how to deal with insufficient memory

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Nishikant Wase

May 27, 2014, 11:26:06 AM5/27/14
Hi i am trying to run mzmatchR for my peaklist. But it struck at insufficient memory. Does anyone has any idea how to deal with this.

I am running mzmatch on a windows R2 server 64bit machine.  

---------------  S Y S T E M  ---------------

OS: Windows Server 2008 R2 , 64 bit Build 7601 Service Pack 1

CPU:total 2 (1 cores per cpu, 2 threads per core) family 15 model 4 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ht, tsc

Memory: 4k page, physical 3659920k(213180k free), swap 9039428k(1879116k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (25.5-b02) for windows-amd64 JRE (1.8.0_05-b13), built on Mar 18 2014 01:08:39 by "java_re" with MS VC++ 10.0 (VS2010)

time: Sat May 24 06:26:06 2014
elapsed time: 52 seconds

This is the error i am getting.  is there a way to get around this?

# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 1048576 bytes for AllocateHeap
# Possible reasons:
#   The system is out of physical RAM or swap space
#   In 32 bit mode, the process size limit was hit
# Possible solutions:
#   Reduce memory load on the system
#   Increase physical memory or swap space
#   Check if swap backing store is full
#   Use 64 bit Java on a 64 bit OS
#   Decrease Java heap size (-Xmx/-Xms)
#   Decrease number of Java threads
#   Decrease Java thread stack sizes (-Xss)
#   Set larger code cache with -XX:ReservedCodeCacheSize=
# This output file may be truncated or incomplete.
#  Out of Memory Error (memory/allocation.inline.hpp:62), pid=948, tid=6900
# JRE version:  (8.0_05-b13) (build )
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.5-b02 mixed mode windows-amd64 compressed oops)
# Core dump written. Default location: Z:\Constance\OA ANALOGUES\FTICR-Final-April 1-2014\20140307CDRNeg\hs_err_pid948.mdmp

Andris Jankevics

May 27, 2014, 11:38:12 AM5/27/14
to Nishikant Wase, Ideom
Hi, as fas as I can see from error message you are using 32-bit Java and R. By default it can allocate only 4 GB per process. So switch to 64-bit software. 

Best Regards,

Andris Jankevics

Research associate
Faculty of Life Sciences, Manchester Institute of Biotechnology, 
University of Manchester,
Manchester, United Kingdom

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