AMBER Archive (2006)

Subject: Re: AMBER: Unit 5 Error on OPEN:

From: Chris Moth (
Date: Sat Dec 16 2006 - 12:25:03 CST

In some pbs environments it is necessary to have a
cd working_directory
command before (in the line above) your invocation of sander.

Otherwise, sander may be trying to open the in an entirely
unexpected directory.

> 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 -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:
> [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 <> 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 -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:
>> [0] MPI Abort by user Aborting program !
>> [0] Aborting program!
>> p0_12655: p4_error: : 1
>> The file 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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