[Iplant-api-dev] Error occurred during initialization of VM

[Damian Gessler]

Hi Liya,

I've been running into those issues also.

I've had some success by using 'idev' on lonestar and 'srun' on stampede 
to get a temporary cluster allocation.

For idev, just type:
	$ idev

and it will set you up w/ a default alloc.

For 'srun', the stampede welcome message shows:

	$ srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

What I do not know is what type of JVM alloc errors a user may get when 
running a Java app under fAPI. Perhaps Rion or Matt can clarify.

D.


On 12/12/13 3:09 PM, Wang, Liya wrote:
> I am trying to parallelize TASSEL via launcher but got this error. Any clue?
>
> Part of the error file:
>
> Memory Settings: -Xms512m -Xmx2536m
> Tassel Pipeline Arguments: -fork1 -NamGwasPlugin -map nam/map.txt -rils nam/markers/chr8.txt -trait /iplant/home//lwang/co59.txt -m out.model.8 -s out.step.8 -fullmodel -founders nam/founders/c8.txt -iterations 10 -start 1 -endPlugin -runfork1
>
> Error occurred during initialization of VM
> Could not reserve enough space for object heap
> Error occurred during initialization of VM
> Could not reserve enough space for object heap
> #
> #
> # There is insufficient memory for the Java Runtime Environment to continue.
> # There is insufficient memory for the Java Runtime Environment to continue.
> # Native memory allocation (malloc) failed to allocate # Native memory allocation (malloc) failed to allocate 1048576 bytes1048576 bytes for E in /HUDSON/workspace/jdk7u21-2-build-linux-amd64-product/jdk7u21/hotspot/src/share/vm/utilities/taskqueue.hpp for
> E in /HUDSON/workspace/jdk7u21-2-build-linux-amd64-product/jdk7u21/hotspot/src/share/vm/utilities/taskqueue.hpp
> # An error report file with more information is saved as:
> # /scratch/0004/iplant/lwang/job-36346-namgwas_analysis1-2013-12-12-21-49-30476/bin/hs_err_pid27026.log
> #
> # There is insufficient memory for the Java Runtime Environment to continue.
> # Native memory allocation (malloc) failed to allocate 1048576 bytes for E in /HUDSON/workspace/jdk7u21-2-build-linux-amd64-product/jdk7u21/hotspot/src/share/vm/utilities/taskqueue.hpp
> # An error report file with more information is saved as:
> # /scratch/0004/iplant/lwang/job-36346-namgwas_analysis1-2013-12-12-21-49-30476/bin/hs_err_pid27099.log
> # An error report file with more information is saved as:
> # /scratch/0004/iplant/lwang/job-36346-namgwas_analysis1-2013-12-12-21-49-30476/bin/hs_err_pid27095.log
> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> #  SIGSEGV (0xb) at pc=0x0000000000000000, pid=27096, tid=1095551296
> #
> # JRE version: 7.0_21-b11
> # Java VM: Java HotSpot(TM) 64-Bit Server VM (23.21-b01 mixed mode linux-amd64 compressed oops)
> # Problematic frame:
> # C  0x0000000000000000
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