Re: [galaxy-dev] Jobs don't run for one user

2016-12-02 Thread Nate Coraor 
Hi Brad,

Absolutely nothing about these jobs in the handler logs?

--nate

On Wed, Nov 30, 2016 at 8:20 PM, Langhorst, Brad  wrote:

>
> On Nov 30, 2016, at 4:27 PM, Nate Coraor  wrote:
>
> Seems on the up 'n up. Can you check the `handler` column of the job table
> in the database for the jobs in question?
>
>
>id   |create_time |  state  | handler  |
>  537202 | 2016-11-30 05:49:35.363694 | new | handler0 |
>  537201 | 2016-11-30 05:40:08.343855 | new | handler0 |
>  537200 | 2016-11-30 05:39:20.394128 | new | handler1 |
>  537199 | 2016-11-30 05:38:03.913992 | new | handler0 |
>
>
> So hander0 and handler1
>
> Brad
>
>
> On Wed, Nov 30, 2016 at 4:14 PM, Langhorst, Brad 
> wrote:
>
>> nope -
>> I limit local jobs to 8, but no jobs go to that destination
>>
>> 2 handlers, a few jobs that reserve more cores.
>>
>> here’s my job.conf
>>
>> 
>> 
>> 
>> 
>> > load="galaxy.jobs.runners.local:LocalJobRunner"
>> workers="4"/>
>> > load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
>> 
>> /opt/g
>> ridengine/lib/linux-x64/libdrmaa.so
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> > tags="rockscluster">
>> True
>> 
>> 
>> > tags="rockscluster,8cores">
>> True
>> -pe smp 8
>> 
>> 
>> > tags="rockscluster,16cores">
>> True
>> -pe smp 16
>> 
>> 
>> > tags="rockscluster,16cores,longrun">
>> True
>> -pe smp 16 -P
>> longrun
>> 
>> 
>> > tags="rockscluster,32cores,longrun">
>> True
>> -pe smp 32 -P
>> longrun
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> > id="local">8
>> 
>> 
>>
>>
>> Brad
>> —
>> Brad Langhorst, Ph.D.
>> Development Scientist
>> New England Biolabs
>>
>>
>>
>>
>> On Nov 30, 2016, at 4:05 PM, Nate Coraor  wrote:
>>
>> Hi Brad,
>>
>> Do you have any kind of strange job mapping going on, or job limits
>> configured?
>>
>> --nate
>>
>> On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad 
>> wrote:
>>
>>> Hi:
>>>
>>> I have one user who’s jobs won’t execute on my local instance.
>>>
>>> The user was mysteriously listed as inactive.
>>> I reactivated and restored the handlers, still jobs are not executing.
>>> The user has plenty of quota (82%  used)
>>>
>>> Anybody have an idea about what might be wrong with this user?
>>>
>>> I have impersonated the user, jobs can be added
>>>
>>> galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to
>>> create dynamic subclass for , None: metaclass conflict:
>>> the metaclass of a derived class must be a (non-strict) subclass of the
>>> metaclasses of all its bases
>>> galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output
>>> (153.865 ms)
>>> galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to
>>> datasets (5.648 ms)
>>> galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool [
>>> toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0] created job
>>> [537201] (384.040 ms)
>>> galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for
>>> tool request: (413.473 ms)
>>> 10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools
>>> HTTP/1.0" 200 - "http://galaxy.neb.com/"; "Mozilla/5.0 (Macintosh; Intel
>>> Mac OS X 10_12_1) AppleWebKit/537.36 (KHTML, like Gecko)
>>> Chrome/54.0.2840.99 Safari/537.36 OPR/41.0.2353.69”
>>>
>>> but they never get scheduled or run.
>>>
>>> Nothing else in the logs after submitting the job.
>>>
>>> They just remain in this state:
>>> This is a new dataset and not all of its data are available yet
>>>
>>> Any ideas?
>>> Brad
>>>
>>> ___
>>> 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:
>>>   https://lists.galaxyproject.org/
>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>>
>
>
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Re: [galaxy-dev] Jobs don't run for one user

2016-11-30 Thread Langhorst, Brad 

On Nov 30, 2016, at 4:27 PM, Nate Coraor 
mailto:n...@bx.psu.edu>> wrote:

Seems on the up 'n up. Can you check the `handler` column of the job table in 
the database for the jobs in question?

   id   |create_time |  state  | handler  |
 537202 | 2016-11-30 05:49:35.363694 | new | handler0 |
 537201 | 2016-11-30 05:40:08.343855 | new | handler0 |
 537200 | 2016-11-30 05:39:20.394128 | new | handler1 |
 537199 | 2016-11-30 05:38:03.913992 | new | handler0 |


So hander0 and handler1

Brad


On Wed, Nov 30, 2016 at 4:14 PM, Langhorst, Brad 
mailto:langho...@neb.com>> wrote:
nope -
I limit local jobs to 8, but no jobs go to that destination

2 handlers, a few jobs that reserve more cores.

here’s my job.conf








/opt/gridengine/lib/linux-x64/libdrmaa.so













True



True
-pe smp 8



True
-pe smp 16



True
-pe smp 16 -P longrun



True
-pe smp 32 -P longrun
















8




Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs




On Nov 30, 2016, at 4:05 PM, Nate Coraor 
mailto:n...@bx.psu.edu>> wrote:

Hi Brad,

Do you have any kind of strange job mapping going on, or job limits configured?

--nate

On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad 
mailto:langho...@neb.com>> wrote:
Hi:

I have one user who’s jobs won’t execute on my local instance.

The user was mysteriously listed as inactive.
I reactivated and restored the handlers, still jobs are not executing.
The user has plenty of quota (82%  used)

Anybody have an idea about what might be wrong with this user?

I have impersonated the user, jobs can be added

galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to create 
dynamic subclass for , None: metaclass conflict: the metaclass 
of a derived class must be a (non-strict) subclass of the metaclasses of all 
its bases
galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output (153.865 ms)
galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to datasets 
(5.648 ms)
galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool 
[toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0]
 created job [537201] (384.040 ms)
galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for tool 
request: (413.473 ms)
10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools HTTP/1.0" 200 - 
"http://galaxy.neb.com/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_1) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99 Safari/537.36 
OPR/41.0.2353.69”

but they never get scheduled or run.

Nothing else in the logs after submitting the job.

They just remain in this state:
This is a new dataset and not all of its data are available yet

Any ideas?
Brad

___
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Re: [galaxy-dev] Jobs don't run for one user

2016-11-30 Thread Nate Coraor 
Seems on the up 'n up. Can you check the `handler` column of the job table
in the database for the jobs in question?

On Wed, Nov 30, 2016 at 4:14 PM, Langhorst, Brad  wrote:

> nope -
> I limit local jobs to 8, but no jobs go to that destination
>
> 2 handlers, a few jobs that reserve more cores.
>
> here’s my job.conf
>
> 
> 
> 
> 
>  load="galaxy.jobs.runners.local:LocalJobRunner"
> workers="4"/>
> 
> 
> /opt/gridengine/lib/linux-x64/
> libdrmaa.so
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>  tags="rockscluster">
> True
> 
> 
>  tags="rockscluster,8cores">
> True
> -pe smp 8
> 
> 
>  tags="rockscluster,16cores">
> True
> -pe smp 16
> 
> 
>  tags="rockscluster,16cores,longrun">
> True
> -pe smp 16 -P
> longrun
> 
> 
>  tags="rockscluster,32cores,longrun">
> True
> -pe smp 32 -P
> longrun
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>  id="local">8
> 
> 
>
>
> Brad
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Nov 30, 2016, at 4:05 PM, Nate Coraor  wrote:
>
> Hi Brad,
>
> Do you have any kind of strange job mapping going on, or job limits
> configured?
>
> --nate
>
> On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad 
> wrote:
>
>> Hi:
>>
>> I have one user who’s jobs won’t execute on my local instance.
>>
>> The user was mysteriously listed as inactive.
>> I reactivated and restored the handlers, still jobs are not executing.
>> The user has plenty of quota (82%  used)
>>
>> Anybody have an idea about what might be wrong with this user?
>>
>> I have impersonated the user, jobs can be added
>>
>> galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to
>> create dynamic subclass for , None: metaclass conflict:
>> the metaclass of a derived class must be a (non-strict) subclass of the
>> metaclasses of all its bases
>> galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output (153.865
>> ms)
>> galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to
>> datasets (5.648 ms)
>> galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool [
>> toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0] created job
>> [537201] (384.040 ms)
>> galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for
>> tool request: (413.473 ms)
>> 10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools HTTP/1.0"
>> 200 - "http://galaxy.neb.com/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
>> 10_12_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99
>> Safari/537.36 OPR/41.0.2353.69”
>>
>> but they never get scheduled or run.
>>
>> Nothing else in the logs after submitting the job.
>>
>> They just remain in this state:
>> This is a new dataset and not all of its data are available yet
>>
>> Any ideas?
>> Brad
>>
>> ___
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
___
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Re: [galaxy-dev] Jobs don't run for one user

2016-11-30 Thread Langhorst, Brad 
nope -
I limit local jobs to 8, but no jobs go to that destination

2 handlers, a few jobs that reserve more cores.

here’s my job.conf








/opt/gridengine/lib/linux-x64/libdrmaa.so













True



True
-pe smp 8



True
-pe smp 16



True
-pe smp 16 -P longrun



True
-pe smp 32 -P longrun
















8




Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs




On Nov 30, 2016, at 4:05 PM, Nate Coraor 
mailto:n...@bx.psu.edu>> wrote:

Hi Brad,

Do you have any kind of strange job mapping going on, or job limits configured?

--nate

On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad 
mailto:langho...@neb.com>> wrote:
Hi:

I have one user who’s jobs won’t execute on my local instance.

The user was mysteriously listed as inactive.
I reactivated and restored the handlers, still jobs are not executing.
The user has plenty of quota (82%  used)

Anybody have an idea about what might be wrong with this user?

I have impersonated the user, jobs can be added

galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to create 
dynamic subclass for , None: metaclass conflict: the metaclass 
of a derived class must be a (non-strict) subclass of the metaclasses of all 
its bases
galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output (153.865 ms)
galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to datasets 
(5.648 ms)
galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool 
[toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0]
 created job [537201] (384.040 ms)
galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for tool 
request: (413.473 ms)
10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools HTTP/1.0" 200 - 
"http://galaxy.neb.com/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_1) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99 Safari/537.36 
OPR/41.0.2353.69”

but they never get scheduled or run.

Nothing else in the logs after submitting the job.

They just remain in this state:
This is a new dataset and not all of its data are available yet

Any ideas?
Brad

___
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in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Jobs don't run for one user

2016-11-30 Thread Nate Coraor 
Hi Brad,

Do you have any kind of strange job mapping going on, or job limits
configured?

--nate

On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad  wrote:

> Hi:
>
> I have one user who’s jobs won’t execute on my local instance.
>
> The user was mysteriously listed as inactive.
> I reactivated and restored the handlers, still jobs are not executing.
> The user has plenty of quota (82%  used)
>
> Anybody have an idea about what might be wrong with this user?
>
> I have impersonated the user, jobs can be added
>
> galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to
> create dynamic subclass for , None: metaclass conflict:
> the metaclass of a derived class must be a (non-strict) subclass of the
> metaclasses of all its bases
> galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output (153.865
> ms)
> galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to
> datasets (5.648 ms)
> galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool [
> toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0] created job
> [537201] (384.040 ms)
> galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for
> tool request: (413.473 ms)
> 10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools HTTP/1.0"
> 200 - "http://galaxy.neb.com/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
> 10_12_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99
> Safari/537.36 OPR/41.0.2353.69”
>
> but they never get scheduled or run.
>
> Nothing else in the logs after submitting the job.
>
> They just remain in this state:
> This is a new dataset and not all of its data are available yet
>
> Any ideas?
> Brad
>
> ___
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
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[galaxy-dev] Jobs don't run for one user

2016-11-29 Thread Langhorst, Brad 
Hi:

I have one user who’s jobs won’t execute on my local instance.

The user was mysteriously listed as inactive.
I reactivated and restored the handlers, still jobs are not executing.
The user has plenty of quota (82%  used)

Anybody have an idea about what might be wrong with this user?

I have impersonated the user, jobs can be added

galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to create 
dynamic subclass for , None: metaclass conflict: the metaclass 
of a derived class must be a (non-strict) subclass of the metaclasses of all 
its bases
galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output (153.865 ms)
galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to datasets 
(5.648 ms)
galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool 
[toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0]
 created job [537201] (384.040 ms)
galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for tool 
request: (413.473 ms)
10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools HTTP/1.0" 200 - 
"http://galaxy.neb.com/"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_1) 
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99 Safari/537.36 
OPR/41.0.2353.69”

but they never get scheduled or run.

Nothing else in the logs after submitting the job.

They just remain in this state:
This is a new dataset and not all of its data are available yet

Any ideas?
Brad
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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