EGAN hangs, crashes or doesn't start
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ucsf egan
Jul 2, 2010, 8:40:28 PM7/2/10
to UCSF EGAN
EGAN users,
About 99% of all user-reported issues with EGAN are a result of EGAN
requesting too much or not having enough memory (AKA RAM).
Here's a quick guide:
If EGAN doesn't start at all, it's likely that the EGAN .jnlp file is
requesting more memory than your computer has available. See "how to
edit the jnlp" below and reduce the default number to request less
memory for EGAN at startup. Try to find a number that gives EGAN as
much memory as possible, but still allows EGAN to run.
If EGAN crashes, there may be a problem with your OS' version of the
JVM, but it is most likely due to EGAN not having enough memory to
accommodate all specified data sets. See "how to edit the jnlp" below
and raise the default number to request more memory for EGAN at
startup. But not too much that EGAN doesn't start at all.
If EGAN hangs or seems to run very slowly, there are two likely
causes: 1) EGAN is running out of available memory and is about to
crash, or 2) EGAN has enough available memory, but other programs
running on your computer have filled up the entire amount of system
memory, and your OS is attempting to use your hard drive for overflow
as "virtual memory" (AKA "paging"). Close all other programs that you
can and restart EGAN (you can also choose to just wait for the OS to
put all of EGAN's data back in RAM, but that may take a while).
Otherwise, you can also "edit the jnlp" (see below) and raise the
default number to request more memory for EGAN at startup.
How to Edit the JNLP
1) Download one of the .jnlp files that you regularly use from the
EGAN Downloads page. (they're the ones entitled "Launch") You'll
want to save the file to your local computer, say to the Desktop.
2) Open the JNLP file in a text editor and edit the following line:
<j2se version="1.6+" max-heap-size="1400M" java-vm-args="-Xincgc"></
j2se>
See the part that says max-heap-size="1400M"? That means that EGAN
will request 1400 megabytes of RAM from your computer. All you need
to do is change this number and save the file. On 32-bit operating
systems, the maximum amount of RAM you can request is around 1535M.
On 64-bit systems, I'm not sure what the maximum is, but it's huge in
comparison. You may want to experiment with the number to find a the
best amount - and know that EGAN running with different data set
configurations will require different amounts of memory.
One last tip:
You can always reduce the amount of memory that EGAN requires by
removing datasets from EGAN in the Launch EGAN Wizard. The biggest
memory hogs are the Conserved Domain and MeSH association nodes (in
the Association Data tab) and the PubMed Co-occurrence edges (also in
the Association Data tab). Click the row to select the offending data
set and click the "Remove Selected Sets" button.
Hope this helps,
Jesse
About 99% of all user-reported issues with EGAN are a result of EGAN
requesting too much or not having enough memory (AKA RAM).
Here's a quick guide:
If EGAN doesn't start at all, it's likely that the EGAN .jnlp file is
requesting more memory than your computer has available. See "how to
edit the jnlp" below and reduce the default number to request less
memory for EGAN at startup. Try to find a number that gives EGAN as
much memory as possible, but still allows EGAN to run.
If EGAN crashes, there may be a problem with your OS' version of the
JVM, but it is most likely due to EGAN not having enough memory to
accommodate all specified data sets. See "how to edit the jnlp" below
and raise the default number to request more memory for EGAN at
startup. But not too much that EGAN doesn't start at all.
If EGAN hangs or seems to run very slowly, there are two likely
causes: 1) EGAN is running out of available memory and is about to
crash, or 2) EGAN has enough available memory, but other programs
running on your computer have filled up the entire amount of system
memory, and your OS is attempting to use your hard drive for overflow
as "virtual memory" (AKA "paging"). Close all other programs that you
can and restart EGAN (you can also choose to just wait for the OS to
put all of EGAN's data back in RAM, but that may take a while).
Otherwise, you can also "edit the jnlp" (see below) and raise the
default number to request more memory for EGAN at startup.
How to Edit the JNLP
1) Download one of the .jnlp files that you regularly use from the
EGAN Downloads page. (they're the ones entitled "Launch") You'll
want to save the file to your local computer, say to the Desktop.
2) Open the JNLP file in a text editor and edit the following line:
<j2se version="1.6+" max-heap-size="1400M" java-vm-args="-Xincgc"></
j2se>
See the part that says max-heap-size="1400M"? That means that EGAN
will request 1400 megabytes of RAM from your computer. All you need
to do is change this number and save the file. On 32-bit operating
systems, the maximum amount of RAM you can request is around 1535M.
On 64-bit systems, I'm not sure what the maximum is, but it's huge in
comparison. You may want to experiment with the number to find a the
best amount - and know that EGAN running with different data set
configurations will require different amounts of memory.
One last tip:
You can always reduce the amount of memory that EGAN requires by
removing datasets from EGAN in the Launch EGAN Wizard. The biggest
memory hogs are the Conserved Domain and MeSH association nodes (in
the Association Data tab) and the PubMed Co-occurrence edges (also in
the Association Data tab). Click the row to select the offending data
set and click the "Remove Selected Sets" button.
Hope this helps,
Jesse
ucsf egan
Jul 22, 2010, 1:01:03 PM7/22/10
to UCSF EGAN
Another issue might be that you have an older version of Java. EGAN
requires Java 1.6 or higher. Go to http://java.com for the latest
version.
requires Java 1.6 or higher. Go to http://java.com for the latest
version.
ucsf egan
Jul 22, 2010, 1:20:12 PM7/22/10
to UCSF EGAN
Some people running Internet Explorer will find the "Save as..."
option unavailable for .jnlp files. I'm not sure how to configure IE
to allow the "Save as..." option for JNLP, so my best workaround
suggestion at this point would be that you download the .jnlp files
for editing using a different browser (Firefox/Chrome/Safari/etc.)
option unavailable for .jnlp files. I'm not sure how to configure IE
to allow the "Save as..." option for JNLP, so my best workaround
suggestion at this point would be that you download the .jnlp files
for editing using a different browser (Firefox/Chrome/Safari/etc.)
christoph...@ucsf.edu
Feb 13, 2014, 2:09:11 PM2/13/14
to ucsf...@googlegroups.com
I'm getting this:
java.lang.NullPointerException
at edu.ucsf.cc.icore.app.egan.EganFrame.getBackground(EganFrame.java:118)
at java.awt.Window.setBackground(Window.java:3798)
at java.awt.Frame.setBackground(Frame.java:988)
at javax.swing.JFrame.frameInit(JFrame.java:259)
at javax.swing.JFrame.<init>(JFrame.java:225)
at edu.ucsf.cc.icore.app.egan.EganFrame.<init>(EganFrame.java:84)
at edu.ucsf.cc.icore.app.egan.EganState.constructEganFrame(EganState.java:86)
at edu.ucsf.cc.icore.app.egan.EganState.<init>(EganState.java:67)
at edu.ucsf.cc.icore.app.egan.launch.LaunchEgan.constructEganState(LaunchEgan.java:348)
at edu.ucsf.cc.icore.app.egan.launch.LaunchEganThread.run(LaunchEganThread.java:142)
at java.lang.Thread.run(Thread.java:744)
ucsf egan
Feb 13, 2014, 2:16:43 PM2/13/14
to ucsf...@googlegroups.com
Hi Christopher,
This is a known issue between EGAN and Java 7 and will be fixed soon. In the meantime, here are the workarounds:
Jesse
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