RE: CUDA simulation memory usage

From: Jesper Sørensen (
Date: Wed May 18 2011 - 07:23:28 CDT

Thanks Norman - I don't have a problem with an increase in memory during the simulation, so I don't know exactly what is going on...
I would prefer not upgrading to NAMD 2.8 until it is a "final" (or at least not beta) version. NAMD will be shared by many users on our cluster, so I prefer not to have test-versions out there, people can have those on their own desktops if there are new functionalities they would like to check out before the final release (in my opinion).

Best regards,

-----Original Message-----
From: [] On Behalf Of Norman Geist
Sent: 18. maj 2011 14:11
To: 'Jesper Sørensen'
Cc: Namd Mailing List
Subject: AW: namd-l: CUDA simulation memory usage

Hi Jesper,

For me the memory consumption of the cuda namd is also a bit greater than on cpu but I think that’s quite normal. I had a problem with a constant increase of memory during the simulation, maybe it’s the same to you. For me the newer nightly build solved the problem while fixing a memory leak in trajectory output. Maybe try the newer NAMD 2.8b2.

Best regards

Norman Geist.

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag von Jesper Sørensen
Gesendet: Mittwoch, 18. Mai 2011 13:15
Cc: 'namd-l'
Betreff: RE: namd-l: CUDA simulation memory usage

Thanks, but that doesn't really solve my problem with NAMD...


-----Original Message-----
From: []
Sent: 18. maj 2011 13:09
To: lists
Subject: Re: namd-l: CUDA simulation memory usage

Dear Sir,
I used the command "nvidia-smi" to view the performance of my gpu card. Then I found that the performance of NAMD2.8b2 was very low (~ 13%). But the performance of ACEMD was very high (~ 100%).

-----Original message-----
From:Jesper Sørensen <>
To:'namd-l' <>
Date:Wed, 18 May 2011 12:03:17 +0200
Subject:namd-l: CUDA simulation memory usage


I have just been benchmarking our new cluster with GPUs and the memory usage that NAMD prints out at the end of the simulation run is MUCH larger with GPU's than without the GPU's.

With CUDA:
WallClock: 1246.348877 CPUTime: 1246.348877 Memory: 41306.324219 MB

Without CUDA
WallClock: 4025.868896 CPUTime: 4025.868896 Memory: 350.937500 MB

I am assuming that the Memory number with CUDA is wrong - mostly because I know that we don't have that much memory in these new machines. Is it taking memory on the GFX-card into account, or what is going on?

I've looked through the mailinglist, but I haven't been able to find anything on this issue...

Best regards,

Jesper Sørensen
Dept. of Chemistry
Aarhus University, Denmark

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