CI for ray

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CI for ray

Nadiya Sitdykova
Hello Andreas, 

I added autopkgtest test-suite for ray package. Tests that run ray on one core run perfectly well, but when I tried:
  mpiexec -n 2 Ray -k 31 -p ecoli_1K_1.fq ecoli_1K_2.fq -o test3

the same error arises as with mpi-mrbayes:
--------------------------------------------------------------------------
The value of the MCA parameter "plm_rsh_agent" was set to a path
that could not be found:

  plm_rsh_agent: ssh : rsh

Please either unset the parameter, or check that the path is correct
--------------------------------------------------------------------------

So I also added ssh to dependencies and in fixed the problem.

Regards, Nadiya
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Re: CI for ray

Graham Inggs-3
Hi Nadiya

On 28 July 2017 at 05:35, Nadiya Sitdykova <[hidden email]> wrote:

> --------------------------------------------------------------------------
> The value of the MCA parameter "plm_rsh_agent" was set to a path
> that could not be found:
>
>   plm_rsh_agent: ssh : rsh
>
> Please either unset the parameter, or check that the path is correct
> --------------------------------------------------------------------------
>
> So I also added ssh to dependencies and in fixed the problem.

I recall this seeing this message in other packages in debian-science
and debichem.  An alternate solution would be to add the following
line near the beginning of debian/tests/run-unit-test:

export OMPI_MCA_plm_rsh_agent=/bin/false

I believe that ssh is only required when MPI processes execute on
different hosts.  It should not be required when the MPI processes all
execute on the same host, like a buildd or a CI tester.

codesearch.debian.net has many examples:
https://codesearch.debian.net/search?q=path%3Adebian%2F*+OMPI_MCA_plm_rsh_agent
and more specifically for autopkgtests:
https://codesearch.debian.net/search?q=path%3Adebian%2Ftests%2F*+OMPI_MCA_plm_rsh_agent

Regards
Graham

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Re: CI for ray

Nadiya Sitdykova
Hello all,

Graham, thank you for your advice and those examples. It really makes sense to get rid of ssh dependency for a whole package, since it could be used on the same host.

Andreas, I removed ssh from dependencies and added mention by Graham line to the run-unit-test.

Regards, Nadiya

On Thu, Jul 27, 2017 at 11:46 PM, Graham Inggs <[hidden email]> wrote:
Hi Nadiya

On 28 July 2017 at 05:35, Nadiya Sitdykova <[hidden email]> wrote:
> --------------------------------------------------------------------------
> The value of the MCA parameter "plm_rsh_agent" was set to a path
> that could not be found:
>
>   plm_rsh_agent: ssh : rsh
>
> Please either unset the parameter, or check that the path is correct
> --------------------------------------------------------------------------
>
> So I also added ssh to dependencies and in fixed the problem.

I recall this seeing this message in other packages in debian-science
and debichem.  An alternate solution would be to add the following
line near the beginning of debian/tests/run-unit-test:

export OMPI_MCA_plm_rsh_agent=/bin/false

I believe that ssh is only required when MPI processes execute on
different hosts.  It should not be required when the MPI processes all
execute on the same host, like a buildd or a CI tester.

codesearch.debian.net has many examples:
https://codesearch.debian.net/search?q=path%3Adebian%2F*+OMPI_MCA_plm_rsh_agent
and more specifically for autopkgtests:
https://codesearch.debian.net/search?q=path%3Adebian%2Ftests%2F*+OMPI_MCA_plm_rsh_agent

Regards
Graham

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Re: CI for ray

Andreas Tille-5
Hi Nadiya,

On Fri, Jul 28, 2017 at 06:35:44PM -0700, Nadiya Sitdykova wrote:
> Graham, thank you for your advice and those examples. It really makes sense
> to get rid of ssh dependency for a whole package, since it could be used on
> the same host.

I agree that it is better to stay with less dependencies but finally it
does not real practical harm if the package pulls ssh.  I admit I would
consider it a bug that openmpi-bin is not even suggesting ssh - I
personally would even go with Recommends if I would be the maintainer.
 
> Andreas, I removed ssh from dependencies and added mention by Graham line
> to the run-unit-test.

I've created a new changelog entry for this change since the package was
uploaded and leave it as is until we might have another reason to upload.

Thanks for your work on this

      Andreas.

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