[AMBER] MMPBSA.py: "fork()" system call to create a child process

From: Lennart Gundelach <L.Gundelach.soton.ac.uk>
Date: Tue, 24 Nov 2020 07:02:44 +0000


I am trying to run MMPBSA.py.MPI in Amber16 and whenever I submit my job, SLURM freaks out with the following (I have asked the HPC system sysadmins and they have no idea:
A process has executed an operation involving a call to the
"fork()" system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host: [[16072,1],0] (PID 207509)

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.

After this warning the calculation crashes with the following error:
File "/local/software/amber/amber16/bin/MMPBSA.py.MPI", line 99, in <module>
  File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/local/software/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line 76, in make_trajectories
    raise MMPBSA_Error('Must have at least as many frames as processors!')
MMPBSA_Error: Must have at least as many frames as processors!
Error occured on rank 0.

Which to me makes no sense, given my mmpbas.in file:
Sample input file for GB and PB calculation
startframe=1, endframe=1000000, interval=1000,
verbose=2, keep_files=0,
igb=5, saltcon=0.0,
nmstartframe=1, nmendframe=1000000, nminterval=1000
maxcyc=1000, drms=0.0001

But maybe I am just missing something obvious here.


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Received on Mon Nov 23 2020 - 23:30:02 PST
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