On 8/16/13 11:51 AM, vidhya sankar wrote:
Dear justin Thank you for your previous reply
When i run the md in gromacs 4.6.2 with plumed1.3 Plugin i have got the
error as follows
The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin thread to
cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run
multiple jobs).
Back Off! I just backed up CNTPEPRSOLIONSfull.trr to
./#CNTPEPRSOLIONSfull.trr.3#
Back Off! I just backed up CNTPEPRSOLIONSfull.edr to
./#CNTPEPRSOLIONSfull.edr.3#
WARNING: This run will generate roughly 273370 Mb of data
starting mdrun 'C225N99O45 in water'
100000000 steps, 200000.0 ps.
!!!!! PLUMED ERROR: PluMed dead with errors: check log file
!!!!! ABORTING RUN
Segmentation fault (core dumped)
To avoid this May i use -pin on ?
It's easier to try it and see (and have an answer in seconds) rather than wait
several hours to get a reply...
The specific answer depends on your hardware and whether or not you are going to
see any benefit. I don't really know the mechanics of this process, though
there have been numerous discussions in recent weeks and months. First, upgrade
to 4.6.3, then try again.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
