[Swift-user] Swift is stuck with 5K jobs

[Andriy Fedorov]

Thanks, Allan. Now I have a different exception:

class org.globus.cog.abstraction.impl.file.coaster.buffers.NIOChannelReadBuffer
throws exception in doStuff. Fix it!
java.lang.NullPointerException
	at org.globus.cog.abstraction.impl.file.coaster.commands.PutFileCommand.error(PutFileCommand.java:95)
	at org.globus.cog.abstraction.impl.file.coaster.buffers.ReadBuffer.error(ReadBuffer.java:79)
	at org.globus.cog.abstraction.impl.file.coaster.buffers.NIOChannelReadBuffer.doStuff(NIOChannelReadBuffer.java:42)
	at org.globus.cog.abstraction.impl.file.coaster.buffers.Buffers.run(Buffers.java:133)



On Mon, Mar 14, 2011 at 11:15, Allan Espinosa <aespinosa at cs.uchicago.edu> wrote:
> Hello Andriy,
>
> The default package may have a small max heap limit.  Usually, I apply
> this patch whenever I get a new version of Swift:
>
> --- old/bin/swift       2010-10-12 12:18:47.000000000 -0500
> +++ new/bin/swift       2010-10-12 12:18:37.000000000 -0500
> @@ -9,7 +9,7 @@
>
>  CYGWIN=
>  CPDELIM=":"
> -HEAPMAX=256M
> +HEAPMAX=4096M
>
>  if echo `uname` | grep -i "cygwin"; then
>   CYGWIN="yes"
>
>
> Works well with 800K jobs.
>
> -Allan
>
> 2011/3/14 Andriy Fedorov <fedorov at bwh.harvard.edu>:
>> Hi,
>>
>> I am using swift with coasters on NCSA Abe. I use binary build of
>> swift 0.92. My script should generate about 5K individual jobs. When I
>> try to run it, I have
>>
>> Swift svn swift-r4157 cog-r3056
>>
>> RunID: 20110314-0951-f3c45zja
>> Progress:
>> Exception in thread "Timer-0" java.lang.OutOfMemoryError: Java heap space
>>
>> Exception in thread "SIGINT handler"
>> Exception in thread "SIGINT handler" Exception in thread "SIGTERM handler"
>>
>> After this error, I am not able to terminate the script, and no jobs
>> get scheduled to pbs apparently.
>>
>> Am I hitting some limit? Is 5K jobs too much?
>>
>> How do I terminate swift now not to waste cycles of the head node?
>>
>> Thanks
>> --
>> Andriy Fedorov, Ph.D.
>>
>> Research Fellow
>> Brigham and Women's Hospital
>> Harvard Medical School
>> 75 Francis Street
>> Boston, MA 02115 USA
>> fedorov at bwh.harvard.edu
>> (617) 525-6258 (office)
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
>>
>>
>
>
>
> --
> Allan M. Espinosa <http://amespinosa.wordpress.com>
> PhD student, Computer Science
> University of Chicago <http://people.cs.uchicago.edu/~aespinosa>
>