8:35 a.m.
Hi,
On our local install, we've just enabled bowtie NGS mapping and although
the search runs fine and the output is viewable in Galaxy, any attempt
to save it brings down the server.
The only error in paster.log is:
galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
mimetype in data factory sam
Tried it on large files and small files with the same effect.
Trying save as fails with an 'unable to read file error'. Anyone have
any ideas?
Cheers,
Chris
1:32 p.m.
Hi Chris,
Can you confirm that you have a recent changeset (today we're at
3192:828d9f9dcb29)? If you're using an earlier version, either update
or check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains
the following line:
'sam' : 'text/plain',
(it should be line 164, as part of the self.mimetypes_by_extension
dictionary definition).
In either case, make sure the line:
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam"
display_in_upload="true"/>
appears in <Galaxy root>/datatypes_conf.xml. It should be around line
51, inside the tag:
<registration converters_path="lib/galaxy/datatypes/converters">
Let us know what you find.
Regards,
Kelly
On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
Hi,
On our local install, we've just enabled bowtie NGS mapping and
although the search runs fine and the output is viewable in Galaxy,
any attempt to save it brings down the server.
The only error in paster.log is:
galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
mimetype in data factory sam
Tried it on large files and small files with the same effect.
Trying save as fails with an 'unable to read file error'. Anyone
have any ideas?
Cheers,
Chris
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
3:18 a.m.
Hi Kelly,
Just getting back to this following the holidays.
On 22/12/09 21:32, Kelly Vincent wrote:
Hi Chris,
Can you confirm that you have a recent changeset (today we're at
3192:828d9f9dcb29)?
'hg tip' returns 3137:ddd9d5ac0457
If you're using an earlier version, either update or
check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains the
following line:
'sam' : 'text/plain',
(it should be line 164, as part of the self.mimetypes_by_extension
dictionary definition).
Yup, it's there
In either case, make sure the line:
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam"
display_in_upload="true"/>
appears in <Galaxy root>/datatypes_conf.xml. It should be around line
51, inside the tag:
<registration converters_path="lib/galaxy/datatypes/converters">
Nope. Not in there.
I've added it and it works for small files, but not large ones. Small is
119 lines and large 20 million lines. There are no errors in paster.log,
now. Galaxy simply falls over.
Would an update solve it?
Thanks for your help,
Chris
Let us know what you find.
Regards,
Kelly
On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
> Hi,
>
> On our local install, we've just enabled bowtie NGS mapping and
> although the search runs fine and the output is viewable in Galaxy,
> any attempt to save it brings down the server.
>
> The only error in paster.log is:
> galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
> mimetype in data factory sam
>
> Tried it on large files and small files with the same effect.
>
> Trying save as fails with an 'unable to read file error'. Anyone have
> any ideas?
> Cheers,
>
> Chris
8:58 a.m.
Bump.
Anyone got ideas regarding the issue below, please? ATM we're not able
to use Galaxy as we would like.
Thanks,
Chris
On 05/01/10 11:18, Chris Cole wrote:
Hi Kelly,
Just getting back to this following the holidays.
On 22/12/09 21:32, Kelly Vincent wrote:
> Hi Chris,
>
> Can you confirm that you have a recent changeset (today we're at
> 3192:828d9f9dcb29)?
'hg tip' returns 3137:ddd9d5ac0457
> If you're using an earlier version, either update or
> check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains the
> following line:
> 'sam' : 'text/plain',
> (it should be line 164, as part of the self.mimetypes_by_extension
> dictionary definition).
Yup, it's there
> In either case, make sure the line:
> <datatype extension="sam" type="galaxy.datatypes.tabular:Sam"
> display_in_upload="true"/>
> appears in <Galaxy root>/datatypes_conf.xml. It should be around line
> 51, inside the tag:
> <registration converters_path="lib/galaxy/datatypes/converters">
Nope. Not in there.
I've added it and it works for small files, but not large ones. Small is
119 lines and large 20 million lines. There are no errors in paster.log,
now. Galaxy simply falls over.
Would an update solve it?
Thanks for your help,
Chris
> Let us know what you find.
>
> Regards,
> Kelly
>
>
> On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
>
>> Hi,
>>
>> On our local install, we've just enabled bowtie NGS mapping and
>> although the search runs fine and the output is viewable in Galaxy,
>> any attempt to save it brings down the server.
>>
>> The only error in paster.log is:
>> galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
>> mimetype in data factory sam
>>
>> Tried it on large files and small files with the same effect.
>>
>> Trying save as fails with an 'unable to read file error'. Anyone have
>> any ideas?
>> Cheers,
>>
>> Chris
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
9:33 a.m.
Chris Cole wrote:
Bump.
Anyone got ideas regarding the issue below, please? ATM we're not able
to use Galaxy as we would like.
Hi Chris,
Are you using 'run.sh --daemon' or just 'run.sh' (and
daemonizing/backgrounding through some other method, like 'screen')?
I'm asking because it's odd that there's no traceback or even something
like a segfault (which would only be seen if run in the foreground).
If you're starting with --daemon, could you start in the foreground,
cause the crash, and see if anything is output when it happens?
Thanks,
--nate
Thanks,
Chris
On 05/01/10 11:18, Chris Cole wrote:
> Hi Kelly,
>
> Just getting back to this following the holidays.
>
> On 22/12/09 21:32, Kelly Vincent wrote:
>> Hi Chris,
>>
>> Can you confirm that you have a recent changeset (today we're at
>> 3192:828d9f9dcb29)?
>
> 'hg tip' returns 3137:ddd9d5ac0457
>
>> If you're using an earlier version, either update or
>> check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains the
>> following line:
>> 'sam' : 'text/plain',
>> (it should be line 164, as part of the self.mimetypes_by_extension
>> dictionary definition).
>
> Yup, it's there
>
>> In either case, make sure the line:
>> <datatype extension="sam"
type="galaxy.datatypes.tabular:Sam"
>> display_in_upload="true"/>
>> appears in <Galaxy root>/datatypes_conf.xml. It should be around line
>> 51, inside the tag:
>> <registration converters_path="lib/galaxy/datatypes/converters">
>
> Nope. Not in there.
>
> I've added it and it works for small files, but not large ones. Small is
> 119 lines and large 20 million lines. There are no errors in paster.log,
> now. Galaxy simply falls over.
>
> Would an update solve it?
> Thanks for your help,
>
> Chris
>
>> Let us know what you find.
>>
>> Regards,
>> Kelly
>>
>>
>> On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
>>
>>> Hi,
>>>
>>> On our local install, we've just enabled bowtie NGS mapping and
>>> although the search runs fine and the output is viewable in Galaxy,
>>> any attempt to save it brings down the server.
>>>
>>> The only error in paster.log is:
>>> galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
>>> mimetype in data factory sam
>>>
>>> Tried it on large files and small files with the same effect.
>>>
>>> Trying save as fails with an 'unable to read file error'. Anyone
have
>>> any ideas?
>>> Cheers,
>>>
>>> Chris
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
7:59 a.m.
Hi Nate,
We tried a BWA run this morning and this time it gave an error rather
than a crash. Below is just the python error output, I can give a
sanitised full output if you prefer.
However, I can't do any more testing for the time being as the hardware
on our development server has gone to the Great Cluster in the Sky RIP.
We do have a replacement which will be in place soon.
In the meantime, any help appreciated.
Chris
Server Error
URL:
http://wsdev.compbio.dundee.ac.uk:3216/datasets/ec351b7f7460a3bb/display?...
Module paste.exceptions.errormiddleware:143 in __call__
<< try:
__traceback_supplement__ = Supplement, self, environ
app_iter = self.application(environ, start_response)
return self.make_catching_iter(app_iter, environ)
except:>> app_iter = self.application(environ, start_response)
Module paste.debug.prints:97 in __call__
<< threadedprint.register(replacement_stdout)
try:
status, headers, body = wsgilib.intercept_output(
environ, self.app)
if status is None:>> status, headers, body =
wsgilib.intercept_output(
Module paste.wsgilib:552 in intercept_output
<< if len(data) < 2:
data.append(None)
data.append(output.getvalue())
return data>> data.append(output.getvalue())
MemoryError:
extra data
Hi Chris,
Are you using 'run.sh --daemon' or just 'run.sh' (and
daemonizing/backgrounding through some other method, like 'screen')? I'm
asking because it's odd that there's no traceback or even something like
a segfault (which would only be seen if run in the foreground).
If you're starting with --daemon, could you start in the foreground,
cause the crash, and see if anything is output when it happens?
Thanks,
--nate
> Thanks,
>
> Chris
>
> On 05/01/10 11:18, Chris Cole wrote:
>> Hi Kelly,
>>
>> Just getting back to this following the holidays.
>>
>> On 22/12/09 21:32, Kelly Vincent wrote:
>>> Hi Chris,
>>>
>>> Can you confirm that you have a recent changeset (today we're at
>>> 3192:828d9f9dcb29)?
>>
>> 'hg tip' returns 3137:ddd9d5ac0457
>>
>>> If you're using an earlier version, either update or
>>> check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains the
>>> following line:
>>> 'sam' : 'text/plain',
>>> (it should be line 164, as part of the self.mimetypes_by_extension
>>> dictionary definition).
>>
>> Yup, it's there
>>
>>> In either case, make sure the line:
>>> <datatype extension="sam"
type="galaxy.datatypes.tabular:Sam"
>>> display_in_upload="true"/>
>>> appears in <Galaxy root>/datatypes_conf.xml. It should be around line
>>> 51, inside the tag:
>>> <registration
converters_path="lib/galaxy/datatypes/converters">
>>
>> Nope. Not in there.
>>
>> I've added it and it works for small files, but not large ones. Small is
>> 119 lines and large 20 million lines. There are no errors in paster.log,
>> now. Galaxy simply falls over.
>>
>> Would an update solve it?
>> Thanks for your help,
>>
>> Chris
>>
>>> Let us know what you find.
>>>
>>> Regards,
>>> Kelly
>>>
>>>
>>> On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
>>>
>>>> Hi,
>>>>
>>>> On our local install, we've just enabled bowtie NGS mapping and
>>>> although the search runs fine and the output is viewable in Galaxy,
>>>> any attempt to save it brings down the server.
>>>>
>>>> The only error in paster.log is:
>>>> galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
>>>> mimetype in data factory sam
>>>>
>>>> Tried it on large files and small files with the same effect.
>>>>
>>>> Trying save as fails with an 'unable to read file error'. Anyone
have
>>>> any ideas?
>>>> Cheers,
>>>>
>>>> Chris
8:02 a.m.
Do you have 'debug = True' in universe_wsgi.ini on this server? This
enables middleware that will attempt to load the entire response into
memory.
--nate
Chris Cole wrote:
Hi Nate,
We tried a BWA run this morning and this time it gave an error rather
than a crash. Below is just the python error output, I can give a
sanitised full output if you prefer.
However, I can't do any more testing for the time being as the hardware
on our development server has gone to the Great Cluster in the Sky RIP.
We do have a replacement which will be in place soon.
In the meantime, any help appreciated.
Chris
Server Error
URL:
http://wsdev.compbio.dundee.ac.uk:3216/datasets/ec351b7f7460a3bb/display?...
Module paste.exceptions.errormiddleware:143 in __call__
<< try:
__traceback_supplement__ = Supplement, self, environ
app_iter = self.application(environ, start_response)
return self.make_catching_iter(app_iter, environ)
except:>> app_iter = self.application(environ, start_response)
Module paste.debug.prints:97 in __call__
<< threadedprint.register(replacement_stdout)
try:
status, headers, body = wsgilib.intercept_output(
environ, self.app)
if status is None:>> status, headers, body =
wsgilib.intercept_output(
Module paste.wsgilib:552 in intercept_output
<< if len(data) < 2:
data.append(None)
data.append(output.getvalue())
return data>> data.append(output.getvalue())
MemoryError:
extra data
> Hi Chris,
>
> Are you using 'run.sh --daemon' or just 'run.sh' (and
> daemonizing/backgrounding through some other method, like 'screen')? I'm
> asking because it's odd that there's no traceback or even something like
> a segfault (which would only be seen if run in the foreground).
>
> If you're starting with --daemon, could you start in the foreground,
> cause the crash, and see if anything is output when it happens?
>
> Thanks,
> --nate
>
>> Thanks,
>>
>> Chris
>>
>> On 05/01/10 11:18, Chris Cole wrote:
>>> Hi Kelly,
>>>
>>> Just getting back to this following the holidays.
>>>
>>> On 22/12/09 21:32, Kelly Vincent wrote:
>>>> Hi Chris,
>>>>
>>>> Can you confirm that you have a recent changeset (today we're at
>>>> 3192:828d9f9dcb29)?
>>>
>>> 'hg tip' returns 3137:ddd9d5ac0457
>>>
>>>> If you're using an earlier version, either update or
>>>> check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains
the
>>>> following line:
>>>> 'sam' : 'text/plain',
>>>> (it should be line 164, as part of the self.mimetypes_by_extension
>>>> dictionary definition).
>>>
>>> Yup, it's there
>>>
>>>> In either case, make sure the line:
>>>> <datatype extension="sam"
type="galaxy.datatypes.tabular:Sam"
>>>> display_in_upload="true"/>
>>>> appears in <Galaxy root>/datatypes_conf.xml. It should be around
line
>>>> 51, inside the tag:
>>>> <registration
converters_path="lib/galaxy/datatypes/converters">
>>>
>>> Nope. Not in there.
>>>
>>> I've added it and it works for small files, but not large ones.
>>> Small is
>>> 119 lines and large 20 million lines. There are no errors in
>>> paster.log,
>>> now. Galaxy simply falls over.
>>>
>>> Would an update solve it?
>>> Thanks for your help,
>>>
>>> Chris
>>>
>>>> Let us know what you find.
>>>>
>>>> Regards,
>>>> Kelly
>>>>
>>>>
>>>> On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> On our local install, we've just enabled bowtie NGS mapping and
>>>>> although the search runs fine and the output is viewable in Galaxy,
>>>>> any attempt to save it brings down the server.
>>>>>
>>>>> The only error in paster.log is:
>>>>> galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown
>>>>> mimetype in data factory sam
>>>>>
>>>>> Tried it on large files and small files with the same effect.
>>>>>
>>>>> Trying save as fails with an 'unable to read file error'.
Anyone have
>>>>> any ideas?
>>>>> Cheers,
>>>>>
>>>>> Chris
2:02 a.m.
On 11/01/10 16:02, Nate Coraor wrote:
Do you have 'debug = True' in universe_wsgi.ini on this
server? This
enables middleware that will attempt to load the entire response into
memory.
Yup.
Ok. Tried it again with new hardware and now Galaxy brought down the
whole machine!
This is the sum total from the session while running in non-daemon mode:
Starting server in PID 12466.
serving on http://xxxxx.dundee.ac.uk:3216
10.31.1.120 - - [12/Jan/2010:09:34:53 +0100] "GET / HTTP/1.1" 200 -
"-"
"Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1.6) Gecko/20091206
SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:34:54 +0100] "GET /root/tool_menu
HTTP/1.1" 200 - "http://xxxxxx.dundee.ac.uk:3216/" "Mozilla/5.0 (X11;
U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:34:54 +0100] "GET /history HTTP/1.1" 200
- "http://xxxxxxxxxx.dundee.ac.uk:3216/" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:34:58 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:01 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:04 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:08 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:11 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:14 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:17 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:20 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:23 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxxdundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
For reference our universe_wsgi.ini is attached also (sensitive info
removed).
Our hardware spec. is a dual cpu Opteron 248 server with 4Gb RAM, is
that a problem? The files we're trying to save are between 3-4Gb each.
Thanks for your help.
Chris
6:10 a.m.
Chris Cole wrote:
On 11/01/10 16:02, Nate Coraor wrote:
> Do you have 'debug = True' in universe_wsgi.ini on this server? This
> enables middleware that will attempt to load the entire response into
> memory.
Yup.
Okay, give it a shot with debug = False and see if this solves it.
--nate
Ok. Tried it again with new hardware and now Galaxy brought down the
whole machine!
This is the sum total from the session while running in non-daemon mode:
Starting server in PID 12466.
serving on http://xxxxx.dundee.ac.uk:3216
10.31.1.120 - - [12/Jan/2010:09:34:53 +0100] "GET / HTTP/1.1" 200 -
"-"
"Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1.6) Gecko/20091206
SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:34:54 +0100] "GET /root/tool_menu
HTTP/1.1" 200 - "http://xxxxxx.dundee.ac.uk:3216/" "Mozilla/5.0 (X11;
U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:34:54 +0100] "GET /history HTTP/1.1" 200
- "http://xxxxxxxxxx.dundee.ac.uk:3216/" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:34:58 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:01 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:04 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:08 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:11 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:14 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:17 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:20 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
10.31.1.120 - - [12/Jan/2010:09:35:23 +0100] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://xxxxxxxxxxdundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U; Linux
i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
For reference our universe_wsgi.ini is attached also (sensitive info
removed).
Our hardware spec. is a dual cpu Opteron 248 server with 4Gb RAM, is
that a problem? The files we're trying to save are between 3-4Gb each.
Thanks for your help.
Chris
8:39 a.m.
On 12/01/10 14:10, Nate Coraor wrote:
Chris Cole wrote:
> On 11/01/10 16:02, Nate Coraor wrote:
>> Do you have 'debug = True' in universe_wsgi.ini on this server? This
>> enables middleware that will attempt to load the entire response into
>> memory.
>
> Yup.
Okay, give it a shot with debug = False and see if this solves it.
Yes it did. Thanks very much!
Cheers,
Chris
--nate
> Ok. Tried it again with new hardware and now Galaxy brought down the
> whole machine!
>
> This is the sum total from the session while running in non-daemon mode:
>
> Starting server in PID 12466.
> serving on http://xxxxx.dundee.ac.uk:3216
> 10.31.1.120 - - [12/Jan/2010:09:34:53 +0100] "GET / HTTP/1.1" 200 -
> "-" "Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1.6)
> Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:34:54 +0100] "GET /root/tool_menu
> HTTP/1.1" 200 - "http://xxxxxx.dundee.ac.uk:3216/" "Mozilla/5.0
(X11;
> U; Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:34:54 +0100] "GET /history HTTP/1.1"
> 200 - "http://xxxxxxxxxx.dundee.ac.uk:3216/" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:34:58 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
Linux
> i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:01 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:04 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:08 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:11 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:14 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:17 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:20 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxxxxx.dundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
> 10.31.1.120 - - [12/Jan/2010:09:35:23 +0100] "POST
> /root/history_item_updates HTTP/1.1" 200 -
> "http://xxxxxxxxxxdundee.ac.uk:3216/history" "Mozilla/5.0 (X11; U;
> Linux i686; en-US; rv:1.9.1.6) Gecko/20091206 SeaMonkey/2.0.1"
>
> For reference our universe_wsgi.ini is attached also (sensitive info
> removed).
> Our hardware spec. is a dual cpu Opteron 248 server with 4Gb RAM, is
> that a problem? The files we're trying to save are between 3-4Gb each.
> Thanks for your help.
>
> Chris
>
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days inactive
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galaxy-dev@lists.galaxyproject.org
9 comments
3 participants
participants (3)
-
Chris Cole -
Kelly Vincent -
Nate Coraor