java.io (Too many open files) error during Reconciling

[Thad Guidry]

Notice in the attached file that it could not find some files,  sometimes in /PC Axis and also /extensions and /gdata  /blah... however the files were/are accessible on the server on Amazon, as I just checked....so something with the Refine reconciling process, or perhaps too many connection drops on Freebase's end during the 1.5 days of reconciling this ?

and Refine is stuck in a loop right now at 100% completion on Reconciling with 1 column 1 property on 125000 rows after running for 1.5 days.  It was progressing well yesterday when I intermittently checked on it, but didn't check after around 50% completion.

I wonder if it is the log4j Receivers package or something similar such as what this guy found ?  (See his Edit 1 and Edit 2) 

http://stackoverflow.com/questions/2272908/java-io-filenotfoundexception-too-many-open-files

Thoughts ?

-- 

-Thad
http://www.freebase.com/view/en/thad_guidry

[David Huynh]

+stefanom explicitly as it seems like a Butterfly issue.

David

[Stefano Mazzocchi]

Something is leaking file descriptors, hard to know what without some deeper profiling.

I just ran "./refine findbugs" and while a few issues were added since the last time I checked, there doesn't seem to be anything in Refine that does that... so it might indeed be butterfly.

Thad, I suspect you're running this from the command line, in that case, try commenting out line 635 in refine.sh, basically changing

        add_option "-Drefine.autoreload=true -Dbutterfly.autoreload=true"

to

        #add_option "-Drefine.autoreload=true -Dbutterfly.autoreload=true"

(note the # sign in front)

And see if the problem goes away (you'll have to restart refine for this to have any effect).

--
Stefano Mazzocchi  <stef...@google.com>
Software Engineer, Google Inc.

[Thad Guidry]

OK, sure thing.. I'll try that... :) another 1.5 days ...here we go.

--
-Thad
http://www.freebase.com/view/en/thad_guidry

[Thad Guidry]

got

Syntax error line 636 "fi" unexpected  ??

--
-Thad
http://www.freebase.com/view/en/thad_guidry

[Thad Guidry]

Fixed it and got past that... it starts now, but...wondering about this 827: /tmp/refine.gLjkKFx: unexpected operator   ??

./refine: 636: Syntax error: "fi" unexpected

ubuntu@ip-1x-xx-xxx-xx:~/Desktop/Working/grefine$ ./refine -m 12000m -i 1x.xx.xxx.xx

./refine: 636: Syntax error: "fi" unexpected

ubuntu@ip-xx-xx-xxx-xx:~/Desktop/Working/grefine$ ./refine -m 12000m -i 1x.xx.xxx.xx

[: 827: /tmp/refine.gLjkKFx: unexpected operator

Starting Google Refine at 'http://1x.xx.xxx.xx:xxxx/'

20:01:34.614 [            refine_server] Starting Server bound to '1x.xx.xxx.xx:xxxx' (0ms)

20:01:34.615 [            refine_server] refine.memory size: 12000m JVM Max heap: 11184832512 (1ms)

20:01:34.631 [            refine_server] Initializing context: '/' from '/media/ebs2/scraping/Working/grefine/main/webapp' (16ms)

20:01:35.170 [                   refine] Starting Google Refine 2.5 [TRUNK]... (539ms)

Xlib:  extension "RANDR" missing on display ":1.0".

20:01:42.129 [                   refine] POST /command/core/get-importing-configuration (6959ms)

20:01:42.146 [                   refine] GET /command/core/get-all-project-metadata (17ms)

20:01:42.167 [                   refine] GET /command/core/get-version (21ms)

--
-Thad
http://www.freebase.com/view/en/thad_guidry

[Thad Guidry]

For what it's worth...I fixed it this way:

    if [ -d $REFINE_CLASSES_DIR ] ; then

IGNOREME=B

        #add_option "-Drefine.autoreload=true -Dbutterfly.autoreload=true"

    fi

--
-Thad
http://www.freebase.com/view/en/thad_guidry

[Stefano Mazzocchi]

On Fri, Dec 9, 2011 at 12:13 PM, Thad Guidry <thadg...@gmail.com> wrote:

For what it's worth...I fixed it this way:

    if [ -d $REFINE_CLASSES_DIR ] ; then

IGNOREME=B

        #add_option "-Drefine.autoreload=true -Dbutterfly.autoreload=true"

    fi

ah, sure, that works.

Or you could comment out the if and fi lines as well... or turn the "true" into "false" inside the add_option call.

 

On Fri, Dec 9, 2011 at 2:09 PM, Thad Guidry <thadg...@gmail.com> wrote:

Fixed it and got past that... it starts now, but...wondering about this 827: /tmp/refine.gLjkKFx: unexpected operator   ??

./refine: 636: Syntax error: "fi" unexpected

ubuntu@ip-1x-xx-xxx-xx:~/Desktop/Working/grefine$ ./refine -m 12000m -i 1x.xx.xxx.xx

./refine: 636: Syntax error: "fi" unexpected

ubuntu@ip-xx-xx-xxx-xx:~/Desktop/Working/grefine$ ./refine -m 12000m -i 1x.xx.xxx.xx

[: 827: /tmp/refine.gLjkKFx: unexpected operator

Starting Google Refine at 'http://1x.xx.xxx.xx:xxxx/'

20:01:34.614 [            refine_server] Starting Server bound to '1x.xx.xxx.xx:xxxx' (0ms)

20:01:34.615 [            refine_server] refine.memory size: 12000m JVM Max heap: 11184832512 (1ms)

20:01:34.631 [            refine_server] Initializing context: '/' from '/media/ebs2/scraping/Working/grefine/main/webapp' (16ms)

20:01:35.170 [                   refine] Starting Google Refine 2.5 [TRUNK]... (539ms)

Xlib:  extension "RANDR" missing on display ":1.0".

20:01:42.129 [                   refine] POST /command/core/get-importing-configuration (6959ms)

20:01:42.146 [                   refine] GET /command/core/get-all-project-metadata (17ms)

20:01:42.167 [                   refine] GET /command/core/get-version (21ms)

--
-Thad
http://www.freebase.com/view/en/thad_guidry

--
-Thad
http://www.freebase.com/view/en/thad_guidry

[Paul Makepeace]

On Fri, Dec 9, 2011 at 19:33, Stefano Mazzocchi <stef...@google.com> wrote:
> I just ran "./refine findbugs"

All software should have a "findbugs" option!

Paul

[Thad Guidry]

Still wondering about that 827 expected error, however... any ideas ?

[Stefano Mazzocchi]

Probably something in your refine.ini file that your shell doesn't like.