From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Mar 19 2019 - 14:22:44 CDT
Thanks Gerard, that helps. I have also seen others do:
module load openmpi
Does the openmpi need to be loaded explicitly like this in the submit script for ORCA/NAMD parallel to work?
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: McGuire, Kelly
Sent: Monday, March 18, 2019 9:57 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu
Subject: Re: Parallel Simulation Question
Is the SCRATCH directory necessary to get ORCA to work in parallel? If so, what files need to be in the SCRATCH directory?
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Saturday, March 16, 2019 10:30 PM
To: namd-l
Subject: namd-l: Parallel Simulation Question
I was able to get ORCA set up for running in parallel with my QMMM simulation. I specified 16 processors for ORCA to use. But, it seems to be taking longer than one processor. One processor was able to finish one step of my 100 step QMMM minimization in 35 minutes. With 16 processors in parallel, it has bee running for 1 hour and is still running. This is still the first step of the 100 minimization steps. My ORCA output seems to be stopped a certain spot and nothing seems to be progressing. Here is what the ORCA output shows:
************************************************************
* Program running with 16 parallel MPI-processes *
* working on a common directory *
************************************************************
One Electron integrals ... done
Pre-screening matrix ... done
I hasn't progressed from this point so far (1 hour runtime). I don't see any errors or warnings.
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
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