Hmm, no luck on the large uploads.
I tried using a recent version of Google Chrome.
I added these settings to /etc/httpd/conf/httpd.conf
Timeout 6000
LimitRequestBody 32147483647
And restarted apache.
But when I try to upload a 3.7GB file I get this error in Galaxy:
"Bad Gateway
The proxy server received an invalid response from an upstream server."
Now I do see this error in the Galaxy log, so I'm thinking I'm not
hitting an Apache issue, and I'm not hitting a browser issue. Perhaps
it's a paste issue?
Exception happened during processing of request from ('127.0.0.1', 52128)
Traceback (most recent call last):
File
"/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/local/python27/lib/python2.7/SocketServer.py", line 323,
in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/local/python27/lib/python2.7/SocketServer.py", line 639,
in __init__
self.handle()
File
"/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 432, in handle
BaseHTTPRequestHandler.handle(self)
File "/usr/local/python27/lib/python2.7/BaseHTTPServer.py", line
337, in handle
self.handle_one_request()
File
"/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 427, in handle_one_request
self.wsgi_execute()
File
"/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 287, in wsgi_execute
self.wsgi_start_response)
File
"/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
line 202, in __call__
return app(environ, start_response)
File
"/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
File
"/misc/local/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
line 164, in __call__
app_iter = self.application(environ, start_response)
File
"/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
line 68, in __call__
return self.application(environ, replacement_start_response)
File
"/misc/local/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 226, in __call__
return self.respond(environ, start_response)
File
"/misc/local/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 399, in respond
if self.xmlhttp_key in req.params:
File "build/bdist.linux-x86_64/egg/webob/__init__.py", line 900, in params
params = self.str_params
File "build/bdist.linux-x86_64/egg/webob/__init__.py", line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File "build/bdist.linux-x86_64/egg/webob/__init__.py", line 818, in str_POST
keep_blank_values=True)
File "/usr/local/python27/lib/python2.7/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File "/usr/local/python27/lib/python2.7/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File "/usr/local/python27/lib/python2.7/cgi.py", line 510, in __init__
self.read_single()
File "/usr/local/python27/lib/python2.7/cgi.py", line 647, in read_single
self.read_lines()
File "/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py",
line 268, in read_lines
self.read_lines_to_outerboundary()
File "/usr/local/python27/lib/python2.7/cgi.py", line 697, in
read_lines_to_outerboundary
line = self.fp.readline(1<<16)
File
"/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 467, in readline
data = self.file.readline(self.length - self._consumed)
File "/usr/local/python27/lib/python2.7/socket.py", line 412, in readline
bline = buf.readline(size)
OverflowError: signed integer is greater than maximum
On Thu, Nov 29, 2012 at 11:26 AM, greg <[email protected]> wrote:
> This says Google Chrome can support uploads larger than 4 GB.
> http://www.motobit.com/help/scptutl/pa98.htm
>
> Maybe I just need to configure Apache?
>
> I'll let you guys know what I find.
>
> -Greg
>
> On Thu, Nov 29, 2012 at 11:22 AM, greg <[email protected]> wrote:
>> Follow up question. What's the deal with the 2GB limit it mentions?
>>
>> I think it would be pretty convienent to allow larger uploads. We're
>> on a fast local network so even 10 or 20 GB uploads pretty fast.
>>
>> Can I increase the limit in Apache? Which browsers are limited? This
>> is an internal install so I can tell users to only use certain
>> browsers for uploads.
>>
>> -Greg
>>
>> On Thu, Nov 29, 2012 at 11:01 AM, Nate Coraor <[email protected]> wrote:
>>> On Nov 29, 2012, at 10:54 AM, greg wrote:
>>>
>>>> Thanks. That seemed to have worked. Can you explain what happened?
>>>> (I'm curious)
>>>
>>> It's due to a bug that we've done quite a bit of work to investigate, but
>>> haven't yet found the cause. It seems to have cropped up more frequently
>>> in the past few weeks, so we'll be working on it in depth in the next few
>>> days.
>>>
>>> --nate
>>>
>>>>
>>>> -Greg
>>>>
>>>> On Thu, Nov 29, 2012 at 8:43 AM, Nate Coraor <[email protected]> wrote:
>>>>> On Nov 28, 2012, at 1:23 PM, greg wrote:
>>>>>
>>>>>> I just finished setting up a local install on our cluster but I'm
>>>>>> having trouble uploading files.
>>>>>>
>>>>>> I was able to (successfully?) upload one 160MB fasta file. But any
>>>>>> further uploads I try, they just hang.
>>>>>
>>>>> Hi Greg,
>>>>>
>>>>> Could you try the following:
>>>>>
>>>>> Open tools/data_source/upload.xml
>>>>>
>>>>> In the following line, set 'ajax-upload="false"':
>>>>>
>>>>> <param name="file_data" type="file" size="30" label="File"
>>>>> ajax-upload="false" help="TIP: Due to browser limitations, uploading
>>>>> files larger than 2GB is guaranteed to fail. To upload large files, use
>>>>> the URL method (below) or FTP (if enabled by the site administrator).">
>>>>>
>>>>> Then restart Galaxy and retry the upload and let us know if it succeeds.
>>>>>
>>>>> --nate
>>>>>
>>>>>>
>>>>>> Here's the information from the log file:
>>>>>>
>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:15:18,190
>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>> galaxy.tools.actions.upload_common INFO 2012-11-28 12:20:36,597 tool
>>>>>> upload1 created job id 4
>>>>>> galaxy.jobs.handler INFO 2012-11-28 12:20:38,386 (4) Job dispatched
>>>>>> galaxy.jobs.runners.drmaa INFO 2012-11-28 12:20:38,930 (4) queued as
>>>>>> 3718641
>>>>>> galaxy.objectstore CRITICAL 2012-11-28 12:21:03,071
>>>>>> /home/galaxy/job_working_directory/000/4 delete error [Errno 39]
>>>>>> Directory not empty: '/home/galaxy/job_working_directory/000/4'
>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:21:55,763
>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:28:26,466
>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:35:09,662
>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:46:35,565
>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>>
>>>>>>
>>>>>> The first upload that worked was around 12:20 (above), and the second
>>>>>> failed one was at 12:40. The log file doesn't seem to even mention
>>>>>> it? Could that error have killed the server somehow?
>>>>>>
>>>>>> Let me know if I can provide more info.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Greg
>>>>>> ___________________________________________________________
>>>>>> 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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