AMBER Archive (2006)

Subject: Re: AMBER: Unit 5 Error on OPEN: md.in

From: Rachel (comeonsos_at_googlemail.com)
Date: Sat Dec 16 2006 - 12:01:12 CST

Dear all,

I tried to recompile amber8 and tried to narrow the problem down, I found
out that if I use exactly same command:

$AMBERHOME/exe/sander -O -i md.in -o md.out -c model_min.rst -p
model.prmtop-r model_md.rst -x model_md.mdcrd

after the installation of serial part (without parallel part), it is OK. And
if i use it after finishing the parallel installation of amber, then I got
error message:

 Unit 5 Error on OPEN: md.in
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_12655: p4_error: : 1

Anyone can tell me what is wrong please? really appreciate your help.

Regards,
Rachel

On 12/13/06, Rachel <comeonsos_at_googlemail.com> wrote:
>
> Dear all,
>
> I have compiled amber8 on a beowulf cluster using ifort, both serial and
> parallel compilation were OK and all the tests passed without any errors.
>
> However, when I tried to just run an interactive job using:
> $AMBERHOME/exe/sander -O -i md.in -o md.out -p model.prmtop -c
> model_min.rst -r model_md.rst -x model_md.mdcrd
>
> I got error message as:
> Unit 5 Error on OPEN: md.in
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_12655: p4_error: : 1
>
> The file md.in is in the directory where I ran this job.
>
> I know it is a problem caused by MPI, however, I don't quite know how to
> get rid of this error. For your information, because the mpich under the
> cluster root directory was not compiled by ifort, therefore when I tried to
> use that to compile parallel amber, I got some errors, and searched in the
> mailing list, found out that I need an mpich compiled using the same
> compiler. Therefore I installed a new MPICH using ifort under my own home
> directory and set MPICH_HOME to the MPICH in my own directory when I
> compiled amber8.
>
> Thanks in advance for your help.
> Best regards,
> Rachel
>

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