Hi Martin, David,
If the error is reproducible, I would like to take a look at it in detail. But
I will need your cooperation.
Could you prepare a ZIP archive of your raw files, and send it to me e.g. via
rapidshare.com, dropbox.com or some other sharing website?
Also, please include the exact settings in your startMZmine script, and the
exact steps and parameters you used for processing.
Thanks a lot!
Tomas
On Dec 20, 2011, at 9:06 PM, Martin Wagner wrote:
> Hej MZmine team,
>
> It appears I am having a similar problem like David Lyon (posted on
> 2011-12-14).
>
> I have run some environmental samples on an LTQ Velos in full scan,
> data-dependent MSn and PDA. The size of the raw files is circa 180 MB in the
> negative mode and 40 MB in positive ionization.
>
> I am working with MZmine 2.4 on an octacore server with 16 GB RAM running
> Ubuntu (64Bit). My heap size is 14 GB. Processing of the data according to
> the workflow works fine until the RAM gets full. The fuller it is the slower
> the processing. This appears when I run the mass detection (exact mass) even
> with only 16 samples. Chromatogram detection is even worse. It takes app. 6 h
> computation with the local minimum algorithm. Sometimes the computer manages
> the calculation (when I wait long enough), sometimes it produces an
> "outofmemoryerror: gc overhead" error.
>
> I have tried the following without any improvement:
> - calculate on a Windows 7 machine and on MacOS X
> - calculate with MZmine 2.3
> - increase noise level during mass detection
> - crop the PDA and MSn data from the raw files (files don't get really
> smaller)
> - convert to mzXML (files get much smaller, from 180 MB to 30 MB, but same
> problem)
>
> I did similar calculations with similar samples in MZmine 2.2 and never
> experienced problems. Now I'm running out of ideas. It appears to be a
> problem with the JavaVM rather than with MZmine but I don't know how to solve
> that.
>
> Thanks for your help & all the best from snowy Germany!
>
> Martin
>
>
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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
TEL: +81-98-966-8684
------------------------------------------------------------------------------
Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create
new or port existing apps to sell to consumers worldwide. Explore the
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
http://p.sf.net/sfu/intel-appdev
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