||
| # EasyBuild 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 | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with EasyBuild. If not, see <http://www.gnu.org/licenses/>. | ||
| ## | ||
| """ | ||
| EasyBuild support for CUDA, implemented as an easyblock | ||
|
|
@@ -20,6 +32,7 @@ | |
| @author: Kenneth Hoste (Ghent University) | ||
| @author: Damian Alvarez (Forschungszentrum Juelich) | ||
| @author: Ward Poelmans (Free University of Brussels) | ||
| @author: Robert Mijakovic (LuxProvide S.A.) | ||
| """ | ||
| import os | ||
| import stat | ||
|
|
@@ -29,10 +42,10 @@ | |
| from easybuild.easyblocks.generic.binary import Binary | ||
| from easybuild.framework.easyconfig import CUSTOM | ||
| from easybuild.tools.build_log import EasyBuildError | ||
| from easybuild.tools.filetools import adjust_permissions, patch_perl_script_autoflush | ||
| from easybuild.tools.filetools import remove_file, which, write_file | ||
| from easybuild.tools.filetools import adjust_permissions, copy_dir, patch_perl_script_autoflush | ||
| from easybuild.tools.filetools import remove_file, symlink, which, write_file | ||
| from easybuild.tools.run import run_cmd, run_cmd_qa | ||
| from easybuild.tools.systemtools import POWER, X86_64, get_cpu_architecture, get_shared_lib_ext | ||
| from easybuild.tools.systemtools import AARCH64, POWER, X86_64, get_cpu_architecture, get_shared_lib_ext | ||
|
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| # Wrapper script definition | ||
| WRAPPER_TEMPLATE = """#!/bin/sh | ||
|
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@@ -62,10 +75,12 @@ def extra_options(): | |
| def __init__(self, *args, **kwargs): | ||
| """ Init the cuda easyblock adding a new cudaarch template var """ | ||
| myarch = get_cpu_architecture() | ||
| if myarch == X86_64: | ||
| cudaarch = '' | ||
| if myarch == AARCH64: | ||
| cudaarch = '_sbsa' | ||
| elif myarch == POWER: | ||
| cudaarch = '_ppc64le' | ||
| elif myarch == X86_64: | ||
| cudaarch = '' | ||
| else: | ||
| raise EasyBuildError("Architecture %s is not supported for CUDA on EasyBuild", myarch) | ||
|
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||
|
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@@ -179,7 +194,7 @@ def create_wrapper(wrapper_name, wrapper_comp): | |
| for comp in (self.cfg['host_compilers'] or []): | ||
| create_wrapper('nvcc_%s' % comp, comp) | ||
|
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| ldconfig = which('ldconfig') | ||
| ldconfig = which('ldconfig', log_ok=False, log_error=False) | ||
| sbin_dirs = ['/sbin', '/usr/sbin'] | ||
| if not ldconfig: | ||
| # ldconfig is usually in /sbin or /usr/sbin | ||
|
|
@@ -195,23 +210,28 @@ def create_wrapper(wrapper_name, wrapper_comp): | |
| path = os.environ.get('PATH', '') | ||
| raise EasyBuildError("Unable to find 'ldconfig' in $PATH (%s), nor in any of %s", path, sbin_dirs) | ||
|
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| stubs_dir = os.path.join(self.installdir, 'lib64', 'stubs') | ||
| # Run ldconfig to create missing symlinks in the stubs directory (libcuda.so.1, etc) | ||
| cmd = ' '.join([ldconfig, '-N', os.path.join(self.installdir, 'lib64', 'stubs')]) | ||
| cmd = ' '.join([ldconfig, '-N', stubs_dir]) | ||
| run_cmd(cmd) | ||
|
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||
| # GCC searches paths in LIBRARY_PATH and the system paths suffixed with ../lib64 or ../lib first | ||
| # This means stubs/../lib64 is searched before the system /lib64 folder containing a potentially older libcuda. | ||
| # See e.g. https://github.com/easybuilders/easybuild-easyconfigs/issues/12348 | ||
| # Workaround: Create a copy that matches this pattern | ||
| new_stubs_dir = os.path.join(self.installdir, 'stubs') | ||
| copy_dir(stubs_dir, os.path.join(new_stubs_dir, 'lib64')) | ||
| # Also create the lib dir as a symlink | ||
| symlink('lib64', os.path.join(new_stubs_dir, 'lib'), use_abspath_source=False) | ||
|
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| super(EB_CUDA, self).post_install_step() | ||
|
|
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| def sanity_check_step(self): | ||
| """Custom sanity check for CUDA.""" | ||
|
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| shlib_ext = get_shared_lib_ext() | ||
|
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| chk_libdir = ["lib64"] | ||
|
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| # Versions higher than 6 do not provide 32 bit libraries | ||
| if LooseVersion(self.version) < LooseVersion("6"): | ||
| chk_libdir += ["lib"] | ||
|
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| chk_libdir = ["lib64", "lib"] | ||
| culibs = ["cublas", "cudart", "cufft", "curand", "cusparse"] | ||
| custom_paths = { | ||
| 'files': [os.path.join("bin", x) for x in ["fatbinary", "nvcc", "nvlink", "ptxas"]] + | ||
|
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@@ -259,7 +279,7 @@ def make_module_req_guess(self): | |
| guesses.update({ | ||
| 'PATH': bin_path, | ||
| 'LD_LIBRARY_PATH': lib_path, | ||
| 'LIBRARY_PATH': ['lib64', os.path.join('lib64', 'stubs')], | ||
| 'LIBRARY_PATH': ['lib64', os.path.join('stubs', 'lib64')], | ||
| 'CPATH': inc_path, | ||
| }) | ||
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