AMBER Archive (2004)

Subject: Re: AMBER: -p4pg problem

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Sat Jun 26 2004 - 05:59:53 CDT

> ... 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 previously..now,
> what i want to know is....is 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.
http://structbio.vanderbilt.edu/archives/amber-archive/2004/1077.phtml
the changes were made to pmemd 3.1 sources, i guess, but they could be
useful for you.

regards, 

-- 
Lubos
_@_"
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