FAQ - Revision history

Smith: /* Q. Can I run geWorkbench on a 32/64-bit Windows system? */

2015-01-23T23:39:52Z

‎Q. Can I run geWorkbench on a 32/64-bit Windows system?

Smith: /* Q. How do I increase the amount of memory available to Java to run geWorkbench? */

2015-01-23T20:32:04Z

‎Q. How do I increase the amount of memory available to Java to run geWorkbench?

Smith: /* Q. Can I run geWorkbench on a 32/64-bit Windows system? */

2015-01-23T20:25:16Z

‎Q. Can I run geWorkbench on a 32/64-bit Windows system?

Smith: /* Q. How do I increase the amount of memory available to Java to run geWorkbench? */

2015-01-23T18:30:14Z

‎Q. How do I increase the amount of memory available to Java to run geWorkbench?

Smith: /* Q. I get a Java error when I try to start geWorkbench. */

2015-01-23T18:22:51Z

‎Q. I get a Java error when I try to start geWorkbench.

Smith: /* Q. Can I run geWorkbench on a 64-bit Windows system? */

2015-01-23T18:21:47Z

‎Q. Can I run geWorkbench on a 64-bit Windows system?

Smith: /* Q. How do I increase the amount of memory available to Java to run geWorkbench? */

2013-11-13T21:47:41Z

‎Q. How do I increase the amount of memory available to Java to run geWorkbench?

Smith: /* Q. How do I increase the amount of memory available to Java to run geWorkbench? */

2013-11-12T18:10:22Z

‎Q. How do I increase the amount of memory available to Java to run geWorkbench?

Smith: /* Q. How can I download the geWorkbench source? */

2013-11-04T19:46:09Z

‎Q. How can I download the geWorkbench source?

Smith: /* Q. How can I download the geWorkbench source? */

2013-11-04T19:45:54Z

‎Q. How can I download the geWorkbench source?

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 A. Yes.  geWorkbench can run on both 32 and 64-bit systems.  Starting with geWorkbench 2.6.0, both 32 and 64-bit installers are provided for Windows.  The 64-bit version is preferred as it allows larger data sets to be used.  Mac OS X itself only supports 64-bit versions.  For Linux, a 64-bit installer is provided; for 32-bit, please use the "noJRE" Linux installer.  In that case you will need to install the Java 7 JRE yourself, which can be downloaded from java.oracle.com.
 Further instructions can be found on the [[Download_and_Installation|Download and Installation]] page.
 ===Q. Will calculations run faster using a 64-bit JVM than on a 32-bit JVM?===

@@ Line 55: / Line 55: @@
 ===Q. How do I increase the amount of memory available to Java to run geWorkbench?===
-A. It depends on how you are running geWorkbench.
+A. Windows and Mac OS X versions of geWorkbench now include .bat and .command files, respectively, in the installation directory, which allow directly starting geWorkbench with anywhere from 1 to 16 GB of Java Heap Memory.
-Windows and Mac OS X versions of geWorkbench now include .bat and .command files, respectively, in the installation directory, which allow directly starting geWorkbench with anywhere from 1 to 16 GB of Java Heap Memory.
+. If you wish to instead change the default  maximum amount of Java heap memory when using the InstallAnywhere launcher, you can edit the "geworkbench.lax" file.  This does not apply to the Mac OS X version.  However, the values found in the geworkbench.lax files are already set to the maximum values that work with the InstallAnywhere launchers, depending on whether the 32-bit or 64-bit version is being used.
 '''lax.nl.java.option.java.heap.size.max=950MB''' (32-bit versions)
-'''lax.nl.java.option.java.heap.size.max=2147483647''' (64-bit versions)
+'''lax.nl.java.option.java.heap.size.max=2147483647''' (64-bit versions) (can also be entered as "2G".
-. If you are running geWorkbench from the Generic or source distributions using Ant, you can edit the build.xml file found in the geWorkbench root directory to alter the memory requested using the variable '''jvmarg''':
+. If you are running geWorkbench from the Generic or source distributions using Ant, you can edit the build.xml file found in the geWorkbench root directory to alter the memory requested using the jvmarg value="-Xmx1024M" option:
   <target name="run" depends="init" description="Runs geWorkbench.">

← Older revision		Revision as of 20:25, 23 January 2015
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	===Q. Can I run geWorkbench on a 32/64-bit Windows system?===		===Q. Can I run geWorkbench on a 32/64-bit Windows system?===

−	A. Yes. geWorkbench can run on both 32 and 64-bit systems. Starting with geWorkbench 2.6.0, both 32 and 64-bit installers are provided for Windows. ~~the~~ 64-bit version is preferred. Mac OS X itself only supports 64 bit versions. For Linux, a 64-bit installer is provided; for 32-bit, please use the "noJRE" Linux installer. ~~You~~ will need to install the Java 7 JRE yourself, which can be downloaded from java.oracle.com.	+	A. Yes. geWorkbench can run on both 32 and 64-bit systems. Starting with geWorkbench 2.6.0, both 32 and 64-bit installers are provided for Windows. The 64-bit version is preferred as it allows larger data sets to be used. Mac OS X itself only supports 64-bit versions. For Linux, a 64-bit installer is provided; for 32-bit, please use the "noJRE" Linux installer. In that case you will need to install the Java 7 JRE yourself, which can be downloaded from java.oracle.com.

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 ===Q. How do I increase the amount of memory available to Java to run geWorkbench?===
 A. It depends on how you are running geWorkbench.
 . If you are running a packaged distribution of geWorkbench (created using InstallAnywhere) (but not on Macintosh), there is a file in the geWorkbench root directory called '''geWorkbench.lax''' (in earlier versions it was called UILauncher.lax).  There is a line there which specifies the Java heap size:
-'''lax.nl.java.option.java.heap.size.max=1073741824'''
+'''lax.nl.java.option.java.heap.size.max=950MB''' (32-bit versions)
-Here it is shown set to 1 GB.  You can experiment with increasing this, subject to the amount of memory in your machine and demands on it from other applications.  On Windows or Linux, it is best to switch to a 64-bit JVM to allow larger amounts of memory to be allocated.  Use the version of geWorkbench without JVM included, and install your own 64-bit Java JVM.
+You can experiment with edit this, subject to the amount of memory in your machine and demands on it from other applications.  On Windows or Linux, you must be using a 64-bit JVM to allow larger amounts of memory to be allocated.
 . If you are running geWorkbench from the Generic or source distributions using Ant, you can edit the build.xml file found in the geWorkbench root directory to alter the memory requested using the variable '''jvmarg''':
   <target name="run" depends="init" description="Runs geWorkbench.">

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 ===Q. I get a Java error when I try to start geWorkbench.===
-A. This is almost always caused by the Sun Java JRE not being installed or not being found (when you use a version of geWorkbench that does not include the JRE).  You can either try a geWorkbench installer that includes the JRE, or make sure that an appropriate JRE is installed on your system.
+A. This is almost always caused by the Java JRE not being installed or not being found (when you use a version of geWorkbench that does not include the JRE).  You can either try a geWorkbench installer that includes the JRE, or make sure that an appropriate JRE is installed on your system.
 ===Q. Where can I obtain the latest annotation files for my microarray platform?===

@@ Line 1: / Line 1: @@
 ==Using geWorkbench==
-===Q. Can I run geWorkbench on a 64-bit Windows system?===
+===Q. Can I run geWorkbench on a 32/64-bit Windows system?===
-A. Yes.  As of release 2.0.0, geWorkbench has been tested on both 64-bit Windows 7/Vista operating systems, as well as 32-bit Windows XP.  The formal release testing for Windows is done using the 32-bit Java JRE6.    However, geWorkbench has also been tested with the 64-bit Java JRE6 on the 64-bit Windows 7 platforms, and only minor compatibility issues have been found.  These are listed in the [[Known_Issues | Known Issues]] section.
+A. Yes.  geWorkbench can run on both 32 and 64-bit systems.  Starting with geWorkbench 2.6.0, both 32 and 64-bit installers are provided for Windows.  the 64-bit version is preferred.  Mac OS X itself only supports 64 bit versions.  For Linux, a 64-bit installer is provided; for 32-bit, please use the "noJRE" Linux installer.  You will need to install the Java 7 JRE yourself, which can be downloaded from java.oracle.com.
-The prebuilt installers with JRE6 all include the 32-bit JRE.  If you wish to try the 64-bit JRE, please use a version of the geWorkbench installer which does not include the JRE.  Further instructions can be found on the [[Download_and_Installation|Download and Installation]] page.
 ===Q. Will calculations run faster using a 64-bit JVM than on a 32-bit JVM?===

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 ===Q. How can I download the geWorkbench source?===
 <span id="download_geworkbench_code"></span>
 A. The latest geWorkbench source code can be downloaded from Github.  Please see the instructions on the  [[Download_and_Installation#Download_the_geWorkbench_Source_Code |Download the geWorkbench Source Code]] section of the [[Download_and_Installation|Download and Installation page]].  Instructions for compiling the code are available on the same page at [[Download_and_Installation#Compiling_the_geWorkbench_Source_Code | Compiling the geWorkbench Source Code]].

← Older revision		Revision as of 19:45, 4 November 2013
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−	~~===~~A. The latest geWorkbench source code can be downloaded from Github. Please see the instructions on the [[Download_and_Installation#Download_the_geWorkbench_Source_Code \|Download the geWorkbench Source Code]] section of the [[Download_and_Installation\|Download and Installation page]]. Instructions for compiling the code are available on the same page at [[Download_and_Installation#Compiling_the_geWorkbench_Source_Code \| Compiling the geWorkbench Source Code]].	+	A. The latest geWorkbench source code can be downloaded from Github. Please see the instructions on the [[Download_and_Installation#Download_the_geWorkbench_Source_Code \|Download the geWorkbench Source Code]] section of the [[Download_and_Installation\|Download and Installation page]]. Instructions for compiling the code are available on the same page at [[Download_and_Installation#Compiling_the_geWorkbench_Source_Code \| Compiling the geWorkbench Source Code]].

	===Q. How do I turn on logging in installer-based versions of geWorkbench?===		===Q. How do I turn on logging in installer-based versions of geWorkbench?===