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I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows:

#!/bin/bash
#SBATCH -Jgromacs_cpu 
#SBATCH -Axxxxxxxxxxxx #account name
#SBATCH -N1 --ntasks-per-node=1
#SBATCH --cpus-per-task=4 
#SBATCH --mem-per-cpu=10G 
#SBATCH -t4:00:00
#SBATCH -pxxxxxxx #queue name                    
#SBATCH -oggpu.out      # output file name
#SBATCH --mail-type=BEGIN,END,FAIL              # Mail preferences
#SBATCH [email protected]        # E-mail address for notifications

#name of the executable
exe="gmx_mpi"
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

pwd
module load gromacs
cd nvt
pwd

srun $exe grompp -f inputs/nvt.mdp -c peg.gro -p topol.top -o nvt.tpr -maxwarn 1
srun -bootstrap slurm -n $SLURM_NTASKS $exe mdrun -s nvt.tpr

P.S.- I am new to GROMACS, and the last line is throwing error. In fact that is the line that my university's HPC cluster has reccomended to run MD simulations.

The error thrown is as follows:

There was 1 note

There was 1 warning

Back Off! I just backed up nvt.tpr to ./#nvt.tpr.29#

GROMACS reminds you: "If humanity has fled shivering from the starry spaces, it has become minutely at home in the interstices of the speck that it inhabits for an instant" (George H. Mead)

Setting the LD random seed to -419561833

Generated 18 of the 28 non-bonded parameter combinations

Excluding 2 bonded neighbours molecule type 'PEG'

turning H bonds into constraints...

Velocities were taken from a Maxwell distribution at 300 K Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K

Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm

Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 25x25x25, spacing 0.120 0.120 0.120

Estimate for the relative computational load of the PME mesh part: 0.81

This run will generate roughly 2 Mb of data Invalid time specification (pos=0): ootstrap srun: error: Invalid --begin specification [atl1-1-01-010-3-0.pace.gatech.edu:mpi_rank_0][MPID_Init] [Performance Suggestion]: Application has requested for multi-thread capability. If allocating memory from different pthreads/OpenMP threads, please consider setting MV2_USE_ALIGNED_ALLOC=1 for improved performance. Use MV2_USE_THREAD_WARNING=0 to suppress this error message.

Please can y'all help me with the same.

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  • $\begingroup$ Please first use gmx grompp ... instead of srun gmx_mpi grompp ... and report back. The GROMACS preprocessor does not write .tpr files in parallel -- instead you have $NTASKS instances all trying to write to the same file at once, and together with GROMACS's file backup behaviour, you are almost certainly getting an error from that step. $\endgroup$ Feb 2 at 10:16

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