AMBER Archive (2007)

Subject: AMBER: Re: RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: on PATH)

From: Alexandar T Tzanov (alex.tzanov_at_nyu.edu)
Date: Fri Jun 29 2007 - 09:48:13 CDT

Hi Ross,

Well I dig a bit more in the issue and seems to me the problem comes from
g++ which 9.1.047 uses. I got similar bad behaviour on other
codes. For example many OpenMP codes which are running fine under 9.1.043
crash. My compilation of Amber was done first serial (all tests pass) due to auxiliary
tools and the error cited below happened when I tried to build the parallel
version using mpich. I used sgi_altix option but no -static.

Thanks

Alex

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Thursday, June 28, 2007 12:55 pm
Subject: RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: $AMBERHOME on PATH)
To: amber_at_scripps.edu

> Hi Alex,
>
> > Hi guys
> > I am installing Amber9 on Altix under Suse10 and I am getting
> > from the test:
>
> > cd qmmm2/crambin_2; ./Run.crambin
> > *** glibc detected *** ../../../exe/sander: malloc(): memory
> > corruption: 0x6000000000e75c90 ***
> > ======= Backtrace: =========
> >
> > Anybody to see such a thing before under Intel 9.1.047?
>
> I have come across problems before with certain versions of the Intel
> compilers and the QM/MM code on Altix. The issue has been with the compiler
> misvectorizing loops. A couple of things to check before we dig any deeper.
>
> 1) Have you applied all the lastest bugfixes and made clean / recompiled?
> There are several workarounds in these bugfixes to address certain
> intel
> compiler bugs.
>
> 2) Is this running in serial or in parallel?
>
> Please take a look at the following page:
>
> http://amber.ch.ic.ac.uk/archive/200702/0389.html
>
> and see if the suggestions in here fix the problem.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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