Re: AMBER: pmemd and mpich - myrinet

From: Lubos Vrbka <>
Date: Fri, 23 Apr 2004 19:33:32 +0200


thanks for quick reply.

> 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)
ok, i'll try that...

> 2) ... Find where libgm.a is installed on your system, and set
> MPICH_LIBDIR2 to point at it. ...
this stuff about MPICH_LIBDIR2 was exactly the thing i needed to know...
i wasn't sure whether it isn't used for some other purposes, but if i
can redefine it i'll make use of it...

> 3) 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).
well, the build proceeded fine... i want this binary mainly for tests,
since not all nodes at clusters i use possess myrinet... sometimes i
experience that pmemd with mpich-p4 isn't putting the maximal load on
the processors - and i guess this could be related to slow ethernet
communication - myrinet should tell me, whether it is really so...

once more, thanks for your help. have a nice weekend,

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Received on Fri Apr 23 2004 - 18:53:00 PDT
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