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

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 12 May 2010 11:51:23 -0300

Hi Lachele,

Just to be sure, in your case, the hang happens *only* in the parallel
version, right? Do all serial tests pass just fine?

Apparently, we're the only ones reporting hangs, so it seems to only
be happening to us (although in my case the hang is random). I wonder
if it could be a bad combination of MPI implementation + specific
hardware + Ubuntu 9.10. Or, it could be that for some reason we're the
only ones being affected by Bug #504659:
https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/504659.

Is there anyone else on the list using the same combination of Unbuntu
9.10 + OpenMPI + gnu compilers?

-- 
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Tue, May 11, 2010 at 5:41 PM, Lachele Foley <lfoley.ccrc.uga.edu> wrote:
> Yes, using gcc44/g++44/gfortran44, etc., all 4.4.0, we still get the hang on the same neb test.
>
> Many thanks to Arunima for the testing.
>
> :-) 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: case
> [mailto:case.biomaps.rutgers.edu]
> To: AMBER Developers Mailing List
> [mailto:amber-developers.ambermd.org]
> Sent: Tue, 11 May 2010 09:00:16
> -0400
> Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in
> Ubuntu 9.10
>
>
>> On Mon, May 10, 2010, Lachele Foley wrote:
>> >
>> > 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.
>>
>> Red Hat is distributing gcc4.4 officially, as I understand it.  Also, the
>> newer 4.4 version is scheduled to be the default in the next RHEL release.
>> Anyway, this is what my sysadmin told me...see message below.
>>
>> ....dave
>>
>>
>> >From kabbey.biomaps.rutgers.edu  Fri Apr 23 22:26:11 2010
>>
>> RedHat 6.0 beta just became available on the 21st.
>> The gcc version is 4.4.3 as listed in the Packages directory.
>>
>> I'd estimate at least 2 months before RH6 is released and CentOS 6 to be
>> 4-8 weeks later.
>>
>>
>> Red Hat Enterprise Linux 6 Beta Available Today for Public Download
>> April 21st, 2010
>> by Red Hat Enterprise Linux Team
>> http://press.redhat.com/2010/04/21/red-hat-enterprise-linux-6-beta-available-today-for-public-download/
>>
>>
>> RedHat 6.0 beta
>>
>> Base installation
>> ftp://ftp.redhat.com/pub/redhat/rhel/beta/6.0/x86_64/os/
>> ftp://ftp.redhat.com/pub/redhat/rhel/beta/6/x86_64/os/Packages/
>>
>> Optional packages
>> ftp://ftp.redhat.com/pub/redhat/rhel/beta/6/optional/x86_64/os/Packages/
>>
>>
>> DVD
>> ftp://ftp.redhat.com/pub/redhat/rhel/beta/6.0/x86_64/iso/
>>
>> Starting with RH 5.4,
>> gcc44, 4.4.0, is available (and installed on casegroup1)
>> from RH/CentOS to co-exist with the default 4.1.2
>>
>> The default will not change until RH 6 is released later this year. A
>> beta RH 6 is not yet available.
>> I assume that RH 6 will use the 4.4.x series since it is now available
>> in RH 5.4.
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Received on Wed May 12 2010 - 08:00:04 PDT