NAMD: Difference between revisions

Finally, you have to ask whether to run with or without GPUs for this simulation.  From our numbers we can see that using a full GPU node of Graham (32 cores, 2 gpus) the job runs faster than it would on 4 non-GPU nodes of Graham.  Since a GPU node on Graham costs about twice what a non-GPU node costs, in this case it is more cost effective to run with GPUs.  You should run with GPUs if possible, however, given that there are fewer GPU than CPU nodes, you may need to consider submitting non-GPU jobs if your waiting time for GPU jobs is too long.

NAMD 3 is now available as an ALPHA release.  It might offer better performance for certain system configurations.

To use it, you can download the binary from the NAMD website and modify it so it can run on Alliance systems, like this (change alpha version as needed):

  cd NAMD_3.0alpha11_Linux-x86_64-multicore-CUDA

  setrpaths.sh  --path .

After this the namd3 executable located in that directory will be linking to the correct libraries on our systems.

You can then submit a GPU job that uses that executable.

In order to enable high-performance GPU-resident integration, you must add the following keyword to the configuration file:  

'''CUDASOAintegrate on'''