TPP on cluster - Petunia running remotely?

[Joshua Dunham]

Hi Everyone,

  TPP has been successfully installed on my cluster and am now trying to get Petunia up. I'd like to run petunia as a remote process, not on the cluster; is this possible?

  -Josh

[Joseph Slagel]

Josh,

Its easily possible to run it as a remote process, not on the cluster.  The trick of course is having it actually run jobs on the cluster.  And I just recently did some work to make this a little easier.  Which clustering software do you use?

-Joe

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/groups/opt_out.

--

Joe Slagel
Institute for Systems Biology
jsl...@systemsbiology.org
(206) 732-1362

[Gary Smith]

We're using UNIVA Grid Engine (aka. SGE).

 

      --g

 

[Joseph Slagel]

Gary/Josh,

That's good to hear since we're using the last open source version of SGE and the commands should all be similar.  Recently I've made to the Petunia web interface (tpp_gui.pl) that should also work for you.   What I've done is made two simple modifications  The first will prepend the "qrsh" to the list of commands.  That way the commands are submitted to the cluster instead of running locally on the web server.  The second (and more controversial) change does yet another prepend to the command list, this time using "sudo" to switch to the logged in user.  Since Petunia already has a undocumented feature that allows you to change its authentication mechanism  (we happen to use this to use LDAP to authenticate our TPP users) this then allows one to make sure jobs are submitted as the appropriate user.

I've tested this out on our development systems here at ISB and it seems to work pretty well.  We haven't deployed it into production yet for as you can imagine the security implications of having a CGI script using sudo and being tied to a cluster are significant.  We do intend to eventually roll some solution like this but only after we can change our current system configuration.  (Our IT wants to ensure the web server node is locked down and strictly controlled before they'll let any program use sudo so freely).

If your interested I could share the code with you now -- or you can wait until we release 4.7 which will have said hooks in place with hopefully some documentation.

-Joe

On Tue, Nov 12, 2013 at 7:25 AM, Gary Smith <grack...@gmail.com> wrote:

We're using UNIVA Grid Engine (aka. SGE).

 

      --g

 

--

You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/groups/opt_out.

[Joshua Dunham]

I think it would be handy to try out your modifications. Since we have a small user base that would need this we could probably make some further modifications to accommodate just their use.

-J