On Mon, Apr 6, 2009 at 5:21 PM, Gus Correa <gus_at_[hidden]> wrote:
> 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.
I have found the "examples". Should they be compiled? how? This is my
only question here. What's below is info. Although amber parallel
would have not compiled with faulty openmpi, I'll run openmpi tests as
soon as I understand how.
> 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.
there is no other accessible MPI (one application, DOT2, has mpich but
it is a static compilation; DOT2 parallelizatuion requires thar the
computer knows itself, i.e." ssh hostname date" should afford the date
passwordless. The reported issues in testing amber have destroyed this
situation: now deb64 has port22 closed, evem to itself.
> 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.
With amber I use the parallel computer directly and the amber
installation is chown to me. The ssh connection, in this case, only
serves to get file from. or send files to, my desktop.
In my .bashrc:
if [ "$LD_LIBRARY_PATH" ] ; then
There is also
this is for DOCK, which, with this env variabl, accepts openmpi (at
lest it was so with v 1.2.6)
the intel compilers (compiled ifort and icc, are sourced in both my
.bashrc and root home .bashrc.
Thanks and apologies for my low level in these affairs. It is the
first time I am faced by such problems, with amd64, same intel
compilers, and openmpi 1.2.6 everything was in order.
> 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,
> /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
>> Â MCA affinity: libnuma (MCA v 2.0, API 2.0)
>> ompi_info | grep maffinity
>> Â MCA affinity: first use (MCA as above)
>> Â 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 Â < /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 ..
>> francesco pietra
>> users mailing list
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