Running namd on linux in cpu+gpu mode

From: James Starlight (
Date: Sat Jan 19 2013 - 01:19:53 CST

Dear Namd Users!

I have some questions about ussing NAMD on the linux-64 bit
workstation on which some other MD package have been installed.

1) I want to use NAMD with the CUDA-gpu acceleration on my core-i5 +
GTX 670 work-station.

I've downloaded and install latest NAMD binaries where found library.

The main problem is that on that work-station I have had already
installed latest cuda-5 libraries in /local/usr/cuda-5/ dir on which
some another software is dependend

Consequently in the bashrc I have

 export LD_LIBRARY_PATH=/usr/local/openmm/lib:/usr/local/cuda-5.0/lib64:/usr/local/cuda-5.0/lib:/usr/lib/nvidia:$LD_LIBRARY_PATH

So I dont wont to add /home/own/NAMD (where cuda so libraries for
namd is located) becauce of possible conflct between two cuda's as
well as software on which depend it. Should I compile NAMD for
binaries with my Cuda or is there any other possibilities of solving
such problem ?

2) When I test installed NAMD binaries from the NAMD dir by means of
./namd2 +idlepoll +p4 +devices 0

I've obtained

Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.5.0-beta1-28-gabc7887
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.004 seconds.

Charm++> Warning: the number of SMP threads is greater than the number
of physical cores, use +CmiNoProcForComThread runtime option.

Info: NAMD CVS-2013-01-18 for Linux-x86_64-multicore-CUDA
Info: Please visit
Info: for updates, documentation, and support information.
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60401 for multicore-linux64-iccstatic
Info: Built Fri Jan 18 02:25:42 CST 2013 by jim on
Info: 1 NAMD CVS-2013-01-18 Linux-x86_64-multicore-CUDA 4 starlight own
Info: Running on 4 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.019299 s
Pe 2 physical rank 2 binding to CUDA device 0 on starlight: 'GeForce
GTX 670' Mem: 2047MB Rev: 3.0
Pe 3 physical rank 3 will use CUDA device of pe 2
Pe 1 physical rank 1 will use CUDA device of pe 2
Pe 0 physical rank 0 will use CUDA device of pe 2
FATAL ERROR: No simulation config file specified on command line.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: No simulation config file specified on command line.

Does it meas that my gpu was recognized correctly ? ( actually I want
to run simulation in the gpu+cpu (4 cores) mode ). Could you also
provide me with the test configure file and some test system suitable
for simulation on GPU?

Thanks for help,


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