heatherkellyucl

> An InfiniBand network is highly recommended when running CUDA-accelerated NAMD across multiple nodes. You will need either an ibverbs NAMD binary (available for download) or an MPI NAMD binary...

When in doubt, check Compute Canada: https://docs.computecanada.ca/wiki/NAMD/en#Parallel_GPU_jobs They use OFI GPU on their OmniPath interconnect machine and UCX GPU on Infiniband machines. If we need to do that, we aren't...

Top priority is now to get NAMD OFI CPU working on Young with gerun using charmrun - then we can make the OFI CUDA one work when the GPUs exist.

Notes on charmrun and SGE: https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnGridEngine

This is quite handy, about building multiple versions and comparing them: https://docs.hpc.wvu.edu/text/609.CHARM++_NAMD.html Note: in our Linux-x86_64-icc.arch we have `-qopenmp-simd` (and so does the link above, which are CPU versions). Compute...

On Young: - [x] NAMD 2.14 ofi-smp with openmp-simd - [x] benchmarking jobs - [x] NAMD 2.14 ofi-smp without openmp-simd - [x] benchmarking jobs On Myriad: - [x] NAMD 2.14...

Submitted a job with the first ofi-smd version.

Young, apoa1, `namd_ofismp_nosimd_12`, end of second run ``` Running on 6 processors: namd2 apoa1.namd ++ppn2 charmrun> /bin/setarch x86_64 -R mpirun -np 6 namd2 apoa1.namd ++ppn2 Charm++>ofi> provider: psm2 Charm++>ofi> control...

Trying to get them working multi-node, I am somewhat confused: the charmrun that NAMD has installed is calling mpirun itself, and so the examples that suggest doing this kind of...

Need to try getting qrsh to launch the correct number of processes on the nodes.