Hi DJ,
the message
Error occurred during initialization of VM
Could not reserve enough space for object heap
means that the program cannot start because it is not able to reserve
enough main memory (RAM).
FInd out how much memory yourlinux machine has, then edit the script
startMZmine_Linux.sh:
in line 7 you find
HEAP_SIZE=`free -m | awk '/Mem:/ {print int($2 / 2)}'`
change that to something like
HEAP_SIZE=1024
(1024 for reserving 1024 MB, i.e. 1 GByte for the program)
You may have to experiment with different numbers.
HTH
Matthias
On Tue, Feb 5, 2013 at 10:14 PM, Dian Jiao <oscarj...@gmail.com> wrote:
> Hi,
>
> I was trying to run MZmine with command line on a Linux machine. It is a
> remote machine and it does not support X server. Therefore, I prepared the
> input xml file on a local computer and copied it over to the Linux machine.
> I did "startMZmine_Linux.sh myfile.xml" and got the following error. Is
> java VM really needed for command-line mode? If not is there a way to
> disable it? If java VM is indeed needed, how do I increase the heap size?
>
> Error occurred during initialization of VM
> Could not reserve enough space for object heap
> Error: Could not create the Java Virtual Machine.
> Error: A fatal exception has occurred. Program will exit.
> Error occurred during initialization of VM
> Could not reserve enough space for object heap
> Error: Could not create the Java Virtual Machine.
> Error: A fatal exception has occurred. Program will exit.
>
> Another question is, does this startMZmine script execute all three
> steps: mass detection, chromatogram building and perk deconvolution? Is it
> possible to manually run them one by one (by option/flag)?
>
> Thanks,
>
> DJ
>
>
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