Re: Re: ORCA NAMD Parallel

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Mar 15 2019 - 17:22:08 CDT

Thanks Marcelo, what is the command for specifying the machinefile in the qmConfigLine?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Marcelo C. R. Melo <melomcr_at_gmail.com>
Sent: Friday, March 15, 2019 3:20 PM
To: NAMD; McGuire, Kelly
Subject: Re: namd-l: Re: ORCA NAMD Parallel

You can use the qmConfigLine to specify the machinefile. ORCA expects the machinefile to be in the directory where ORCA is executed, that is, the path you select for "qmExecPath" + "/0" (for QM region 0, for example).
Best

---
Marcelo Cardoso dos Reis Melo, PhD
Postdoctoral Research Associate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu<mailto:crdsdsr2_at_illinois.edu>
+1 (217) 244-5983
On Fri, 15 Mar 2019 at 10:55, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
Thanks for the response.  By Orca execution directory, do you mean where ORCA is located or where I am running my simulations?  Also, specifying the machine file in the Orca input, meaning in my NAMD config file for my QMMM simulation, would that be specified in the qmConfigLine?
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: Gerard Rowe <GerardR_at_usca.edu<mailto:GerardR_at_usca.edu>>
Sent: Friday, March 15, 2019 8:45 AM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; McGuire, Kelly
Subject: Re: ORCA NAMD Parallel
You can specify a machinefile in your Orca input by placing a file called MyInp.nodes in the orca execution directory.  In your case, it might be useful to play a little scripting magic to copy the one created by SLURM and remove the instances of the node being used by NAMD.  You could hard-code the machinefile if you're on a smaller cluster and know which nodes you'll be assigned.
This is assuming that node allocation is the source of your error.  What you pasted in is a generic "Orca crashed" message.  The cause of the crash is usually found immediately above that message.
-Gerard
________________________________
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>>
Sent: Thursday, March 14, 2019 3:51 AM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
Subject: namd-l: ORCA NAMD Parallel
I am trying to use PAL8 in my qmConfigLine for ORCA QMMM, but get in my ORCA output :
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
  Process name: [[51120,1],0]
  Exit code:    127
--------------------------------------------------------------------------
[file orca_main/gtoint.cpp, line 137]: ORCA finished by error termination in ORCA_GTOInt
Is this probably due to ORCA and NAMD fighting for the same threads?  I haven't figured out how, yet, to tell ORCA which nodes are available.  We use SLURM.
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602

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