AMBER Archive (2009)

Subject: [AMBER] ssh and make test.parallel

From: Francesco Pietra (
Date: Mon Apr 06 2009 - 04:58:39 CDT

I am at recompiling amber10 from scratch on debian amd64 lenny because
on the upgrading from amd64 etch to lenny, ambertools did no more pass
the tests.

AmberTools 1.2 compiled plainly with gcc (initial attempts with
icc/icpc - which was ok with previous amd64 etch - failed here).

Serial compilation of amber10 was done with ifort. All tests passed.
(I skipped QMMM)

For parallel compilation (openmpi 1.3.1) no errors with

./configure_amber -openmpi -nobintray ifort

make parallel


I am having problems with parallel tests

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) (
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. I found that strange because deb64 knew
itself ("ssh deb64 name" gave the date passwordless (as required by
the parallelization of DOT2); now port 22 is closed even to such ssh).
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.

Question: does makefile contain any ssh command that may require the
-n flag? If so, I would appreciate how to edit makefile(s) or the make
command, or what else is better.

If the answer is that a network expert should intervene locally, I'll

francesco pietra

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