AMBER Archive (2009)

Subject: Re: [AMBER] ssh and make test.parallel

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Apr 06 2009 - 09:29:19 CDT

Do you mean that the flag -openmpi in ./configure (which was ok for
openmpi 1.2.6) is no good for version 1.3.1, as I used now?

As far as the installation of openmpi 1.3.1 is concerned, the 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.

thanks
francesco

On Mon, Apr 6, 2009 at 12:33 PM, Atro Tossavainen
<atro.tossavainen+amber_at_helsinki.fi> wrote:
>> cd cytosine && ./Run.cytosine
>> The authenticity of host deb64 (which is the hostname) (127.0.1.1)
>> can't be established.
>> RSA fingerprint .....
>> connecting ?
>
> You need to learn to operate your MPI installation.  This is not an
> AMBER problem.
>
>> 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.
>
> AMBER Makefiles do not contain anything to do with SSH, which you
> may clearly see by reading the files yourself.  Your local MPI
> installation is doing this.
>
> --
> Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
> Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
> +358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
>
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