AMBER Archive (2006)

Subject: Re: AMBER: mpich Amber7 problem

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Wed Jan 11 2006 - 03:27:01 CST

Hello,

try these ...
1) use full path to sander executable
2) do not use & at the end of command line
3) be sure that mpirun is from mpich and not from other mpi system
installed on your computer

Petr

Jan Dohnalek wrote:
> Hi,
> I think I have successfully compiled Amber7 sander with Mpich 1.2.7.
> However I am still getting this error (run out of web/google options how
> to fix this now):
>
> [dohnalek_at_m2 6cpus_mpich]$ mpirun -np 6 sander -O -i mdin -o mdout -p
> prmtop -c prmcrd -x mdcrd -v mdvel -e mden -inf mdinfo &
> [1] 25998
> [dohnalek_at_m2 6cpus_mpich]$ Warning: Command line arguments for program
> should be given
> after the program name. Assuming that -O is a
> command line argument for the program.
> Warning: Command line arguments for program should be given
> after the program name. Assuming that -i is a
> command line argument for the program.
> Unrecognized argument sander ignored.
> /home/dohnalek/amber/md_penta/6cpus_mpich/mdin: line 1: syntax error
> near unexpected token `&'
> /home/dohnalek/amber/md_penta/6cpus_mpich/mdin: line 1: `&cntrl'
>
> [1] Exit 2 mpirun -np 6 sander -O -i mdin -o
> mdout -p prmtop -c prmcrd -x mdcrd -v mdvel ...
> [dohnalek_at_m2 6cpus_mpich]$
>
>
>
> Please, please. Anyone familiar with this problem?
> Jan
>
>
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-- 
##################################################
   Petr Kulhanek
  ------------------------------------------------
   E-mail: kulhanek_at_chemi.muni.cz
   WWW: http://www.ncbr.chemi.muni.cz/~kulhanek
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   National Centre for Biomolecular Research
   Masaryk University in Brno
   Kotlarska 2, CZ-611 37 Brno
   Czech Republic
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