How to access GROMACS in Expanse Sanjoy Paul https://conferences.xsede.org/c/message_boards/find_message?p_l_id=&messageId=2774108 2021-07-20T21:20:33Z 2021-07-20T21:20:33Z

I found that GROMACS 2019 and 2020 are available in Expanse. I was trying to access it by loading all the necessary modules. However, after loading the required modules including gromacs/2019.6, I was able to get gmx_mpi executable but unable to run simple commands like gmx_mpi -version etc. It is showing the following error-<br /><br />By default, for Open MPI 4.0 and later, infiniband ports on a device<br />are not used by default. The intent is to use UCX for these devices.<br />You can override this policy by setting the btl_openib_allow_ib MCA parameter<br />to true.<br /><br /> Local host: exp-7-60<br /> Local adapter: mlx5_0<br /> Local port: 1<br /><br />--------------------------------------------------------------------------<br />--------------------------------------------------------------------------<br />WARNING: There was an error initializing an OpenFabrics device.<br /><br /> Local host: exp-7-60<br /> Local device: mlx5_0<br />--------------------------------------------------------------------------<br />srun: error: PMK_KVS_Barrier duplicate request from task 0<br /><br />Here are the currently loaded modules-<br />Currently Loaded Modules:<br /> 1) shared 2) DefaultModules 3) gpu/0.15.4 4) openmpi/4.0.4 5) slurm/expanse/20.02.3 6) sdsc/1.0 7) gromacs/2019.6<br /><br />Inactive Modules:<br /> 1) gcc/10.2.0<br /><br />I would appreciate if anyone can tell me how to run gromacs job in Expanse. <br />Thanks,<br />Sanjoy Paul<br />Boston University<br />email: sanjoypaul25@gmail.com

Sanjoy Paul 2021-07-20T21:20:33Z