AMBER Archive (2004)

Subject: Re: AMBER: -p4pg problem

From: spookie (
Date: Sat Jun 26 2004 - 09:00:48 CDT

well, thanx lubos..the link you gave was
informative..but in the third thread as you mentioned,
you said that the modification of code pertains to
running jobs using PBS and mpiexec..but, i'm trying to
run my parallel jobs using mpirun and without pbs..i'm
actually trying to run the default benchmark given by
the amber8 distro, using DO_PARALLEL
variable looks like this..

DO_PARALLEL="mpirun -np 2 -machinefile

i cannot see anything wrong with this declaration..but
i observed another strange thing we know, a
parallel job creates a temporary file with the process
id of sander as its name and lists all the nodes on
which the job is being run...till amber7, sander used
to accept nodes in powers of two..but now, my
DO_PARALLEL variable started accepting any number of
nodes irrespective of it being a power of two or
not....i'm wondering if it is a modification in the
source code that has been brought about in amber8 or
it is a compilation error on my cluster !!

and i could not find an appropriate correction to my
mdfil.f file (excluding usage of pbs, mpiexec etc)

thanks in anticipation..

--- Lubos Vrbka <> wrote: > > ...
previously i modified the mdfil.f file to add
> the
> > -p4pg flag so that sander ignores the flag even
> when
> > it is habitually added to the flag list by
> mpich..i
> > added the following lines to mdfil.f in
> > $AMBERHOME/src/sander
> >
> > else if (arg == '-p4pg')
> > continue
> >
> > and when i recompiled sander with this
> modification, i
> > could surpass the error i mentioned
> > what i want to know this the way to
> surpass
> > this error, and is this modification the cause of
> the
> > parallel job problem of sander...please give me
> some
> > more suggestions...
> >
> hi,
> i think i faced very similar problem when using
> mpiexec instead of
> mpirun with pmemd. i had to change the code by
> myself - if you're
> interested see the follwing thread in the amber mail
> reflector. i guess
> the third post contains the changes i made to the
> code.
> the changes were made to pmemd 3.1 sources, i guess,
> but they could be
> useful for you.
> regards,
> --
> Lubos
> _@_"
> The AMBER Mail Reflector
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