*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 <[email protected]> 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 > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. >
-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
