Hi,
What is the exact command you are using to run cpptraj? It seems like
you might be running this in a parallel environment (like MPI; looks
like maybe 4 threads?). Note that MPI is not supported for cpptraj;
certain actions are OpenMP-enabled, but 2drms is not one of them yet.
Also, based on the # of RMSDs to be calculated (739182025) you will
need about 5.6 GB of free memory to successfully run the just the
Rms2d command. By running in parallel, each thread is requesting 5.6
GB so you may be blowing the system memory.
Try running single-threaded, and potentially reduce the # of frames
for which you're calculating 2drms (for example taking the RMSD of
every other frame, 'trajin 1 last 2', should give you a similar
picture and drastically reduce the amount of memory used).
Hope this helps,
-Dan
On Sat, Jan 12, 2013 at 4:49 AM, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
> Hello,
>
>
> AMBER users,
>
> I am trying to calculate RMS2D using cpptraj but getting no output and come up with following error. If anyone know, kindly help me out. I have re-compiled the amber package as following error says something like ...
>
> --------------------------
> CTION OUTPUT:
> RMS2D: Calculating RMSDs between each frame (739182025 total).
> 0% 10% 10% 10% 10% 10% 10% 10% 10% 20% 20% 20% 20% 20% 20% 20% 20% 30% 30% 30% 30% 30% 30% 30% 30% 40% 40% 40% 40% 40% 40% 40% 40% 50% 50% 50% 50% 50% 50% 50% 60% 60% 60% 60% 60% 60% 70% 70% 70% 70% 70% 70% 80% 80% 80% 80% 80% 90% 90% 90% 90% 100% 100% 100% 100%
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = EXIT CODE: 9
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
> -------------------------------------------------------------------------
>
> The syntax for the rms2d, I used is as follows..
> ----------
> rms2d first rmsout comt-backbone.rms2d.gnu .C,CA,N time 1
> --------------
>
> Thanks in advance
> Regards
>
> Tarique
>
>
>
> -----------------------------
> Syed Tarique Moin, Ph.D.
> Post Doctoral Fellow,
>
> Institute of General, Inorganic and Theoretical Chemistry
> Center for Chemistry and Biomedicine
> University of Innsbruck
> Innrain 80-82
> A-6020 Innsbruck
> AUSTRIA
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 12 2013 - 10:30:03 PST
