Hi,
I' have just purchased another gpu in order to run two molecular dynamics simulation through Desmond in parallel.
Here's my set-up
OS : Linux / Ubuntu
Package : Schrodinger 2016-4 / Maestro + Desmond
GPU: NVIDIA GTX1070 *2
(One is configured as gpu0, and the other as gpu1)
Every time I try to submit Desmond MD jobs through maestro, gpu for each job is automatically selected to be gpu0.
Which means, after submitting two jobs through maestro-task option, both jobs goes to the same gpu : which is gpu0.
Is there any way that I can choose which GPUs to use for every task through maestro?
If there isn't, can any one help me with the command line submitting the Desmond job for each GPUs?
(In trying to run it for 10ns, 2000 frames recording-5ps interval)
Thanks :)
Hi,
this could happened because your GPUs are set up in "normal mode". So the software is not able splitting the jobs on different GPUs.
You need to switch your GPUs in "exclusive mode" by using the following command:
#sudo nvidia-smi -c 3
Generally this command is enough to obtain what you want. You don't event need to edit the host file.
My suggestion is to launch your job from command line. Let you write the the your_md.sh from the GUI Molecular Dynamics panel e launch it from command line.
It works very well! Thank you :) I can see both GPUs busy through nvidia-smi.
Could you recommend me a book or websites where I can learn basics of MD simulations? I really want to understand some logic and theories while running my simulations, as well as advanced techniques if necessary.
Thanks again :)
Hi,
in my opinion there are some very interesting video regarding MD on YouTube. This way to acquire new skills is less boring than others...
Enjoy!
Hi Eunsoo, I would be curious to know the performance of Desmond in Nvidia 1070? i am planing to buy 280ti although..
@Carmine Talarico . I have run the command
Nvidia-smi -c 3
But my both GPUs are not working only 1 is showing
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