Re: Tutorial example of replica exchange

From: Dr. Eddie (eackad_at_gmail.com)
Date: Thu Mar 10 2016 - 09:46:50 CST

Thank you Norman, that helps!

For anyone else who had the same/similar problem I solved it by compiling
Namd (2.11) from source and got it working with mpi (not CUDA) with the
steps above. All multicore binaries (w/wo cuda) failed with those errors
(see above).

Now that it runs, I cannot find any information on periodic BC or using a
Piston with REMD. Is there some limitation?
Thanks,
Eddie

On Thu, Mar 10, 2016 at 2:03 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Hey,
>
>
>
> 1) The jobX.conf will just put together the *_base.namd the
> *_remd.namd and and will source the replica.namd script which actually does
> the REMD. Also it is used to source additional restart.files from job1 and
> higher. You will get output files named like the job. So it’s just some
> kind of output separation if you want to restart the simulation multiple
> times.
>
> 2) Shouldn’t you specify how many processes to launch or threads to
> use? Otherwise try to use a non GPU version an see if it helps. There’s
> seems to be a problem with CUDA REMD, especially when using GBIS.
>
>
>
> Let us know
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Dr. Eddie
> *Gesendet:* Dienstag, 8. März 2016 23:56
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Tutorial example of replica exchange
>
>
>
> Hi all,
>
> I am trying to learn how to REMD with namd 2.11 by following the (spartan)
> tutorial <http://www.ks.uiuc.edu/Research/namd/2.11/ug/node69.html>. I
> have two problems:
>
> 1) I don't understand what jobX.conf are doing exactly and why two are
> commands are needed (first job0.conf then job1.conf)
>
> 2) I can't get it to run:
>
> ~/bin/NAMD_2.11_Linux-x86_64-multicore-CUDA/lib/replica/example$ mpirun
> ../../../namd2 +idlepoll +replicas 8 job0.conf +stdout output/%d/job0.%d.log
>
> Charm++: standalone mode (not using charmrun)
>
> Charm++> Running in Multicore mode: 1 threads
>
> --------------------------------------------------------------------------
>
> mpirun noticed that process rank 0 with PID 23811 on node heartofgold
> exited on signal 11 (Segmentation fault).
>
> --------------------------------------------------------------------------
>
>
>
> Nothing comes out so I can't see any errors:
>
>
>
> ~/bin/NAMD_2.11_Linux-x86_64-multicore-CUDA/lib/replica/example$ ls
> output/*
>
> output/0:
>
> total 0
>
>
>
> output/1:
>
> total 0
>
>
>
> output/2:
>
> total 0
>
>
>
> output/3:
>
> total 0
>
>
>
> output/4:
>
> total 0
>
>
>
> output/5:
>
> total 0
>
>
>
> output/6:
>
> total 0
>
>
>
> output/7:
>
> total 0
>
>
>
>
>
> I've tried using +idlepoll since this is a gpu build, but this changed
> nothing. Any help or idea would be most welcome!
>
> Thanks,
>
> Eddie
>

-- 
Eddie

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