Project

General

Profile

Bug #1870

pme_loadbal_do called at an interval != nstlist

Added by himanshu khandelia about 4 years ago. Updated almost 4 years ago.

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

Description

I am using 5.1 on a cluster with two Intel E5-2680v3 CPUs each with 12 CPU cores. The issue is also seen on the same nodes with 2 GPU cards. Attached are the log and tpr files for the GPU simulations.
Please let me know what additional info is needed,

Thank you !

err.txt (12.1 KB) err.txt log file GPU himanshu khandelia, 12/06/2015 09:28 AM
4mq1.tpr (3.28 MB) 4mq1.tpr tpr file GPU himanshu khandelia, 12/06/2015 09:28 AM
err_cpu.txt (53.5 KB) err_cpu.txt log file cpu only himanshu khandelia, 12/06/2015 09:31 AM
phos1_4lmn.tpr (3.35 MB) phos1_4lmn.tpr tpr file cpu only (different simulation) himanshu khandelia, 12/06/2015 09:31 AM
phos1_4lmn.log (9.07 MB) phos1_4lmn.log gromacs log file. himanshu khandelia, 03/11/2016 12:28 PM

Related issues

Related to GROMACS - Task #1781: re-design benchmarking functionalityAccepted

Associated revisions

Revision 9836b1eb (diff)
Added by Berk Hess almost 4 years ago

Avoid assertion failure in pme_loadbal_do

When ir->init_step % ir->nstlist != 0 an assertion would fail in
pme_loadbal_do. If it does not fail every time, the assertion can safely
be replaced by a conditional return, which is now done in this case.

Fixes #1870.

Change-Id: Ie586022c87d3993f2de5a6fdf9210ae56aa7855b

History

#1 Updated by Mark Abraham almost 4 years ago

Sorry for the delay in looking at this. I have not been able to reproduce this yet.

Can you please share the actual md.log files, rather than just the terminal output? There's a lot of useful diagnostics we'd like to know about. Thanks!

#2 Updated by Mark Abraham almost 4 years ago

  • Related to Task #1781: re-design benchmarking functionality added

#3 Updated by Gerrit Code Review Bot almost 4 years ago

Gerrit received a related patchset '1' for Issue #1870.
Uploader: Szilárd Páll ()
Change-Id: I8268b0f6213fc2b4210a31c3f14bbc95dfb9c86c
Gerrit URL: https://gerrit.gromacs.org/5705

First upload to wrong branch, correct gerrit url:
https://gerrit.gromacs.org/#/c/5706

#4 Updated by himanshu khandelia almost 4 years ago

Have uploaded the log file now.

#5 Updated by Szilárd Páll almost 4 years ago

Thanks. THis may be useful, although the ideal thing would be having the two separate log files, one for the continued run and one for the continuation run. Do you happen to have such a run or do you always run with -append?

#6 Updated by Gerrit Code Review Bot almost 4 years ago

Gerrit received a related patchset '1' for Issue #1870.
Uploader: Berk Hess ()
Change-Id: Ie586022c87d3993f2de5a6fdf9210ae56aa7855b
Gerrit URL: https://gerrit.gromacs.org/5721

#7 Updated by himanshu khandelia almost 4 years ago

Hi
Unfortunately this is the only .log file at the moment. I may have overwritten and then deleted the old one. If it is critical, I can generate new log files,

Himanshu

#8 Updated by Berk Hess almost 4 years ago

  • Status changed from New to Resolved

#9 Updated by Erik Lindahl almost 4 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF