From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Tue Nov 09 2021 - 10:58:01 CST
Look for a “Benchmark” line (grep Benchmark *log). Those will tell you how fast the simulation is progressing.
-Josh
From: Amir Zeb <zebamir85_at_gmail.com>
Date: Monday, November 8, 2021 at 10:02 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Subject: Re: namd-l: Why simulation running on linux is damn slow??
Thanks dear Josh,
would you please like to let me know how do I find the estimated completion time of the simulation run?
I tried to check in xxx.log file but couldn't find it.
On Tue, Nov 9, 2021, 10:57 AM Vermaas, Josh <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
Hi Amir,
This is a bigish system, being run only on CPUs on a single node. This is going to be pretty slow. If you get CUDA operational, the 960 might help, but the 960 is also a bit old, so it may actually be a bottleneck itself. The ultimate solution is to get more hardware to throw at the problem, either by buying time, or by proposing your science to a supercomputing site.
-Josh
From: <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of Amir Zeb <zebamir85_at_gmail.com<mailto:zebamir85_at_gmail.com>>
Reply-To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>, Amir Zeb <zebamir85_at_gmail.com<mailto:zebamir85_at_gmail.com>>
Date: Monday, November 8, 2021 at 8:41 PM
To: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
Subject: namd-l: Why simulation running on linux is damn slow??
Hello NAMD users,
I have a system of ~250000 atoms and I want to run simulation for 100 ns. The time step is 2, so I put run = 50000000 in config file. It took 4 days and hardly completed 6400000 steps, this means it'll take >20 days to complete 100 ns simulation with this speed. The command I used is:
namd2 +idle poll +p10 +devices 0 config.
namd > xxx.log
Details of my system:
Linux, Ubuntu
CPU(s) 40, online cups list 0-39, Core(s) per socket 10, Sockets 2,
NVIDIA GM206 [GeForce GTX 960] (rev a1).
but when I put the command nvidia-smi,
it prints 'not found', but can be installed with: sudo aor install nvidia-340
and many others.
Please let me know what should I do to speed up the simulation?
kind regards
Amir
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