You might first try and see if you can run something other than amber
with your new installation. Make sure you have the PATH and
LD_LIBRARY_PATH set correctly on the remote node, or add --prefix to
your mpirun cmd line.
Also, did you remember to install the OMPI 1.3 libraries on the remote
One thing I see below is that host deb64 was resolved to the loopback
interface - was that correct? Seems unusual - even if you are on that
host, it usually would resolve to some public IP address.
On Apr 6, 2009, at 8:51 AM, 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 ..
> francesco pietra
> users mailing list