AMBER Archive (2009)

Subject: Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade

From: Jason Swails (jason.swails_at_gmail.com)
Date: Mon Nov 02 2009 - 06:15:19 CST

It could be that the new version of mvapich broke the previous installation,
since the libraries could easily have changed (and if it's really, in fact,
a new version, I'd bet on it since there's not much else that could
'change'). Did you try recompiling?

Do the test cases still pass? If not, I'd say your only options are to
recompile amber/pmemd in parallel or revert back to the old version of
mvapich if it's still on the cluster.

Good luck!
Jason

On Mon, Nov 2, 2009 at 4:17 AM, Dmitri Nilov <nilovdm_at_gmail.com> wrote:

> Hello!
> Sander.MPI tasks are crushing just after launch since mvapich software was
> upgraded on cluster.
> Sander.MPI.out contains:
>
> MPI process terminated unexpectedly
> Exit code -5 signaled from node-23-06
> Killing remote processes...forrtl: error (69): process interrupted (SIGINT)
> Image PC Routine Line
> Source
> libpthread.so.0 00007F2132C1EB00 Unknown Unknown Unknown
> libpthread.so.0 00007F2132C1DB7E Unknown Unknown Unknown
> libmpich.so.1.0 00007F21334CB1AC Unknown Unknown Unknown
> libmpich.so.1.0 00007F21334E1ADE Unknown Unknown Unknown
> libmpich.so.1.0 00007F21334C050A Unknown Unknown Unknown
> libmpich.so.1.0 00007F21334A2DED Unknown Unknown Unknown
> libmpich.so.1.0 00007F21334A1DC6 Unknown Unknown Unknown
> sander.MPI 000000000093A0EF Unknown Unknown Unknown
> sander.MPI 00000000004BC222 Unknown Unknown Unknown
> sander.MPI 000000000041E05C Unknown Unknown Unknown
> libc.so.6 00007F213216ACF4 Unknown Unknown Unknown
> sander.MPI 000000000041DF69 Unknown Unknown Unknown
> forrtl: error (69): process interrupted (SIGINT)
> and so on..
>
> I've found similar problem at
> http://archive.ambermd.org/200907/0092.html, that seems to be still
> unsolved.
> I don't think it's infiniband problem. So what i have to do?
>
> Thanks a lot!
> Dmitri Nilov,
> Lomonosov Moscow State University
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber