Fedora Linux Support Community & Resources Center
  #1  
Old 3rd July 2012, 06:36 AM
trotel Offline
Registered User
 
Join Date: Jan 2012
Location: Lima, Perú
Posts: 21
linuxfirefox
Java JVM installation 64-bit

Hi, I completly newer in Java and I need to run a program that requiere Java Virtual Machine,
It is doesn't installed by default in my F17 64-bit because when I run my program it show me that.

Code:
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
So I folowed the instructions from http://www.java.com/en/download/help...ad_options.xml. There said in 32-bit but I suppouse that is similar for 64-bit, so I dowload jre-7u5-linux-x64.rpm and .... the instructions said that I have to type ./jre-7u5-linux-x64.rpm.bin but my file doesn't have ***.bin, it doesn't work for me.

I type rpm -ivh jre-7u5-linux-x64.rpm but it show me that is already installed

But when I run again my program, this show me tha same error.

So, How can I install JVM in F17 for 64-bits, please?

Last edited by trotel; 6th July 2012 at 11:07 PM. Reason: (SOLVED)
Reply With Quote
  #2  
Old 3rd July 2012, 02:38 PM
CoffeeNKeyboard Offline
Registered User
 
Join Date: Sep 2011
Location: TheCloud
Posts: 25
windows_7firefox
Re: Java JVM installation 64-bit

I think the instructions are out of sync with the downloads available. I couldn't locate the rpm.bin download on the Java site. I remember, they used to have these for Java 6. This can feel overwhelming to a new user.

I prefer the approach documented here. Give this a go. Ask here if you get stuck, with the output you get.

Install Sun/Oracle Java JDK/JRE 7u5 on Fedora 17/16, CentOS/RHEL 6.2/5.8

=== Summarised for your scenario ===

1. su -
2. rpm -Uvh /path/to/binary/jre-7u5-linux-x64.rpm
3. Step 4b (go with the absolute version for now)
4. Relevant checks in step 5. Check for javac is not relevant if you are installing the JRE
5. Step 6 may not be necessary, but it is worth running the commands to verify everything is in order. Just run the command (i.e. alternatives --config java) and review the output. If the + sign is next to the JRE you want, just press ENTER once.
6. Post install configuration

Last edited by CoffeeNKeyboard; 3rd July 2012 at 02:59 PM.
Reply With Quote
  #3  
Old 3rd July 2012, 03:00 PM
marko Offline
Registered User
 
Join Date: Jun 2004
Location: Laurel, MD USA
Posts: 6,050
linuxfirefox
Re: Java JVM installation 64-bit

Java is in the Default Fedora repositories, it would be much easier to just run:

Quote:
su -
<root password>
yum install java-1.7.0-openjdk.x86_64
If one of your programs has an obscure problem with the Open JDK, then you can resort to the Oracle JDK. See also these instructions which talks about both these options:


http://www.mjmwired.net/resources/mj...-f17.html#java
Reply With Quote
  #4  
Old 3rd July 2012, 05:37 PM
trotel Offline
Registered User
 
Join Date: Jan 2012
Location: Lima, Perú
Posts: 21
linuxfirefox
Re: Java JVM installation 64-bit

Quote:
Originally Posted by CoffeeNKeyboard View Post
...
I prefer the approach documented here. Give this a go. Ask here if you get stuck, with the output you get.

Install Sun/Oracle Java JDK/JRE 7u5 on Fedora 17/16, CentOS/RHEL 6.2/5.8
Thank for the link, I followed the instruction, and your instructions, but when I run my program, it show me the same error.

My program is: http://apollo.berkeleybop.org/current/index.html

---------- Post added at 04:37 PM ---------- Previous post was at 04:34 PM ----------

Quote:
Originally Posted by marko View Post
Java is in the Default Fedora repositories, it would be much easier to just run:
If one of your programs has an obscure problem with the Open JDK, then you can resort to the Oracle JDK. See also these instructions which talks about both these options:
http://www.mjmwired.net/resources/mj...-f17.html#java
Thanks, I folloed the instructions in that link, is the same that http://www.if-not-true-then-false.co...#comment-33160 but it show the same error.
Reply With Quote
  #5  
Old 3rd July 2012, 05:55 PM
CoffeeNKeyboard Offline
Registered User
 
Join Date: Sep 2011
Location: TheCloud
Posts: 25
windows_7firefox
Re: Java JVM installation 64-bit

Quote:
Originally Posted by trotel View Post
Which Apollo Linux installer did you download? One has JVM included.

It might be easier to help if you list out the procedure you followed in as much detail as possible, perhaps copy/paste the text from the terminal as well.

How far did you get with the commands on the link I posted? Can you paste the output here for each step?
Reply With Quote
  #6  
Old 3rd July 2012, 08:13 PM
trotel Offline
Registered User
 
Join Date: Jan 2012
Location: Lima, Perú
Posts: 21
linuxfirefox
Re: Java JVM installation 64-bit

Quote:
Originally Posted by CoffeeNKeyboard View Post
Which Apollo Linux installer did you download? One has JVM included.

It might be easier to help if you list out the procedure you followed in as much detail as possible, perhaps copy/paste the text from the terminal as well.

How far did you get with the commands on the link I posted? Can you paste the output here for each step?
Thanks, this is my procedure:

1. I download the Apollo_linux_with_jre.sh (includes Java VM)
2. I move that in: /usr/local/bioinfo/dir/apollo/ and I gave it permissions
3. I run: /bin/sh Apollo_linux_with_jre.sh
4. When I run that it ask me about the directory where it was installled and the symlink
- My directory is: /usr/local/bioinfo/dir/apollo/
- My symlink location is: /usr/local/bioinfo/bin/
5. When I want to run that it show me.
Code:
$ apollo 
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
6. I try to install the JMV, so I dowload this.
- jdk-7u5-linux-x64.rpm
For mistake I type this, it is for JDK,
Code:
alternatives --install /usr/bin/java java /usr/java/latest/jre/bin/java 20000
and when I typed java -version it show me that java command not found.
So I installed java again yum -y install java and yum -y install icedtea-web
7. In case I download these both and I tyed to installed those, I move both in /usr/local/java/
- jdk-7u5-linux-x64.rpm
- jre-7u5-linux-x64.rpm
And I installed
Code:
rpm -Uvh jdk-7u5-linux-x64.rpm
rpm -Uvh jre-7u5-linux-x64.rpm
8. Installation. This step, here occurs something very rare, first I follow the intructions for "latest version (/usr/java/latest)" and when I typed javaws it show me an error.
Code:
alternatives --install /usr/bin/javaws javaws /usr/java/latest/jre/bin/javaws 20000
failed to read link /usr/bin/javaws: No such file or directory
the second time occurs the same (second time with absolute version (/usr/java/jre1.7.0_05)) but in the third time ("latest version (/usr/java/latest)" again) all was ok, it was the result for the third time.
Code:
alternatives --install /usr/bin/java java /usr/java/latest/jre/bin/java 20000
alternatives --install /usr/bin/javaws javaws /usr/java/latest/jre/bin/javaws 20000
alternatives --install /usr/lib64/mozilla/plugins/libjavaplugin.so libjavaplugin.so.x86_64 /usr/java/latest/jre/lib/amd64/libnpjp2.so 20000
alternatives --install /usr/bin/java java /usr/java/latest/bin/java 20000
alternatives --install /usr/bin/javaws javaws /usr/java/latest/bin/javaws 20000
alternatives --install /usr/lib64/mozilla/plugins/libjavaplugin.so libjavaplugin.so.x86_64 /usr/java/latest/lib/amd64/libnpjp2.so 20000
9. I sheck
Code:
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)
10. I choose the alternatives
Code:
alternatives --config java

There are 5 programs which provide 'java'.

  Selection    Command
-----------------------------------------------
   1           /usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java
*+ 2           /usr/java/latest/jre/bin/java
   3           /usr/java/latest/bin/java
   4           /usr/java/jre1.7.0_05/bin/java
   5           /usr/java/jdk1.7.0_05/jre/bin/java

Enter to keep the current selection[+], or type selection number: 2
Code:
alternatives --config javaws

There are 3 programs which provide 'javaws'.

  Selection    Command
-----------------------------------------------
*+ 1           /usr/java/latest/jre/bin/javaws
   2           /usr/java/latest/bin/javaws
   3           /usr/java/jdk1.7.0_05/jre/bin/javaws

Enter to keep the current selection[+], or type selection number: 1
Code:
alternatives --config libjavaplugin.so.x86_64 

There are 5 programs which provide 'libjavaplugin.so.x86_64'.

  Selection    Command
-----------------------------------------------
   1           /usr/lib64/IcedTeaPlugin.so
*+ 2           /usr/java/latest/jre/lib/amd64/libnpjp2.so
   3           /usr/java/latest/lib/amd64/libnpjp2.so
   4           /usr/java/jre1.7.0_05/lib/amd64/libnpjp2.so
   5           /usr/java/jdk1.7.0_05/jre/lib/amd64/libnpjp2.so

Enter to keep the current selection[+], or type selection number: 2
Code:
alternatives --config javac                    # nothing happened
11. I add a variable in my file /etc/profile.d/bioinfo.sh
Code:
## export JAVA_HOME JDK/JRE ##
export JAVA_HOME="/usr/java/latest"
12. I restart my machine and test the variable and run my program again.
Code:
$ echo $JAVA_HOME
/usr/java/latest
Code:
$ apollo 
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
Well, what was my mistake?

Last edited by trotel; 3rd July 2012 at 08:34 PM.
Reply With Quote
  #7  
Old 3rd July 2012, 09:59 PM
CoffeeNKeyboard Offline
Registered User
 
Join Date: Sep 2011
Location: TheCloud
Posts: 25
linuxfirefox
Re: Java JVM installation 64-bit

I think you made more effort than you needed to Don't worry, we learn by making mistakes and come out more confident in the process.

Alright, I'll step you through it bit by bit, so let's focus on one thing at a time. There may be a few things we can tidy up with JDK, but for now it appears you have managed to get a working one. So let's focus on Apollo first. Post your output if something doesn't work as expected.

Below is how I managed to install Apollo. Looks like you missed (or didn't understand the significance) the notes in Linux instructions and the FAQ.

It might be a good idea to move /usr/bin/bioinfo to somewhere like /tmp. I don't think it is needed. But better to move it to /tmp just in case we need it.

Since you have a JVM installed, download Apollo_unix.sh

Maybe it is fine to run it from where it was downloaded, but I like to follow a clean approach, so I moved the downloaded file to a temporary location /tmp in case the installer generates a load of temporary files when it runs.

At a terminal (as a regular user), type
Code:
cp ~/Downloads/Apollo_unix.sh /tmp
then run the installer as root, like so
Code:
su - 
Password: <-- enter password
cd /tmp
[root@phenom2 tmp]# /bin/sh Apollo_unix.sh 
testing JVM in /usr/java/jdk1.6.0_32 ...
Starting Installer ...
Apollo installer window appears. Step through the installer wizard with the defaults (the defaults I got are shown in the screenshots):

Apollo installer Step 1

Apollo installer Step 2

Apollo installer Step 3
I chose Don't create symlinks, although I don't think there is any harm if you do (see Apollo > Linux Instructions > Notes).

Apollo installer Step 4

We are done as root. So exit the root shell and drop back to the ordinary shell.
Go to the folder we chose as default in the installer wizard
Code:
[coffeenkeyboard@phenom2 ~]$ cd /opt/Apollo/
And launch Apollo.

Note: I get an error, but I believe it can be ignored. Maybe Apollo doesn't like something about my network configuration.
Code:
[coffeenkeyboard@phenom2 Apollo]$ ./bin/apollo 
APOLLO_ROOT set to /opt/Apollo
Couldn't find JavaPath line in apollo.cfg file, trying to guess path to java...
./bin/apollo: line 212: unalias: java: not found
Using version of Java in /usr: /usr/bin/java
Web browser = netscape
Starting apollo (memory = 800M)...
/usr/bin/java -ms50M -Xmx800M -classpath /opt/Apollo/jars/apollo.jar:/opt/Apollo/jars/bbop.jar:/opt/Apollo/jars/biojava.jar:/opt/Apollo/jars/ecp1_0beta.jar:/opt/Apollo/jars/ensj.jar:/opt/Apollo/jars/jakarta-oro-2.0.6.jar:/opt/Apollo/jars/jaxp.jar:/opt/Apollo/jars/jnlp.jar:/opt/Apollo/jars/junit.jar:/opt/Apollo/jars/log4j-1.2.14.jar:/opt/Apollo/jars/macify-1.1.jar:/opt/Apollo/jars/mysql-connector-java-3.1.8-bin.jar:/opt/Apollo/jars/oboedit.jar:/opt/Apollo/jars/obo.jar:/opt/Apollo/jars/org.mortbay.jetty.jar:/opt/Apollo/jars/patbinfree153.jar:/opt/Apollo/jars/pg74.213.jdbc3.jar:/opt/Apollo/jars/psgr2.jar:/opt/Apollo/jars/servlet-tomcat.jar:/opt/Apollo/jars/te-common.jar:/opt/Apollo/jars/xerces.jar:/opt/Apollo/data: -DAPOLLO_ROOT=/opt/Apollo -Dorg.xml.sax.driver=org.apache.crimson.parser.XMLReaderImpl -Dlog4j.configuration=file:///opt/Apollo/conf/log4j.properties apollo.main.Apollo
WARN : UnknownHostException calling getLocalHost()
java.net.UnknownHostException: phenom2.coffeenkeyboard.no-ip.org: phenom2.coffeenkeyboard.no-ip.org
	at java.net.InetAddress.getLocalHost(InetAddress.java:1360)
	at apollo.main.Apollo.setLog4JDiagnosticContext(Apollo.java:314)
	at apollo.main.Apollo.main(Apollo.java:94)
INFO : APOLLO_ROOT: /opt/Apollo
INFO : OS name: Linux
INFO : OS arch: amd64
INFO : Java version: 1.6.0_32
INFO : reading config file conf/apollo.cfg
INFO : Couldn't find history file /home/coffeenkeyboard/.apollo/apollo.history; copying default history file /opt/Apollo/data/history.default to /home/coffeenkeyboard/.apollo/apollo.history
INFO : using history file /home/coffeenkeyboard/.apollo/apollo.history
INFO : using backup file /home/coffeenkeyboard/.apollo/apollo.backup
INFO : this is Apollo Genome Annotation and Curation Tool, version 1.11.6, last updated May 12 2010
WARN : UnknownHostException calling getLocalHost()
java.net.UnknownHostException: phenom2.coffeenkeyboard.no-ip.org: phenom2.coffeenkeyboard.no-ip.org
	at java.net.InetAddress.getLocalHost(InetAddress.java:1360)
	at apollo.main.Apollo.setLog4JDiagnosticContext(Apollo.java:314)
	at apollo.main.Apollo$1.run(Apollo.java:170)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:646)
	at java.awt.EventQueue.access$000(EventQueue.java:84)
	at java.awt.EventQueue$1.run(EventQueue.java:607)
	at java.awt.EventQueue$1.run(EventQueue.java:605)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:616)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
WARN : UnknownHostException calling getLocalHost()
java.net.UnknownHostException: phenom2.coffeenkeyboard.no-ip.org: phenom2.coffeenkeyboard.no-ip.org
	at java.net.InetAddress.getLocalHost(InetAddress.java:1360)
	at apollo.main.Apollo.setLog4JDiagnosticContext(Apollo.java:314)
	at apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:748)
	at org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)
	at java.lang.Thread.run(Thread.java:662)
INFO : Trying to open GAME XML file data/example.xml
INFO : set style to conf/fly.style; style file source(s): conf/fly.style, conf/game.style
INFO : using tiers file /opt/Apollo/conf/fly.tiers
INFO : Starting XML parse
INFO : Species style override. Setting style to conf/fly.style for species Drosophila melanogaster
INFO : Completed XML parse of 3R:1178000-1230000
WARN : UnknownHostException calling getLocalHost()
java.net.UnknownHostException: phenom2.coffeenkeyboard.no-ip.org: phenom2.coffeenkeyboard.no-ip.org
	at java.net.InetAddress.getLocalHost(InetAddress.java:1360)
	at apollo.main.Apollo.setLog4JDiagnosticContext(Apollo.java:314)
	at apollo.gui.AutoSaveThread.run(AutoSaveThread.java:51)
And I get the Apollo launch screen

Screen 1

Screen 2

---------- Post added at 09:59 PM ---------- Previous post was at 09:04 PM ----------

I am creating a separate post for comments on the JDK setup, to help make it clear for you. While you are installing Oracle JDK, I would suggest you also try running Apollo on open-JDK once you get it running, as the two code bases are fast becoming identical.

IMPORTANT: When JDK is being installed, there is no need to run the JRE installer as well. JRE is a subset of the JDK. When JDK is installed, JRE is automatically present.

Quote:
Originally Posted by trotel View Post
7. In case I download these both and I tyed to installed those, I move both in /usr/local/java/
- jdk-7u5-linux-x64.rpm
- jre-7u5-linux-x64.rpm
When rpm or any installer is run it will unpack and place the files in the appropriate locations within /usr hierarchy. Downloaded rpm files do not go here. I would put these files in /tmp instead, and as root run rpm -Uvh jdk-7u5-linux-x64.rpm If you still have the rpm files in /usr/local/java, please delete them.

To give a simplified explanation, Alternatives is a mechanism of allowing installation and switching different flavours of a software (like JDK for example) through symbolic links

Quote:
Originally Posted by trotel View Post
10. I choose the alternatives
/usr/java/latest and /usr/java/default are symbolic links to an actual installation created by the Oracle installer (rpm). In this case they point to /usr/java/jdk1.7.0_05

For this command, I would choose either Option 1 or Option 5 depending on whether I wanted to use java command from the OpenJDK JRE or Oracle JDK installations

Last edited by CoffeeNKeyboard; 3rd July 2012 at 10:19 PM.
Reply With Quote
  #8  
Old 3rd July 2012, 10:18 PM
marko Offline
Registered User
 
Join Date: Jun 2004
Location: Laurel, MD USA
Posts: 6,050
linuxfirefox
Re: Java JVM installation 64-bit

The FAQ ( http://apollo.berkeleybop.org/current/faq.html ) mentions one person reported problems on 64bit "Red Hat Java", which I guess means the OpenJDK 64bit version.

Also the FAQ says you need at least 164MB of system RAM.
The warning message you're seeing implies to me not that the JDK is installed incorrectly but the Apollo configuration isn't setting or can't set the maximum heap big enough.

For example, -Xmx1G would set the maximum heap limit to 1 GB

See "java -X" for the available options

The JVM computes a Xmx size depending on the amount of ram the machine has, one explanation is your PC has a small enough RAM size that the Xmx is defaulting too small.
Please post what your ram size is ( "free -m" would show it)

Last edited by marko; 3rd July 2012 at 10:25 PM.
Reply With Quote
  #9  
Old 4th July 2012, 05:03 AM
trotel Offline
Registered User
 
Join Date: Jan 2012
Location: Lima, Perú
Posts: 21
linuxfirefox
Re: Java JVM installation 64-bit

Finally I can run my program.
Thanks CoffeeNKeyboard and Marko, now I understand more this installation.
Well I have 8GB on my RAM (Marko wants to know)
Code:
$ free -m
             total       used       free     shared    buffers     cached
Mem:          7784       2826       4957          0         94       1591
-/+ buffers/cache:       1140       6643
Swap:         1023          0       1023
I have only one question. CoffeeNKeyboard, you run the Apollo/bin/apollo and that work but if I choose symlink in the installation, the path to this symlink is Apollo/apollo not Apollo/bin/apollo, I run Apollo/apollo (just curious) and it work too. So what is the difference?

Just in case I run the previous installation, with Apollo_linux_with_jre.sh, and when I run the Apollo/bin/apollo it work, but when I run Apollo/apollo it show me the error at first.

Well I just want to understand that.
Reply With Quote
  #10  
Old 4th July 2012, 12:10 PM
CoffeeNKeyboard Offline
Registered User
 
Join Date: Sep 2011
Location: TheCloud
Posts: 25
windows_7firefox
Re: Java JVM installation 64-bit

Marko has a valid observation. Even more so, since you confirm that your system has 8GB RAM. I am intrigued. I too get the feeling that Apollo script may not be handling some scenario like it ought to.

I'll have a look at the installed Apollo folder once I get home after work.

Quote:
Originally Posted by trotel View Post
Just in case I run the previous installation, with Apollo_linux_with_jre.sh, and when I run the Apollo/bin/apollo it work, but when I run Apollo/apollo it show me the error at first
I am not sure I follow this comment. Do you mean that once you had Apollo installed and working using Apollo_unix.sh installer, you ran the Apollo_linux_with_jre.sh installer?
If that is the case, you'll need to check Apollo_linux_with_jre.sh to see what it is doing. I am guessing that it is changing symbolic links and your Apollo installation ends up broken. I may be wrong.
Reply With Quote
  #11  
Old 4th July 2012, 04:27 PM
trotel Offline
Registered User
 
Join Date: Jan 2012
Location: Lima, Perú
Posts: 21
linuxfirefox
Re: Java JVM installation 64-bit

Quote:
Originally Posted by CoffeeNKeyboard View Post
Marko has a valid observation. Even more so, since you confirm that your system has 8GB RAM. I am intrigued. I too get the feeling that Apollo script may not be handling some scenario like it ought to.

I'll have a look at the installed Apollo folder once I get home after work.

I am not sure I follow this comment. Do you mean that once you had Apollo installed and working using Apollo_unix.sh installer, you ran the Apollo_linux_with_jre.sh installer?
If that is the case, you'll need to check Apollo_linux_with_jre.sh to see what it is doing. I am guessing that it is changing symbolic links and your Apollo installation ends up broken. I may be wrong.
Yes, I had Apollo installed and working using Apollo_unix.sh installer, and then I used the executables of the Apollo_linux_with_jre.sh installer.
The symlink is not broken I cheked that.
I'm checking the Apollo_linux_with_jre.sh but I only know a little of bash shell programming.
Reply With Quote
  #12  
Old 4th July 2012, 04:32 PM
marko Offline
Registered User
 
Join Date: Jun 2004
Location: Laurel, MD USA
Posts: 6,050
linuxfirefox
Re: Java JVM installation 64-bit

I installed it on my PC which has 64bit Fedora 17 and 64bit JDK 1.7.0_05 (4GB of RAM, Sony Vaio laptop) and I get errors about missing
style files and it says it can't run with Java version 1.7.0_05

Quote:
ERROR: JVM 1.7.0_05 doesn't support data adapter apollo.dataadapter.ensj.EnsJAdapter
WARN : apollo.dataadapter.ensj.EnsJAdapter can't run with Java version 1.7.0_05
ERROR: Failed to set style apollo.dataadapter.ensj.EnsJAdapter--couldn't find style file. This could be a problem!
WARN : Failed to set style apollo.dataadapter.ensj.EnsJAdapter--couldn't find style file. This could be a problem!
ERROR: JVM 1.7.0_05 doesn't support data adapter apollo.dataadapter.synteny.SyntenyAdapter
WARN : apollo.dataadapter.synteny.SyntenyAdapter can't run with Java version 1.7.0_05
ERROR: Failed to set style apollo.dataadapter.synteny.SyntenyAdapter--couldn't find style file. This could be a problem!
WARN : Failed to set style apollo.dataadapter.synteny.SyntenyAdapter--couldn't find style file. This could be a problem!
INFO : using history file /home/mos/.apollo/apollo.history
INFO : using backup file /home/mos/.apollo/apollo.backup
INFO : this is Apollo Genome Annotation and Curation Tool, version 1.11.6, last updated May 12 2010
my apollo.vmoptions file contains:
Quote:
-Xms80m
-Xmx1973m
However it does run well enough that I get to that main window and before that it shows the load data dialogs.

Note, I used the "without JVM" shell install file because I wanted to use my own jdk.

Last edited by marko; 4th July 2012 at 04:38 PM.
Reply With Quote
  #13  
Old 4th July 2012, 05:29 PM
trotel Offline
Registered User
 
Join Date: Jan 2012
Location: Lima, Perú
Posts: 21
linuxfirefox
Re: Java JVM installation 64-bit

Quote:
Originally Posted by marko View Post
I installed it on my PC which has 64bit Fedora 17 and 64bit JDK 1.7.0_05 (4GB of RAM, Sony Vaio laptop) and I get errors about missing
style files and it says it can't run with Java version 1.7.0_05

my apollo.vmoptions file contains:
However it does run well enough that I get to that main window and before that it shows the load data dialogs.

Note, I used the "without JVM" shell install file because I wanted to use my own jdk.
When I ran, it show me the same like you, with Apollo/apollo, and when I ran Apollo/bin/apollo it show me similar but with: (with Apollo_unix.sh)
Code:
...
Couldn't find JavaPath line in apollo.cfg file, trying to guess path to java...
/tmp/Apollo/bin/apollo: line 212: unalias: java: not found
...
Starting apollo (memory = 800M)...
/usr/bin/java -ms50M -Xmx800M
....
Reply With Quote
  #14  
Old 5th July 2012, 12:04 AM
CoffeeNKeyboard Offline
Registered User
 
Join Date: Sep 2011
Location: TheCloud
Posts: 25
linuxfirefox
Re: Java JVM installation 64-bit

Sorry, I stand corrected. According to the User Guide

./bin/apollo <- for Windows / Mac
./apollo <- Linux / UNIX (A should be lower case in the manual)

Apollo has been very generous with the max heap size in my case, since the PC that I installed it on has 12GB RAM
Code:
-Xms80m
 -Xmx5757m
Perhaps someone who hasn't got a JVM installed can run the jvm included version and report their findings.
Reply With Quote
Reply

Tags
64bit, installation, java, jvm

Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
Java installation techdawg270 Programming & Packaging 11 9th August 2007 10:14 AM
Java Sun installation fruity_kiwi Using Fedora 11 6th August 2007 11:40 PM
Sun Java Installation omidkamangar Using Fedora 7 9th November 2006 01:28 PM
Java 1.5.0.6 installation help pkpanda Installation, Upgrades and Live Media 13 8th May 2006 11:21 PM
Java installation rcallan515 Using Fedora 4 7th February 2006 04:29 AM


Current GMT-time: 21:52 (Friday, 19-09-2014)

TopSubscribe to XML RSS for all Threads in all ForumsFedoraForumDotOrg Archive
logo

All trademarks, and forum posts in this site are property of their respective owner(s).
FedoraForum.org is privately owned and is not directly sponsored by the Fedora Project or Red Hat, Inc.

Privacy Policy | Term of Use | Posting Guidelines | Archive | Contact Us | Founding Members

Powered by vBulletin® Copyright ©2000 - 2012, vBulletin Solutions, Inc.

FedoraForum is Powered by RedHat