AMBER Archive (2007)

Subject: Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out"

From: Khatcharin Siriwong (skhatcha_at_kku.ac.th)
Date: Sat Apr 21 2007 - 22:57:18 CDT

> > I obtained error as "Unit 6 Error on OPEN: md.out2" from both
> > commands.
> > As I know, this error message concerns overwrite output.
> > However, I am sure that I have added a flag "-O" (a letter O,
not
> > zero). Any suggestion?

>
> Manually remove any files that would need to be overwritten
(e.g. md.out2),
> and try again?
>
> ....dac
>

Dear Dr.David Case,
File md.out2 was never existed. However, now I realize that
sander.MPI (using mpirun.ch_gm device) read/write the input and
output files in directory $AMBERHOME/exe. It works fine if I enter

mpirun.ch_gm -s -np 2 -machinefile m1.gm
$AMBERHOME/exe/sander.MPI -O -i $PWD/gbin -o $PWD/md.out2 -
c $PWD/md12.x -p $PWD/prmtop -r $PWD/restrt -inf $PWD/mdinf

Of course, without "$PWD", it is not success, because sander will
write output (i.e. mdinf and restrt files) into directory
$AMBERHOME/exe which is allowed only for administrator.
How can I run sander.MPI using mpirun.ch_gm without
adding "$PWD"? Note that, It works fine for mpirun.ch_p4 without
adding $PWD.
Many thanks in advance.

Best Regards,
Khatcharin

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