Commit 82c9da41 authored by Lukáš Krupčík's avatar Lukáš Krupčík
Browse files

Merge branch 'it4i-salomon'

parents 2cf5b016 7f366a52
# Copyright 2009-2018 Ghent University
# Copyright 2015-2018 Stanford University
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (,
# with support of Ghent University (,
# the Flemish Supercomputer Centre (VSC) (,
# the Hercules foundation (
# and the Department of Economy, Science and Innovation (EWI) (
# 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
# 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 <>.
EasyBuild support for Amber, implemented as an easyblock
Original author: Benjamin Roberts (The University of Auckland)
Modified by Stephane Thiell (Stanford University) for Amber14
Enhanced/cleaned up by Kenneth Hoste (HPC-UGent)
import os
import as env
import as toolchain
from easybuild.easyblocks.generic.configuremake import ConfigureMake
from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
from easybuild.framework.easyconfig import CUSTOM, MANDATORY, BUILD
from import EasyBuildError
from import get_software_root, get_software_version
from import run_cmd
class EB_Amber(ConfigureMake):
"""Easyblock for building and installing Amber"""
def extra_options(extra_vars=None):
"""Extra easyconfig parameters specific to ConfigureMake."""
extra_vars = dict(ConfigureMake.extra_options(extra_vars))
# 'Amber': [True, "Build Amber in addition to AmberTools", CUSTOM],
'patchlevels': ["latest", "(AmberTools, Amber) updates to be applied", CUSTOM],
# The following is necessary because some patches to the Amber update
# script update the update script itself, in which case it will quit
# and insist on being run again. We don't know how many times will
# be needed, but the number of times is patchlevel specific.
'patchruns': [1, "Number of times to run Amber's update script before building", CUSTOM],
# enable testing by default
'runtest': [True, "Run tests after each build", CUSTOM],
return ConfigureMake.extra_options(extra_vars)
def __init__(self, *args, **kwargs):
"""Easyblock constructor: initialise class variables."""
super(EB_Amber, self).__init__(*args, **kwargs)
self.build_in_installdir = True
self.pylibdir = None
self.with_cuda = False
self.with_mpi = False
env.setvar('AMBERHOME', self.installdir)
def extract_step(self):
"""Extract sources; strip off parent directory during unpack"""
self.cfg.update('unpack_options', "--strip-components=1")
super(EB_Amber, self).extract_step()
def patch_step(self, *args, **kwargs):
"""Patch Amber using 'update_amber' tool, prior to applying listed patch files (if any)."""
if self.cfg['patchlevels'] == "latest":
cmd = "./update_amber --update"
# Run as many times as specified. It is the responsibility
# of the easyconfig author to get this right, especially if
# he or she selects "latest". (Note: "latest" is not
# recommended for this reason and others.)
for _ in range(self.cfg['patchruns']):
run_cmd(cmd, log_all=True)
for (tree, patch_level) in zip(['AmberTools', 'Amber'], self.cfg['patchlevels']):
if patch_level == 0:
cmd = "./update_amber --update-to %s/%s" % (tree, patch_level)
# Run as many times as specified. It is the responsibility
# of the easyconfig author to get this right.
for _ in range(self.cfg['patchruns']):
run_cmd(cmd, log_all=True)
super(EB_Amber, self).patch_step(*args, **kwargs)
def configure_step(self):
"""Configuring Amber is done in install step."""
def build_step(self):
"""Building Amber is done in install step."""
def test_step(self):
"""Testing Amber build is done in install step."""
def install_step(self):
"""Custom build, test & install procedure for Amber."""
# unset $LIBS since it breaks the build
# define environment variables for MPI, BLAS/LAPACK & dependencies
mklroot = get_software_root('imkl')
openblasroot = get_software_root('OpenBLAS')
if mklroot:
env.setvar('MKL_HOME', mklroot)
elif openblasroot:
lapack = os.getenv('LIBLAPACK')
if lapack is None:
raise EasyBuildError("LIBLAPACK (from OpenBLAS) not found in environement.")
env.setvar('GOTO', lapack)
mpiroot = get_software_root(self.toolchain.MPI_MODULE_NAME[0])
if mpiroot and self.toolchain.options.get('usempi', None):
env.setvar('MPI_HOME', mpiroot)
self.with_mpi = True
if self.toolchain.mpi_family() == toolchain.INTELMPI:
self.mpi_option = '-intelmpi'
self.mpi_option = '-mpi'
common_configopts = [self.cfg['configopts'], '--no-updates', '-noX11']
if == 'Amber':
netcdfroot = get_software_root('netCDF')
if netcdfroot:
common_configopts.extend(["--with-netcdf", netcdfroot])
pythonroot = get_software_root('Python')
if pythonroot:
common_configopts.extend(["--with-python", os.path.join(pythonroot, 'bin', 'python')])
self.pylibdir = det_pylibdir()
pythonpath = os.environ.get('PYTHONPATH', '')
env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))
comp_fam = self.toolchain.comp_family()
if comp_fam == toolchain.INTELCOMP:
comp_str = 'intel'
elif comp_fam == toolchain.GCC:
comp_str = 'gnu'
raise EasyBuildError("Don't know how to compile with compiler family '%s' -- check EasyBlock?", comp_fam)
# The NAB compiles need openmp flag
if self.toolchain.options.get('openmp', None):
env.setvar('CUSTOMBUILDFLAGS', self.toolchain.get_flag('openmp'))
# compose list of build targets
build_targets = [('', 'test')]
if self.with_mpi:
build_targets.append((self.mpi_option, 'test.parallel'))
# hardcode to 4 MPI processes, minimal required to run all tests
env.setvar('DO_PARALLEL', 'mpirun -np 4')
cudaroot = get_software_root('CUDA')
if cudaroot:
env.setvar('CUDA_HOME', cudaroot)
self.with_cuda = True
build_targets.append(('-cuda', 'test.cuda'))
if self.with_mpi:
build_targets.append(("-cuda %s" % self.mpi_option, 'test.cuda_parallel'))
ld_lib_path = os.environ.get('LD_LIBRARY_PATH', '')
env.setvar('LD_LIBRARY_PATH', os.pathsep.join([os.path.join(self.installdir, 'lib'), ld_lib_path]))
for flag, testrule in build_targets:
# configure
cmd = "%s ./configure %s" % (self.cfg['preconfigopts'], ' '.join(common_configopts + [flag, comp_str]))
(out, _) = run_cmd(cmd, log_all=True, simple=False)
# build in situ using 'make install'
# note: not 'build'
super(EB_Amber, self).install_step()
# test
if self.cfg['runtest']:
run_cmd("make %s" % testrule, log_all=True, simple=False)
# clean, overruling the normal 'build'
run_cmd("make clean")
def sanity_check_step(self):
"""Custom sanity check for Amber."""
binaries = ['sander', 'tleap']
if == 'Amber':
if self.with_cuda:
if self.with_mpi:
if self.with_mpi:
if == 'Amber':
custom_paths = {
'files': [os.path.join(self.installdir, 'bin', binary) for binary in binaries],
'dirs': [],
super(EB_Amber, self).sanity_check_step(custom_paths=custom_paths)
def make_module_extra(self):
"""Add module entries specific to Amber/AmberTools"""
txt = super(EB_Amber, self).make_module_extra()
txt += self.module_generator.set_environment('AMBERHOME', self.installdir)
if self.pylibdir:
txt += self.module_generator.prepend_paths('PYTHONPATH', self.pylibdir)
return txt
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