NAMD 2.9 with CUDA runs

From: Ashley Chew (
Date: Fri Aug 31 2012 - 04:02:48 CDT

Hi this is my first post in regards to NAMD

I was wondering if anyone in the community was having problems with NAMD built with CUDA (Using a single Tesla M2075 6gb, node has 72GB of Ram) once it passes a certain point (In his case pass 320k steps)

In our case one of the researcher notice the errors returned in the output are common internal errors to do with unstable simulations but if they checkpoint and stop the runs prior to 320K steps, and then restart from the restart files internally generated by NAMD, the restarted simulation runs past the previous crash point.

I have even rebuilt the NAMD from CVS 20120828 build with fftw3 (which works) but it pretty much did the same things once it passes a certain point.

Ashley Chew
HPC System Administrator
iVEC_at_UWA (MBDP: M024)
The University of Western Australia
35 Stirling Highway

P: +61 8 6488 8742
F: +61 8 6488 1015

CRICOS Provider Code: 00126G


Confidentiality and Privacy Notice
The contents of this email are strictly private and intended only for the addressee. This email may contain legally privileged or confidential information. If you receive this communication in error, please notify the sender immediately by reply email and delete both emails and any attachments contained therein. No further disclosure, copying or relaying of any part of this correspondence is permitted without the express permission of the sender. The contents of this email, and any response or further correspondence, may be stored on an electronic filing record system pursuant to the privacy statement for records at The University of Western Australia. The University accepts no liability in connection with computer virus, data corruption, delay, interruption, unauthorized access or unauthorized amendment. This notice should not be removed.

P Save a tree...please don't print this e-mail unless you really need to


This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:00 CST