Re: [galaxy-dev] drmaa resubmission

[John Chilton]

We've done a lot of work in Galaxy dev on this problem over the last
few years - I'm not sure how much concrete progress we have made.

Nate started it and I did some work at the end of last year. Just to
summarize my most recent work on this - in
https://github.com/galaxyproject/galaxy/pull/3291/commits/b78287f1508db2c06f0c309ed8d3747adb4d17fa
I added some test cases for the existing job runner resubmission stuff
- it was just my sense to understand what was there - hopefully the
examples in the form of test cases help you as well.. This includes a
little test job_conf.xml file that describes how you can catch job
walltime and memory limit hits registered by the job runner and send
jobs to different destinations. This requires the job runner knows how
to record these problems - which the SLURM job runner does - other job
runners like the generic drmaa runner may need to be subclassed to
check for these things in general.

In 
https://github.com/galaxyproject/galaxy/pull/3291/commits/7d52b28ab2ab0314cd4fa31108a6750cb9750ef3
I created a little DSL for resubmissions to make what can be expressed
in job_conf more powerful. Then I added variables to expressions
language such as seconds_since_queued,
seconds_running(https://github.com/galaxyproject/galaxy/pull/3291/commits/18eb1c8d0e4c3f7616d44fd177c90943695b7053),
and attempt number
(https://github.com/galaxyproject/galaxy/pull/3291/commits/7e338d790964f594ae67b33e6a72e1777e774b8c).
I also added the ability to resubmit on unknown job runner problems
here 
(https://github.com/galaxyproject/galaxy/pull/3291/commits/0559cff6e94b250ddd98275b119ab51b36491e34).

None of this is really documented outside the test cases - it is
waiting for someone to come along and find it useful.

I think the next thing I'd like to see for job resubmission besides
documentation and more job runner support for common runners is
described in this issue
(https://github.com/galaxyproject/galaxy/issues/3320) - all the
existing resubmission logic is based on errors detected from job
runners - if the underlying error exhibits itself as a tool failure -
we need a way to reason about that and we cannot currently.

Hope this helps.

-John

On Thu, Jun 15, 2017 at 10:37 AM, Matthias Bernt  wrote:
> Dear list,
>
> I was thinking about implementing the job resubmission feature for drmaa.
>
> I hope that I can simplify the job configuration for our installation (and
> probably others as well) by escalating through different queues (or
> ressource limits). Thereby I hope to reduce the number of special cases that
> I need to take care.
>
> I was wondering if there are others
>
> - who are also interested in this feature and want to join? I would try to
> give this project a head start in the next week.
>
> - that may have started to work on this feature or just started to think
> about it and want to share code/experience
>
> Best,
> Matthias
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Re: [galaxy-dev] Galaxy slurm error

[Nate Coraor]

If slurm accounting is configured, `sacct` might reveal more. You might
also check the slurmd logs on the execution host where the job ran.

--nate

On Thu, Jun 15, 2017 at 11:47 AM, Hoover , David (NIH/CIT) [E] <
hoove...@helix.nih.gov> wrote:

> I would guess something about the slurm job exceeded some allocated
> resource (memory, cpu, time) and slurm killed the job.
>
> David Hoover
> HPC @ NIH
>
> On Jun 15, 2017, at 11:28 AM, Nate Coraor  wrote:
>
> Hi Evan,
>
> Are there any other details logged for this job?
>
> --nate
>
> On Thu, Jun 15, 2017 at 9:20 AM, evan clark  wrote:
>
>> Has anyone ever encountered an error such as this when running galaxy
>> with slurm and submitting files for upload and unzip.
>>
>> slurmstepd: get_exit_code task 0 died by signal
>>
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>
>
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>
>
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Re: [galaxy-dev] Galaxy slurm error

[Hoover , David (NIH/CIT) [E]]

I would guess something about the slurm job exceeded some allocated resource 
(memory, cpu, time) and slurm killed the job.

David Hoover
HPC @ NIH

> On Jun 15, 2017, at 11:28 AM, Nate Coraor  wrote:
> 
> Hi Evan,
> 
> Are there any other details logged for this job?
> 
> --nate
> 
> On Thu, Jun 15, 2017 at 9:20 AM, evan clark  > wrote:
> Has anyone ever encountered an error such as this when running galaxy with 
> slurm and submitting files for upload and unzip.
> 
> slurmstepd: get_exit_code task 0 died by signal
> 
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Re: [galaxy-dev] drmaa job status

[Hendrickson, Curtis (Campus)]

Matthias, 

We have had this problem on our SGE based installation for years. We referred 
to it as the "green screen of death" - as it would allow a biologist to 
continue analysis using output that was partial, at best, often resulting in 
seemingly successful completion of the entire analysis, but completely bogus 
results (say, cuffdiff killed half way through the genome, but it's green in 
galaxy, so no transcripts on the smaller chromosomes, but no error, either).  

We ended up implementing an external reaper that detected these killed jobs 
from SGE, and notified the user and galaxy post-hoc. It was not a very 
satisfactory solution. We are currently moving to SLURM for other reasons and 
hope the problem will not be present there. 

Regards, 
Curtis


-Original Message-
From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Matthias Bernt
Sent: Thursday, June 15, 2017 9:27 AM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] drmaa job status

Dear list,

I have two question for all DRMAA users. Here is the first one.

I was checking how our queuing system (univa GridEngine) and Galaxy react if 
jobs are submitted that exceed run time or memory limits.

I found out that the python drmaa library cannot query the job status after the 
job is finished (for both successful and unsuccessful jobs).

In lib/galaxy/jobs/runners/drmaa.py the call gives an exception
 self.ds.job_status( external_job_id )

Is this always the case? Or might this be a problem with our GridEngine?

I have attached some code for testing. Here the first call to
s.jobStatus(jobid) works, but the second after s.wait(...) doesn't.
But I get "drmaa.errors.InvalidJobException: code 18: The job specified by the 
'jobid' does not exist."

The same error pops up in the Galaxy logs. The consequence is that jobs that 
reached the limits are shown as completed successfully in Galaxy.

Interestingly, quite a bit of information can be obtained from the return value 
of s.wait. I was wondering if this can be used to differentiate successful from 
failed jobs. In particular hasExited, hasSignal, and terminateSignal are 
different in the two cases.

Cheers,
Matthias

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Re: [galaxy-dev] Galaxy slurm error

[Nate Coraor]

Hi Evan,

Are there any other details logged for this job?

--nate

On Thu, Jun 15, 2017 at 9:20 AM, evan clark  wrote:

> Has anyone ever encountered an error such as this when running galaxy with
> slurm and submitting files for upload and unzip.
>
> slurmstepd: get_exit_code task 0 died by signal
>
> ___
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Re: [galaxy-dev] drmaa job status

[Nate Coraor]

Hi Matthias,

I can't speak for GridEngine's specific behavior because I haven't used it
in a long time, but it's not surprising that jobs "disappear" as soon as
they've exited. Unfortunately, Galaxy uses periodic polling rather than
waiting on completion. We'd need to create a thread-per-submitted job
unless you can still get job exit details by looping over jobs with a
timeout wait.

You can gain some control over how Galaxy handles InvalidJobException
exceptions with drmaa job runner plugin params, see here:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L9

However, if normally finished jobs also result in InvalidJobException, that
probably won't help. Alternatively, you could create a DRMAAJobRunner
subclass for GridEngine like we've done for Slurm that does some digging to
learn more about terminal jobs.

--nate

On Thu, Jun 15, 2017 at 10:27 AM, Matthias Bernt  wrote:

> Dear list,
>
> I have two question for all DRMAA users. Here is the first one.
>
> I was checking how our queuing system (univa GridEngine) and Galaxy react
> if jobs are submitted that exceed run time or memory limits.
>
> I found out that the python drmaa library cannot query the job status
> after the job is finished (for both successful and unsuccessful jobs).
>
> In lib/galaxy/jobs/runners/drmaa.py the call gives an exception
> self.ds.job_status( external_job_id )
>
> Is this always the case? Or might this be a problem with our GridEngine?
>
> I have attached some code for testing. Here the first call to
> s.jobStatus(jobid) works, but the second after s.wait(...) doesn't.
> But I get "drmaa.errors.InvalidJobException: code 18: The job specified
> by the 'jobid' does not exist."
>
> The same error pops up in the Galaxy logs. The consequence is that jobs
> that reached the limits are shown as completed successfully in Galaxy.
>
> Interestingly, quite a bit of information can be obtained from the return
> value of s.wait. I was wondering if this can be used to differentiate
> successful from failed jobs. In particular hasExited, hasSignal, and
> terminateSignal are different in the two cases.
>
> Cheers,
> Matthias
>
>
> ___
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> and other Galaxy lists, please use the interface at:
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>
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>   http://galaxyproject.org/search/
>
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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[Nicola Soranzo]

According to the same documentation, you need it only if using the 
|mod_proxy| Apache module with HTTP transport, but I'm using nginx, not 
Apache, so I'm not the best person to ask.


Cheers,
Nicola

On 15/06/17 15:55, Fernandez Edgar wrote:


Thanks Nicola for the comfirmation.

Would you mind explaining a little more:

ProxyPass / http://127.0.0.1:8080/

Should I add this too?

*Edgar Fernandez*

System Administrator (Linux)

Technologies de l'Information*//*

*/Université de Montréal/*

*//*

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : *1-514-343-6111 poste 16568//*

*From:*Nicola Soranzo [mailto:nicola.sora...@gmail.com] *On Behalf Of 
*Nicola Soranzo

*Sent:* June 15, 2017 10:44 AM
*To:* SAPET, Frederic ; Fernandez Edgar 
; galaxy-...@bx.psu.edu
*Subject:* Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught 
error.


Hi Edgar, Frederic,
if you are using Apache as proxy for your Galaxy server, then you 
should probably add


|AllowEncodedSlashes NoDecode|


to your Apache config, see 
https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls


Cheers,
Nicola

On 15/06/17 15:35, SAPET, Frederic wrote:

Hi

Same for me.

But It looks like to be related with tools installed via the
toolshed (Ie : bedtools, emboss, blast+ suite…).

My own tools seem to be ok.

Just like you Edgar, nothing in the log…

Fred

*De :*galaxy-dev
[mailto:galaxy-dev-boun...@lists.galaxyproject.org] *De la part
de* Fernandez Edgar
*Envoyé :* mercredi 14 juin 2017 17:11
*À :* galaxy-...@bx.psu.edu 
*Objet :* [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.

It starts properly and I installed some tools.

But when I try to test any tools I get and “Uncaught error” (see
picture).

I can’t find anywhere in the logs what is happening.

Any ideas?

Regards,

*Edgar Fernandez*

System Administrator (Linux)

Technologies de l'Information

*/Université de Montréal/*

*//*

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : *1-514-343-6111 poste 16568*




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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[Nicola Soranzo]

Hi Fred,

It was already needed for data manager tools in 17.01, it seems it's 
needed for all tools installed from the ToolShed since 17.05, but I use 
nginx, not Apache.


Cheers,
Nicola

On 15/06/17 15:57, SAPET, Frederic wrote:


Hello,

Thank you as well,

Is that a new behavior with 17.05 ?  I use the Apache proxy since a 
while without any problem, with previous versions of Galaxy.


Regards,

Fred

*De :*Nicola Soranzo [mailto:nicola.sora...@gmail.com] *De la part de* 
Nicola Soranzo

*Envoyé :* jeudi 15 juin 2017 16:44
*À :* SAPET, Frederic ; Fernandez Edgar 
; galaxy-...@bx.psu.edu

*Objet :* Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Edgar, Frederic,
if you are using Apache as proxy for your Galaxy server, then you 
should probably add


|AllowEncodedSlashes NoDecode|


to your Apache config, see 
https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls


Cheers,
Nicola

On 15/06/17 15:35, SAPET, Frederic wrote:

Hi

Same for me.

But It looks like to be related with tools installed via the
toolshed (Ie : bedtools, emboss, blast+ suite…).

My own tools seem to be ok.

Just like you Edgar, nothing in the log…

Fred

*De :*galaxy-dev
[mailto:galaxy-dev-boun...@lists.galaxyproject.org] *De la part
de* Fernandez Edgar
*Envoyé :* mercredi 14 juin 2017 17:11
*À :* galaxy-...@bx.psu.edu 
*Objet :* [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.

It starts properly and I installed some tools.

But when I try to test any tools I get and “Uncaught error” (see
picture).

I can’t find anywhere in the logs what is happening.

Any ideas?

Regards,

*Edgar Fernandez*

System Administrator (Linux)

Technologies de l'Information

*/Université de Montréal/*

*//*

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : *1-514-343-6111 poste 16568*




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   http://galaxyproject.org/search/



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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[Fernandez Edgar]

Thanks Nicola for the comfirmation.

Would you mind explaining a little more:

ProxyPass / http://127.0.0.1:8080/
Should I add this too?

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568

From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola 
Soranzo
Sent: June 15, 2017 10:44 AM
To: SAPET, Frederic ; Fernandez Edgar 
; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Edgar, Frederic,
if you are using Apache as proxy for your Galaxy server, then you should 
probably add

AllowEncodedSlashes NoDecode

to your Apache config, see 
https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls

Cheers,
Nicola

On 15/06/17 15:35, SAPET, Frederic wrote:
Hi

Same for me.
But It looks like to be related with tools installed via the toolshed (Ie : 
bedtools, emboss, blast+ suite...).
My own tools seem to be ok.

Just like you Edgar, nothing in the log...

Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de Fernandez Edgar
Envoyé : mercredi 14 juin 2017 17:11
À : galaxy-...@bx.psu.edu
Objet : [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.
It starts properly and I installed some tools.
But when I try to test any tools I get and "Uncaught error" (see picture).

I can't find anywhere in the logs what is happening.

Any ideas?

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568





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To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/

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Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[SAPET, Frederic]

Hello,

Thank you as well,

Is that a new behavior with 17.05 ?  I use the Apache proxy since a while 
without any problem, with previous versions of Galaxy.

Regards,

Fred


De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola 
Soranzo
Envoyé : jeudi 15 juin 2017 16:44
À : SAPET, Frederic ; Fernandez Edgar 
; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Edgar, Frederic,
if you are using Apache as proxy for your Galaxy server, then you should 
probably add

AllowEncodedSlashes NoDecode

to your Apache config, see 
https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls

Cheers,
Nicola

On 15/06/17 15:35, SAPET, Frederic wrote:
Hi

Same for me.
But It looks like to be related with tools installed via the toolshed (Ie : 
bedtools, emboss, blast+ suite...).
My own tools seem to be ok.

Just like you Edgar, nothing in the log...

Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de Fernandez Edgar
Envoyé : mercredi 14 juin 2017 17:11
À : galaxy-...@bx.psu.edu
Objet : [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.
It starts properly and I installed some tools.
But when I try to test any tools I get and "Uncaught error" (see picture).

I can't find anywhere in the logs what is happening.

Any ideas?

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568





___

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in your mail client.  To manage your subscriptions to this

and other Galaxy lists, please use the interface at:

  https://lists.galaxyproject.org/



To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/

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Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[SAPET, Frederic]

Hello,

Nice !
Thank you for the help.

Regards,

Fred

De : Fernandez Edgar [mailto:edgar.fernan...@umontreal.ca]
Envoyé : jeudi 15 juin 2017 16:41
À : SAPET, Frederic ; galaxy-...@bx.psu.edu
Objet : RE: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hello Frederic,

I actually just fixed the problem not 5 minutes ago...
In your file: /etc/httpd/vhosts.d/galaxy_prod.conf
Add the following line: AllowEncodedSlashes NoDecode

Please let me know what you think...

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568

From: SAPET, Frederic [mailto:frederic.sa...@biogemma.com]
Sent: June 15, 2017 10:36 AM
To: Fernandez Edgar 
mailto:edgar.fernan...@umontreal.ca>>; 
galaxy-...@bx.psu.edu
Subject: RE: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi

Same for me.
But It looks like to be related with tools installed via the toolshed (Ie : 
bedtools, emboss, blast+ suite...).
My own tools seem to be ok.

Just like you Edgar, nothing in the log...

Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de Fernandez Edgar
Envoyé : mercredi 14 juin 2017 17:11
À : galaxy-...@bx.psu.edu
Objet : [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.
It starts properly and I installed some tools.
But when I try to test any tools I get and "Uncaught error" (see picture).

I can't find anywhere in the logs what is happening.

Any ideas?

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568

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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[Nicola Soranzo]

Hi Edgar, Frederic,
if you are using Apache as proxy for your Galaxy server, then you should 
probably add


|AllowEncodedSlashes NoDecode|


to your Apache config, see 
https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls


Cheers,
Nicola

On 15/06/17 15:35, SAPET, Frederic wrote:


Hi

Same for me.

But It looks like to be related with tools installed via the toolshed 
(Ie : bedtools, emboss, blast+ suite…).


My own tools seem to be ok.

Just like you Edgar, nothing in the log…

Fred

*De :*galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] 
*De la part de* Fernandez Edgar

*Envoyé :* mercredi 14 juin 2017 17:11
*À :* galaxy-...@bx.psu.edu
*Objet :* [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.

It starts properly and I installed some tools.

But when I try to test any tools I get and “Uncaught error” (see picture).

I can’t find anywhere in the logs what is happening.

Any ideas?

Regards,

*Edgar Fernandez*

System Administrator (Linux)

Technologies de l'Information*//*

*/Université de Montréal/*

*//*

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : *1-514-343-6111 poste 16568//*



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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[Fernandez Edgar]

Hello Frederic,

I actually just fixed the problem not 5 minutes ago...
In your file: /etc/httpd/vhosts.d/galaxy_prod.conf
Add the following line: AllowEncodedSlashes NoDecode

Please let me know what you think...

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568

From: SAPET, Frederic [mailto:frederic.sa...@biogemma.com]
Sent: June 15, 2017 10:36 AM
To: Fernandez Edgar ; galaxy-...@bx.psu.edu
Subject: RE: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi

Same for me.
But It looks like to be related with tools installed via the toolshed (Ie : 
bedtools, emboss, blast+ suite...).
My own tools seem to be ok.

Just like you Edgar, nothing in the log...

Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de Fernandez Edgar
Envoyé : mercredi 14 juin 2017 17:11
À : galaxy-...@bx.psu.edu
Objet : [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.
It starts properly and I installed some tools.
But when I try to test any tools I get and "Uncaught error" (see picture).

I can't find anywhere in the logs what is happening.

Any ideas?

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568

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[galaxy-dev] drmaa resubmission

[Matthias Bernt]

Dear list,

I was thinking about implementing the job resubmission feature for drmaa.

I hope that I can simplify the job configuration for our installation 
(and probably others as well) by escalating through different queues (or 
ressource limits). Thereby I hope to reduce the number of special cases 
that I need to take care.


I was wondering if there are others

- who are also interested in this feature and want to join? I would try 
to give this project a head start in the next week.


- that may have started to work on this feature or just started to think 
about it and want to share code/experience


Best,
Matthias
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Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

[SAPET, Frederic]

Hi

Same for me.
But It looks like to be related with tools installed via the toolshed (Ie : 
bedtools, emboss, blast+ suite...).
My own tools seem to be ok.

Just like you Edgar, nothing in the log...

Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de Fernandez Edgar
Envoyé : mercredi 14 juin 2017 17:11
À : galaxy-...@bx.psu.edu
Objet : [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hey Guys,

Hope everyone is doing ok.

I have a small issue with a brand new installation of galaxy-1705.
It starts properly and I installed some tools.
But when I try to test any tools I get and "Uncaught error" (see picture).

I can't find anywhere in the logs what is happening.

Any ideas?

Regards,

Edgar Fernandez
System Administrator (Linux)
Technologies de l'Information
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
*  Bur. : 1-514-343-6111 poste 16568

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[galaxy-dev] drmaa job status

[Matthias Bernt]

Dear list,

I have two question for all DRMAA users. Here is the first one.

I was checking how our queuing system (univa GridEngine) and Galaxy 
react if jobs are submitted that exceed run time or memory limits.


I found out that the python drmaa library cannot query the job status 
after the job is finished (for both successful and unsuccessful jobs).


In lib/galaxy/jobs/runners/drmaa.py the call gives an exception
self.ds.job_status( external_job_id )

Is this always the case? Or might this be a problem with our GridEngine?

I have attached some code for testing. Here the first call to 
s.jobStatus(jobid) works, but the second after s.wait(...) doesn't.
But I get "drmaa.errors.InvalidJobException: code 18: The job specified 
by the 'jobid' does not exist."


The same error pops up in the Galaxy logs. The consequence is that jobs 
that reached the limits are shown as completed successfully in Galaxy.


Interestingly, quite a bit of information can be obtained from the 
return value of s.wait. I was wondering if this can be used to 
differentiate successful from failed jobs. In particular hasExited, 
hasSignal, and terminateSignal are different in the two cases.


Cheers,
Matthias

#!/usr/bin/env python

from __future__ import print_function
import drmaa
import os


def main():
   """Submit a job.
   Note, need file called sleeper.sh in current directory.
   """
   with drmaa.Session() as s:
   print('Creating job template')
   jt = s.createJobTemplate()
   
   jt.jobName = "foo"
   jt.workingDirectory = "/home/songalax/"
   jt.remoteCommand = '/home/songalax/sleeper.sh'
   jt.args = ['30','Simon_says']
   jt.joinFiles=True
   jt.nativeSpecification = "-l h_rt=10 -l h_vmem=1G -pe smp 2 -w n"
#
   jobid = s.runJob(jt)
   print('Your job has been submitted with id ' + jobid)

   decodestatus = {drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
drmaa.JobState.RUNNING: 'job is running',
drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
drmaa.JobState.DONE: 'job finished normally',
drmaa.JobState.FAILED: 'job finished, but failed'}
   print(decodestatus[s.jobStatus(jobid)])

   retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER)
   print('Job: {0} finished with status {1}'.format(retval.jobId, retval.hasExited))
   print("exitStatus {0}\nhasCoreDump {1}\nhasExited {2}\nhasSignal {3}\njobId {4}\nresourceUsage {5}\nterminatedSignal {6}wasAborted {7}\n".format(retval.exitStatus, retval.hasCoreDump, retval.hasExited, retval.hasSignal, retval.jobId, retval.resourceUsage, retval.terminatedSignal, retval.wasAborted))
   print(decodestatus[s.jobStatus(jobid)])


   print('Cleaning up')
   s.deleteJobTemplate(jt)

if __name__=='__main__':
 main() 


sleeper.sh
Description: application/shellscript
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[galaxy-dev] Galaxy slurm error

[evan clark]

Has anyone ever encountered an error such as this when running galaxy 
with slurm and submitting files for upload and unzip.


slurmstepd: get_exit_code task 0 died by signal

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Re: [galaxy-dev] Singularity Container forks ?

[Nikos Nikoloutsakos]

Hi,

It's seems like you got me ! yey ! :D  I was already working on my fork 
for singularity ,
since we don't need any sudo rights for the galaxy user "setup manually 
by the admin and the paths hard-coded for each tool "


I will test it out and let you know !

Best regards from Greece,
Nikos



On 14/06/2017 07:46 μμ, John Chilton wrote:
Sorry for the late response - but earlier this week Björn Grüning and 
I added various support to Galaxy's development branch for Singularity.


The following pull request added Singularity support in job running 
(https://github.com/galaxyproject/galaxy/pull/4175) - here job 
destinations may describe the paths to Singularity containers. It may 
also work with Singularity 2.3 to just specify Docker containers and 
let it auto-convert - I haven't tested that.


For "best practice" tools - these are tools that have only 
requirements that can resolve via Conda in the best practice Conda 
channels we can do even more - we can build Singularity containers and 
use them automatically - either ahead of time or build on the demand 
during job execution.


Here is the PR that added the on-demand building support for such 
Singularity containers to Galaxy 
https://github.com/galaxyproject/galaxy/pull/4185 and here is the 
tooling PR (https://github.com/galaxyproject/galaxy-lib/pull/64) and 
cached container PR 
(https://github.com/galaxyproject/galaxy/pull/4179) support. If you or 
anyone has a chance to try it out and beta test - let the list know 
how it goes. I plan to talk a little about this work and related 
Docker and Conda work at the GCC so I hope to see you there!


-John



On Tue, May 2, 2017 at 8:51 AM, Nikos Nikoloutsakos 
mailto:nikolou...@admin.grnet.gr>> wrote:


Hello,

Are there any galaxy forks using Singularity images instead of
Docker ?
Is it trivial enough to replace "docker run" with "singularity exec" ?

Thank you,
Nikos


-- 
Nikos Nikoloutsakos

Greek Research and Technology Network (GRNET)
☎ +30 210 7471127 
✉ nikolou...@grnet.gr 
hpc.grnet.gr 

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--
Nikos Nikoloutsakos
Greek Research and Technology Network (GRNET)
☎ +30 210 7471127
✉ nikolou...@grnet.gr
 hpc.grnet.gr

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