AMBER Archive (2006)

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

From: bertrand russell (betrussell23_at_gmail.com)
Date: Wed Dec 20 2006 - 23:09:48 CST

Dear Ross,

                Thank you very much for your immediate reply. I issued the
following command as instructed by you. I am getting the following error
message.

#############################################################################
bash-2.05b$ export DO_PARALLEL='mpirun -np 4'
bash-2.05b$ make test.parallel
export TESTsander=/pludisk1/facs/sanjib/AMBER9/amber9/exe/sander.MPI; make
test.sander.BASIC
make[1]: Entering directory `/pludisk1/facs/sanjib/AMBER9/amber9/test'
cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
MPI: asgetnetinfo_array('(null)') failed : request failed - authentication
failure
  ./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/pludisk1/facs/sanjib/AMBER9/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2

###############################################################################

What might be the problem?
On 12/21/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Hi Bertrand,
>
> Ah I see, you need to include quotes. Do the following:
>
> cd $AMBERHOME/test/
> export DO_PARALLEL='mpirun -np 4'
> make test.parallel
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *bertrand russell
> *Sent:* Wednesday, December 20, 2006 20:13
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: Installation help - SGI Altix 350
>
> Dear Ross,
>
> As you suggested I issued >which mpirun command. It
> showed /usr/bin/mpirun.
>
> bash-2.05b$ which mpirun
> /usr/bin/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
> follows,
>
> 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 < ross_at_rosswalker.co.uk> 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:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | 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:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > Behalf Of *bertrand russell
> > *Sent:* Wednesday, December 20, 2006 02:47
> > *To:* amber_at_scripps.edu
> > *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
> Bertrand.P.S.Russell
>
> 

-- 
Live Life; Don't pass it
Bertrand.P.S.Russell

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