AMBER Archive (2006)

Subject: Re: AMBER: mpich Amber7 problem

From: Jan Dohnalek (dohnalek_at_imc.cas.cz)
Date: Wed Jan 11 2006 - 04:32:18 CST


Dear all,
I got now Amber7 run in the parallel mode on Linux.

1. I have compiled mpich 1.2.7p1 with --with-device=ch_p4 --with-arch=LINUX
--with-comm=shared

2. I have used the Machine.g77_mpich file. I.e. made a link called
MACHINE in the Amber src dir.
Edited the Machine.g77_mpich to point to the mpich directory.

3. Did "make install" in the src dir.

4. I run the jobs by saying
mpirun -machinefile xxx -np 4 /usr/local/protein/amber7_mpich/exe/sander
-O -i mdin -o mdout -p prmtop -c prmcrd -x mdcrd -v mdvel -e mden -inf
mdinfo &

This may not be the optimal way to do things (I do not have pgf77) but
it works.
Stating the full path of the sander binary was crucial to have it run.
Jan

linfu wrote:

>Hi Jan Dohnalek!
>You have successfully compiled Amber7 sander with Mpich 1.2.7,So
>Could you give me some details about how to compile Amber7 with Mpich in Linux system!
>
>Thank you very much!
>
>BEST WISHES
>
>Fu Lin
>
>
>
>======= 2006-01-10 22:31:38 艇壓栖佚嶄亟祇=======
>
>
>
>>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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>
>= = = = = = = = = = = = = = = = = = = =
>
>
>        崑
>撰
>
>
>        linfu
>        linfu3200_at_mail.sioc.ac.cn
>          2006-01-11
>
>-----------------------------------------------------------------------
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