Re: [AMBER-Developers] sander.MPI tests randomly stall in Ubuntu 9.10

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Mon, 10 May 2010 19:21:02 -0400

> could you try different compiler?

On that machine? Not easily, unless there's an rpm for it. A new gcc from sources would take time I can't easily spare right now. The student is pretty good... I can ask her. Know of an rpm?? Sigh...

I realize the 4.1.x compilers aren't so great, but that's what comes with RHEL, even the newest. UGA has a site license, etc. I might consider a different distro.

:-) Lachele

--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Volodymyr Babin
[mailto:vbabin.ncsu.edu]
To: AMBER Developers Mailing List
[mailto:amber-developers.ambermd.org]
Sent: Mon, 10 May 2010 18:37:03
-0400
Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
Ubuntu 9.10
> Hi Lachele,
> 
> could you try different compiler?
> 
> Best,
> 
> Volodymyr
> 
> On Mon, May 10, 2010 16:23, Lachele Foley wrote:
> > Sorry I've been quiet lately... very overwhelmed.
> >
> > A student did some testing, and she got a similar hang.  For us, the hangs
> > weren't random:
> >
> > ==============================================================
> > make[2]: Leaving directory `/usr/local/amber11_20100507/test'
> > cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial
> >
> >  Running multisander version of sander Amber11
> >     Total processors =     4
> >     Number of groups =     4
> > .......
> >
> > She said she tried it twice, and I confirmed it a third time just for fun.
> >  The serial tests went mostly well with 13 failures (all ncsu stuff) and
> > one error (I think DFTB).
> >
> > Info of relevance (64-bit something?):
> >
> > Linux aarya.woods.ccrc 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST
> > 2010 x86_64 x86_64 x86_64 GNU/Linux
> >
> > GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
> >
> > gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
> >
> > mpirun (Open MPI) 1.4.1
> >
> > mpicc -showme
> > gcc -I/usr/local/include -pthread -L/usr/local/lib -lmpi -lopen-rte
> > -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> >
> > mpif90 -showme
> > gfortran -I/usr/local/include -pthread -I/usr/local/lib -L/usr/local/lib
> > -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic
> > -lnsl -lutil -lm -ldl
> >
> > mpif77 -showme
> > gfortran -I/usr/local/include -pthread -L/usr/local/lib -lmpi_f77 -lmpi
> > -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> >
> >
> > She says she'll try on the machine in Ireland (64-bit with the wiggy file
> > system), tonight.
> >
> > :-) Lachele
> > --
> > B. Lachele Foley, PhD '92,'02
> > Assistant Research Scientist
> > Complex Carbohydrate Research Center, UGA
> > 706-542-0263
> > lfoley.ccrc.uga.edu
> >
> >
> > ----- Original Message -----
> > From: Gustavo Seabra
> > [mailto:gustavo.seabra.gmail.com]
> > To: AMBER Developers Mailing List
> > [mailto:amber-developers.ambermd.org]
> > Sent: Mon, 10 May 2010 14:40:54
> > -0400
> > Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
> > Ubuntu 9.10
> >
> >
> >> Hi,
> >>
> >> Here's what I have:
> >> $ uname -a
> >> Linux TIE1 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:05:01 UTC
> >> 2009 x86_64 GNU/Linux
> >>
> >> $ gfortran --version
> >> GNU Fortran (Ubuntu 4.4.1-4ubuntu9) 4.4.1
> >>
> >> $ gcc --version
> >> gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1
> >>
> >> $ mpirun --version
> >> mpirun (Open MPI) 1.3.2
> >>
> >> The serial version works just fine. I only see this with the parallel
> >> version. The machine is a dual core AMD  Athlon(tm) II X2 B22
> >> Processor 800MHz, and I was running the tests with 4 mpi processes.
> >>
> >> Thanks,
> >> Gustavo.
> >>
> >> On Fri, May 7, 2010 at 10:46 PM, Daniel Roe wrote:
> >> > I personally havent seen this before. What compiler(s) are you using,
> >> and
> >> > what MPI implementation?
> >> >
> >> > -Dan
> >> >
> >> > On Fri, May 7, 2010 at 2:14 PM, Gustavo Seabra
> >> <gustavo.seabra.gmail.com>wrote:
> >> >
> >> >> Hi All,
> >> >>
> >> >> I have compiled and tested Amber11 (release version) serial with no
> >> >> problems on Ubuntu 9.10. Now, when I try the parallel version, it
> >> >> compiles fine but some tests just stall. The processes keep running
> >> >> (from "top" I can stil see the sander.MPI processes using all the
> >> >> processor they need), but the calculation never advances.
> >> >>
> >> >> Which test will be a problem is random: I had with PIMD, then when I
> >> >> try again it happens with QM tests, then something else, etc.
> >> >>
> >> >> I have found the following message on the archives:
> >> >> http://structbio.vanderbilt.edu/archives/amber-archive/2009/5928.php
> >> >>
> >> >> But with no replies.
> >> >>
> >> >> Does anyone else experience such problems?
> >> >>
> >> >> Thanks,
> >> >>
> >> >> --
> >> >> Gustavo Seabra
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> 
> 
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Received on Mon May 10 2010 - 16:30:05 PDT