[Bug-gmx_MMPBSA]: Error in function returning the inconsistency warning

Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/

GNU General Public License v3.0

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[Bug-gmx_MMPBSA]: Error in function returning the inconsistency warning #217

Closed Ahmsame closed 2 years ago

Ahmsame commented 2 years ago

Bug summary

I get nothing written in the output file however the run seems to take all the time it needs.

Terminal output

I get this as the last line in my slurm file as I am running it on a supercomputer. 
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
Error occurred on rank 0.
Exiting. All files have been retained.
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

gmx_MMPBSA.log

Operating system

HPC linux based system

gmx_MMPBSA Version

gmx_MMPBSA v1.5.0.3

Python version

Python 3.9.7

Installation

No response

marioernestovaldes commented 2 years ago

Please, check this thread... you can run gmx_MMPBSA using the --rewrite-output flag once you update the program:

gmx_MMPBSA --rewrite-output

let us know if that solves the problem...

cheers!

Ahmsame commented 2 years ago

I will try it and keep you updated, however, I would like to know whether this warning Is normal or not! ib_md.c:1161 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued. [1650069523.119334] [comp032:18553:0] ib_md.c:1162 UCX WARN IB: data corruption might occur when using registered memory. progress.log as this upsets me!

Valdes-Tresanco-MS commented 2 years ago

It seems similar to this issue. We are thinking of removing the use of h5py since we have noticed that it has some performance issues with nested dictionaries as is our case. We are sorry to hear about these issues. The problem is that our tests are on our PCs, so we have no way to identify these problems in HPC. Right now I am working on improving the performance of gmx_MMPBSA_ana, but as soon as I finish it I will work on removing h5py to see if the problem persists. I think it could also be related to the platform.platform() call that creates threads to get the values. If you want, you can try commenting out these lines and see if the warnings are not displayed.

https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/blob/59bff94de67fb2d2a7f9ce944860309231760150/GMXMMPBSA/utils.py#L702-L705

marioernestovaldes commented 2 years ago

closing this... feel free to reopen if the issue persists...