Viswanath Vittaladevaram
Oct 9, 2023, 8:39:04 AM10/9/23
to gmx_MMPBSA
Iam getting this error below.
Need help on this!
warnings.warn('receptor_mask overwritten with default\n')
File "/ichec/packages/amber/18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /ichec/packages/amber/18/bin/sander failed with prmtop ../protein-surface.parm7!
Error occured on rank 23.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 23
slurmstepd: error: Detected 2 oom-kill event(s) in StepId=1174669.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.
File "/ichec/packages/amber/18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/ichec/packages/amber/18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /ichec/packages/amber/18/bin/sander failed with prmtop ../protein-surface.parm7!
Error occured on rank 23.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 23
slurmstepd: error: Detected 2 oom-kill event(s) in StepId=1174669.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.
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