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
nodes?
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 ..
thanks
francesco pietra
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