Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham <Iry.Witham@jax.orgmailto:Iry.Witham@jax.org> Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason <MMason@benaroyaresearch.orgmailto:MMason@benaroyaresearch.org> Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham <iry.witham@jax.orgmailto:iry.witham@jax.org>, "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham <Iry.Witham@jax.orgmailto:Iry.Witham@jax.org> Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Okay - I just checked out a clean Galaxy without modifications and I don't see any problems with uploads. So this is likely something to do with your setup - if I had to guess I would guess that your job_conf.xml configuration is somehow incorrect - the job is getting creating but nothing is running it. Can you verify this by looking in the logs? I would imagine you do see lines like:
galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool upload1 created job id 2
for the uploads but nothing like:
galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is: python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py ....
You could also verify this is the problem by doing something other than uploading - maybe a data source tool? I have attached a tool that doesn't require any existing files or external data sources that I use for testing stuff like this - maybe see if it runs?
If no jobs run - can you attach your job_conf.xml and we can try to debug the problem from there.
If other tools run than it is likely not a job related problem - in that case can you answer some questions - Are you using a proxy - if so which one? Can you attach the configuration? Is the upload.xml tool in your tool_conf.xml? Have you made modifications to it?
-John
On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham Iry.Witham@jax.org wrote:
I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason MMason@benaroyaresearch.org Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham iry.witham@jax.org, "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham Iry.Witham@jax.org Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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/
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Hi John,
It looks like it may be related to PBS and Torque. I am currently running torque-4.2.5. I scrambled the pbs-python eggs and it is now running pbs-python 4.3.5. The good thing is I am now getting an attempt to submit to pbs, but all jobs are failing. This is the error:
galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs runner galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination (destination id: pbs:////-l nodes=1:ppn=1,walltime=20:00:00) galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS server for submit failed: 15007: No permission
Iry
On 8/15/14 12:11 PM, "John Chilton" jmchilton@gmail.com wrote:
Okay - I just checked out a clean Galaxy without modifications and I don't see any problems with uploads. So this is likely something to do with your setup - if I had to guess I would guess that your job_conf.xml configuration is somehow incorrect - the job is getting creating but nothing is running it. Can you verify this by looking in the logs? I would imagine you do see lines like:
galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool upload1 created job id 2
for the uploads but nothing like:
galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is: python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py ....
You could also verify this is the problem by doing something other than uploading - maybe a data source tool? I have attached a tool that doesn't require any existing files or external data sources that I use for testing stuff like this - maybe see if it runs?
If no jobs run - can you attach your job_conf.xml and we can try to debug the problem from there.
If other tools run than it is likely not a job related problem - in that case can you answer some questions - Are you using a proxy - if so which one? Can you attach the configuration? Is the upload.xml tool in your tool_conf.xml? Have you made modifications to it?
-John
On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham Iry.Witham@jax.org wrote:
I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason MMason@benaroyaresearch.org Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham iry.witham@jax.org, "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham Iry.Witham@jax.org Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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/
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
I have not seen this before - are you able to submit things as your Galaxy user from the command line? Are their logs on the PBS side that give any more clues?
-John
On Fri, Aug 15, 2014 at 2:01 PM, Iry Witham Iry.Witham@jax.org wrote:
Hi John,
It looks like it may be related to PBS and Torque. I am currentlyrunning torque-4.2.5. I scrambled the pbs-python eggs and it is now running pbs-python 4.3.5. The good thing is I am now getting an attempt to submit to pbs, but all jobs are failing. This is the error:
galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs runner galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination (destination id: pbs:////-l nodes=1:ppn=1,walltime=20:00:00) galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS server for submit failed: 15007: No permission
Iry
On 8/15/14 12:11 PM, "John Chilton" jmchilton@gmail.com wrote:
Okay - I just checked out a clean Galaxy without modifications and I don't see any problems with uploads. So this is likely something to do with your setup - if I had to guess I would guess that your job_conf.xml configuration is somehow incorrect - the job is getting creating but nothing is running it. Can you verify this by looking in the logs? I would imagine you do see lines like:
galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool upload1 created job id 2
for the uploads but nothing like:
galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is: python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py ....
You could also verify this is the problem by doing something other than uploading - maybe a data source tool? I have attached a tool that doesn't require any existing files or external data sources that I use for testing stuff like this - maybe see if it runs?
If no jobs run - can you attach your job_conf.xml and we can try to debug the problem from there.
If other tools run than it is likely not a job related problem - in that case can you answer some questions - Are you using a proxy - if so which one? Can you attach the configuration? Is the upload.xml tool in your tool_conf.xml? Have you made modifications to it?
-John
On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham Iry.Witham@jax.org wrote:
I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason MMason@benaroyaresearch.org Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham iry.witham@jax.org, "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham Iry.Witham@jax.org Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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/
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
Hi John,
I was able to work through this since it was related to pbs on the cluster. However, I am still having issues. This is the error I am getting:
galaxy.tools.genome_index DEBUG 2014-08-18 09:31:56,819 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2014-08-18 09:31:56,825 Starting job handler galaxy.jobs INFO 2014-08-18 09:31:56,825 Handler 'handler1' will load all configured runner plugins galaxy.jobs.runners DEBUG 2014-08-18 09:31:56,829 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2014-08-18 09:31:57,073 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners DEBUG 2014-08-18 09:31:57,104 Starting 3 LWRRunner workers galaxy.jobs.runners.lwr_client.manager INFO 2014-08-18 09:31:57,197 Setting LWR client class to standard, non-caching variant. galaxy.jobs DEBUG 2014-08-18 09:31:57,228 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr' Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/bu ildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 144, in __init__ self.job_manager = manager.JobManager( self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 31, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 583, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py" , line 496, in get_job_runner_plugins module = __import__( module_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs. py", line 32, in <module> raise Exception( egg_message % str( e ) ) Exception:
The 'pbs' runner depends on 'pbs_python' which is not installed or not configured properly. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
Additional errors may follow: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-l inux-x86_64-ucs4.egg/_pbs.so: undefined symbol: log_record
Removing PID file handler1.pid
I am running the following:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> qsub --about HomeDir: /var/spool/torque InstallDir: /usr/local Server: rockhopper BuildDir: /root/torque-4.2.5 BuildUser: root BuildHost: galaxy2 BuildDate: Sat Aug 16 11:17:00 EDT 2014 Version: 4.2.5 Commit: 39f78e588b3a47a6c7bed1004ec7b5d0ccf24288
The handler.pid are being removed.
Thanks, Iry
On 8/18/14 9:16 AM, "John Chilton" jmchilton@gmail.com wrote:
I have not seen this before - are you able to submit things as your Galaxy user from the command line? Are their logs on the PBS side that give any more clues?
-John
On Fri, Aug 15, 2014 at 2:01 PM, Iry Witham Iry.Witham@jax.org wrote:
Hi John,
It looks like it may be related to PBS and Torque. I amcurrently running torque-4.2.5. I scrambled the pbs-python eggs and it is now running pbs-python 4.3.5. The good thing is I am now getting an attempt to submit to pbs, but all jobs are failing. This is the error:
galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs runner galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination (destination id: pbs:////-l nodes=1:ppn=1,walltime=20:00:00) galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS server for submit failed: 15007: No permission
Iry
On 8/15/14 12:11 PM, "John Chilton" jmchilton@gmail.com wrote:
Okay - I just checked out a clean Galaxy without modifications and I don't see any problems with uploads. So this is likely something to do with your setup - if I had to guess I would guess that your job_conf.xml configuration is somehow incorrect - the job is getting creating but nothing is running it. Can you verify this by looking in the logs? I would imagine you do see lines like:
galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool upload1 created job id 2
for the uploads but nothing like:
galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is: python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py ....
You could also verify this is the problem by doing something other than uploading - maybe a data source tool? I have attached a tool that doesn't require any existing files or external data sources that I use for testing stuff like this - maybe see if it runs?
If no jobs run - can you attach your job_conf.xml and we can try to debug the problem from there.
If other tools run than it is likely not a job related problem - in that case can you answer some questions - Are you using a proxy - if so which one? Can you attach the configuration? Is the upload.xml tool in your tool_conf.xml? Have you made modifications to it?
-John
On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham Iry.Witham@jax.org wrote:
I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason MMason@benaroyaresearch.org Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham iry.witham@jax.org, "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham Iry.Witham@jax.org Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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/
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
On Aug 18, 2014, at 9:55 AM, Iry Witham Iry.Witham@jax.org wrote:
Hi John,
I was able to work through this since it was related to pbs on the cluster. However, I am still having issues. This is the error I am getting:
galaxy.tools.genome_index DEBUG 2014-08-18 09:31:56,819 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2014-08-18 09:31:56,825 Starting job handler galaxy.jobs INFO 2014-08-18 09:31:56,825 Handler 'handler1' will load all configured runner plugins galaxy.jobs.runners DEBUG 2014-08-18 09:31:56,829 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2014-08-18 09:31:57,073 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners DEBUG 2014-08-18 09:31:57,104 Starting 3 LWRRunner workers galaxy.jobs.runners.lwr_client.manager INFO 2014-08-18 09:31:57,197 Setting LWR client class to standard, non-caching variant. galaxy.jobs DEBUG 2014-08-18 09:31:57,228 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr' Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/bu ildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 144, in __init__ self.job_manager = manager.JobManager( self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 31, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 583, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py" , line 496, in get_job_runner_plugins module = __import__( module_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs. py", line 32, in <module> raise Exception( egg_message % str( e ) ) Exception:
The 'pbs' runner depends on 'pbs_python' which is not installed or not configured properly. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
Additional errors may follow: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-l inux-x86_64-ucs4.egg/_pbs.so: undefined symbol: log_record
Hi Iry,
It looks like we need to upgrade to pbs_python 4.4.0: https://oss.trac.surfsara.nl/pbs_python/ticket/34
The pbs_python 4.4.0 source is on our eggs server - could you update the version to 4.4.0 in /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs.ini and re-scramble the egg and let us know if this fixes it?
Thanks, --nate
Removing PID file handler1.pid
I am running the following:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> qsub --about HomeDir: /var/spool/torque InstallDir: /usr/local Server: rockhopper BuildDir: /root/torque-4.2.5 BuildUser: root BuildHost: galaxy2 BuildDate: Sat Aug 16 11:17:00 EDT 2014 Version: 4.2.5 Commit: 39f78e588b3a47a6c7bed1004ec7b5d0ccf24288
The handler.pid are being removed.
Thanks, Iry
On 8/18/14 9:16 AM, "John Chilton" jmchilton@gmail.com wrote:
I have not seen this before - are you able to submit things as your Galaxy user from the command line? Are their logs on the PBS side that give any more clues?
-John
On Fri, Aug 15, 2014 at 2:01 PM, Iry Witham Iry.Witham@jax.org wrote:
Hi John,
It looks like it may be related to PBS and Torque. I amcurrently running torque-4.2.5. I scrambled the pbs-python eggs and it is now running pbs-python 4.3.5. The good thing is I am now getting an attempt to submit to pbs, but all jobs are failing. This is the error:
galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs runner galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination (destination id: pbs:////-l nodes=1:ppn=1,walltime=20:00:00) galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS server for submit failed: 15007: No permission
Iry
On 8/15/14 12:11 PM, "John Chilton" jmchilton@gmail.com wrote:
Okay - I just checked out a clean Galaxy without modifications and I don't see any problems with uploads. So this is likely something to do with your setup - if I had to guess I would guess that your job_conf.xml configuration is somehow incorrect - the job is getting creating but nothing is running it. Can you verify this by looking in the logs? I would imagine you do see lines like:
galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool upload1 created job id 2
for the uploads but nothing like:
galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is: python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py ....
You could also verify this is the problem by doing something other than uploading - maybe a data source tool? I have attached a tool that doesn't require any existing files or external data sources that I use for testing stuff like this - maybe see if it runs?
If no jobs run - can you attach your job_conf.xml and we can try to debug the problem from there.
If other tools run than it is likely not a job related problem - in that case can you answer some questions - Are you using a proxy - if so which one? Can you attach the configuration? Is the upload.xml tool in your tool_conf.xml? Have you made modifications to it?
-John
On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham Iry.Witham@jax.org wrote:
I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason MMason@benaroyaresearch.org Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham iry.witham@jax.org, "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham Iry.Witham@jax.org Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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Hi Nate,
We were able to get upgraded to pbs-python 4.4.0 after having to modify some c++ code that was causing errors with the _py.so. We now have it running, but I am trying to get the references to work for the tools I have installed from the tool shed. They can't seem to find the correct path.
Thanks, Iry
Sent from my iPhone
On Aug 18, 2014, at 5:08 PM, "Nate Coraor" <nate@bx.psu.edumailto:nate@bx.psu.edu> wrote:
On Aug 18, 2014, at 9:55 AM, Iry Witham <Iry.Witham@jax.orgmailto:Iry.Witham@jax.org> wrote:
Hi John,
I was able to work through this since it was related to pbs on the cluster. However, I am still having issues. This is the error I am getting:
galaxy.tools.genome_index DEBUG 2014-08-18 09:31:56,819 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2014-08-18 09:31:56,825 Starting job handler galaxy.jobs INFO 2014-08-18 09:31:56,825 Handler 'handler1' will load all configured runner plugins galaxy.jobs.runners DEBUG 2014-08-18 09:31:56,829 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2014-08-18 09:31:57,073 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners DEBUG 2014-08-18 09:31:57,104 Starting 3 LWRRunner workers galaxy.jobs.runners.lwr_client.manager INFO 2014-08-18 09:31:57,197 Setting LWR client class to standard, non-caching variant. galaxy.jobs DEBUG 2014-08-18 09:31:57,228 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr' Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/bu ildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 144, in __init__ self.job_manager = manager.JobManager( self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__ self.job_handler = handler.JobHandler( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 31, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", line 583, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py" , line 496, in get_job_runner_plugins module = __import__( module_name ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs. py", line 32, in <module> raise Exception( egg_message % str( e ) ) Exception:
The 'pbs' runner depends on 'pbs_python' which is not installed or not configured properly. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
Additional errors may follow: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pbs_python-4.3.5-py2.6-l inux-x86_64-ucs4.egg/_pbs.so: undefined symbol: log_record
Hi Iry,
It looks like we need to upgrade to pbs_python 4.4.0: https://oss.trac.surfsara.nl/pbs_python/ticket/34
The pbs_python 4.4.0 source is on our eggs server - could you update the version to 4.4.0 in /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs.ini and re-scramble the egg and let us know if this fixes it?
Thanks, --nate
Removing PID file handler1.pid
I am running the following:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> qsub --about HomeDir: /var/spool/torque InstallDir: /usr/local Server: rockhopper BuildDir: /root/torque-4.2.5 BuildUser: root BuildHost: galaxy2 BuildDate: Sat Aug 16 11:17:00 EDT 2014 Version: 4.2.5 Commit: 39f78e588b3a47a6c7bed1004ec7b5d0ccf24288
The handler.pid are being removed.
Thanks, Iry
On 8/18/14 9:16 AM, "John Chilton" <jmchilton@gmail.commailto:jmchilton@gmail.com> wrote:
I have not seen this before - are you able to submit things as your Galaxy user from the command line? Are their logs on the PBS side that give any more clues?
-John
On Fri, Aug 15, 2014 at 2:01 PM, Iry Witham <Iry.Witham@jax.orgmailto:Iry.Witham@jax.org> wrote: Hi John,
It looks like it may be related to PBS and Torque. I am currently running torque-4.2.5. I scrambled the pbs-python eggs and it is now running pbs-python 4.3.5. The good thing is I am now getting an attempt to submit to pbs, but all jobs are failing. This is the error:
galaxy.jobs.handler DEBUG 2014-08-15 13:10:37,822 (16) Dispatching to pbs runner galaxy.jobs DEBUG 2014-08-15 13:10:41,110 (16) Persisting job destination (destination id: pbs:////-l nodes=1:ppn=1,walltime=20:00:00) galaxy.jobs.handler INFO 2014-08-15 13:10:41,145 (16) Job dispatched galaxy.tools.deps DEBUG 2014-08-15 13:10:42,338 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-08-15 13:10:42,339 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.pbs ERROR 2014-08-15 13:11:33,507 Connection to PBS server for submit failed: 15007: No permission
Iry
On 8/15/14 12:11 PM, "John Chilton" <jmchilton@gmail.commailto:jmchilton@gmail.com> wrote:
Okay - I just checked out a clean Galaxy without modifications and I don't see any problems with uploads. So this is likely something to do with your setup - if I had to guess I would guess that your job_conf.xml configuration is somehow incorrect - the job is getting creating but nothing is running it. Can you verify this by looking in the logs? I would imagine you do see lines like:
galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool upload1 created job id 2
for the uploads but nothing like:
galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is: python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py ....
You could also verify this is the problem by doing something other than uploading - maybe a data source tool? I have attached a tool that doesn't require any existing files or external data sources that I use for testing stuff like this - maybe see if it runs?
If no jobs run - can you attach your job_conf.xml and we can try to debug the problem from there.
If other tools run than it is likely not a job related problem - in that case can you answer some questions - Are you using a proxy - if so which one? Can you attach the configuration? Is the upload.xml tool in your tool_conf.xml? Have you made modifications to it?
-John
On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham <Iry.Witham@jax.orgmailto:Iry.Witham@jax.org> wrote: I have checked and everything appears correct. I did notice that in the /database/tmp/upload_store/ there are files that when I cat them they are the files I am/have attempted to upload. However, they do not get moved to the /ftp directory. I am wondering if this is due to a misconfiguration in the universe.wsgi.ini or if it could be related to proftpd or postgres. Unfortunately I am under a very tight deadline and need to figure this out. Any assistance will be appreciated.
Thanks, Iry
From: Michael Mason <MMason@benaroyaresearch.orgmailto:MMason@benaroyaresearch.org> Date: Thursday, August 14, 2014 12:48 PM To: Iry Witham <iry.witham@jax.orgmailto:iry.witham@jax.org>, "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this.
From: Iry Witham <Iry.Witham@jax.orgmailto:Iry.Witham@jax.org> Date: Thursday, August 14, 2014 9:34 AM To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Upload file not working with new install
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution?
Thanks, Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.orghttp://www.benaroyaresearch.org
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
___________________________________________________________ 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/
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
___________________________________________________________ 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/
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
galaxy-dev@lists.galaxyproject.org
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Iry Witham -
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Michael Mason -
Nate Coraor