Skip to content

Ensure AmberTools will find the correct python library and include dir #4045

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

Merged
boegel merged 2 commits into from
Jan 28, 2026
+19 −3
Merged

Ensure AmberTools will find the correct python library and include dir #4045

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4e35f4d
Ensure AmberTools will find the correct python library and include dir
Crivella Jan 15, 2026
b0aef6d
Fix tests taking all CPUs due to unset OMP_NUM_THREADS
Crivella Jan 15, 2026
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
17 changes: 15 additions & 2 deletions easybuild/easyblocks/a/amber.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,10 @@
from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
from easybuild.framework.easyconfig import CUSTOM
from easybuild.tools.build_log import EasyBuildError
from easybuild.tools.modules import get_software_root
from easybuild.tools.modules import get_software_root, get_software_version
from easybuild.tools.run import run_shell_cmd
from easybuild.tools.filetools import remove_dir, which
from easybuild.tools.systemtools import get_shared_lib_ext


class EB_Amber(CMakeMake):
Expand Down Expand Up @@ -164,13 +165,25 @@ def configure_step(self):

pythonroot = get_software_root('Python')
if pythonroot:
version = get_software_version('Python')
shlib_ext = get_shared_lib_ext()
self.cfg.update('configopts', '-DDOWNLOAD_MINICONDA=FALSE')
self.cfg.update('configopts', '-DPYTHON_EXECUTABLE=%s' % os.path.join(pythonroot, 'bin', 'python'))
Copy link
Contributor Author

@Crivella Crivella Jan 15, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Removed as this is now set by the CMake configure_step


self.pylibdir = det_pylibdir()
pythonpath = os.environ.get('PYTHONPATH', '')
env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))

# AmberTools uses the deprecated FindPythonLibs. Ensure we use the correct library and include dir
version_maj_min = '.'.join(version.split('.')[:2])
python_library = os.path.join(pythonroot, 'lib', f'libpython{version_maj_min}.{shlib_ext}')
python_incdir = os.path.join(pythonroot, 'include', 'python%s' % version_maj_min)
if not os.path.isfile(python_library):
raise EasyBuildError("Cannot find Python library '%s'!" % python_library)
if not os.path.isdir(python_incdir):
raise EasyBuildError("Cannot find Python include directory '%s'!" % python_incdir)
self.cfg.update('configopts', f'-DPYTHON_LIBRARY={python_library}')
self.cfg.update('configopts', f'-DPYTHON_INCLUDE_DIR={python_incdir}')

if get_software_root('FFTW'):
external_libs_list.append('fftw')
if get_software_root('netCDF'):
Expand Down