[AMBER] Temperature-Replica Exchange MD

From: Gilberto Pereira <gilberto.pereiraportugal.gmail.com>
Date: Wed, 24 Oct 2018 16:26:32 +0200

Hello, dear Amber community.

I am currently trying to run replica exchange MD simulations for a complex
in explicit solvent. However, due to the low number of processors in my
desktop, i must resort to a computer cluster, where i want to run the
replicas in two different nodes. However, It returns an error stating that
the number of processes that i wish to run is too big for one single node.
I cannot understand why it is unable to use the cpus on both nodes and
instead allocates all processes to a single node.
Below, please find the script i am currently using:

#! /bin/bash
#SBATCH -p public
#SBATCH --cpus-per-task=1
#SBATCH --ntasks=12
#SBATCH -t 24:00:00
#SBATCH --job-name=REMD
#SBATCH -o slurm.out
#SBATCH -e slurm.err

# Configuration

module purge
module load batch/slurm
module load compilers/intel17
module load mpi/openmpi-2.0.2.i17

# Replace with your current amber16 (or 18) location
source /b/home/isis/dbarreto/software/amber16_failsafe/amber.sh


cd ${RUNDIR}/

mpirun -np 38 pmemd.MPI -ng 38 -groupfile equilibrate.groupfile
-machinefile machines

Hope you can help me figure out a solution.

Thank you so much.

Gilberto Pereira
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Received on Wed Oct 24 2018 - 07:30:02 PDT
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