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howto:gpu_gromacs

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howto:gpu_gromacs [2014/03/17 17:31]
swyngaard Expected output
howto:gpu_gromacs [2014/03/18 08:40] (current)
swyngaard [PBS job script]
Line 46: Line 46:
 mpirun mdrun -s adh_cubic_vsites_pme.tpr -nb gpu_cpu -gpu_id 00 mpirun mdrun -s adh_cubic_vsites_pme.tpr -nb gpu_cpu -gpu_id 00
 </​file>​ </​file>​
-**NOTE:** The ''​-s''​ flag above specifies the input file to be run. The ''​-nb''​ flag specifies that the non-bonded force calculations should be performed on a hybrid GPU-CPU combination which currently yields the best performance. You can optionally set this to ''​gpu''​ if you prefer to perform the non-bonded force calculations exclusively on the GPU or to ''​cpu''​ if you prefer that all calculations are run on the CPU. The parameter to ''​-gpu_id''​ flag denotes the index of the GPU device each MPI process should use. In the above case, there is one GPU device per node and two MPI processes per node. So we specify that each MPI process use the first GPU device by setting the ''​-gpu_id''​ string to ''​00''​.+**NOTE:** The ''​-s''​ flag above specifies the input file to be run. The ''​-nb''​ flag specifies that the non-bonded force calculations should be performed on a hybrid GPU-CPU combination which currently yields the best performance. You can optionally set this to ''​gpu''​ if you prefer to perform the non-bonded force calculations exclusively on the GPU or to ''​cpu''​ if you prefer that all calculations are run on the CPU. The parameter to the ''​-gpu_id''​ flag denotes the index of the GPU device each MPI process should use. In the above case, there is one GPU device per node and two MPI processes per node. So we specify that each MPI process use the first GPU device by setting the ''​-gpu_id''​ string to ''​00''​.
  
 ==== Submit the job ==== ==== Submit the job ====
/var/www/wiki/data/pages/howto/gpu_gromacs.txt · Last modified: 2014/03/18 08:40 by swyngaard