[gmx-users] Normal mode segmentation fault - memory problem ?

[Marlon Sidore]

I would like a second opinion on the cause of this segfault.

I have a protein in a vacuum. All atom. After extensive minimization, I
produced a matrix .mtx.

Then, on the cluster, a simple gmx_mpi nmeig -f normal.mtx -s normal.tpr
leads to:
Reading double precision matrix generated by GROMACS 2018.6
Sparse matrix storage format, nrow=27579, ncols=27579
[n2534:10432:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
 2 0x000000000006ba2c mxm_handle_error()
 /var/tmp/OFED_topdir/BUILD/mxm-3.7.3111/src/mxm/util/debug/debug.c:641
 3 0x000000000006bf7c mxm_error_signal_handler()
 /var/tmp/OFED_topdir/BUILD/mxm-3.7.3111/src/mxm/util/debug/debug.c:616
 4 0x0000000000036280 killpg()  ??:0
 5 0x0000000000642091
_ZN17_INTERNAL3a3192c818nma_sparse_hessianEP16gmx_sparsematrixiPK10t_topologyRKSt6vectorImSaImEEiPfSA_()
 /scratch/DEFAUT/akira/
akira/installs/occigen/applications/gromacs/2018.6/intel/18.1/openmpi/intel/2.0.4/gromacs-2018.6/src/gromacs/gmxana/gmx_nmeig.cpp:220
 6 0x0000000000642091 gmx_nmeig()
 /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018.6/intel/18.1/openmpi/intel/2.0.4/gromacs-201
8.6/src/gromacs/gmxana/gmx_nmeig.cpp:471
 7 0x0000000000431cb9
_ZN3gmx12_GLOBAL__N_122CMainCommandLineModule3runEiPPc()
 /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018
.6/intel/18.1/openmpi/intel/2.0.4/gromacs-2018.6/src/gromacs/commandline/cmdlinemodulemanager.cpp:133
 8 0x0000000000431cb9 _ZN3gmx24CommandLineModuleManager3runEiPPc()
 /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018.6/intel/18.
1/openmpi/intel/2.0.4/gromacs-2018.6/src/gromacs/commandline/cmdlinemodulemanager.cpp:589
 9 0x000000000040f788 main()
 /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018.6/intel/18.1/openmpi/intel/2.0.4/gromacs-2018.6/s
rc/programs/gmx.cpp:60
10 0x00000000000223d5 __libc_start_main()  ??:0
11 0x000000000040f5e9 _start()  ??:0
===================

Either I did something wrong while producing the matrix or I'm doing
something wrong on the nmeig. S

Should I have done something to restrict the analysis on the backbone
(somehow) if it's a memory problem ? I'm still allocacating 100G to
this analysis, I naively thought it was enough.

Best,

Marlon Sidore

PhD - Post-doctoral fellow
Institut d’Électronique et des Systèmes