Respected Team,
I am facing an issue while running the equilibration step of my MD
simulation using AMBER on our server.
When I run the same equilibration input (pmemd.cuda) on my local desktop,
it completes successfully without any error. However, when I run the same
step on the server using the below SLURM script with pmemd.MPI, the job
fails with a *segmentation fault*.
SLURM script used:
#!/bin/sh
#SBATCH -N 1
#SBATCH --ntasks-per-node=64
#SBATCH --job-name=184
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out
#SBATCH --partition=braf
#SBATCH --exclusive
#SBATCH --export=ALL
# Load the Intel toolchain
ml intel/2018_4
# Set OMP threads, if your application is multithreaded
# OMP_NUM_THREADS=$SLURM_NTASKS #Optional, uncomment this line if required.
mpirun -n 64 /home/apps/amber16_intel/bin/pmemd.MPI -O -i equi_50.in -o
equi_50.out -p with_184.parm7 -c heat_hold.rst7 -r equi_50.rst7 -inf
equi_50.info -ref heat_hold.rst7 -x equi_50.mdcrd;
Error in .err file:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
pmemd.MPI 0000000000744BDD Unknown Unknown Unknown
libpthread-2.17.s 00007F1C27DCF630 Unknown Unknown Unknown
pmemd.MPI 000000000046F462 Unknown Unknown Unknown
...
Output in .out file (last lines):
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
Could you please advise on possible causes or solutions? Is this issue
related to MPI configuration, number of cores, or AMBER build?
Thank you for your time and support.
with regards,
Yashika
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Received on Thu Aug 14 2025 - 07:00:03 PDT