We just compiled the non-free version of CHARMM enhanced for GPUs on a machine with 4 NVidia GPUs and 20 Intel CPU cores. When I execute the following command:
/usr/local/bin/mpirun -n 4 /usr/local/software/charmm-parallel/charmm/bin/charmm -i test_parallel_md.test > output.out
on a test MD simulation, I notice the following odd things:
1) The output file shows the output duplicated 4 times (this didn't happen on previously compiled parallel non-GPU versions I have)
2) The GPUs do not seem to be engaged at all
watch -n 0.5 nvidia-smi
shows that the GPUs are not being used at all.
3) When I read the scarce online documentation for running CHARMM on GPUs (am I missing some obvious documentation?), it mentioned adding PARA commands or GRAPe commands, both of which just give me "error" messages -- that these commands aren't recognized.
I definitely obtained the GPU-enhanced (non-free) CHARMM 43b1 officially from Harvard, but it seems like it doesn't even engage my GPUs or understand the commands it should. Can you please provide any insight as to what I might be missing?
Thanks so much!