RE: AMBER: Installation help - SGI Altix 350

From: Ross Walker <>
Date: Wed, 20 Dec 2006 08:38:16 -0800

Dear Bertrand,
We really need some more information about your system and what you are
doing to be able to help out some more. If things compiled okay - I.e. you
built a parallel version with no errors such that you now have a sander.MPI
executable in your $AMBERHOME/exe/ directory then I suspect there is nothing
wrong with the mpi implementation on your machine.
On SGI Altix machines the MPI installation is generally vendor supplied. You
should check which mpirun you have in your path:
which mpirun
You should see /usr/bin/mpirun
Also please show exactly what you are setting for the DO_PARALLEL variable
and exactly what error messages you see when you type make test.parallel.
I suspect that for some reason you don't have mpirun defined in your path or
that it points to a non-standard mpi installation.
All the best

|\oss Walker

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From: [] On Behalf Of
bertrand russell
Sent: Wednesday, December 20, 2006 02:47
Subject: AMBER: Installation help - SGI Altix 350

Dear Amber users,

I am trying to install Amber9 in SGI Altix 350 running in SGI pro pack 2. I
have done all the steps successfully till making sander parallel. I now want
to test my parallel version using >make test.parallel. Before that it seems
that I need to set an environmental variable for DO_PARALLEL it seems. I
gave the command mentioned in the Amber installation instructions file
(Since I am working in bash shell I used export command). But it doesn't
work. I don't know how to set. One more thing is, I don't know what is the
mpi version is in our server. Is the mpi version and its details are
essential for the testing process. If so, It would be very helpful, if
somebody could help me to know the mpi version and complete my installation
successfully. Thanks in advance.

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Received on Sun Dec 24 2006 - 06:07:10 PST
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