Re: [AMBER] Jobs hanging on parallel CUDA without producing output

From: Nils Oberhauser <>
Date: Thu, 26 Sep 2013 08:58:49 +0200

Thank you Jason for your reply.
I finally updated Amber on the other machine. So now both machines run the
latest version.
However, I'm still having the same problem: On one machine the job runs
through without any interruption, while on the other machine I get the
nonbond cells error every time and have to restart the calculation at least
twice. The parallel GPU jobs also still hang after a while on this machine,
but you are right, the parallel GPU processing does not give a lot of
So the only difference between the two machines seems to be the kernel... Is
it possible that this causes the strange behavior?

Maybe someone else in the list has tried the lipid 11 tutorial lately and
can tell me if they had any errors?


-----Original Message-----
From: Jason Swails []
Sent: Montag, 23. September 2013 13:37
To: AMBER Mailing List
Subject: Re: [AMBER] Jobs hanging on parallel CUDA without producing output

On Mon, Sep 23, 2013 at 6:12 AM, Nils Oberhauser

> Hello,
> I am having some trouble running parallel CUDA jobs on 2 and 3 GPUs.
> I'm observing the following problems following the lipid 11 tutorial
> on
> Field_
> Tutorial.html :
> To be sure I did not do anything wrong in the setup, I downloaded the
> example files from the tutorial page as input.
> During the production phase the calculations break up after a short
> time,
> returning:
> "Nonbond cells need to be recalculated, restart simulation
> from previous checkpoint with a higher value for skinnb."
> I restart the calculation, as was suggested by previous posts in the
> mailing list. For a while the calculations seem to be running
> smoothly, but after a certain time period (sometimes minutes,
> sometimes hours) there is no more write access to the trajectory or
> any other output file. The pmemd.cuda.MPI processes keep running
> forever without any output or error message until the process is
> killed manually. Since the jobs just keep running without any output,
> I'm not sure how to further debug this problem...
> When I use only one GPU or 10 parallel CPU cores however, the job
> finishes normally.
> The machine I'm using has 3 GeForce GTX 680 Cards and two Intel Xeon
> E5-2620
> (2 GHz, 6 cores each) CPUs, running CentOS 64bit (kernel:
> 2.6.32-358.14.1.el6.x86_64) and the latest updates of amber12.
> Here is the most confusing part:
> We have another machine with identical hardware but a slightly
> different linux kernel (2.6.32-358.11.1.el6.x86_64) and a not
> up-to-date version of amber12. Since there are currently jobs running
> on the machine, I cannot upgrade the kernel or amber to see if it makes
any difference.
> However when I run the same job from the tutorial as described above
> on this machine, I don't get any errors. The jobs run and terminate
> without any problems on 3 GPUs. Even the "Nonbond cells.." error never
> occurs (maybe because of the older amber version?).
> I ran the jobs several times on both machines, to be quite sure that
> the different outcomes are not due to the non-deterministic algorithms
> of the software, but it is always the same results.

You can check the output of $AMBERHOME/update_amber --version to see what
updates have been applied to which installation.

That said, the indication that the nonbonded cells need to be recalculated
was introduced by an update to address the fact that for certain types of
simulations (particularly lipids built with the CHARMM lipid builder, I
think), the volume changes a _lot_ during constant pressure simulations --
too much for the nonbonded cell decomposition scheme that was originally set

This led to _very_ strange behavior. So if an 'updated' version of Amber
indicates that non-bonded cells need to be updated, then you should either
do your equilibration with that updated version or use CPUs instead (because
the 'old' GPU implementation that does not emit the error will be wrong).
See the description for bugfix.18.bz2 at

So, before I go through all the trouble of installing an older kernel to the
> first machine, I'm asking here for help. Can it at all be the kernel?
> Maybe some has a different suggestion to debug this problem.

Perhaps use only a single GPU to equilibrate the density, then try multiple
GPUs for the production stage if you really need the speed-up of multiple
GPUs (it's quite limited, isn't it?) Also, is the place where the
simulation stalls deterministic (i.e., does it always hang on exactly the
same step each time?)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 26 2013 - 00:00:03 PDT
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