Skip to content

update custom easyblock for NAMD for version >= 3.0 #3248

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
tanmoy1989 wants to merge 6 commits into
base: develop
Choose a base branch
from
Open

update custom easyblock for NAMD for version >= 3.0 #3248

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
ac2c0cb
Update namd.py to run successfully NAMD-3.0b6-foss-2023a-mpi.eb
tanmoy1989 Mar 4, 2024
a7d40d9
Update namd.py - I have revised the code as per suggestions. Please l…
tanmoy1989 Mar 5, 2024
7311289
Update namd.py - making further changes
tanmoy1989 Mar 5, 2024
bc80bf1
Update namd.py - blank line deleted
tanmoy1989 Mar 5, 2024
0046563
Update namd.py
tanmoy1989 Mar 13, 2024
efd5825
Update namd.py
tanmoy1989 Mar 14, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 15 additions & 10 deletions easybuild/easyblocks/n/namd.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,18 +88,20 @@ def extract_step(self):
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)
"""From version 3.0 this is no longer needed."""
if LooseVersion(self.version) < LooseVersion('3.0'):
"""Patch scripts to avoid using hardcoded /bin/csh."""
super(EB_NAMD, self).patch_step(*args, **kwargs)

self.charm_dir = self.charm_tarballs[0][:-4]
self.charm_dir = self.charm_tarballs[0][:-4]

charm_config = os.path.join(self.charm_dir, 'src', 'scripts', 'configure')
apply_regex_substitutions(charm_config, [(r'SHELL=/bin/csh', 'SHELL=$(which csh)')])
charm_config = os.path.join(self.charm_dir, 'src', 'scripts', 'configure')
apply_regex_substitutions(charm_config, [(r'SHELL=/bin/csh', 'SHELL=$(which csh)')])

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*$', '#!/usr/bin/env csh')])
for csh_script in [os.path.join('plugins', 'import_tree'), os.path.join('psfgen', 'import_tree'),
os.path.join(self.charm_dir, 'src', 'QuickThreads', 'time', 'raw')]:
if os.path.exists(csh_script):
apply_regex_substitutions(csh_script, [(r'^#!\s*/bin/csh\s*$', '#!/usr/bin/env csh')])

def configure_step(self):
"""Custom configure step for NAMD, we build charm++ first (if required)."""
Expand All @@ -124,7 +126,7 @@ def configure_step(self):

# 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
# 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')
Expand All @@ -141,6 +143,9 @@ def configure_step(self):
'parallel': self.cfg['parallel'],
}
charm_subdir = '.'.join(os.path.basename(self.charm_tarballs[0]).split('.')[:-1])
# From version 3.0 naming schema changed
if LooseVersion(self.version) >= LooseVersion('3.0'):
charm_subdir = charm_subdir.replace("-", "-v")
self.log.debug("Building Charm++ using cmd '%s' in '%s'" % (cmd, charm_subdir))
run_cmd(cmd, path=charm_subdir)

Expand Down