[gmx-users] : SOLVED GMX_MPI 2020 gmx_mpi segmentation fault

Nicolas GOUDARD nicolas.goudard at univ-amu.fr
Thu Feb 6 07:24:14 CET 2020 

Hello
I solve my problem myself,  with a colleague
The problem was : On CentOS Linux release 8.1.1911 (Core)  the gmx_mpi returned a segmentation  fault, .  
The source of the problem was the openmpi version 4.0.1  provided by CenOS: (dnf install openmpi)
So we have downloaded openmpi 4.0.2 from the OmpenMpi website , then we have compiled Gromacs 2020 with openmpi 4.0.2 
and the problem has been solved !!

Thanks




[alta:23110:0:23110] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f06e1072768)
==== backtrace ====
    0  /usr/lib64/libucs.so.0(+0x18bb0) [0x7f06e0a05bb0]
    1  /usr/lib64/libucs.so.0(+0x18d8a) [0x7f06e0a05d8a]
    2  /usr/lib64/libuct.so.0(+0x1655b) [0x7f06e1f3755b]
    3  /lib64/ld-linux-x86-64.so.2(+0xfd2a) [0x7f06f382cd2a]
    4  /lib64/ld-linux-x86-64.so.2(+0xfe2a) [0x7f06f382ce2a]
    5  /lib64/ld-linux-x86-64.so.2(+0x13e3f) [0x7f06f3830e3f]
    6  /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7]
    7  /lib64/ld-linux-x86-64.so.2(+0x136ae) [0x7f06f38306ae]
    8  /usr/lib64/libdl.so.2(+0x11ba) [0x7f06f0e011ba]
    9  /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7]
   10  /usr/lib64/libc.so.6(_dl_catch_error+0x33) [0x7f06f137c093]
   11  /usr/lib64/libdl.so.2(+0x1939) [0x7f06f0e01939]
   12  /usr/lib64/libdl.so.2(dlopen+0x4a) [0x7f06f0e0125a]
   13  /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f06ee649f05]
   14  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f06ee627b16]
   15  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f06ee626a5a]
   16  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f06ee6323ce]
   17  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f06ee6328b2]
   18  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f06ee632915]
   19  /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f06f23de494]
   20  /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Init_thread+0x55) [0x7f06f240e805]
   21  /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx4initEPiPPPc+0x85) [0x7f06f287dad5]
   22  /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx18initForCommandLineEPiPPPc+0x19) [0x7f06f2cc9449]
   23  gmx_mpi() [0x4052bb]
   24  /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f06f1266873]
   25  gmx_mpi() [0x40538e]
===================
Segmentation fault (core dumped)

Nicolas Goudard - Informaticien UMR CNRS 7313 - ISM2 - Institut des Sciences Moléculaires de Marseille
Aix-Marseille Université - case 561 - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille
Tél: +33(0)4 91 28 82 66
Site : http://www.univ-amu.fr <http://www.univ-amu.fr/> - Email : nicolas.goudard at univ-amu.fr <mailto:nicolas.goudard at univ-amu.fr>
Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire.

> Début du message réexpédié :
> 
> De: Nicolas GOUDARD <nicolas.goudard at univ-amu.fr>
> Objet: [gmx-users] GMX_MPI 2020
> Date: 3 février 2020 à 23:58:14 UTC+1
> À: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Répondre à: <gmx-users at gromacs.org>
> 
> Hello
> On Gromacs 2020 or 2020 beta 1 on centos 8.1 there is a segmentation fault 
> How can I solve it ?
> 
> #cat /etc/redhat-release 
> CentOS Linux release 8.1.1911 (Core) 
> 
> #cat /etc/redhat-release 
> CentOS Linux release 8.1.1911 (Core) 
> [root at alta ~]# 
> [root at alta ~]# cat /usr/share/Modules/modulefiles/gromacs2020_mpi 
> #%Module######################################################################
> ##
> ##      gromacs modulefile
> ##
> proc ModulesHelp { } {
> puts stderr "gromacs 2020"
> return 0
> }
> prepend-path LD_LIBRARY_PATH /share/programs/GROMACS-2020-MPI/lib 
> prepend-path PATH /share/programs/GROMACS-2020-MPI/bin
> 
> 
> #wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta1.tar.gz
> #tar xvzf gromacs-2020-beta1.tar.gz 
> #cd gromacs-2020-beta1/
> #cmake ..  -DGMX_MPI=on  -DCMAKE_INSTALL_PREFIX=/share/programs/GROMACS-2020-MPI  -DCMAKE_INSTALL_LIBDIR=/share/programs/GROMACS-2020-MPI/lib  -DGMX_USE_RDTSCP=ON
> #make -j4
> #make install
> #source /share/programs/GROMACS-2020-MPI/bin/GMXRC
> #module unload gromacs2020_mpi 
> #gmx_mpi
> 
> [alta:23110:0:23110] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f06e1072768)
> ==== backtrace ====
>    0  /usr/lib64/libucs.so.0(+0x18bb0) [0x7f06e0a05bb0]
>    1  /usr/lib64/libucs.so.0(+0x18d8a) [0x7f06e0a05d8a]
>    2  /usr/lib64/libuct.so.0(+0x1655b) [0x7f06e1f3755b]
>    3  /lib64/ld-linux-x86-64.so.2(+0xfd2a) [0x7f06f382cd2a]
>    4  /lib64/ld-linux-x86-64.so.2(+0xfe2a) [0x7f06f382ce2a]
>    5  /lib64/ld-linux-x86-64.so.2(+0x13e3f) [0x7f06f3830e3f]
>    6  /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7]
>    7  /lib64/ld-linux-x86-64.so.2(+0x136ae) [0x7f06f38306ae]
>    8  /usr/lib64/libdl.so.2(+0x11ba) [0x7f06f0e011ba]
>    9  /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7]
>   10  /usr/lib64/libc.so.6(_dl_catch_error+0x33) [0x7f06f137c093]
>   11  /usr/lib64/libdl.so.2(+0x1939) [0x7f06f0e01939]
>   12  /usr/lib64/libdl.so.2(dlopen+0x4a) [0x7f06f0e0125a]
>   13  /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f06ee649f05]
>   14  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f06ee627b16]
>   15  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f06ee626a5a]
>   16  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f06ee6323ce]
>   17  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f06ee6328b2]
>   18  /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f06ee632915]
>   19  /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f06f23de494]
>   20  /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Init_thread+0x55) [0x7f06f240e805]
>   21  /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx4initEPiPPPc+0x85) [0x7f06f287dad5]
>   22  /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx18initForCommandLineEPiPPPc+0x19) [0x7f06f2cc9449]
>   23  gmx_mpi() [0x4052bb]
>   24  /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f06f1266873]
>   25  gmx_mpi() [0x40538e]
> ===================
> Segmentation fault (core dumped)
> 
> Nicolas Goudard - Informaticien UMR CNRS 7313 - ISM2 - Institut des Sciences Moléculaires de Marseille
> Aix-Marseille Université - case 561 - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille
> Tél: +33(0)4 91 28 82 66
> Site : http://www.univ-amu.fr <http://www.univ-amu.fr/> - Email : nicolas.goudard at univ-amu.fr <mailto:nicolas.goudard at univ-amu.fr>
> Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire.
> 
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