[gmx-users] How to run GROMACS in cluster

[Shradheya R.R. Gupta]

 *GROMACS compiled and installed in the shared folder using:-*

cmake .. -DCMAKE_INSTALL_PREFIX=/home/drug/Desktop/share/test
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
-DCMAKE_BUILD_TYPE=Release -DGMX_MPI=ON -DGMX_BUILD_UNITTESTS=ON
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
-DGMX_BUILD_MDRUN_ONLY=ON -DGMX_USE_OPENCL=ON  -DGMX_PREFER_STATIC_LIBS=ON
-DGMX_OPENMP=ON  -DGMX_BUILD_SHARED_EXE=OFF

*MD run command:-*
export OMP_NUM_THREADS=2
mpirun -np 8 --hostfile /etc/hosts  mdrun_mpi -deffnm p_NVT -npme 4 -ntomp
2 -v

*Log File:-*
Please find the attachment.

Thank you

On Fri, 1 Nov 2019 at 18:22, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/1/19 7:40 AM, Shradheya R.R. Gupta wrote:
> > Respected Researchers,
> >
> > I am trying to run GROMACS in parallel. So I have established connection
> > using ssh, nfs and openmpi.
> >
> > The connection is working fine as I have run Autodock Vina-MPI and other
> > test files.
> >
> > I have installed the GROMACS in the mounted directory which is shared by
> > all the computers (not in individual computer).
> >
> > When I run GROMACS in parallel it is showing 10 minutes for 10ps and when
> > run on single computer it is showing 5 minutes.
> >
> > How to resolve this issue?
>
> Without knowing how GROMACS was installed, what your mdrun commands
> were, and the contents of the relevant .log files, no one can provide
> you any insight here. It may also be worth consulting your sysadmin for
> advice specific to your cluster.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
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> Virginia Tech Department of Biochemistry
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>
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