GROMACS version:2022+cp2k interface
basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?
Thank you in advance
I am taking that error :
Command line:
gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt
Compiled SIMD: AVX_256, but for this host/run AVX2_256 might be better (see
log).
Reading file nvt.tpr, VERSION 2022 (double precision)
Changing nstlist from 10 to 50, rlist from 1.2 to 1.302
Using 4 MPI processes
Non-default thread affinity set, disabling internal thread affinity
Using 1 OpenMP thread per MPI process
starting mdrun ‘Protein in water’
50000 steps, 100.0 ps.
step 0
[barbun8:362337:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
2 0x00000000000686ec mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.5.3093/src/mxm/util/debug/debug.c:641
3 0x0000000000068c3c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.5.3093/src/mxm/util/debug/debug.c:616
4 0x0000000000035250 killpg() ??:0
5 0x0000000000b03558 _Z14spread_on_gridPK9gmx_pme_tP11PmeAtomCommPK10pmegrids_tbbPdbi._omp_fn.0() pme_spread.cpp:0
6 0x000000000000dacf GOMP_parallel() /truba/sw/src/gcc/gcc-7-20170326/hamsi_install/x86_64-pc-linux-gnu/libgomp/…/…/./…/libgomp/parallel.c:168
7 0x0000000000b04f42 _Z14spread_on_gridPK9gmx_pme_tP11PmeAtomCommPK10pmegrids_tbbPdbi() ??:0
8 0x0000000000add6f3 _Z10gmx_pme_doP9gmx_pme_tN3gmx8ArrayRefIKNS1_11BasicVectorIdEEEENS2_IS4_EENS2_IKdEES9_S9_S9_S9_S9_PA3_S8_PK9t_commreciiP6t_nrnbP13gmx_wallcyclePA3_dSK_PdSL_ddSL_SL_RKNS1_12StepWorkloadE() ??:0
9 0x0000000001186a47 _ZN24CpuPpLongRangeNonbondeds9calculateEP9gmx_pme_tPK9t_commrecN3gmx8ArrayRefIKNS5_11BasicVectorIdEEEEPNS5_15ForceWithVirialEP14gmx_enerdata_tPA3_KdNS6_ISF_EESA_RKNS5_12StepWorkloadERK22DDBalanceRegionHandler() ??:0
10 0x00000000012c638a _Z8do_forceP8_IO_FILEPK9t_commrecPK14gmx_multisim_tRK10t_inputrecPN3gmx3AwhEP10gmx_enfrotPNSA_10ImdSessionEP6pull_tlP6t_nrnbP13gmx_wallcyclePK14gmx_localtop_tPA3_KdNSA_19ArrayRefWithPaddingINSA_11BasicVectorIdEEEEPK9history_tPNSA_16ForceBuffersViewEPA3_dPK9t_mdatomsP14gmx_enerdata_tNSA_8ArrayRefISQ_EEP10t_forcerecPNSA_21MdrunScheduleWorkloadEPNSA_19VirtualSitesHandlerEPddP9gmx_edsamP24CpuPpLongRangeNonbondedsiRK22DDBalanceRegionHandler() ??:0
11 0x00000000011d9fc7 _ZN3gmx15LegacySimulator5do_mdEv() ??:0
12 0x00000000011d52bd _ZN3gmx15LegacySimulator3runEv() ??:0
13 0x0000000000b26a3d _ZN3gmx8Mdrunner8mdrunnerEv() ??:0
14 0x0000000000585bb9 _ZN3gmx9gmx_mdrunEP19ompi_communicator_tRK13gmx_hw_info_tiPPc() ??:0
15 0x0000000000585ee4 _ZN3gmx9gmx_mdrunEiPPc() ??:0
16 0x000000000063a960 _ZN3gmx24CommandLineModuleManager3runEiPPc() ??:0
17 0x000000000051665c main() ??:0
18 0x0000000000021b35 __libc_start_main() ??:0
19 0x00000000005824d5 _start() ??:0
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
mpirun noticed that process rank 0 with PID 362337 on node barbun8 exited on signal 11 (Segmentation fault).
That is my nvt.mdp file:
; md-qmmm-nvt.mdp - used as input into grompp to generate egfp-qmmm-nvt.tpr
integrator = md ; MD using leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Set output frequency to each step
nstxout = 1000 ; Coordinates to trr
nstvout = 1000 ; Coordinates to trr
nstlog = 1000 ; Energies to md.log
nstcalcenergy = 1000 ; Energies to ener.edr
nstenergy = 1000 ; Energies to ener.edr
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Set cut-offs
nstlist = 50
rlist = 1.302
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 1.0
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw-switch = 1.0
rvdw = 1.2
;Temperature coupling options
tcoupl = v-rescale
nsttcouple = 10
tc-grps = System
tau-t = 0.1
ref-t = 300
; CP2K QMMM parameters
qmmm-cp2k-active = true ; Activate QMMM MdModule
qmmm-cp2k-qmgroup = QMatoms; Index group of QM atoms
qmmm-cp2k-qmmethod = PBE ; Method to use
qmmm-cp2k-qmcharge = 0 ; Charge of QM system
qmmm-cp2k-qmmultiplicity = 1 ; Multiplicity of QM system
that is my slurm for starting job
#!/bin/bash
#SBATCH -p mid2
#SBATCH -J nvt-2-1
#SBATCH --nodes=1
#SBATCH --tasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --time=5-00:00:00
#SBATCH --output=slurm-%j.out
#SBATCH --error=slurm-%j.err
echo “SLURM_NODELIST $SLURM_NODELIST”
echo “NUMBER OF CORES $SLURM_NTASKS”
export OMP_NUM_THREADS=1
export OMPI_MCA_btl_openib_allow_ib=1
module purge
module load centos7.9/comp/gcc/7
module load centos7.9/lib/openmpi/4.1.1-gcc-7
export PATH=/truba/home/gromacs-cp2k/build/bin:$PATH
mpirun -np 4 /truba/home/gromacs-cp2k/build/bin/gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt
exit