Hi Chris,
I checked the code of the baseline correction module, and I think the problem
mentioned below comes from the way how the module deals with the scans.
The module creates a copy of the whole raw data in memory (by creating lots of
SimpleScan instances) and then writes them all to RawDataFileWriter.
If the amount of the data is large, that will cause heap overload.
IMHO scans should be processed one by one and immediately added to the
RawDataFileWriter.
Adding the new scan to the RawDataFileWriter will turn the scan into a
StorableScan and therefore the memory can be reclaimed.
What do you think?
Cheers,
Tomas
On Jul 29, 2012, at 2:34 PM, 石田 和也 wrote:
Dear developpers
My name is Kazuya, and I am researching metabolomics by OrbitrapXL(Thermo) at
CERI.
I am triing to introduce MZmine2 for our processing scheme.
This reason why I am writting this e-mail to you is I would like to ask
questions about Java heap size of MZmine2.
I imported to the software our .raw files(MS scan data about 150Mb/file), then
I performed "Baseline correction"(conditions are following).
But, this processing was aborted at once and diplayed a message "Java heap
space".
I adjusted heap size to 2048 kB(maximum memmory size in our PC is 4MB) , but
this process aborted.
So, could you advise to me how many need a heap size at least?
If you needs other informations to solve this problem, please do not hesitate
to ask.
Processing conditions
Chromatogram type; "TIC"
MS level; "1"
Smoothing; "100,000(=10^5)"
Asymmetry; "0.01"
m/z bin width; "0.01"
Sincerely,
Kazuya
++++++++++++++++++++++++++++++++++++++++++
Kazuya Ishida
Chemicals Evaluation and Research Institute, Japan
Email: ishida-kaz...@ceri.jp<mailto:ishida-kaz...@ceri.jp>
Phone: +81-480-37-2601 Fax: +81-480-37-2521
URL: http://www.cerij.or.jp/ceri_en/index_e4.shtml
++++++++++++++++++++++++++++++++++++++++++
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