[gmx-users] Pull code stalling?

[Justin Lemkul]

On 4/7/14, 10:19 PM, Justin Lemkul wrote:
>
> Hi All,
>
> I have noticed a strange problem involving the pull code, and perhaps other
> types of restraints with version 5.0-beta2.  It seems that use of the pull code
> causes runs to simply stall and produce no output beyond the header of the .log
> file.  A few notes to break down the situation:
>
> 1. I initially suspected a hardware problem, but I have determined that the
> nodes in question work correctly.  I have 64-CPU nodes that are handling these
> jobs.  Runs submitted using version 4.6.3 or 5.0-beta2 without the pull code run
> correctly.
>
> 2. It seems that the runs with the pull code are stalling.  Logging in to the
> node where the job is running reveals that 8 CPU are being used instead of 64,
> but mdrun stays stuck in uninterruptible sleep.  Runs on the same nodes with
> version 4.6.3 with the pull code are correctly using all 64 CPU and are
> producing output at regular intervals.
>
> 3. Gromacs has been compiled with the thread-MPI library, which has worked well
> for previous versions.
>
> 4. The mdrun command is simply mdrun -nt 64 -deffnm pull -px pullx.xvg -pf
> pullf.xvg.  Invoking mdrun -nt 64 for other runs with 5.0-beta2 without the pull
> code works fine with decent performance.  The problem persists with different
> numbers of CPUs/threads.
>
> I have not tried the new release candidate from today, but if that would help
> narrow the problem down, I will gladly do it.
>

To follow up on this, it appears that 5.0-rc1 works properly, so this 
information is mostly an FYI for anyone experiencing problems with 5.0-beta2.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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