On 14/08/2012 6:08 AM, Juliette N. wrote:
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation.
You have to look at the stderr, stdout and .log file for information.
You can't solve the problem without that.
Mark
I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before ( mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
-g -e -x ) but as soon as I include the -cpi flag the it doesn work
and I get:
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
While as I said if I try to start from the very beginning it doesnt crash...
Any ideas..
Thanks
On 13 August 2012 15:51, Matthias Ernst <matthias.ern...@student.kit.edu> wrote:
Am 13.08.2012 21:42, schrieb Juliette N.:
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
I see a "md_prev.cpt". If I presume correctly that this is for the
continuation of the crashed run: Why and did you read what I wrote?
but I dont get any output and the issued command terminates in the
terminal.
Do I have to remove the -o -c -g -e -x flags from the command line?
Appreciate your help,
On 13 August 2012 15:28, Matthias Ernst <matthias.ern...@student.kit.edu>
wrote:
Long story short: backup everything (since it's a backup, and hopefully
you
won't need it), then use the [whatever].cpt file. You don't want to do
work
twice, do you? If you use the [whatever]_prev.cpi file, you will
calculate
some frames *again* that are already there.
If you use an up-to-date version of Gromacs (4.5.5 is the most recent
one),
then the files will be continued and not overwritten. This is stated on
the
page you already found (hint: "remaining output will be appended to the
existing files (energy, trajectory, log, etc).")
Good luck,
Matthias
Am 13.08.2012 21:07, schrieb Juliette N.:
Hello all,
I am going to restart my crashed simulations, but I am not sure which
of *_prev.cpt or *.cpt to use as they contain different written
frames.
*_prev.cpt >>>> Last frame -1 time 7462.900
*.cpt >>>> Last frame -1 time 7468.965
Also on the gmx site it is stated that :
Before doing anything, back up your files! Then use
mdrun -s topol.tpr -cpi state.cpt
What files do I need to back up? the edr. trr .. files that were
written before crash? Is the new run going to overwrite the old files?
Thanks,
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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
