Changing HEAP_SIZE to 2000 did help.
I generated this batch xml file from GUI (batch mode). The scheme includes
raw data input, peak detection, chromatogram builder, and mass detection.
It was saved as test-batch.xml (attached). However when I run in command
line by "startMZmine_Linux.command test-batch.xml" I got the error "can't
read batch file". Why can't the xml file be recognized? How does it know
which raw data file to read in the first place? Is the raw data supposed to
be merged into the batch xml file or it will point to the raw data file in
the batch xml somewhere?
Thanks
On Thu, Feb 7, 2013 at 3:24 AM, Tomas Pluskal <plus...@oist.jp> wrote:
> 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> 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> 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
>>
>>
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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
>
>
<?xml version="1.0" encoding="UTF-8"?>
<batch>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule">
<parameter name="Raw data file names">
<file>/Users/oscar/work/mzmine/SKBRcontrol_merge_mzData.xml</file>
</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.targetedpeakdetection.TargetedPeakDetectionModule">
<parameter name="Raw data files"/>
<parameter name="Name suffix">detectedPeak</parameter>
<parameter name="Peak list file"/>
<parameter name="Field separator">,</parameter>
<parameter name="Ignore first line">false</parameter>
<parameter name="Intensity tolerance">0.01</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>0.0010</absolutetolerance>
<ppmtolerance>5.0</ppmtolerance>
</parameter>
<parameter name="Retention time tolerance" type="absolute">1.0</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule">
<parameter name="Raw data files"/>
<parameter name="Mass list">masses</parameter>
<parameter name="Min time span (min)">0.2</parameter>
<parameter name="Min height">750.0</parameter>
<parameter name="m/z tolerance">
<absolutetolerance>0.0050</absolutetolerance>
<ppmtolerance>20.0</ppmtolerance>
</parameter>
<parameter name="Suffix">chromatograms</parameter>
</batchstep>
<batchstep method="net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule">
<parameter name="Raw data files"/>
<parameter name="Mass detector" selected="Centroid">
<module name="Centroid">
<parameter name="Noise level">300.0</parameter>
</module>
<module name="Exact mass">
<parameter name="Noise level">1000.0</parameter>
</module>
<module name="Local maxima">
<parameter name="Noise level"/>
</module>
<module name="Recursive threshold">
<parameter name="Noise level"/>
<parameter name="Min m/z peak width"/>
<parameter name="Max m/z peak width"/>
</module>
<module name="Wavelet transform">
<parameter name="Noise level">33.0</parameter>
<parameter name="Scale level">3</parameter>
<parameter name="Wavelet window size (%)">0.3</parameter>
</module>
</parameter>
<parameter name="MS level">1</parameter>
<parameter name="Mass list name">masses</parameter>
</batchstep>
</batch>
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