VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Oct 05 2011 - 06:47:08 CDT

Dear VMD users,

I have some strange problems when running VMD on my workstation. There
are 3 symptoms I noticed since a while already and recently they got worse:

1. VMD fails to start stalling while the message "Creating CUDA device
pool and initializing hardware ..." appears on the console
2. VMD stalls causing the freezing of the entire graphics machine upon
loading a structure (3000 atoms, nothing special) ... The console is
blocked with the message "Determining bond structure from distance search".
3. VMD crashes simply with a segmentation fault.

My workstation has 2 AMD, quad-core opterons, 32 GB RAM, NVIDIA Quadro
FX 3800 + NVIDIA 3D kit, 2 monitors SAMSUNG SyncMaster, 3D capable. The
operating system is openSUSE 11.4, the NVIDIA graphics driver version
280.13 (latest).

Tests I performed:
1. Removing the stereo devices (emitter) and starting with no stereo in
the xorg.conf does not solve the problem.
2. Removing 1 monitor does not solve the problem
2. The problem is independent of the NVIDIA graphics driver (I tried
several of them)
2. The problem remains both if using the executable supplied by VMD or
using my own compilation of VMD 1.9 or VMD CVS from 26.09 (CUDA 3.2, GCC
4.5 - default)
3. The problem is not observed on a second machine with exactly the same
operating system but with Intel Xeon CPUs and with Quadro 4000 Graphics
card (neither when using pre-compiled binaries nor my own compilations)...

The worst is that the problem is not always reproducible ... Sometimes,
VMD starts normally, sometimes one of the symptoms described appear.
Lately, the crashes occur more frequently than before. Sometimes symptom
2 blocks the computer as such that I cannot even restart it from a
different machine and I need to shutdown completely ... Sometime, a
flickering in the screens is observed (both when stereo is ON of OFF,
both when 1 or 2 monitors are connected).

My question is: Has somebody observed this behavior before ? Can it be a
graphics card issue ?

Thanks for any thoughts on this

Best wishes
Vlad 

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de