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Bug #613

REMD with distance restrance

Added by Gadzikano empty about 7 years ago. Updated almost 5 years ago.

Status:
Closed
Priority:
Normal
Category:
mdrun
Target version:
Affected version - extra info:
4.5.1
Affected version:
Difficulty:
uncategorized
Close

Description

Created an attachment (id=567)
tpr file

I am trying to do REMD with distance restraints using gromacs-4.5.1. My problem is that if i specify the number of cores which are more than the number of tpr files that i have, my simulations are crushing with a segmentation fault. They seem to run very well if i specify the number of processors which are equal to the number of tpr files . I believe that is how REMD was meant work in versions prior to gromacs-4.0. If i run the same simulation without distance restraints, i can specify as many cores as i want and the simulations seem to run very well.

I am wondering if there is anything i am doing wrong,

I have tried to show the commands that i am using below...i am working with 16 replicas

1. mpprun -np 16 -pd -s md_tpr -multi 16 -replex 5000 -o md_

This one works fine with distance restraints

2. mpprun -np 64 -pd -s md_tpr -multi 16 -replex 5000 -o md_

The second one works fine without distance restraints but crushes with a segmentation fault when i use distance restraints.

My system is made up of two similar peptide molecules in a box. I have 36 nmr distance restraints on each of the peptides.

Thank you for your help

Gadzikano

gb_0.tpr (312 KB) gb_0.tpr tpr file Gadzikano empty, 11/15/2010 11:30 AM
gb_1.tpr (312 KB) gb_1.tpr tpr file Gadzikano empty, 11/15/2010 11:31 AM

Associated revisions

Revision 64600020 (diff)
Added by Mark Abraham almost 5 years ago

Updated code checks with distance restraints

Ensemble-averaged distance restraints require -multi, and it is
also reasonable to do REMD with distance restraints, which also
requires -multi. So checks for the ensemble-averaging case need
to be more sensitive to their context.

In fact, ensemble-averaging is probably functional only with PD and
one processor per system, since that was probably all that was
available when it was built.

Fixes #613, refs #1117

Change-Id: Ia6f1bb4eb82eab3c7c249638cd3a5a5d1f707132

History

#1 Updated by Gadzikano empty about 7 years ago

Created an attachment (id=568)
tpr file

#2 Updated by Gadzikano empty about 7 years ago

(In reply to comment #1)

Created an attachment (id=568) [details]
tpr file

I mistakenly left out the mdrun flag in my command lines

#3 Updated by David van der Spoel about 7 years ago

I fixed a simple bug in the printing which caused the SEGV (commit 74c3d74 in the release branch), however it seems that parallel DR is not compatible with REMD yet, since there is another crash, now in the MPI routine Allreduce. Will check more.

#4 Updated by Rossen Apostolov about 6 years ago

  • Description updated (diff)
  • Assignee deleted (Erik Lindahl)
  • Target version deleted (4.5.1)

#5 Updated by Rossen Apostolov over 5 years ago

  • Assignee set to David van der Spoel
  • Target version set to 4.5.6
  • Affected version - extra info set to 4.5.1

#6 Updated by Teemu Murtola almost 5 years ago

What is the status here, David? From the comments, it seems that something was fixed, but that other issues remain. Have those been fixed later, or should there be a message printed out by mdrun indicating that this combination does not work?

#8 Updated by Mark Abraham almost 5 years ago

  • Status changed from New to Closed

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