From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Jan 20 2016 - 21:12:50 CST
I am using REUS for the system of 42 k atoms. I have a problem in increasing benchmark time for the MD. I have cluster resource in which I have access to 1 node (4 GPU (K20) and 32 cores CPU), therefore, I can run REUS for 16 windows (2 cores 1 window).
I had checked the previously discussed link http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2522.html, it is helpful to some extent but I am not using mpi, the command I am following is:
NAMD_2.11_Linux-x86_64-netlrts/charmrun NAMD_2.11_Linux-x86_64-netlrts/namd2 ++ppn 2 +p32 +replicas 16 job0.conf +stdout output/%d/job0.%d.log
After executing above command the REUS implicated on 32 cores, not on GPU. The system right now on 32 core CPU. The benchmark time right now is 10 day/ns.
Than, I had modified the command and added +devices 0,1,2,3 :
NAMD_2.11_Linux-x86_64-netlrts/charmrun NAMD_2.11_Linux-x86_64-netlrts/namd2 +devices 0,1,2,3 ++ppn 2 +p32 +replicas 16 job0.conf +stdout output/%d/job0.%d.log
It produces error :
Charmrun> scalable start enabled.
Charmrun> started all node programs in 5.236 seconds.
Charm++> Running in non-SMP mode: numPes 32
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Charm++> TORUS A SIZE 32 USING 0 1 2 3 4 5 6 7 8 9...
Charm++> TORUS B SIZE 1 USING 0
Charm++> TORUS C SIZE 1 USING 0
Charm++> TORUS MINIMAL MESH SIZE IS 32 BY 1 BY 1
Redirecting stdout to files output/0/job0.0.log through 15
------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 0 FATAL ERROR: Unknown command-line option +devices
Fatal error on Partition 0 PE 0> REPLICA 0 FATAL ERROR: Unknown command-line option +devices
I want to utilize the GPU with CPU, however I am not able to do it. Can anyone suggest to solve this problem.
Thanks in advance
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
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