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Old 05-08-2013, 08:15 AM   #1
JackieBadger
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Default Installing Newbler 2.7 on Ubuntu 12.04, java problem

Hi,

I realise this question has been addressed previously but the resolutions given have not solved the issue in the versions of Newbler/Ubuntu I am using.

I am trying to install Newbler 2.7 in Ubuntu 12.04

I resolved the "rocks" error by creating a ~/bin and adding to PATH
then

ln -s /bin/true ~/bin/rocks

This launches the Nixstaller, however the following error occurs:


"Verifying checksums...

Installing jre... Failed

A complete log of this installation can be found in:
/tmp/Install_DataAnalysis_2.7_08_May_2013_1306.log

Installation failed.

See log file for details.
=========================

Click "Finish" to exit this installer. "


Detailed from error log:
"Hostname: ubuntu

=============================
[01:06:36 PM] cd /home/mgpl/programs/DataAnalysis_2.7_All; md5sum -c checksum_inst

./setup.sh: OK
./README: OK
./packages/jre-linux-i586-oracle-2.7-1.noarch.rpm: OK
./packages/gsMapper-2.7-1.noarch.rpm: OK
./packages/gsNewbler-2.7-1.i686.rpm: OK
./packages/gsSeqTools-2.7-1.x86_64.rpm: OK
./packages/gsAmplicons-2.7-1.noarch.rpm: OK
./packages/gsNewbler-2.7-1.x86_64.rpm: OK
./packages/amplicons_CLI_2.7.i686.tgz: OK
./packages/gsAssembler-2.7-1.noarch.rpm: OK
./packages/gsSeqTools-2.7-1.i686.rpm: OK
=============================

=============================
[01:06:36 PM] installRpm.sh /home/mgpl/programs/DataAnalysis_2.7_All/packages/jre-linux-i586-oracle-2.7-1.noarch.rpm /home/mgpl/454/apps/jre /home/mgpl/454 other --force --relocate /opt/454/apps/jre/jre1.6.0_30=/

/tmp/selfgz7717/files_extra//installRpm.sh: 12: /tmp/selfgz7717/files_extra//installRpm.sh: Syntax error: "(" unexpected
============================="


I realise its a java related error, and Roche is looking for jre1.6.0_30, which is not available on ubuntu.

I am running
java version "1.7.0_09"
OpenJDK Runtime Environment (IcedTea7 2.3.3) (7u9-2.3.3-0ubuntu1~12.04.1)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

How do I fool Newber around this issue?

ANy help would be much appreciated.
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Old 05-08-2013, 01:52 PM   #2
sklages
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Quote:
Originally Posted by JackieBadger View Post
/tmp/selfgz7717/files_extra//installRpm.sh: 12: /tmp/selfgz7717/files_extra//installRpm.sh: Syntax error: "(" unexpected
============================="
This is probably due to Ubuntu using 'dash' as system shell (invoking 'sh' from within a script invokes 'dash'). Just configure the default system shell being 'bash'. I always do this since 10.04; no performance loss, but less problems with '#!/bin/sh' stuff ;-)

Quote:
I realise its a java related error, and Roche is looking for jre1.6.0_30, which is not available on ubuntu.

I am running
java version "1.7.0_09"
OpenJDK Runtime Environment (IcedTea7 2.3.3) (7u9-2.3.3-0ubuntu1~12.04.1)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)
Get the java JRE/SDK directly from oracle [1] and install it somewhere in your 454 directory structure; change the scripts accordingly to use this specific version of java.

Think about subsituting your openJDK with with Oracle's java 7 systemwide; it is said that performance is better ...

EDIT: hmm, Roche brings its own (32bit) version of java 6. Seems that java 7 is not your problem. Just fix the dash/bash stuff and then see if it works.
For my Roche installations on 64bit Ubuntu I use Oracle's java .. you don't necessarily need it.

java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01, mixed mode)

hth,
Sven

[1]=http://www.oracle.com/technetwork/java/javase/downloads/index.html

Last edited by sklages; 05-08-2013 at 02:19 PM. Reason: Roche brings its own java
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Old 05-08-2013, 02:22 PM   #3
ajthomas
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You might be running into Java issues that I ran across back when I first tried to install the 454 software in Fedora. It worked fine in 32-bit Fedora, but couldn't find Java in 64-bit Fedora. After a bit of back and forth with Roche, they came up with some additional libraries that need to be installed. The installer now tells the user to install those libraries when it discovers that they're needed. I remember one is zlib.i386, but I don't remember the others off the top of my head. I know it's been posted more than once here (try the 454 subforum). You might just need those libraries to solve your problem.
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Old 05-08-2013, 04:13 PM   #4
JackieBadger
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Thanks for the input guys, appreciated.

One more Q.
How do I "configure the default system shell being 'bash' " ?

Cheers

J
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Old 05-08-2013, 05:20 PM   #5
GenoMax
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Quote:
Originally Posted by JackieBadger View Post
How do I "configure the default system shell being 'bash' " ?

Cheers

J
Procedure is described here. Replace with the path for a shell you want to use.
http://ubuntuforums.org/showthread.php?t=2050679

Last edited by GenoMax; 05-08-2013 at 05:22 PM.
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Old 05-08-2013, 05:25 PM   #6
JackieBadger
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Thanks a lot.

J
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Old 05-08-2013, 11:21 PM   #7
sklages
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Quote:
Originally Posted by JackieBadger View Post
Thanks for the input guys, appreciated.

One more Q.
How do I "configure the default system shell being 'bash' " ?

Cheers

J
You don't want to change your login shell, but the system shell:

http://wiki.ubuntuusers.de/Dash

$ sudo dpkg-reconfigure dash

This is asking you if you want to use 'dash' for '/bin/sh'. Answer 'no' to use 'bash' instead.

hth,
Sven
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Old 05-08-2013, 11:25 PM   #8
sklages
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Quote:
Originally Posted by ajthomas View Post
You might be running into Java issues that I ran across back when I first tried to install the 454 software in Fedora. It worked fine in 32-bit Fedora, but couldn't find Java in 64-bit Fedora. After a bit of back and forth with Roche, they came up with some additional libraries that need to be installed. The installer now tells the user to install those libraries when it discovers that they're needed. I remember one is zlib.i386, but I don't remember the others off the top of my head. I know it's been posted more than once here (try the 454 subforum). You might just need those libraries to solve your problem.
If you run into problems with their 32bit java, I'd install my own 64bit oracle java somewhere in the Roche Software tree and alter the corresponding five or so scripts to use that java.

btw, I never installed libs like zlib.i386 which is Roche moaning about; installation proceeds without them.

Sven
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Old 05-09-2013, 06:15 AM   #9
JackieBadger
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Quote:
Originally Posted by sklages View Post
You don't want to change your login shell, but the system shell:

http://wiki.ubuntuusers.de/Dash

$ sudo dpkg-reconfigure dash

This is asking you if you want to use 'dash' for '/bin/sh'. Answer 'no' to use 'bash' instead.

hth,
Sven
Thanks!
This worked..and installation completed with no apparent issues.
Appreciate the help guys!
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Old 05-09-2013, 11:16 AM   #10
JackieBadger
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OK...

So I managed to get the program working on my own machine, but the assembly maxed out the RAM (~29GB in a virtual machine). As such I am trying to now install on a linux dedicated machine that has 64GB.

But I am running into problems again.

The installer says I lack the libraries zlib:i386 Lib xi:i386 Lib xtst:i386 and LibXaw:i386

I can not remember how I installed these on my personal cpu a couple of years ago and am now struggling to find a source for these. It seems they are now obsolete??

If I continue with installation and ignore these, I get the following error when atempting to run gsMapper. Any solution for a non-linux boffin would be very much appreciated

"mgplab@new2012:~/454/apps/mapper/bin$ ./gsMapper
Exception in thread "main" java.lang.UnsatisfiedLinkError: /home/mgplab/454/apps/jre/jre1.6.0_30/lib/i386/xawt/libmawt.so: libXi.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.load0(Unknown Source)
at java.lang.System.load(Unknown Source)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.loadLibrary0(Unknown Source)
at java.lang.System.loadLibrary(Unknown Source)
at sun.security.action.LoadLibraryAction.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.loadLibraries(Unknown Source)
at java.awt.Toolkit.<clinit>(Unknown Source)
at java.awt.Rectangle.<clinit>(Unknown Source)
at com.fourfivefour.ui.Resources.<clinit>(Resources.java:47)
at com.fourfivefour.ui.ResourceFactory.getNewInstance(ResourceFactory.java:79)
at com.fourfivefour.ui.ResourceFactory.get(ResourceFactory.java:66)
at com.fourfivefour.assembly.MapperMain.<clinit>(MapperMain.java:30)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.simontuffs.onejar.Boot.run(Boot.java:340)
at com.simontuffs.onejar.Boot.main(Boot.java:166)
"
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Old 05-09-2013, 11:30 AM   #11
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In Red Hat/Fedora, it's as simple as "yum install zlib.i386..." I don't use Ubuntu, but as i understand, the installation procedure is similar. This thread says to install ia32-libs to get them. Not having done this on Ubuntu myself, however, I can't offer any more help than that.
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Old 05-09-2013, 11:36 AM   #12
JackieBadger
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I actually just tracked the memory usage during while gsMapper indexed the reference reads. The program crashes stating it is out of memory at ~50% of the total available RAM. i.e. ~14GB RAM.

I wonder why this is? Is there anyway to open gsMapper telling it to use all 29GBs?
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Old 05-09-2013, 11:44 AM   #13
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What system are you using for the real 64GB machine?
Go and get Oracle's 64bit Java 6 SDK/JRE, put it somewhere under /home/mgplab/454/, make it known to the scripts and give it a try .. :-)

Roche's suite is a mixture of 32 and 64bit software, .. one step towards 64bit ;-)
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Old 05-09-2013, 11:50 AM   #14
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Quote:
Originally Posted by JackieBadger View Post
I actually just tracked the memory usage during while gsMapper indexed the reference reads. The program crashes stating it is out of memory at ~50% of the total available RAM. i.e. ~14GB RAM.

I wonder why this is? Is there anyway to open gsMapper telling it to use all 29GBs?
No idea if there could be any issues with the VM itself. Maybe some limits:

ulimit -a

should give you a hint about that.
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Old 05-09-2013, 11:51 AM   #15
JackieBadger
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Quote:
Originally Posted by sklages View Post
What system are you using for the real 64GB machine?
Go and get Oracle's 64bit Java 6 SDK/JRE, put it somewhere under /home/mgplab/454/, make it known to the scripts and give it a try .. :-)

Roche's suite is a mixture of 32 and 64bit software, .. one step towards 64bit ;-)
Im using Ubuntu. OK..Ill but the java executables in the 454 tree and take a look at the scripts to edit.
Thanks again
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Old 05-10-2013, 03:06 AM   #16
JackieBadger
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I edited the start up scripts to point in the direction of the new Oracle Java executable, and it seems to initially work.

The GUI looks to start up, with the picture of the 454 machine and "starting...".... but then dissapears without crashing out in the terminal. So the terminal still indicates the program is running but no GUI.

Maybe it is due to the Java version, java/jdk1.7.0_21?
Any ideas?

Cheers

Last edited by JackieBadger; 05-10-2013 at 03:12 AM.
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Old 05-10-2013, 03:35 AM   #17
sklages
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Quote:
Originally Posted by JackieBadger View Post
Maybe it is due to the Java version, java/jdk1.7.0_21?
Any ideas?

Cheers

Yes, it is. Do not use Java 7 with the Roche suite, instead go for 6.

Nevertheless, don't forget to check if there are any limts on your machine,

Code:
ulimit -a
should help ..

Last edited by sklages; 05-10-2013 at 03:58 AM.
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Old 05-10-2013, 03:59 AM   #18
JackieBadger
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Thanks a lot, guys. Its all up and running now.
ulimit -a shows no limits on the machine on the machine with the new installation.

Thanks again
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Old 05-10-2013, 04:22 AM   #19
JackieBadger
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OK so I got the memory crash again on the more powerful machine.

Here is the ulimit -a output:

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 514997
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 514997
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited


My reference file is a genome scaffold consiting of 2,962,365 contigs; 1,555,444,314 bp

My query sequences consit of 1,151,700 contigs: 390,436,936 bp
It is after the Index/screening of my query sequences where the compuation runs out of memory.
On both machines (29GB, and 62GB available respectivly) mapping crashes when it uses a little over 50% of the available RAM

ANy ideas how to remedy?
Maybe I should cut my refernce file in half?

THanks again, guys

Last edited by JackieBadger; 05-10-2013 at 04:27 AM.
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Old 05-10-2013, 04:32 AM   #20
sklages
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Seems gsmapper wants to use more than 64GB RAM .. well, it's a "heavy" reference ...
Just take a few thousands of the largest contigs (is it a cDNA backbone?) and try again, just to see if the installation itself is OK (it probably is).

Finally you need to reduce your reference contigs or look for a more powerful machine.

Just curious, why do you want to map many, many contigs on even more many, many contigs? Maybe you should look for another software to achieve the results you are expecting?

EDIT: Oh, I haven't noticed your 50% issue. Maybe you should contact your sysadm about that. It is worth a try ;-)

Last edited by sklages; 05-10-2013 at 04:36 AM.
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