Cluster jobs running as real user

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Cluster jobs running as real user

Shane Sturrock
Has anyone had any success in getting cluster jobs running as the real user?  I've got our server happily working with LSF via drmaa but all jobs run as the galaxy user and I would like to be able to separate out the jobs on a per user basis.  I've followed the instructions at https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User
but I'm having no luck with it so was wondering if someone would know how I might debug it, like where could I find the script it is trying to execute?  All I'm getting is code 18: invalid LSF job id although it does seem to be creating files in my databases/tmp directory owned by the user.

Shane

--
Dr Shane Sturrock
Senior Scientist
Tel: +64 (0) 9 379 5064
76 Anzac Ave
Auckland
New Zealand


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Cluster jobs running as real user

Charles Girardot
Hi Shane,

We had enabled this feature on our cluster working with PBS but since we switched to LSF, we never managed to have it working again. Same error as yours if I correctly remember. After hours spent looking into LSF, I think we understood that LSF somehow catches the user change and rejects the job. We finally gave up.

I am not sure this helps ...

bw

Charles


On 5 Mar 2014, at 02:55, Shane Sturrock wrote:

> Has anyone had any success in getting cluster jobs running as the real user?  I've got our server happily working with LSF via drmaa but all jobs run as the galaxy user and I would like to be able to separate out the jobs on a per user basis.  I've followed the instructions at https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User
> but I'm having no luck with it so was wondering if someone would know how I might debug it, like where could I find the script it is trying to execute?  All I'm getting is code 18: invalid LSF job id although it does seem to be creating files in my databases/tmp directory owned by the user.
>
> Shane
>
> --
> Dr Shane Sturrock
> [hidden email]
> Senior Scientist
> Tel: +64 (0) 9 379 5064
> 76 Anzac Ave
> Auckland
> New Zealand
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

=====================================
Charles Girardot
Head of Genome Biology Computational Support (GBCS)
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
Fax: +49-(0)6221-387-8166
Email: [hidden email]
Room V205
Meyerhofstra├če 1,
69117 Heidelberg, Germany
=====================================















___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Cluster jobs running as real user

Shane Sturrock
Hi Charles,

That actually helps.  I don't have any choice in running LSF but knowing that it didn't work because LSF is rejecting it helps when I talk to my boss about why I couldn't do it.

Shane

On 5/03/2014, at 10:28 pm, Charles Girardot <[hidden email]> wrote:

Hi Shane,

We had enabled this feature on our cluster working with PBS but since we switched to LSF, we never managed to have it working again. Same error as yours if I correctly remember. After hours spent looking into LSF, I think we understood that LSF somehow catches the user change and rejects the job. We finally gave up.

I am not sure this helps ...

bw

Charles


On 5 Mar 2014, at 02:55, Shane Sturrock wrote:

Has anyone had any success in getting cluster jobs running as the real user?  I've got our server happily working with LSF via drmaa but all jobs run as the galaxy user and I would like to be able to separate out the jobs on a per user basis.  I've followed the instructions at https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User
but I'm having no luck with it so was wondering if someone would know how I might debug it, like where could I find the script it is trying to execute?  All I'm getting is code 18: invalid LSF job id although it does seem to be creating files in my databases/tmp directory owned by the user.

Shane

--
Dr Shane Sturrock
[hidden email]
Senior Scientist
Tel: +64 (0) 9 379 5064
76 Anzac Ave
Auckland
New Zealand

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

=====================================
Charles Girardot
Head of Genome Biology Computational Support (GBCS)
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
Fax: +49-(0)6221-387-8166
Email: [hidden email]
Room V205
Meyerhofstra├če 1,
69117 Heidelberg, Germany
=====================================















--
Dr Shane Sturrock
Senior Scientist
Tel: +64 (0) 9 379 5064
76 Anzac Ave
Auckland
New Zealand


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/