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 --mail-user=johndoe@blabla.edu # E-mail address for notifications#name of the executableexe="gmx_mpi"export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASKpwdmodule load gromacscd nvtpwdsrun $exe grompp -f inputs/nvt.mdp -c peg.gro -p topol.top -o nvt.tpr -maxwarn 1srun -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 starryspaces, it has become minutely at home in the interstices of the speckthat 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 Analysingresidue names: There are: 1 Other residues Analysing residuesnot 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 0.000nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000nm
Note that mdrun will redetermine rlist based on the actual pair-listsetup Calculating fourier grid dimensions for X Y Z Using a fouriergrid 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] [PerformanceSuggestion]: Application has requested for multi-thread capability. Ifallocating memory from different pthreads/OpenMP threads, pleaseconsider setting MV2_USE_ALIGNED_ALLOC=1 for improved performance. UseMV2_USE_THREAD_WARNING=0 to suppress this error message.
Please can y'all help me with the same.