Seeking help on this

[Viswanath Vittaladevaram]

Hi,

Here is my script looks like

#!/bin/sh
#SBATCH --job-name=fnIII-12_SAMoh_T298_1            
#SBATCH -A p200518
#SBATCH -N 1
#SBATCH --qos=default
#SBATCH --cpus-per-task=128
#SBATCH --partition=cpu
#SBATCH -t 24:00:00

# Load the Amber module
module load amber/22-foss-2023a-CUDA-12.2

# Set environment variables if needed
export PATH=$AMBERHOME/bin:$PATH
export LD_LIBRARY_PATH=$AMBERHOME/lib:$LD_LIBRARY_PATH

# Set up MPI parallel execution
export DO_PARALLEL="/apps/USE/easybuild/release/2023.1/software/OpenMPI/4.1.5-GCC-12.3.0/bin/mpirun -np 128"

# Run MM-PBSA for each directory
for X in 1 2  
do
    cd pbsa_${X}
    $DO_PARALLEL $AMBERHOME/bin/MMPBSA.py.MPI -O -i pbsa.in -cp ../protein-surface.parm7 -lp ../protein.parm7 -rp ../surface.parm7 -y ../fnIII-12_SAMoh_T298-nw.${X}.nc
    cd ..
done

and the output I am getting is provided below

/var/spool/parastation/jobs/1233876: line 11: module: command not found
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /bin/MMPBSA.py.MPI
Node: mel0432

while attempting to start process rank 0.
--------------------------------------------------------------------------
128 total processes failed to start
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /bin/MMPBSA.py.MPI
Node: mel0432

while attempting to start process rank 0.
--------------------------------------------------------------------------
128 total processes failed to start

Anyone can help me with this?

Regards,

[mariosergi...@gmail.com]

This group intends to resolve problems related to gmx_MMPBSA, not MMPBSA.py. We recommended using the appropriate channels for this.

I note two points you must pay attention

1. module doesn't exist in your environment, as you can see in the output (/var/spool/parastation/jobs/1233876: line 11: module: command not found). So, probably you don't have access to amber executables like MMPBSA.py.MPI

2. $AMBERHOME is empty since mpirun only sees /bin/MMPBSA.py.MPI as executable and not the complete path (for example, /apps/USE/easybuild/release/2023.1/software/ambertools/...)

Please, note that my comments are intended to help you unofficially and do not correspond to a formal solution or support. For this, you should consult the Amber channels since we will not provide additional support other than this.

All the best