Re: [galaxy-dev] galaxy sge Job output not returned from cluster

[ambarish biswas]

Thanks Chrony,
but do u know a fix, for this problem. Like what configuration
change I should make and where?

With Regards,

Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866




On Wed, Jul 27, 2011 at 4:24 AM, Chorny, Ilya  wrote:

>  Those changes to permission in __init__.py  are only necessary of running
> the job as the actual logged in user and not as the galaxy user. There are
> additional changes that are needed to get actual user name integration to
> work with SGE. ** **
>
> ** **
>
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *ambarish biswas
> *Sent:* Monday, July 25, 2011 11:12 PM
> *To:* galaxy-dev@lists.bx.psu.edu"
> *Subject:* [galaxy-dev] galaxy sge Job output not returned from cluster***
> *
>
> ** **
>
> Hi All,
>
>   I'm getting this error "*Job output not returned from cluster*"*
> ***
>
> ** **
>
> ** **
>
> galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:00:59,552 (4915/17234) state
> change: job is queued and active
>
> galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:03,552 (4915/17234) state
> change: job is running
>
> 139.80.26.223 - - [26/Jul/2011:17:01:03 +1300] "POST
> /galaxy/root/history_item_updates HTTP/1.1" 200 - "
> http://bioanalysis.otago.ac.nz/galaxy/history"; "Mozilla/5.0 (X11; U; Linux
> x86_64; en-US) AppleWebKit/534.16 (KHTML, like Gecko) Chrome/10.0.648.205
> Safari/534.16"
>
> galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 (4915/17234) state
> change: job finished, but failed
>
> galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 Job output not
> returned from cluster
>
> galaxy.jobs DEBUG 2011-07-26 17:01:04,762 job 4915 ended
>
> ** **
>
> ** **
>
> I tried changing permission in __init__.py as mentioned in
>
> http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01613.html
>
> but no luck.
>
> ** **
>
>
> I saw Erick has the same problem, and looks like he got a fix as mentioned
> 
>
>
> http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879580.html
> 
>
> ** **
>
> but no detail of what should be done.
>
> ** **
>
> Thanks in advance.
>
> ** **
>
> ** **
>
>
> With Regards,
> 
> Ambarish Biswas,
> University of Otago
> Department of Biochemistry,
> Dunedin, New Zealand,
> Tel: +64(22)0855647
> Fax: +64(0)3 479 7866
>
> ** **
>
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Re: [galaxy-dev] TEMP variable in cluster install

[Shantanu Pavgi]

On Jul 21, 2011, at 6:24 PM, Shantanu Pavgi wrote:

> 
> We have configured galaxy to work with our SGE cluster using drmaa job runner 
> interface. We are using 'unified method' for this install and 
> both TEMP environment variable and new_file_path in universe_wsgi.ini file 
> have been configured correctly. However, we are seeing some errors where 
> local /tmp space on compute nodes is being referenced by the galaxy tools. 
> Specifically we saw it mentioned in error messages from following tools: 
> * bwa_wrapper and upload tools: 'No space left on device: /tmp...' 
> * sam_to_bam tool: 'Error sorting alignments from /tmp/filename..'
> 
> Shouldn't it be referencing TEMP environment variable or new_file_path 
> configuration value? Is it getting overridden by TMP or TMPDIR variables in 
> python wrapper code? Has anyone else experienced similar issue? 
> 
> 

Further debugging showed that there are two more temporary directory related 
environment variables - TMP and TMPDIR which were pointing local /tmp location 
on compute nodes. We tried to set these variables in our shell environment 
(drmaa URL uses -V to export current shell env) however SGE overwrote TMP and 
TMPDIR before actual job execution. The TEMP variable remained unmodified by 
SGE scheduler.

The galaxy tools seemed to be using temporary directory space pointed by TMP 
and TMPDIR and hence we saw local /tmp related errors mentioned in my earlier 
post. 

We have temporarily fixed this problem by hard coding TEMP, TMP and TMPDIR 
values in job template files - 
1. lib/galaxy/jobs/runners/drmaa.py  
2. lib/galaxy/jobs/runners/sge.py  

This will affect all jobs submitted through the galaxy. It will be helpful to 
know how it can be handled in the tool wrapper scripts. It seems like it can be 
handled in the tool wrapper scripts using directory prefix while creating the 
tempfile ( http://docs.python.org/library/tempfile.html ). Any 
thoughts/comments?  Are there any other SGE users having similar issue? 

Also, there is a similar thread started today regarding usage of temporary 
directory location in tool wrapper scripts. It would be helpful to know how 
galaxy or tool wrappers are using the temporary directory and ways to configure 
it. 

--
Thanks,
Shantanu. 
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Re: [galaxy-dev] GALAXY-GBROWSE : setting up incoming/outcomming functionalities (sharing data)

[Jennifer Jackson]

Hello Ben,

Were you able to get the set up working? This is an older thread, and 
maybe this was resolved already, but I wanted to double check that you 
got help if still needed.


Just in case you didn't see it yet, our wiki has been moved, and this is 
the location of the set-up config for the Galaxy side:

http://wiki.g2.bx.psu.edu/Admin/FAQ#Connect_an_external_datasource_to_Galaxy

Take care,

Jen
Galaxy team

On 6/28/11 5:16 AM, BM wrote:

Hi,
I am trying to set up the galaxy outgoing and incoming funtionalities
in GBROWSE and GALAXY to send data between these applications.

I have local instances of GALAXY and GBROWSE and I wonder how should I
configure these.

How this should look in the GBROWSE user interface (in the "share this
track" section) ?
How this should look in the GALAXY user interface ?

My GBROWSE version : 2.38 and my GALAXY version :
galaxy-galaxy-central-fd3391bcd903
Here the conf I set up :

--MY GALAXY SETTINGS--
I saw in a previous topic posted by nicki
(http://gmod.827538.n3.nabble.com/Send-data-to-GBrowse-td2446346.html)
that some files must be edtited :

1. universe_wsgi.ini
I edited it as follows :
GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
gbrowse_display_sites =
wormbase,tair,modencode_worm,modencode_fly,yeast_sgd,perso

2. tool-data/shared/gbrowse/gbrowse_build_sites.txt
I edited it as follows :
#perso
perso
http://my_host.com/Gbrowse/cgi-bin/gbrowse_details/specie  specie

3.  datatypes_conf.xml
I edited it as follows :
 
 
 
 

I have got the following files in "display_applications/gbrowse/" :
gbrowse_gff.xml
gbrowse_interval_as_bed.xml
gbrowse_wig.xml

--MY GBROWSE SETTINGS--
I have edited the general section of
"/var/www/GBROWSE/conf/specie.conf" according to the documentation
http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options:

[GENERAL]
galaxy outgoing = http:/my_host.com:8080/tool_runner?tool_id=ncbi_blastn_wrapper
galaxy incoming = https://my_host.com/Gbrowse/cgi-bin/gbgff
-
First, I would like to look for the outgoing functionality from
GBROWSE to GALAXY.
Then,  the incoming functionnality : from GALAXY to GBROWSE

I hope someone can help me, I'm new to GALAXY.

Thanks,
greetings

Ben
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--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
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Re: [galaxy-dev] Cluster setup - shared temporary directory

[Luobin Yang]

I benchmarked MrBayes 3.1.2 program on my cluster for two cases:

1. use local /tmp for temporary files
2. use the network shared /home/galaxy/galaxy-dist/database/tmp

MrBayes is about 10 times slower for case 2 than for case 1.  What I did was
to set the network shared folder as the default but in the MrBayes wrapper,
I changed the environment variable TEMP to be a local folder.

Luobin

On Tue, Jul 26, 2011 at 10:39 AM, Peter Cock wrote:

> On Tue, Jul 26, 2011 at 5:16 PM, Duddy, John  wrote:
> > I can give you a very good example - if you are doing alignment and for
> some
> > reason need to convert the input file before operating on them, such that
> you
> > need a complete copy, /tmp may not have enough room. I have had this
> happen
> > to me running lots of instances of an aligner, temporarily using 100G+ of
> temp space.
> >
> > I don't see the need to have a "shared" temp space, but I do see the need
> to
> >  be able to tell the tools where you want them to put temp files.
>
> So in your setup, the cluster nodes are not likely to have 100G+ on /tmp
> (i.e.
> the local hard drive of the node), so you want them to use a temp folder on
> the
> cluster shared storage?
>
> I think needs will differ between tools - in some cases you really want
> a fast local drive for temp files, and putting them on a network drive
> will just kill performance. Using /tmp seems a safe default.
>
> Is there any guidance for tool authors on where to put temp files, and
> how to access any related Galaxy settings? There is nothing currently
> listed here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
>
> Peter
> ___
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>
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[galaxy-dev] DRMAA options for SGE

[Ka Ming Nip]

Hi,

I am trying to configure the proper memory resource requests for my Galaxy tool.
This is what I have under the tool_runners section of universe_wsgi.ini

[galaxy:tool_runners]
...
mytoolname = drmaa://-l mem_free=1G -l mem_token=1G -l h_vmem=1G/
...

When I execute my tool on Galaxy, I get the error below in the shell that I ran 
"sh run.sh":

galaxy.jobs.runners.drmaa ERROR 2011-07-26 09:54:01,930 Uncaught exception 
queueing job
Traceback (most recent call last):
  File "/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", 
line 112, in run_next
self.queue_job( obj )
  File "/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", 
line 177, in queue_job
job_id = self.ds.runJob(jt)
  File 
"/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/__init__.py",
 line 331, in runJob
  File 
"/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/helpers.py",
 line 213, in c
  File 
"/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/errors.py", 
line 90, in error_check
DeniedByDrmException: code 17: error: no suitable queues

All the flags I used work with qsub commands on the SGE cluster I use. The tool 
runs
when I comment out the line in universe_wsgi.ini.

Thanks,
Ka Ming
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Re: [galaxy-dev] Invalid job runner: drmaa

[Ka Ming Nip]

Hi,

You may want to check whether your env variables are exported properly. For 
example,

$ env
DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0

Hope that helps!

Ka Ming


From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
On Behalf Of remy d1 [remy...@gmail.com]
Sent: July 26, 2011 7:44 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Invalid job runner: drmaa

Hi,

I try to configure Galaxy with SGE. It works one time yesterday but now I have 
the following message all the time :

galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 
118 to drmaa runner
galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) 
Invalid job runner: drmaa


[ An error occurred running this job: Unable to run job due to a 
misconfiguration of the Galaxy job running system. Please contact a site 
administrator. ] On the web page.

Here is my universe_wsgi.ini file :


[server:main]
port = 8000
host = X.X.X.X
use_threadpool = True
[filter:proxy-prefix]
prefix = /galaxy
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
filter-with = proxy-prefix
database_connection = 
mysql://galaxy:xx@localhost:3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock
file_path = database/files
new_file_path = database/tmp
job_working_directory = database/users_space/user_galaxy
cluster_files_directory = database/users_space/user_galaxy
use_nglims = False
nglims_config_file = tool-data/nglims.yaml
static_enabled = True
static_cache_time = 360
static_dir = %(here)s/static/
static_images_dir = %(here)s/static/images
static_favicon_dir = %(here)s/static/favicon.ico
static_scripts_dir = %(here)s/static/scripts/
static_style_dir = %(here)s/static/june_2007_style/blue
log_events = True
log_actions = True
debug = True
use_interactive = True
library_import_dir = /home/galaxy/galaxy-dist/tmpdir
user_library_import_dir = True
allow_library_path_paste = True
admin_users = me@...
enable_pages = True
enable_api = True
set_metadata_externally = True
retry_metadata_internally = True
outputs_to_working_directory = True
start_job_runners = drmaa
default_cluster_job_runner = drmaa:///
[galaxy:tool_runners]
biomart = local:///
encode_db1 = local:///
hbvar = local:///
microbial_import1 = local:///
ucsc_table_direct1 = local:///
ucsc_table_direct_archaea1 = local:///
ucsc_table_direct_test1 = local:///
upload1 = local:///
[galaxy_amqp]


I checked many things, but it did not change anything...

Any help would gracefull.

Regards.

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Re: [galaxy-dev] Getting a list of workflows a user can run via the API

[Dannon Baker]

Not currently, though they should be.  I'll add this shortly.

-Dannon

On Jul 25, 2011, at 6:22 PM, Duddy, John wrote:

> I am doing an integration with Galaxy, and part of what I need to do is 
> trigger workflows. To do that, I need to list them.
>  
> I can do this if the user owns the workflows, but the API does not return 
> workflows that have been shared with the user.
>  
> Is there a way via the API to discover the sharing relationships? Or will I 
> need to add this to the API?
>  
> Thanks!
>  
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com
>  
> ___
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> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

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Re: [galaxy-dev] Cluster setup - shared temporary directory

[Peter Cock]

On Tue, Jul 26, 2011 at 5:16 PM, Duddy, John  wrote:
> I can give you a very good example - if you are doing alignment and for some
> reason need to convert the input file before operating on them, such that you
> need a complete copy, /tmp may not have enough room. I have had this happen
> to me running lots of instances of an aligner, temporarily using 100G+ of 
> temp space.
>
> I don't see the need to have a "shared" temp space, but I do see the need to
>  be able to tell the tools where you want them to put temp files.

So in your setup, the cluster nodes are not likely to have 100G+ on /tmp (i.e.
the local hard drive of the node), so you want them to use a temp folder on the
cluster shared storage?

I think needs will differ between tools - in some cases you really want
a fast local drive for temp files, and putting them on a network drive
will just kill performance. Using /tmp seems a safe default.

Is there any guidance for tool authors on where to put temp files, and
how to access any related Galaxy settings? There is nothing currently
listed here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

Peter
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Re: [galaxy-dev] galaxy sge Job output not returned from cluster

[Chorny, Ilya]

Those changes to permission in __init__.py  are only necessary of running the 
job as the actual logged in user and not as the galaxy user. There are 
additional changes that are needed to get actual user name integration to work 
with SGE.

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of ambarish biswas
Sent: Monday, July 25, 2011 11:12 PM
To: galaxy-dev@lists.bx.psu.edu"
Subject: [galaxy-dev] galaxy sge Job output not returned from cluster

Hi All,
  I'm getting this error "Job output not returned from cluster"


galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:00:59,552 (4915/17234) state 
change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:03,552 (4915/17234) state 
change: job is running
139.80.26.223 - - [26/Jul/2011:17:01:03 +1300] "POST 
/galaxy/root/history_item_updates HTTP/1.1" 200 - 
"http://bioanalysis.otago.ac.nz/galaxy/history"; "Mozilla/5.0 (X11; U; Linux 
x86_64; en-US) AppleWebKit/534.16 (KHTML, like Gecko) Chrome/10.0.648.205 
Safari/534.16"
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 (4915/17234) state 
change: job finished, but failed
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 Job output not returned 
from cluster
galaxy.jobs DEBUG 2011-07-26 17:01:04,762 job 4915 ended


I tried changing permission in __init__.py as mentioned in
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01613.html

but no luck.


I saw Erick has the same problem, and looks like he got a fix as mentioned
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879580.html

but no detail of what should be done.

Thanks in advance.



With Regards,

Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866

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Re: [galaxy-dev] Cluster setup - shared temporary directory

[Duddy, John]

I can give you a very good example - if you are doing alignment and for some 
reason need to convert the input file before operating on them, such that you 
need a complete copy, /tmp may not have enough room. I have had this happen to 
me running lots of instances of an aligner, temporarily using 100G+ of temp 
space.

I don't see the need to have a "shared" temp space, but I do see the need to be 
able to tell the tools where you want them to put temp files. 

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock
Sent: Tuesday, July 26, 2011 8:10 AM
To: Galaxy Dev
Subject: [galaxy-dev] Cluster setup - shared temporary directory

Hi all,

I'm reading http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster

Could someone expand a little on this section please:

> Create a shared temporary directory
>
> Some tools make use of temporary files created on the server,
> but accessed on the nodes. For this, you'll need to make a
> directory (galaxy_dist/database/tmp by default) ...

I presume this is talking about the universe_wsgi.ini setting
new_file_path = database/tmp (if so, could that be explicit)?

I would like to know more about this from the tool author point
of view. Could you at least give one example of a tool that uses
this temporary folder? As a tool author I am unclear what the
purpose is (and it would be a shock if I accidentally use this
mapped folder instead of the local temp drive of a node).

Thanks,

Peter
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[galaxy-dev] Cluster setup - shared temporary directory

[Peter Cock]

Hi all,

I'm reading http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster

Could someone expand a little on this section please:

> Create a shared temporary directory
>
> Some tools make use of temporary files created on the server,
> but accessed on the nodes. For this, you'll need to make a
> directory (galaxy_dist/database/tmp by default) ...

I presume this is talking about the universe_wsgi.ini setting
new_file_path = database/tmp (if so, could that be explicit)?

I would like to know more about this from the tool author point
of view. Could you at least give one example of a tool that uses
this temporary folder? As a tool author I am unclear what the
purpose is (and it would be a shock if I accidentally use this
mapped folder instead of the local temp drive of a node).

Thanks,

Peter
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[galaxy-dev] Invalid job runner: drmaa

[remy d1]

Hi,

I try to configure Galaxy with SGE. It works one time yesterday but now I
have the following message all the time :

galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa
runner
galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner:
drmaa


[ An error occurred running this job: *Unable to run job due to a
misconfiguration of the Galaxy job running system. Please contact a site
administrator.* ] On the web page.*
*
Here is my universe_wsgi.ini file :


[server:main]
port = 8000
host = X.X.X.X
use_threadpool = True
[filter:proxy-prefix]
prefix = /galaxy
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
filter-with = proxy-prefix
database_connection = mysql://galaxy:xx@localhost
:3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock
file_path = database/files
new_file_path = database/tmp
job_working_directory = database/users_space/user_galaxy
cluster_files_directory = database/users_space/user_galaxy
use_nglims = False
nglims_config_file = tool-data/nglims.yaml
static_enabled = True
static_cache_time = 360
static_dir = %(here)s/static/
static_images_dir = %(here)s/static/images
static_favicon_dir = %(here)s/static/favicon.ico
static_scripts_dir = %(here)s/static/scripts/
static_style_dir = %(here)s/static/june_2007_style/blue
log_events = True
log_actions = True
debug = True
use_interactive = True
library_import_dir = /home/galaxy/galaxy-dist/tmpdir
user_library_import_dir = True
allow_library_path_paste = True
admin_users = me@...
enable_pages = True
enable_api = True
set_metadata_externally = True
retry_metadata_internally = True
outputs_to_working_directory = True
start_job_runners = drmaa
default_cluster_job_runner = drmaa:///
[galaxy:tool_runners]
biomart = local:///
encode_db1 = local:///
hbvar = local:///
microbial_import1 = local:///
ucsc_table_direct1 = local:///
ucsc_table_direct_archaea1 = local:///
ucsc_table_direct_test1 = local:///
upload1 = local:///
[galaxy_amqp]


I checked many things, but it did not change anything...

Any help would gracefull.

Regards.
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