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compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
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StartUp Error - Java related. #5

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
When I double-click the jar file to install the program (SearchGUI or 
FragmentationAnalyzer), the following error message is showing.
--------------
An error occurred when starting the tool.
Inspect the log file for details: recources/conf/startup.log.
Then go to Java TroubleShooting.
--------------

The "startup.log" has the following message.
---------------
Memory settings read from the user preferences: 3072
args: 
original java.home: C:\Program Files\Java\jre1.8.0_45\bin\
new java.home: C:\Program Files\Java\jre1.8.0_45\bin\

Command line: 
"C:\Program Files\Java\jre1.8.0_45\bin\java" -Xms128M -Xmx3072M -cp 
"E:\FragmentationAnalyzer-1.5.11\FragmentationAnalyzer-1.5.11\FragmentationAnaly
zer-1.5.11.jar" no.uib.fragmentation_analyzer.gui.FragmentationAnalyzer 
Process exitValue: 1
----------------

------------
Memory settings read from the user preferences: 3072
args: 
original java.home: C:\Program Files\Java\jre1.8.0_45\bin\
new java.home: C:\Program Files\Java\jre1.8.0_45\bin\

Command line: 
"C:\Program Files\Java\jre1.8.0_45\bin\java" 
-splash:resources\conf\searchgui-splash.png -Xms128M -Xmx3072M -cp 
"E:\SearchGUI-1.28.1\SearchGUI-1.28.1.jar" eu.isas.searchgui.gui.SearchGUI 
Process exitValue: 1
-------------

I am using Windows 7 with 32 bit. The java version is as follows.
Java version 8 update 45 (build 1.8.0_45-b15)

I tried all the recommandations shown in the Java Troubleshooting, but failed 
to install the program.

Do you have any suggestion?
Thanks.

Original issue reported on code.google.com by jkkim48...@gmail.com on 22 Jun 2015 at 1:34

GoogleCodeExporter commented 9 years ago 
Thanks for telling us about this. The problem seems to be your memory settings, 
as on 32 bit machines you cannot use more than around 2 GB of memory (and often 
even less). Thus using 3 GB (3072 MB) is not possible.

The tools should be able top handle this automatically and set the memory to a 
value that is support on your setup. However, from the path to your Java 
installation it seems like you have installed 64 bit Java? As on the 32 bit 
version is usually installed in "C:\Program Files (x86)\Java\" and not in 
"C:\Program Files\Java\". 

Could you confirm that this is the case? You can do this by opening a command 
line window (Windows key + R > cmd > Enter > "cd C:\Program 
Files\Java\jre1.8.0_45\bin\java" > "java -version"). If you then see something 
like "Java HotSpot(TM) 64-Bit Server VM", you know you have 64 bit Java. If 
there is no 64 bit label, then you have 32 bit.

If you have 64 bit I'd recommend uninstalling all Java versions and only 
installing the latest 32 bit version.

Let me know if this helps.

Original comment by harald.b...@gmail.com on 22 Jun 2015 at 9:29

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 22 Jun 2015 at 9:29

GoogleCodeExporter commented 9 years ago 
I followed what you suggested. When I followed the command that you suggested, 
I don't see any 64 bit label. What I see is as follows.
-----------
java version"1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b15)
Java HotSpot(TM) Client VM (build 25.45-b02, mixed mode)
------------
When I uninstall the java versionm and install the lateste 32 bit version, I 
see the following message.
------------
java version"1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b15)
Java HotSpot(TM) Client VM (build 25.45-b02, mixed mode, sharing)
--------------

But still I couldn't install the program. I see the exactly same error message.
Do you have any other suggestion?
Thanks!

Original comment by jkkim48...@gmail.com on 22 Jun 2015 at 9:52

GoogleCodeExporter commented 9 years ago 
I assume you didn't manually change the memory settings via the JavaOptions.txt 
file in the SearchGUI-X.Y.Z\resources\conf folder? The bottom line in this file 
should read "-Xmx****M". If it says anything else, like "-Xmx3072M", then 
please change it to "-Xmx****M" and try starting SearchGUI again.

If this does not help you can also try changing it to "-Xmx1500M" and see if 
that allows you to start SearchGUI.

Note that I'm highlighting SearchGUI here, as FragmentationAnalyzer uses an 
older version of the utilities backend. So lets get it to work for SearchGUI 
first and then we can move on to FragmentationAnalyzer.

Original comment by harald.b...@gmail.com on 22 Jun 2015 at 11:33

GoogleCodeExporter commented 9 years ago 
When I set the **** value in "-Xmx****M" as 1210, it worked for both SearchGUI 
and 
FragmentationAnalyzer.
Thank you very much.
Now I need to get familiar to the programs.

Original comment by jkkim48...@gmail.com on 22 Jun 2015 at 2:08

GoogleCodeExporter commented 9 years ago 
Great! I will then set the issue as fixed.

However, I'd strongly recommend getting access to a 64 bit machine in order to 
be able to analyze anything but very small proteomics datasets. We recommend 
using at least 4 GB of RAM, but in general the more the better, and the faster 
the analysis will be carried out.

And don't hesitate to ask if you have any questions regarding the use of the 
tools.

Original comment by harald.b...@gmail.com on 22 Jun 2015 at 7:52