Hi Dian,
Please try running the following command on your Linux system:
java -Xms12048m -Xmx12048m -version
If it fails with the same error you saw before, there is something strange with
your system: although the system has 24GB of RAM (as you say), the Java VM
could not allocate 12GB of space.
This might happen in case more than half of your RAM is already occupied and
there is no swap space configured.
Anyway, you can just set the HEAP_SIZE value manually, e.g. to 2000 (=2 GB).
Cheers,
Tomas
On Feb 6, 2013, at 10:52 PM, Dian Jiao
<oscarj...@gmail.com<mailto:oscarj...@gmail.com>> wrote:
Thanks for the reply Tomas.
My Linux is 64 bit. It has 24GB of memory. I tried to print out the HEAP_SIZE
and it shows 12048. Is ~12G memory not enough to load the VM?
Dian
On Wed, Feb 6, 2013 at 3:49 AM, Tomas Pluskal
<plus...@oist.jp<mailto:plus...@oist.jp>> wrote:
Hi Dian,
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?
Java VM is certainly needed, because the whole MZmine code is written in Java.
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.
As Matthias already suggested, check the HEAP_SIZE variable in the startup
script.
The above error means that the Java VM tried to allocate more memory than what
was available from the OS.
How much memory does your Linux machine have? Is it running 32-bit or 64-bit
kernel?
Another question is, does this startMZmine script execute all three steps: mass
detection, chromatogram building and perk deconvolution?
The batch script will execute all modules that you put into your batch, in the
same order as they appear in the batch.
Is it possible to manually run them one by one (by option/flag)?
Sorry, that is not possible. But you can prepare different batches according to
your needs.
Tomas
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684<tel:%2B81-98-966-8684>
Fax: +81-98-966-2890<tel:%2B81-98-966-2890>
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===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
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and get the hardware for free! Learn more.
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