fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK #2212
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boegel
changed the title
akesandgren
reviewed
Nov 11, 2020
boegel
reviewed
Nov 12, 2020
| 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'] |
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Is it OK to always include -lpthread -lm -ldl here?
Can you clarify which error this fixes exactly?
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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.
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Going in, thanks @ostueker! |
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First change eliminates the (wrong) variable
$EBROOTMKLfrom the easyblock as per discussion of @boegel and @mboisson on EasyBuild Slack.Secondly GROMACS 2020.4' cmake was refusing to use MKL as FFT library (using the
gomkl-2020atoolchain), which was fixed by appending-lpthread -lm -ldlto-DMKL_LIBRARIES.