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Modify NAMD to adress new build system of charm-8.0.0
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| ## | ||
| # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild | ||
| # | ||
| # Copyright:: Copyright 2013-2024 CaSToRC, The Cyprus Institute | ||
| # Authors:: George Tsouloupas <[email protected]> | ||
| # License:: MIT/GPL | ||
| # $Id$ | ||
| # | ||
| ## | ||
| """ | ||
| Easybuild support for building NAMD, implemented as an easyblock | ||
| @author: George Tsouloupas (Cyprus Institute) | ||
| @author: Kenneth Hoste (Ghent University) | ||
| """ | ||
| import glob | ||
| import os | ||
| import re | ||
| import shutil | ||
| from easybuild.tools import LooseVersion | ||
|
|
||
| import easybuild.tools.toolchain as toolchain | ||
| from easybuild.easyblocks.generic.makecp import MakeCp | ||
| from easybuild.framework.easyconfig import CUSTOM, MANDATORY | ||
| from easybuild.tools.build_log import EasyBuildError | ||
| from easybuild.tools.config import build_option | ||
| from easybuild.tools.filetools import apply_regex_substitutions, change_dir, extract_file | ||
| from easybuild.tools.modules import get_software_root, get_software_version | ||
| from easybuild.tools.run import run_cmd | ||
| from easybuild.tools.systemtools import POWER, X86_64, get_cpu_architecture | ||
|
|
||
|
|
||
| class EB_NAMD(MakeCp): | ||
| """ | ||
| Support for building NAMD | ||
| """ | ||
| @staticmethod | ||
| def extra_options(): | ||
| """Define extra NAMD-specific easyconfig parameters.""" | ||
| extra = MakeCp.extra_options() | ||
| # files_to_copy is not mandatory here | ||
| extra['files_to_copy'][2] = CUSTOM | ||
| extra.update({ | ||
| # see http://charm.cs.illinois.edu/manuals/html/charm++/A.html | ||
| 'charm_arch': [None, "Charm++ target architecture", MANDATORY], | ||
| 'charm_extra_cxxflags': ['', "Extra C++ compiler options to use for building Charm++", CUSTOM], | ||
| 'charm_opts': ['--with-production', "Charm++ build options", CUSTOM], | ||
| 'cuda': [None, "Enable CUDA build if CUDA is among the dependencies", CUSTOM], | ||
| 'namd_basearch': [None, "NAMD base target architecture (compiler family is appended)", CUSTOM], | ||
| 'namd_cfg_opts': ['', "NAMD configure options", CUSTOM], | ||
| 'runtest': [True, "Run NAMD test case after building", CUSTOM], | ||
| }) | ||
|
|
||
| return extra | ||
|
|
||
| def __init__(self, *args, **kwargs): | ||
| """Custom easyblock constructor for NAMD, initialize class variables.""" | ||
| super(EB_NAMD, self).__init__(*args, **kwargs) | ||
| self.namd_arch = None | ||
|
|
||
| def prepare_step(self, *args, **kwargs): | ||
| """Prepare build environment.""" | ||
| super(EB_NAMD, self).prepare_step(*args, **kwargs) | ||
|
|
||
| if self.cfg['namd_basearch'] is None: | ||
|
|
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| self.log.info("namd_basearch not specified, so determining it based a CPU arch...") | ||
|
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| arch = get_cpu_architecture() | ||
| if arch == X86_64: | ||
| basearch = 'Linux-x86_64' | ||
| elif arch == POWER: | ||
| basearch = 'Linux-POWER' | ||
|
|
||
| self.cfg['namd_basearch'] = basearch | ||
| self.log.info("Derived value for 'namd_basearch': %s", self.cfg['namd_basearch']) | ||
|
|
||
| def extract_step(self): | ||
| """Custom extract step for NAMD, we need to extract charm++ so we can patch it.""" | ||
| super(EB_NAMD, self).extract_step() | ||
|
|
||
| change_dir(self.src[0]['finalpath']) | ||
| self.charm_tarballs = glob.glob('charm-*.tar') | ||
| if len(self.charm_tarballs) != 1: | ||
| raise EasyBuildError("Expected to find exactly one tarball for Charm++, found: %s", self.charm_tarballs) | ||
|
|
||
| srcdir = extract_file(self.charm_tarballs[0], os.getcwd(), change_into_dir=False) | ||
| change_dir(srcdir) | ||
|
|
||
| def patch_step(self, *args, **kwargs): | ||
| """Patch scripts to avoid using hardcoded /bin/csh.""" | ||
| super(EB_NAMD, self).patch_step(*args, **kwargs) | ||
|
|
||
| self.charm_dir = self.charm_tarballs[0][:-4] | ||
|
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||
| # NAMD-3.0 depends on charm-8.0.0 that uses Automake. The 'configure' file was | ||
| # removed in favour of 'configure.ac' | ||
| configure_file_name = 'configure' | ||
| if LooseVersion(self.version) >= LooseVersion('3.0'): | ||
| configure_file_name = 'configure.ac' | ||
|
|
||
| charm_config = os.path.join(self.charm_dir, 'src', 'scripts', configure_file_name) | ||
| apply_regex_substitutions(charm_config, [(r'SHELL=/bin/csh', 'SHELL=$(which csh)')]) | ||
|
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| for csh_script in [os.path.join('plugins', 'import_tree'), os.path.join('psfgen', 'import_tree'), | ||
| os.path.join(self.charm_dir, 'src', 'QuickThreads', 'time', 'raw')]: | ||
| if os.path.exists(csh_script): | ||
| apply_regex_substitutions(csh_script, [(r'^#!\s*/bin/csh\s*$', '#!/usr/bin/env csh')]) | ||
|
|
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| def configure_step(self): | ||
| """Custom configure step for NAMD, we build charm++ first (if required).""" | ||
|
|
||
| # complete Charm ++ and NAMD architecture string with compiler family | ||
| comp_fam = self.toolchain.comp_family() | ||
| if self.toolchain.options.get('usempi', False): | ||
| charm_arch_comp = 'mpicxx' | ||
| else: | ||
| charm_arch_comps = { | ||
| toolchain.GCC: 'gcc', | ||
| toolchain.INTELCOMP: 'icc', | ||
| } | ||
| charm_arch_comp = charm_arch_comps.get(comp_fam, None) | ||
| namd_comps = { | ||
| toolchain.GCC: 'g++', | ||
| toolchain.INTELCOMP: 'icc', | ||
| } | ||
| namd_comp = namd_comps.get(comp_fam, None) | ||
| if charm_arch_comp is None or namd_comp is None: | ||
| raise EasyBuildError("Unknown compiler family, can't complete Charm++/NAMD target architecture.") | ||
|
|
||
| # NOTE: important to add smp BEFORE the compiler | ||
| # charm arch style is: mpi-linux-x86_64-smp-mpicxx | ||
| # otherwise the setting of name_charm_arch below will get things | ||
| # in the wrong order | ||
| if self.toolchain.options.get('openmp', False): | ||
| self.cfg.update('charm_arch', 'smp') | ||
| self.cfg.update('charm_arch', charm_arch_comp) | ||
| self.log.info("Updated 'charm_arch': %s", self.cfg['charm_arch']) | ||
|
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||
| self.namd_arch = '%s-%s' % (self.cfg['namd_basearch'], namd_comp) | ||
| self.log.info("Completed NAMD target architecture: %s", self.namd_arch) | ||
|
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| build_cmd = './build' | ||
|
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| cmd = "%(build_cmd)s charm++ %(arch)s %(opts)s --with-numa -j%(parallel)s '%(cxxflags)s'" % { | ||
| 'build_cmd': build_cmd, | ||
| 'arch': self.cfg['charm_arch'], | ||
| 'cxxflags': os.environ['CXXFLAGS'] + ' -DMPICH_IGNORE_CXX_SEEK ' + self.cfg['charm_extra_cxxflags'], | ||
| 'opts': self.cfg['charm_opts'], | ||
| 'parallel': self.cfg['parallel'], | ||
| } | ||
| charm_subdir = '.'.join(os.path.basename(self.charm_tarballs[0]).split('.')[:-1]) | ||
| self.log.debug("Building Charm++ using cmd '%s' in '%s'" % (cmd, charm_subdir)) | ||
| run_cmd(cmd, path=charm_subdir) | ||
|
|
||
| # compiler (options) | ||
| self.cfg.update('namd_cfg_opts', '--cc "%s" --cc-opts "%s"' % (os.environ['CC'], os.environ['CFLAGS'])) | ||
| cxxflags = os.environ['CXXFLAGS'] | ||
| if LooseVersion(self.version) >= LooseVersion('2.12'): | ||
| cxxflags += ' --std=c++11' | ||
| self.cfg.update('namd_cfg_opts', '--cxx "%s" --cxx-opts "%s"' % (os.environ['CXX'], cxxflags)) | ||
|
|
||
| # NAMD dependencies: CUDA, TCL, FFTW | ||
| cuda = get_software_root('CUDA') | ||
| if cuda and (self.cfg['cuda'] is None or self.cfg['cuda']): | ||
| self.cfg.update('namd_cfg_opts', "--with-cuda --cuda-prefix %s" % cuda) | ||
| elif not self.cfg['cuda']: | ||
| self.log.warning("CUDA is disabled") | ||
| elif not cuda and self.cfg['cuda']: | ||
| raise EasyBuildError("CUDA is not a dependency, but support for CUDA is enabled.") | ||
|
|
||
| tcl = get_software_root('Tcl') | ||
| if tcl: | ||
| self.cfg.update('namd_cfg_opts', '--with-tcl --tcl-prefix %s' % tcl) | ||
| tclversion = '.'.join(get_software_version('Tcl').split('.')[0:2]) | ||
| tclv_subs = [(r'-ltcl[\d.]*\s', '-ltcl%s ' % tclversion)] | ||
|
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| apply_regex_substitutions(os.path.join('arch', '%s.tcl' % self.cfg['namd_basearch']), tclv_subs) | ||
|
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||
| fftw = get_software_root('FFTW') | ||
| if fftw: | ||
| if LooseVersion(get_software_version('FFTW')) >= LooseVersion('3.0'): | ||
| if LooseVersion(self.version) >= LooseVersion('2.9'): | ||
| self.cfg.update('namd_cfg_opts', "--with-fftw3") | ||
| else: | ||
| raise EasyBuildError("Using FFTW v3.x only supported in NAMD v2.9 and up.") | ||
| else: | ||
| self.cfg.update('namd_cfg_opts', "--with-fftw") | ||
| self.cfg.update('namd_cfg_opts', "--fftw-prefix %s" % fftw) | ||
|
|
||
| namd_charm_arch = "--charm-arch %s" % '-'.join(self.cfg['charm_arch'].strip().split()) | ||
| cmd = "./config %s %s %s " % (self.namd_arch, namd_charm_arch, self.cfg["namd_cfg_opts"]) | ||
| run_cmd(cmd) | ||
|
|
||
| def build_step(self): | ||
| """Build NAMD for configured architecture""" | ||
| super(EB_NAMD, self).build_step(path=self.namd_arch) | ||
|
|
||
| def test_step(self): | ||
| """Run NAMD test case.""" | ||
| if self.cfg['runtest']: | ||
|
|
||
| if not build_option('mpi_tests'): | ||
| self.log.info("Skipping testing of NAMD since MPI testing is disabled") | ||
| return | ||
|
|
||
| namdcmd = os.path.join(self.cfg['start_dir'], self.namd_arch, 'namd%s' % self.version.split('.')[0]) | ||
| if self.cfg['charm_arch'].startswith('mpi'): | ||
| namdcmd = self.toolchain.mpi_cmd_for(namdcmd, 2) | ||
| ppn = '' | ||
| if self.toolchain.options.get('openmp', False): | ||
| ppn = '+ppn 2' | ||
| cmd = "%(pretestopts)s %(namd)s %(ppn)s %(testopts)s %(testdir)s" % { | ||
| 'namd': namdcmd, | ||
| 'ppn': ppn, | ||
| 'pretestopts': self.cfg['pretestopts'], | ||
| 'testdir': os.path.join(self.cfg['start_dir'], self.namd_arch, 'src', 'alanin'), | ||
| 'testopts': self.cfg['testopts'], | ||
| } | ||
| out, ec = run_cmd(cmd, simple=False) | ||
| if ec == 0: | ||
| test_ok_regex = re.compile(r"(^Program finished.$|End of program\s*$)", re.M) | ||
| if test_ok_regex.search(out): | ||
| self.log.debug("Test '%s' ran fine." % cmd) | ||
| else: | ||
| raise EasyBuildError("Test '%s' failed ('%s' not found), output: %s", | ||
| cmd, test_ok_regex.pattern, out) | ||
| else: | ||
| self.log.debug("Skipping running NAMD test case after building") | ||
|
|
||
| def install_step(self): | ||
| """Install by copying the correct directory to the install dir""" | ||
| srcdir = os.path.join(self.cfg['start_dir'], self.namd_arch) | ||
| try: | ||
| # copy all files, except for .rootdir (required to avoid cyclic copying) | ||
| for item in [x for x in os.listdir(srcdir) if x not in ['.rootdir']]: | ||
| fullsrc = os.path.join(srcdir, item) | ||
| if os.path.isdir(fullsrc): | ||
| shutil.copytree(fullsrc, os.path.join(self.installdir, item), symlinks=False) | ||
| elif os.path.isfile(fullsrc): | ||
| shutil.copy2(fullsrc, self.installdir) | ||
| except OSError as err: | ||
| raise EasyBuildError("Failed to copy NAMD build from %s to install directory: %s", srcdir, err) | ||
|
|
||
| def make_module_extra(self): | ||
| """Add the install directory to PATH""" | ||
| txt = super(EB_NAMD, self).make_module_extra() | ||
| txt += self.module_generator.prepend_paths("PATH", ['']) | ||
| return txt | ||
|
|
||
| def sanity_check_step(self): | ||
| """Custom sanity check for NAMD.""" | ||
| custom_paths = { | ||
| 'files': ['charmrun', 'flipbinpdb', 'flipdcd', 'namd%s' % self.version.split('.')[0], 'psfgen'], | ||
| 'dirs': ['inc'], | ||
| } | ||
| super(EB_NAMD, self).sanity_check_step(custom_paths=custom_paths) |