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Subject: Re: [OMPI users] ssh MPi and program tests
From: Gus Correa (gus_at_[hidden])
Date: 2009-04-06 11:21:18


Hi Francesco

Did you try to run examples/connectivity_c.c,
or examples/hello_c.c before trying amber?
They are in the directory where you untarred the OpenMPI tarball.
It is easier to troubleshoot
possible network and host problems
with these simpler programs.

Also, to avoid confusion,
you may use a full path name to mpirun,
in case you have other MPI flavors in your system.
Often times the mpirun your path is pointing to is not what you
may think it is.

I don't know if you want to run on amd64 alone (master node?)
or on a cluster.
In any case, you may use a list of hosts
or a hostfile on the mpirun command line,
to specify where you want to run.

Do "/full/path/to/openmpi/bin/mpirun --help" for details.

I am not familiar to amber, but how does it find your openmpi
libraries and compiler wrappers?
Don't you need to give it the paths during configuration,
say,
/configure_amber -openmpi=/full/path/to/openmpi
or similar?

I hope this helps.
Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------

Francesco Pietra wrote:
> I have compiled openmpi 1.3.1 on debian amd64 lenny with icc/ifort
> (10.1.015) and libnuma. Tests passed:
>
> ompi_info | grep libnuma
> MCA affinity: libnuma (MCA v 2.0, API 2.0)
>
> ompi_info | grep maffinity
> MCA affinity: first use (MCA as above)
> MCA affinity: libnuma as above.
>
> Then, I have compiled parallel a molecular dynamics package, amber10,
> without error signals but I am having problems in testing the amber
> parallel installation.
>
> amber10 configure was set as:
>
> ./configure_amber -openmpi -nobintray ifort
>
> just as I used before with openmpi 1.2.6. Could you say if the
> -openmpi should be changed?
>
> cd tests
>
> export DO_PARALLEL='mpirun -np 4'
>
> make test.parallel.MM < /dev/null
>
> cd cytosine && ./Run.cytosine
> The authenticity of host deb64 (which is the hostname) (127.0.1.1)
> can't be established.
> RSA fingerprint .....
> connecting ?
>
> I stopped the ssh daemon, whereby tests were interrupted because deb64
> (i.e., itself) could no more be accessed. Further attempts under these
> conditions failed for the same reason. Now, sshing to deb64 is no more
> possible: port 22 closed. In contrast, sshing from deb64 to other
> computers occurs passwordless. No such problems arose at the time of
> amd64 etch with the same
> configuration of ssh, same compilers, and openmpi 1.2.6.
>
> I am here because the warning from the amber site is that I should to
> learn how to use my installation of MPI. Therefore, if there is any
> clue ..
>
> thanks
> francesco pietra
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