FileNotFoundException (Too many open files)

[ca...@distillanalytics.ca]

Hello!

I tried googling, searching the group's topics and the wiki and I am happy to report that I didn't find anything for this!

I'm starting to get a stream of these exceptions in my log:

java.io.FileNotFoundException: /mnt/refine/workspace.temp.json (Too many open files)

        at java.io.FileOutputStream.open(Native Method)

        at java.io.FileOutputStream.<init>(FileOutputStream.java:221)

        at java.io.FileOutputStream.<init>(FileOutputStream.java:171)

        at java.io.FileWriter.<init>(FileWriter.java:90)

        at com.google.refine.io.FileProjectManager.saveToFile(FileProjectManager.java:274)

        at com.google.refine.io.FileProjectManager.saveWorkspace(FileProjectManager.java:243)

        at com.google.refine.ProjectManager.save(ProjectManager.java:212)

        at com.google.refine.RefineServlet$AutoSaveTimerTask.run(RefineServlet.java:94)

        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)

        at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304)

        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178)

        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:745)

17:55:16.616 [       FileProjectManager] Failed to save workspace (4200016ms)

So I investigated how many files I had open and what my ulimits are!

ulimit -Hn

4096

ulimit -Hs

unlimited

ulimit -a

core file size          (blocks, -c) 0

data seg size           (kbytes, -d) unlimited

scheduling priority             (-e) 0

file size               (blocks, -f) unlimited

pending signals                 (-i) 257614

max locked memory       (kbytes, -l) 64

max memory size         (kbytes, -m) unlimited

open files                      (-n) 1024

pipe size            (512 bytes, -p) 8

POSIX message queues     (bytes, -q) 819200

real-time priority              (-r) 0

stack size              (kbytes, -s) 8192

cpu time               (seconds, -t) unlimited

max user processes              (-u) 257614

virtual memory          (kbytes, -v) unlimited

file locks                      (-x) unlimited

I used the list of file descriptors under /proc/{pid}/fd to count the file descriptors... They seem to be climbing! When I started composing this message I was at 349, now they've risen to 1136!

In the past, I've had success trying to up the memory for java in order to accommodate large datasets... Should I also be upping the number of files it is possible to open?

Cheers,

Caleb

PS: I've got a large custom text facet that includes a hefty regexp. And I'm trying to add a column based on the matches of said regexp. I can characterize what that regexp is if you may find it useful for debugging.

[qi cui]

It's not about the limit of your OS. It's more about why the process(s) trigger so many "save" action. 

You can check how often do you see this exception. Also the if you can provide the size of data set and the action you tried to apply etc that will be helpful.

[qi cui]

One more thing, which File system do you attached to? If the mount point detached silently, you may come across this issue.

On Thursday, June 9, 2016 at 2:35:30 PM UTC-4, ca...@distillanalytics.ca wrote:

[Caleb Buxton]

Thanks for these tips! The next time it happens I'll check all these. However, as I haven't been able to reproduce recently, I'm going to lean on file system detaching silently. *shrug*

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