GROMACS
===================================

Following version is available.

.. csv-table:: Large-scale Parallel Computing Server
   :header: "version", "module","execution queue"
   :widths: 20, 79, 1

   "2025.4", "/work/app/GROMACS/gromacs-2025.4_cpu/bin/GMXRC.bash", "P_030 TP_002 MP_001 CP_001 DP_002 S_001 CS_001"

.. attention::
  Execute following command in advance.

  ``module load oneapi/2025.0.1``

.. csv-table:: Accelerator server
   :header: "version", "module","execution queue"
   :widths: 20, 79, 1

   "2025.4", "/work/app/GROMACS/gromacs-2025.4_gpu/bin/GMXRC.bash", "A_002 CA_001 DA_002"

.. attention::
  Execute following command in advance.

  ``module load oneapi/2025.0.1``

  ``module load cuda/12.8``


- Job Submission Script

・Large-scale Parallel Computing Server

.. code-block :: none

   #!/bin/sh 
   #PBS -l select=nodes
   #PBS -q queue 
   #PBS -N jobname

   module -s load oneapi/2025.0.1
   
   cd ${PBS_O_WORKDIR}

   source /work/app/GROMACS/gromacs-2025.4_cpu/bin/GMXRC.bash
   mpirun [ -np MPI total tasks ] [ -ppn MPI tasks per node ] -hostfile $PBS_NODEFILE gmx_mpi mdrun input file > output file 2> error file

・Accelerator server

.. code-block :: none

   #!/bin/sh
   #PBS -l select=1[:ncpus=number of CPUs][:ngpus=number of GPUs][:mem=amount of memory]
   #PBS -q CA_001
   #PBS -N jobname

   module -s load oneapi/2025.0.1
   module -s load cuda/12.8

   cd ${PBS_O_WORKDIR}

   source /work/app/GROMACS/gromacs-2025.4_gpu/bin/GMXRC.bash
   mpirun [ -np MPI total tasks ] [ -N MPI tasks per node ] -hostfile $PBS_NODEFILE gmx_mpi mdrun input file > output file 2> error file


- Example

・Large-scale Parallel Computing Server

.. code-block :: none

   #!/bin/sh 
   #PBS -l select=1 
   #PBS -q P_030
   #PBS -N gromacs

   module -s load oneapi/2025.0.1

   cd ${PBS_O_WORKDIR}

   source /work/app/GROMACS/gromacs-2025.4_cpu/bin/GMXRC.bash
   mpirun -np 112 -ppn 112 -hostfile $PBS_NODEFILE gmx_mpi mdrun -s input.tpr > gromacs.out 2> gromacs.err

・Accelerator server

.. code-block :: none

   #!/bin/sh
   #PBS -l select=1:ncpus=2:ngpus=2:mem=32gb
   #PBS -q CA_001
   #PBS -N gromacs

   module -s load oneapi/2025.0.1
   module -s load cuda/12.8

   cd ${PBS_O_WORKDIR}
   
   source /work/app/GROMACS/gromacs-2025.4_gpu/bin/GMXRC.bash
   mpirun -np 2 -ppn 2 -hostfile $PBS_NODEFILE gmx_mpi mdrun -s input.tpr > gromacs.out 2> gromacs.err