Hi Edgar,

Please make sure you have disabled the developer options `use_interactive`
and `debug` in galaxy.ini, then restart your Galaxy server and try the
upload again.

Also, please try out the modal upload dialog as I suggested, it should
prevent a "stuck" upload in the future.

--nate



On Thu, Jan 22, 2015 at 10:25 AM, Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

>  Hello Nate,
>
>
>
>
>
> Thank you for answer so quickly.
>
> My apache logs (/var/log/httpd/galaxy-prod-access_log) looks like this
>
> *ip_addr - - [22/Jan/2015:10:17:31 -0500] "POST
> /galaxy-prod/tool_runner/upload_async_create HTTP/1.1" 200 37*
>
> *ip_addr - - [22/Jan/2015:10:17:32 -0500] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235*
>
> *ip_addr - - [22/Jan/2015:10:17:32 -0500] "GET
> /galaxy-prod/tool_runner/upload_async_message HTTP/1.1" 200 1401*
>
> *ip_addr - - [22/Jan/2015:10:17:36 -0500] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235*
>
> *ip_addr - - [22/Jan/2015:10:17:40 -0500] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235*
>
> *ip_addr - - [22/Jan/2015:10:17:44 -0500] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235*
>
> *ip_addr - - [22/Jan/2015:10:17:48 -0500] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 235*
>
>
>
> And my galaxy logs (/home/galaxy/galaxy-prod/config/main.log):
>
> ip_addr - - [22/Jan/2015:10:17:31 -0400] "POST
> /galaxy-prod/tool_runner/upload_async_create HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:32 -0400] "POST
> /galaxy-prod/tool_runner/index HTTP/1.1" 500 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> Error - <type 'exceptions.OverflowError'>: signed integer is greater than
> maximum
>
> ip_addr - - [22/Jan/2015:10:17:32 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:32 -0400] "GET
> /galaxy-prod/tool_runner/upload_async_message HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> URL: http://esiservera.esi.umontreal.ca:8081/galaxy-prod/tool_runner/index
>
> File
> '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>
>   app_iter = self.application(environ, sr_checker)
>
> File
> '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
> line 84 in __call__
>
>   return self.application(environ, start_response)
>
> File
> '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
> line 633 in __call__
>
>   return self.application(environ, start_response)
>
> File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 132
> in __call__
>
>   return self.handle_request( environ, start_response )
>
> File '/home/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 185
> in handle_request
>
>   kwargs = trans.request.params.mixed()
>
> File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 900 in
> params
>
> File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 892 in
> str_params
>
> File 'build/bdist.linux-x86_64-ucs4/egg/webob/__init__.py', line 818 in
> str_POST
>
> File '/usr/lib64/python2.6/cgi.py', line 508 in __init__
>
>   self.read_multi(environ, keep_blank_values, strict_parsing)
>
> File '/usr/lib64/python2.6/cgi.py', line 635 in read_multi
>
>   headers = rfc822.Message(self.fp)
>
> File '/usr/lib64/python2.6/rfc822.py', line 108 in __init__
>
>   self.readheaders()
>
> File '/usr/lib64/python2.6/rfc822.py', line 155 in readheaders
>
>   line = self.fp.readline()
>
> File
> '/home/galaxy/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py',
> line 482 in readline
>
>   data = self.file.readline(max_read)
>
> File '/usr/lib64/python2.6/socket.py', line 415 in readline
>
>   bline = buf.readline(size)
>
> OverflowError: signed integer is greater than maximum
>
>
>
>
>
> CGI Variables
>
> -------------
>
>   CONTENT_LENGTH: '2625522525'
>
>   CONTENT_TYPE: 'multipart/form-data;
> boundary=----WebKitFormBoundary9c9hOVrAGAXKJtdd'
>
>   HTTP_ACCEPT: '*/*'
>
>   HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>
>   HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8'
>
>   HTTP_CONNECTION: 'Keep-Alive'
>
>   HTTP_COOKIE:
> 'galaxysession=d122f4f53e5da72f16add67ded507460da12cda8c8b0781476c9ddbea84bd40a1e299b3d9b7a9e3a;
> galaxysession=d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e'
>
>   HTTP_HOST: 'esiservera.esi.umontreal.ca:8081'
>
>   HTTP_ORIGIN: 'http://esiservera.esi.umontreal.ca:8081'
>
>   HTTP_REFERER: 'http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root'
>
>   HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36
> (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36'
>
>   HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
>
>   PATH_INFO: '/tool_runner/index'
>
>   REMOTE_ADDR: 'ip_addr'
>
>   REQUEST_METHOD: 'POST'
>
>   SCRIPT_NAME: '/galaxy-prod'
>
>   SERVER_NAME: 'esiservera.esi.umontreal.ca'
>
>   SERVER_PORT: '7112'
>
>   SERVER_PROTOCOL: 'HTTP/1.1'
>
>
>
>
>
> WSGI Variables
>
> --------------
>
>   application: <paste.recursive.RecursiveMiddleware object at
> 0x7fd1500e9b10>
>
>   is_api_request: False
>
>   paste.cookies: (<SimpleCookie:
> galaxysession='d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e'>,
> 'galaxysession=d122f4f53e5da72f16add67ded507460da12cda8c8b0781476c9ddbea84bd40a1e299b3d9b7a9e3a;
> galaxysession=d122f4f53e5da72f439b77b098b6a77c8fe4c3cee6d2a1f587a8445290a468f305b3911dd27efa9e')
>
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object
> at 0x7fd1500e9550>
>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x7ef2850>
>
>   paste.recursive.forward: <paste.recursive.Forwarder from /galaxy-prod>
>
>   paste.recursive.include: <paste.recursive.Includer from /galaxy-prod>
>
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
> /galaxy-prod>
>
>   paste.recursive.script_name: '/galaxy-prod'
>
>   paste.throw_errors: True
>
>   request_id: 'c93de906a24911e4bd5d002264f83610'
>
>   webob._parsed_query_vars: (MultiDict([]), '')
>
>   wsgi process: 'Multithreaded'
>
> ------------------------------------------------------------
>
> ip_addr - - [22/Jan/2015:10:17:36 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:40 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:44 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:48 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:52 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:17:59 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:18:04 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:18:10 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:18:29 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
> ip_addr - - [22/Jan/2015:10:18:36 -0400] "GET
> /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "
> http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/40.0.2214.91 Safari/537.36"
>
>
>
> However, I still see on my galaxy webpage the document in blue with the
> arrow going up constantly.
>
>
>
> Do you think it’s an apache configuration error or galaxy or both?
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Nate Coraor [mailto:n...@bx.psu.edu]
> *Envoyé :* January-22-15 10:10 AM
> *À :* Fernandez Edgar
> *Cc :* John Chilton; galaxy-...@bx.psu.edu
>
> *Objet :* Re: [galaxy-dev] galaxy and torque - resource allocation
>
>
>
> Hi Edgar,
>
>
>
> I'd suggest checking your Apache logs to see if the upload was denied by
> the server configuration (possibly for being too large).
>
>
>
> Also, please try using the modal upload method to see whether the upload
> is actually completing. This can be found by clicking the icon of a box
> with an up arrow at the top of the tool panel.
>
>
>
> There are multiple steps to an upload - the first is sending the data to
> the server. After that, Galaxy creates a job and detects metadata about the
> uploaded dataset. Prior to the modal upload, a (purple "uploading") history
> item would be created as soon as the upload started, but if the transfer to
> the server was interrupted the history item may remain "stuck" in that
> state without providing feedback to the user that the upload was no longer
> progressing. The modal provides an upload progress bar, and only once all
> the data has been sent to the server does it create a history item (in the
> gray "queued") state.
>
>
>
>
>
> On Thu, Jan 22, 2015 at 8:50 AM, Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
>
> Hello John,
>
> This is totally excellent!
> This gave me a great idea for my little torque installation.
>
> I hope you don't mind but I have an unrelated issue with torque that I do
> not seem to grasp.
> My issue is that it take a rediculious amount of time to upload a 2Gb file.
> I tried many different configurations of apache to upload that 2Gb file
> without success.
> Galaxy keeps showing that arrow going up constantly (over 12h).
> And this is an upload from a file located on the server running galaxy.
>
> Here is some information from my installation.
> 1. Server redhat6 with galaxy behind an Apache HTTP Server proxy like
> described on your website.
> 2. I have Apache HTTP Server running as the galaxy user with
>         a. Serving Galaxy at a sub directory
>         b. Compression and caching
>         c. Sending files using Apache
>
> You will see in attachment my apache's galaxy, deflate, expire and
> xsendfile configuration file.
> Furthermore, I've changed the following in galaxy.ini:
>         apache_xsendfile = True
>         upstream_gzip = False
>
> Any suggestions?
> Any information I missed?
> PLEASE HELP!!!
>
> Cordialement / Regards,
> Edgar Fernandez
>
>
> -----Message d'origine-----
> De : John Chilton [mailto:jmchil...@gmail.com]
> Envoyé : January-21-15 9:34 PM
>
> À : Fernandez Edgar
> Cc : galaxy-...@bx.psu.edu
> Objet : Re: [galaxy-dev] galaxy and torque - resource allocation
>
> Was hoping someone with an actual torque cluster would respond. I think
> the way you would configure this might be for instance might be setting
> native_specification like "-l nodes=1:ppn=n". Depending on how things are
> configured or simply because I am ignorant - this may be wrong - but I
> think what you really want should look a lot like your arguments to qsub.
> So let say you have defined a job runner plugin called pbs_drmaa at the top
> of your job_conf.xml file. Then you could default everything to a single
> core by default and send "big" jobs to a destination with 8 cores with
> destinations and tool sections that look something like this...
>
> ...
>
>   <destinations default="singlecore">
>         <destination id="singlecore" runner="pbs_drmaa">
>           <param id="native_specification">-l nodes=1:ppn=1</param>
>         </destination>
>         <destination id="multicore" runner="pbs_drmaa">
>           <param id="native_specification">-l nodes=1:ppn=8</param>
>         </destination>
>   </destinations>
>
> and ...
>
>   <tools>
>     <tool id="bowtie2" destination="multicore" />
>     <tool id="bowtie" destination="multicore" />
>     <tool id="deeptools" destination="multicore" />
>     <tool id="cufflinks"destination="multicore" />
>     <tool id="cuffdiff" destination="multicore" />
>     <tool id="cuffmerge" destination="multicore" />
>     <tool id="tophat2" destination="multicore" />
>   </tools>
>
> Again - that native specification could be wrong - probably best to test
> it out locally (or maybe Nate or JJ will step in and correct me).
>
> Hope this helps,
> -John
>
>
> On Mon, Jan 19, 2015 at 8:05 AM, Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
> > Hello gents,
> >
> > Once again I would like to convey my most sincere appreciation for your
> help!!!
> > And yes I would like to hear your elaboration on my DRMAA runner which
> is what I'm using.
> > So my installation looks like: galaxy --> pbs_drmaa --> torque
> >
> > Cordialement / Regards,
> > Edgar Fernandez
> >
> > -----Message d'origine-----
> > De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : January-18-15
> > 8:59 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re:
> > [galaxy-dev] galaxy and torque - resource allocation
> >
> > Galaxy generally defers to the DRM (torque in your case) for dealing
> with these things. In your job_conf.xml you can specify limits for memory
> or CPUs and Galaxy will pass these along to the DRM at which point it is up
> to the DRM to enforce these - details depend on if you are using the PBS
> runner or the DRMAA runner (let me know which and I can try to elobrate if
> that would be useful).
> >
> > In your particular case - I don't believe torque "schedules" RAM so
> > things will generally only be... throttled... by CPUs counts. This is
> > what I was told by the admins at MSI when I worked there anyway. If
> > you want to place hard limits on RAM I think you need to "upgrade" to
> > the MOAB scheduler or switch over to a different DRM entirely like
> > SLURM. Even for DRMs that deal more directly with memory - Galaxy
> > doesn't provide a general mechanism for passing this along to the tool
> > (https://trello.com/c/3RkTDnIn) - so it would be up to the tool to
> interact with the environment variables your DRM sets .
> >
> > This sounds really terrible in the abstract - but it reality it usually
> isn't an issue - most of Galaxy's multi-core mappers say have relatively
> low memory per CPU usage - and for things like assemblers where this is
> more important - one can usually just assign them to their own CPU or
> something like that to ensure they get all the memory available.
> >
> > Unlike memory - Galaxy will attempt to pass the number of slots
> allocated to a job to the tools by setting the GALAXY_SLOTS environment
> variable. All of the multiple core devteam Galaxy tools at this point use
> this and so should work - as should probably most multi-core tools from the
> tool shed - at least the most popular ones.
> >
> > Hope this helps,
> >
> > -John
> >
> >
> > On Tue, Jan 13, 2015 at 11:52 AM, Fernandez Edgar <
> edgar.fernan...@umontreal.ca> wrote:
> >> Hello gents,
> >>
> >>
> >>
> >> Hope everyone had a great holiday break!
> >>
> >> Wish you guys all the best for 2015!
> >>
> >>
> >>
> >> I have a couple of questions about how resources (CPU and memory) is
> >> allocated when you have a galaxy and torque installation.
> >>
> >>
> >>
> >> So I’ve setup torque with some default and maximum amount of CPU and
> >> memory allocations.
> >>
> >> However, I have some worries when it comes to application (like
> >> tophat for example).
> >>
> >> By default, it takes half the CPU of a server unless specified
> otherwise.
> >>
> >> How is the CPU allocation is specified to application like tophat
> >> through galaxy?
> >>
> >>
> >>
> >> Also, how does galaxy react if a job needs more memory than the limit
> >> set by torque?
> >>
> >>
> >>
> >> Any information would help me a lot!
> >>
> >>
> >>
> >> My sincere salutations to you all!!!
> >>
> >>
> >>
> >> Cordialement / Regards,
> >>
> >>
> >>
> >> Edgar Fernandez
> >>
> >> System Administrator (Linux)
> >>
> >> Direction Générale des Technologies de l'Information et de la
> >> Communication
> >>
> >> (  Bur. : 1-514-343-6111 poste 16568
> >>
> >>
> >>
> >> Université de Montréal
> >>
> >> PAVILLON ROGER-GAUDRY, bureau X-218
> >>
> >>
> >>
> >>
> >> ___________________________________________________________
> >> 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"
> 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:
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>
>
>
___________________________________________________________
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