I’d check the receptor mdout file for rank 39. I’m guessing there is something unusual in that file near the end. Hopefully an error message that would be helpful to diagnose the problem.
-Bill
> On Jan 2, 2024, at 12:31 AM, Kriti Shukla via AMBER <amber.ambermd.org> wrote:
>
> Hello, Amber community,
> I've been trying to use MMPBSA.py.MPI for my 10-lac
> frame system. In order to do that, I installed mpi4py, modified the route
> via which it can load the mpi4py module in MMPBSA.py.MPI file, and
> recompiled Amber22. However, after a few of hours of operation, I
> encountered the error listed below, with some temporary files being
> generated.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /home/srabanicy/amber22/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> File "/home/srabanicy/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File
> "/home/srabanicy/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/srabanicy/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/srabanicy/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> line 428, in run
> error_list = [s.strip() for s in out.split('\n')
> TypeError: a bytes-like object is required, not 'str'
> Error occurred on rank 39.
>
> Fatal Error!
> All files have been retained for your error investigation:
> You should begin by examining the output files of the first failed
> calculation.
> Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> manual for file naming conventions.
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Received on Tue Jan 02 2024 - 19:30:02 PST
