[gmx-users] K20 test

Hi! When I run gromacs-4.6.1 with k20. I meet a question. I have 6 nodes.And each node has one K20.And I use one process on one node with one gpu. But the test result shows that the runtime of one node is less than that of six nodes.Is the scalability of GPU not good? Thanks! -- gmx-users ma

[gmx-users] About parallelization

How to run combinedMPI/OPENMP parallelization with 2 or 4 Openmp threads per MPI process? -DGMX_MPI and -DGMX_THREAD_MPI can be use at the same time? How to run? Thanks for you help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please se

[gmx-users] About gpu

I have tested gromacs-4.6.1 with k20. But when I run the mdrun, I met some problems. 1.Configure options are -DGMX_MPI=ON ,-DGMX_DOUBLE=ON -DGMX_GPU=OFF . But if I run parallely with mpirun, it would get wrong. "Note: file tpx version 58, software tpx version 83 Fatal error in PMPI_Bcast: Inval

[gmx-users] About 4.6.1

I have tested gromacs-4.6.1 with k20. But when I run the mdrun, I met some problems. 1.GPU only support float accelerating? 2.Configure options are -DGMX_MPI ,-DGMX_DOUBLE . But if I run parallely with mpirun, it would get wrong with PMPI_Broadcast. 3. Configure options are -DGMX_MPI ,-DGMX_GPU.But

[gmx-users] About k20

Hi! I want to improve my mdrun performance with k20.But there is something wrong. My gromacs version is 4.6.1. My openmm version is 5.0.1. The wrong message is "include could not find load file: ../contrib/BuildMdrunOpenMM" Can the openmm version match k20? Thanks! -- gmx-users mailing

[gmx-users] Improve performance

Hi! I have 6 nodes. Each node has two CPUs,12 cores totally. How should I set the options like -rdd,-rcon,-dds,-gcom to improve the performance? Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Fwd: Improve performance

Hi! I have some questions. 1. Is there any method for me to improve my mdrun performance? I have read the manual,and tested some option of mdrun,such as -rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that. 2. Can gromacs 4.6.1 support K20? I want to use CPU+GPU. But I met

[gmx-users] About PP/PME

I'm running gromacs in parallel.I have 6 nodes.There are 96 cores. But hoiw to reduce the load imbalance and improve the performance? The PME-node is 16 and the PP-node is 80.How to divide? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Ple