Skip to content
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

fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK #2212

Merged
merged 3 commits into from
Nov 23, 2020
Merged

fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK #2212

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6201d85
gromacs.py: fix two bugs when using GCC & MKL for FFT and BLAS/LAPACK
ostueker Oct 28, 2020
4bed307
appeasing hound
ostueker Oct 28, 2020
c89d02d
implementing suggestions by reviewers
ostueker Nov 12, 2020
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
8 changes: 5 additions & 3 deletions easybuild/easyblocks/g/gromacs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -326,12 +326,14 @@ def configure_step(self):
else:
self.cfg.update('configopts', "-DGMX_OPENMP=OFF")

if get_software_root('imkl'):
imkl_root = get_software_root('imkl')
if imkl_root:
# using MKL for FFT, so it will also be used for BLAS/LAPACK
self.cfg.update('configopts', '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$EBROOTMKL/mkl/include" ')
imkl_include = os.path.join(imkl_root, 'mkl', 'include')
self.cfg.update('configopts', '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="%s" ' % imkl_include)
libs = os.getenv('LAPACK_STATIC_LIBS').split(',')
mkl_libs = [os.path.join(os.getenv('LAPACK_LIB_DIR'), lib) for lib in libs if lib != 'libgfortran.a']
mkl_libs = ['-Wl,--start-group'] + mkl_libs + ['-Wl,--end-group']
mkl_libs = ['-Wl,--start-group'] + mkl_libs + ['-Wl,--end-group -lpthread -lm -ldl']
Copy link
Member

Choose a reason for hiding this comment

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

Is it OK to always include -lpthread -lm -ldl here?

Can you clarify which error this fixes exactly?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

When trying to compile GROMACS 2020.4 with the gomkl-2020a (GCC + MKL) toolchain (which we found to produce an mdrun that runs a bit faster than the foss-toolchain), cmake wasn't finding the FFT provided by MKL unless I added the -lpthread -lm -ldl flags:

  Linking with MKL was requested, but was not successful: The include path to
  mkl.h in MKL_INCLUDE_DIR, and the link libraries in
  MKL_LIBRARIES=-Wl,--start-group;/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/lib/intel64/libmkl_gf_lp64.a;/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/lib/intel64/libmkl_sequential.a;/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/lib/intel64/libmkl_core.a;-Wl,--end-group
  need to match what the MKL documentation says you need for your system: Use
  full paths to library files, in the right order, and separated by
  semicolons.
Call Stack (most recent call first):
  CMakeLists.txt:716 (include)

I used the MKL advisor to suggest the linker-flags, which is how I came to try adding -lpthread -lm -ldl, which solved the above error.

self.cfg.update('configopts', '-DMKL_LIBRARIES="%s" ' % ';'.join(mkl_libs))
else:
for libname in ['BLAS', 'LAPACK']:
Expand Down