AMBER Archive (2004)

Subject: Re: AMBER: pmemd and mpich - myrinet

From: Robert Duke (
Date: Fri Apr 23 2004 - 11:23:37 CDT

Lubos -
1) There is no machinefile for xeons with myrinet simply because I did not
have access to a xeons + myrinet installation. It is easy to make the
appropriate modifications to Machine.mpich_gm_ifc (diff Machine.mpich_ifc
and Machine.mpich_ifc_p4, and craft up your own Machine.mpich_gm_ifc_p4)
2) PMEMD, and all of amber, very specifically don't make use of
mpicc/mpif77/mpif90 because we don't want to be subjected to the vagaries of
how this stuff is configured (well that is true for me, and I am assuming
that is true for the rest of the amber guys too). You could maybe get it to
work, but there is no need. Find the mpich_gm dir and set MPICH_HOME in the
script to it. Find where libgm.a is installed on your system, and set
MPICH_LIBDIR2 to point at it. A good first place to look is /usr/local/lib.
Otherwise, plow around, bug your system staff, or decipher the library paths
used in mpif90.
3) Beware that mpich-gm had to be built to use ifc. If it is not, linking
will very likely fail. Bug your system staff. Look at the pmemd 3.00
release notes on for particulars.
By the way, this is the hardest of all the possible pmemd or amber installs
in my opinion, due to the conjunction of linux, ifc, and mpich-gm and all
the vageries/incompatibilities that are possible (sorry, really nothing I
can do about it).
Regards - Bob

----- Original Message -----
From: "Lubos Vrbka" <>
To: <>
Sent: Friday, April 23, 2004 11:59 AM
Subject: AMBER: pmemd and mpich - myrinet

> hi guys,
> i have got 2 questions regarding pmemd-3.1 and myrinet.
> 1) why is there no machinefile for xeons with myrinet?
> 2) i'm just building the pmemd with myrinet communication and experience
> problems with it - compiler cannot find myrinet related libraries. these
> are in different place than mpich-gm libraries.
> i asked at our computer facility and they said that i should use
> mpicc/mpif77 compilers that are used within gm package (as they set up
> the library path correctly), but i was not able to find, how to force
> pmemd installation to use them, or even check which compilers are used
> for parallel pmemd build (i use ifc as the compiler for the pmemd).
> when i modified the LOADLIB variable with the correct paths it worked
> so is it possible to find out which mpi compiler is used for the build?
> is it possible to change it?
> thanks for your time. regards,
> --
> Lubos
> _@_"
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