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> 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
> Fax: +81-98-966-2890
>
>
------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
