[gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler
Glenn (Gedaliah) Wolosh
gwolosh at njit.edu
Fri Dec 6 15:30:06 CET 2019
> On Dec 6, 2019, at 9:12 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> Hi,
>
> If the environment is sufficiently well constructed to do the necessary
> dynamic linking, then things like gmx -version and gmx editconf should not
> segfault. Do they? My guess is that the appropriate Intel libraries, or
> perhaps the gcc libstdc++ libraries that icc requires are actually not
> available in the environment.
These command do not segfault. The dynamic linking is fine.
kong-183 lysozyme >: module list
Currently Loaded Modulefiles:
1) sge 3) intel/parallel_studio/2019.4 5) gromacs/intel/2019.4
2) singularity/3.2.1 4) gcc/5.4.0
kong-184 lysozyme >: which gmx
/afs/cad/linux/gromacs/intel/2019.4/bin/gmx
kong-185 lysozyme >: ldd /afs/cad/linux/gromacs/intel/2019.4/bin/gmx
linux-vdso.so.1 => (0x00007ffd08584000)
libmkl_intel_lp64.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so (0x00002afa6906e000)
libmkl_sequential.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_sequential.so (0x00002afa69be6000)
libmkl_core.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_core.so (0x00002afa6b180000)
libgromacs.so.4 => /afs/cad/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 (0x00002afa6f455000)
libm.so.6 => /lib64/libm.so.6 (0x00000038cc400000)
libstdc++.so.6 => /afs/cad/linux/gcc-5.4.0-sl6/lib64/libstdc++.so.6 (0x00002afa706fe000)
libiomp5.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libiomp5.so (0x00002afa70a8c000)
libgcc_s.so.1 => /afs/cad/linux/gcc-5.4.0-sl6/lib64/libgcc_s.so.1 (0x00002afa70e76000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000038cbc00000)
libc.so.6 => /lib64/libc.so.6 (0x00000038cb800000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000038cc000000)
librt.so.1 => /lib64/librt.so.1 (0x00000038cc800000)
libimf.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libimf.so (0x00002afa7108e000)
libsvml.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libsvml.so (0x00002afa7162f000)
libirng.so => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libirng.so (0x00002afa72fd3000)
libintlc.so.5 => /afs/cad/linux/intel/parallel_studio_cluster_edition_2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x00002afa73345000)
/lib64/ld-linux-x86-64.so.2 (0x00005613d5ea5000)
This seems specific to the Scientific Linux 6.x OS. When built and installed on a 7.x version, cmx grompp works fine.
GW
>
> Mark
>
> On Thu, 5 Dec 2019 at 21:36, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu <mailto:gwolosh at njit.edu>>
> wrote:
>
>> Thanks for the quick response. I do have the environment properly prepare
>> via modules.
>>
>> GW
>>
>>
>>> On Dec 5, 2019, at 3:24 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>>
>>> Hi,
>>>
>>> I suspect you need to prepare the intel environment at run time like you
>>> did before compilation. Probably you (or a module you loaded) source-d a
>>> compilervars.sh file, and that's probably what you need here.
>>>
>>> Mark
>>>
>>> On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu
>> <mailto:gwolosh at njit.edu <mailto:gwolosh at njit.edu>>>
>>> wrote:
>>>
>>>>
>>>> Also posted on the intel forum:
>>>>
>>>> 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/ <
>>>> http://www.mdtutorials.com/gmx/lysozyme/ <
>> http://www.mdtutorials.com/gmx/lysozyme/ <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.
>>>>
>>>>
>>>> GW
>>>> --
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