AMBER Archive (2007)

Subject: Re: AMBER: make test.parallel not complete

From: Prem Prakash Pathak (prempolymer_at_gmail.com)
Date: Thu Dec 20 2007 - 03:59:03 CST

Dear Ross,

I applied bugfix.all and it worked. thank you for your help. Thanks a lot.

regards
prem

On 12/13/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Hi Prem,
>
> 1) Are you using an Intel compiler? - There is a bug in it which
> miscompiles one of the qmmm loops in the parallel code.
>
> 2) Have you applied all the bugfixes - especially bugfix.30 which
> includes:
>
> 1) Workaround for some dodgy Intel compiler that can cause a
> QMMM MPI hang at printing kvector distribution in mdout
> file.
> 2) Fix QMMM PIMD MPI_Gather error in parallel.
> http://amber.scripps.edu/bugfixes90.html
>
> This will hopefully implement a workaround for this compiler bug.
>
> If you have done all this and still have problems then please send me some
> more details about your machine, os, compilers, mpi library (with version
> numbers etc). Also please send me the contents of
> $AMBERHOME/test/qmmm2/1NLN_periodic_lnk_atoms after the test has hung for a
> couple of minutes.
>
> 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 |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Prem Prakash Pathak
> *Sent:* Thursday, December 13, 2007 00:10
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: make test.parallel not complete
>
>
> Dear AMBER user,
>
> I have amber9 when i tried to configure the it on 4 processor tower
> server, and tried to check by giving the command
>
> > make test.parallel,
>
> the checking process stucks
>
> >./run.1NLN_min
>
> what could be the reason.
> I am not getting any error message, programme doesnot proceeds further.
>
> thaks
>
>

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