AMBER Archive (2005)

Subject: Re: AMBER: compiling pmemd on dual xeon

From: Tiziano Tuccinardi (tuccinardi_at_farm.unipi.it)
Date: Tue May 17 2005 - 13:05:49 CDT

Robert Duke wrote:

> Tiziano -
> Have you set 'stacksize unlimited' in your .cshrc (or done the
> equivalent things if you use the Bourne shell)?
> Regards - Bob Duke
>
> ----- Original Message -----
> *From:* Tiziano Tuccinardi <mailto:tuccinardi_at_farm.unipi.it>
> *To:* amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> *Sent:* Tuesday, May 17, 2005 1:28 PM
> *Subject:* AMBER: compiling pmemd on dual xeon
>
> Dear all,
> I'm trying to compile amber8 on a dual Xeon 3.4 GHz using Fedora
> core 3, mpich-1.2.6 and intel fortrand compiler 8.1
> I hadn't any problem with the parallel version of sander, but I
> have some problem with pmemd:
> I use this file config.h
> ------------------------------------------------------
> #!/bin/csh -f
> setenv MPICH_HOME /usr/local/mpich-1.2.6
> setenv MPICH_INCLUDE $MPICH_HOME/include
> setenv MPICH_LIBDIR $MPICH_HOME/lib
> setenv MPILIB "-L$MPICH_LIBDIR -lmpich"
>
> setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_VECT_OPT"
>
> setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"
>
> setenv OPT_LO "ifort -c -auto -tpp7 -O0"
> setenv OPT_MED "ifort -c -auto -tpp7 -O2"
> setenv OPT_HI "ifort -c -auto -tpp7 -xW -mp1 -ip -O3"
>
> setenv LOAD "ifort"
> setenv LOADLIB " -limf -lsvml $MPILIB"
> -----------------------------------------------------------
>
> The compilation doesn't give me any error, but when I launch a
> calculation I have this error:
> --------------------------------------------------------
>
>p0_31812: p4_error: interrupt SIGSEGV: 11
>p1_31841: p4_error: interrupt SIGSEGV: 11
>------------------------------------------
>
>
>
> Anyone else experience something like this?
>
> Thanks in advanced
> Tiziano
>
>
> --
>
> +++++++++++++++++++++++++++
> Dr. Tiziano Tuccinardi
> Dip. Scienze Farmaceutiche
> Via Bonanno, 6
> 56126 PISA
> Tel ++39 050 2219572
> E-mail tuccinardi_at_farm.unipi.it <mailto:tuccinardi_at_farm.unipi.it>
> +++++++++++++++++++++++++++
>
>
> --
> Il messaggio e' stato analizzato alla ricerca di virus o
> contenuti pericolosi da *MailScanner*
> <http://www.mailscanner.info/>, ed e'
> risultato non infetto.
>
>
> --
> Il messaggio e' stato analizzato alla ricerca di virus o
> contenuti pericolosi da *MailScanner* <http://www.mailscanner.info/>,
> ed e'
> risultato non infetto.

Yes, I've set 'limit stacksize unlimited' in my .cshrc
Regards, Tiziano 

-- 

+++++++++++++++++++++++++++
Dr. Tiziano Tuccinardi
Dip. Scienze Farmaceutiche
Via Bonanno, 6
56126 PISA
Tel ++39 050 2219572
E-mail tuccinardi_at_farm.unipi.it <mailto:tuccinardi_at_farm.unipi.it>
+++++++++++++++++++++++++++

-- 
Il messaggio e' stato analizzato alla ricerca di virus o
contenuti pericolosi da MailScanner, ed e'
risultato non infetto.

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