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Below are steps for compiling GROMACS 2016 on ikt:

(1) put below lines in your ikt .bashrc

         alias icpc="icpc -std=c++11"

    alias icc="icc -std=c++11"

(2) logout of all ikt terminals

(3) login to ikt

(4) get an interactive build node:

srun -p build --time=2:00:00 --mem=10G --pty /bin/bash

(5) source /opt/rh/devtoolset-2/enable

(6) module load icc_17-impi_2017

(7) compile GROMACS 2016


gromacs has two levels of parallelism: OpenMP and MPI. If you use both levels then gromacs will require (number MPI processes) x (number of openmp threads) cores. Hence the CPU and memory on a node can get overloaded. In order to avoid this overloading of the node, you can turn off the OpenMP parallelism and reduce the grid size.


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