Hi Dr. Case,
I’ve reproduce the error message, which only appears if I try to run on GPUs. The mdout file quits with:
Number of triangulated 3-point waters found: 7200
Sum of charges from parm topology file = 0.00001521
Forcing neutrality...
And the slurm log file (I’m running on an HPC) states:
/var/spool/slurmd/job3989454/slurm_script: line 0: unalias: easy_install-3.6: not found
/var/spool/slurmd/job3989454/slurm_script: line 0: unalias: pip3.6: not found
/var/spool/slurmd/job3989454/slurm_script: line 0: unalias: pip3: not found
/var/spool/slurmd/job3989454/slurm_script: line 0: unalias: python3.6: not found
/var/spool/slurmd/job3989454/slurm_script: line 0: unalias: python3.6m: not found
gpu_neighbor_list_setup :: Small box detected, with <= 2 cells in one or more
dimensions. The current GPU code has been deemed
unsafe for these situations. Please alter the
cutoff to increase the number of hash cells, make
use of the CPU code, or (if absolutely necessary)
run pmemd.cuda with the -AllowSmallBox flag. This
behavior will be corrected in a forthcoming patch.
Can you please explain a bit more about what this error message means? How would you recommend proceeding?
Best,
Matthew
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Received on Tue Jan 05 2021 - 19:30:02 PST
