This appears to be a known issue. It was already reported on the github issue tracker.
https://github.com/merzlab/QUICK/issues/392
________________________________
From: Timothy Giese via AMBER <amber.ambermd.org>
Sent: Wednesday, September 24, 2025 10:47 AM
To: YASHIKA . via AMBER <amber.ambermd.org>
Subject: Re: [AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations
Thanks for the report. I was able to reproduce the symptom. When commsander is the same thing as mpi_comm_world, quick appears to run fine, but when doing an alchemical "bookend" simulation (mm -> qm/mm) using a groupfile, the communicator that quick should be using is a subset of the available processes. It appears that quick is using mpi_comm_world, however.
Here are my observations:
1. "mpirun -n 2 sander.MPI -ng 2 -groupfile groupfile" hangs when using icfe=1 for both the mm and qm/mm
2. "mpirun -n 2 sander.MPI -ng 2 -groupfile groupfile" will successfully run the mm simulation the mm simulation when icfe=0; however, the qm/mm simulation hangs.
3. "mpirun -n 2 sander.MPI -O -p parm7 -c inp.rst7 -i qm.mdin ...." will successfully run the qm/mm simulation.
The quick code needs to be changed to accept a mpi communicator as an argument and exclusively use that communicator. ...at least that is my current working hypothesis.
-Tim
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Received on Wed Sep 24 2025 - 08:00:03 PDT
