AMBER Archive (2006)

Subject: Re: AMBER: Installation help - SGI Altix 350

From: bertrand russell (
Date: Wed Dec 20 2006 - 22:13:03 CST

Dear Ross,

                  As you suggested I issued >which mpirun command. It showed

bash-2.05b$ which mpirun

And I am not getting any errors while testing the pararllel. I don't know
how to set the environment pvariable for DO_PARALLEL. Details on this is as

bash-2.05b$ DO_PARALLEL=mpirun -np 4
bash: -np: command not found
 What should I do to overcome this problem? Many thanks for your reply.

On 12/20/06, Ross Walker <> wrote:
> 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
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on request |
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
> ------------------------------
> *From:* [] *On
> Behalf Of *bertrand russell
> *Sent:* Wednesday, December 20, 2006 02:47
> *To:*
> *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.
> --
> Live Life; Don't pass it
> Bertrand.P.S.Russell

Live Life; Don't pass it

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