Respected Team
I try to do energy minimization using pmemd.MPI (AMBER20 compiled with
Intel compiler 18.0.3 and Intel MPI 2018). The run crashes with the
following error in my output (out.txt):
/scf-data/compilers/intel/
18.0.3.222/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpir$1
Intel(R) MPI Library, Version 2018 Update 3 Build 20180411 (id: 18329)
Copyright (C) 2003-2018 Intel Corporation. All rights reserved.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libifcoremt.so.5 00007FE4F56FD46C for__signal_handl Unknown Unknown
libpthread-2.17.s 00007FE4F5C765E0 Unknown Unknown Unknown
pmemd.MPI 000000000058C1A5 Unknown Unknown Unknown
pmemd.MPI 00000000004CECB3 Unknown Unknown Unknown
pmemd.MPI 0000000000405F02 Unknown Unknown Unknown
libc-2.17.so 00007FE4F4802C05 __libc_start_main Unknown Unknown
pmemd.MPI 0000000000405E09 Unknown Unknown Unknown
real 0m3.923s
user 0m24.735s
sys 0m11.150s
Intel(R) MPI Library, Version 2018 Update 3 Build 20180411 (id: 18329)
Copyright (C) 2003-2018 Intel Corporation. All rights reserved.
*Important note: *
*When I run **the same input files** with pmemd.cuda on my desktop machine,
the job runs correctly without any errors. *
So the problem only appears when I run pmemd.MPI in the HPC environment.
Here is my input shell script below, which I use to submit the job:
#!/bin/bash
#PBS -S /bin/bash
#PBS -N m2
#PBS -l select=1:ncpus=32
#PBS -l walltime=240:00:00
#PBS -q externalq
#PBS -o out.txt
#PBS -e err.txt
#PBS -joe
# ## export environment variable from current session to job run-time ...
better to use this always.
#PBS -V
#module load intel/2019.1.144
#module load intel/2018.1.163
module load intel/2018.3.222
cd $PBS_O_WORKDIR
which mpirun
NPROCS=`wc -l < $PBS_NODEFILE`
echo $NPROCS
export OMP_NUM_THREADS=32
export I_MPI_PRINT_VERSION=1
#time mpirun /scf-data/apps/namd/NAMD_2.13-Linux-x86_64-icc/charmrun
/scf-data/apps/namd/NAMD_2.13-Linux-x86_64-icc/namd2
/scf-data/hridoy/Namd/NAMD_2.12_Win64-multicore/GMP-bound-conformation/2BLE/Restart-E-min-Heating.namd>
/scf-data/hridoy/Namd/NAMD_2.12_Win64-multicore/GMP-bound-conformation/2BLE/output/restart-eneregy_heat-emin.lOg
time mpirun -np 32 pmemd.MPI -O -i min_500.in -o min_500.out -c
with_184.rst7 -p with_184.parm7 -r min_500.rst7 -inf min_500.info -ref
with_184.rst7 -x min_500.mdcrd
Could anyone suggest why this error occurs and how to resolve it?
I have already checked my input file and topology/coordinate consistency.
Is this related to file permissions or MPI I/O in Intel MPI 2018?
with regards
Yashika
NSUT,Delhi
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Received on Tue Sep 09 2025 - 23:00:02 PDT
