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Beginner
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Seg Fault with Gromacs gmx grompp command

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.

 

 

 

 

 

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3 Replies
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Moderator
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We would need to have a reproducible test case to investigate. 

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Beginner
33 Views

What other information do you need?

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Moderator
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An attached test case that we can compile and execute to see the SegFault

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