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This problem is consistent with the following gromacs/compiler versions:
Gromacs 2019.4/Intel Parallel Studio 2019.4
Gromacs 2019.4/Intel 2017.2
Gromacs 2018.2/Intel Parallel Studio 2019.4
Gromacs 2018.5/Intel Parallel Studio 2019.4
The command to build and install gromacs in all cases is
export CC=icc
export CXX=icpc
export FC=ifort
cmake .. -DGMX_FFT_LIBRARY=mkl \
-DCMAKE_INSTALL_PREFIX=$HOME/sw/gromacs/intel/<version> && make VERBOSE=1 && make install
The gcc version in the PATH is 5.4.0
The OS is:
Scientific Linux release 6.10 (Carbon)
I am running the lysozyme tutorial: http://www.mdtutorials.com/gmx/lysozyme/
The command that seg faults is
gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr -maxwarn 2
The gmx grompp command succeeds when using a version of gromacs compiled with GCC
Any help would be greatly appreciated.
- Tags:
- CC++
- Development Tools
- Intel® C++ Compiler
- Intel® Parallel Studio XE
- Intel® System Studio
- Optimization
- Parallel Computing
- Vectorization
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We would need to have a reproducible test case to investigate.
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What other information do you need?
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An attached test case that we can compile and execute to see the SegFault

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