119. Installing sun java/Oracle java in debian

Update 23 March 2013:  the java.com file isn't distributed as a .bin file anymore. Just replace all instances of .bin with .tar.gz and it works just as well.

This basically follows http://sylvestre.ledru.info/blog/sylvestre/2012/02/29/java_package_replacement_of_sun_java6

While a few applications (Grix and Grisu) I was playing with which require java 1.5 or better should work fine with openjdk-7 (1.6.0_24), they didnt. I had to run it using binary packages which I downloaded from java.com and then installed locally.

I'd like a better solution, and here it is:

1. sudo apt-get install java-package

2. Download the java files from java.com, e.g. jre-6u31-linux-x64.bin or jre-7u17-linux-x64.tar.gz
http://java.com/en/download/manual.jsp?locale=en

3. Make-jpkg
Run make-jpkg on the downloaded file, whether it's ending in .bin or .tar.gz:

make-jpkg jre-6u31-linux-x64.bin

Create debian package:
    dh_testdir
    dh_testroot
    dh_installchangelogs
    dh_installdocs
    dh_compress
    dh_fixperms
    dh_installdeb
    dh_shlibdeps
dpkg-shlibdeps: warning: Can't extract name and version from library name `libjvm.so'
[..]
dpkg-shlibdeps: warning: Can't extract name and version from library name `libjvm.so'
[..]
dpkg-shlibdeps: warning: Can't extract name and version from library name `libjli.so'
dpkg-shlibdeps: warning: package could avoid a useless dependency if /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/native_threads/libhpi.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libjava.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libdt_socket.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnet.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/bin/javaws /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libhprof.so were not linked against libnsl.so.1 (they use none of the library's symbols).
dpkg-shlibdeps: warning: package could avoid a useless dependency if /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libjawt.so was not linked against libmawt.so (it uses none of the library's symbols).
    dh_gencontrol
    dh_md5sums
    dh_builddeb
dpkg-deb: building package `oracle-j2re1.6' in `/tmp/make-jpkg.9XTCruNvKM/oracle-j2re1.6_1.6.0+update31_amd64.deb'.
    copy oracle-j2re1.6_1.6.0+update31_amd64.deb into directory /home/me/Downloads/
The Debian package has been created in the current directory. You can
install the package as root (e.g. dpkg -i oracle-j2re1.6_1.6.0+update31_amd64.deb). 

4. sudo dpkg -i oracle-j2re1.6_1.6.0+update31_amd64.deb 

Selecting previously unselected package oracle-j2re1.6.
(Reading database ... 561777 files and directories currently installed.)
Unpacking oracle-j2re1.6 (from oracle-j2re1.6_1.6.0+update31_amd64.deb) ...
Setting up oracle-j2re1.6 (1.6.0+update31) ...
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/bin/ControlPanel to provide /usr/bin/ControlPanel (ControlPanel) in auto mode.
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so to provide /usr/lib/iceweasel/plugins/libjavaplugin.so (iceweasel-javaplugin.so) in auto mode.
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so to provide /usr/lib/chromium/plugins/libjavaplugin.so (chromium-javaplugin.so) in auto mode.

5a. sudo update-alternatives --config java

There are 5 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status------------------------------------------------------------* 0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode  1            /usr/bin/gij-4.4                                 1044      manual mode  2            /usr/bin/gij-4.6                                 1046      manual mode  3            /usr/lib/jvm/j2re1.6-oracle/bin/java             314       manual mode  4            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode  5            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual modePress enter to keep the current choice[*], or type selection number: 3update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/bin/java to provide /usr/bin/java (java) in manual mode.

5b. 

 sudo update-alternatives --config javaws

There are 2 choices for the alternative javaws (providing /usr/bin/javaws).
  Selection    Path                                              Priority   Status
------------------------------------------------------------
* 0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      auto mode
  1            /usr/lib/jvm/j2re1.6-oracle/bin/javaws             314       manual mode
  2            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      manual mode
Press enter to keep the current choice[*], or type selection number: 1
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/bin/javaws to provide /usr/bin/javaws (javaws) in manual mode.
update-alternatives: warning: skip creation of /usr/share/man/man1/javaws.1.gz because associated file /usr/lib/jvm/j2re1.6-oracle/man/man1/javaws.1.gz (of link group javaws) doesn't exist.

6.  Verification
java -version

java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01, mixed mode)

Go to http://java.com/en/download/installed.jsp

Iceweasel worked fine at this stage.

7. To get Chrome to work I did the following:
sudo updatedb
locate libjavaplugin.so

/usr/lib/chromium/plugins/libjavaplugin.so
/usr/lib/iceweasel/plugins/libjavaplugin.so
/usr/lib/mozilla/plugins/libjavaplugin.so

 ls -lah /usr/lib/chromium/plugins/libjavaplugin.so etc.

/usr/lib/chromium/plugins/libjavaplugin.so -> /etc/alternatives/chromium-javaplugin.so
/usr/lib/iceweasel/plugins/libjavaplugin.so -> /etc/alternatives/iceweasel-javaplugin.so
/usr/lib/mozilla/plugins/libjavaplugin.so -> /etc/alternatives/mozilla-javaplugin.so

ls -lah /etc/alternatives/chromium-javaplugin.so etc.

/etc/alternatives/chromium-javaplugin.so -> /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so
/etc/alternatives/iceweasel-javaplugin.so -> /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so
/etc/alternatives/mozilla-javaplugin.so -> /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so

sudo rm /etc/alternatives/mozilla-javaplugin.so

sudo ln -s /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so /etc/alternatives/mozilla-javaplugin.so

And you're done.

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Links to this post:
https://www.linuxquestions.org/questions/debian-26/which-java-for-wheezy-4175469043/

118. Solution to nwchem: SHMMAX too small

Update: also see this post: http://verahill.blogspot.com.au/2012/10/shmmax-revisited-and-shmall-shmmni.html

When running nwchem using mpirun I've occasionally encountered this error.

Error:
******************* ARMCI INFO ************************

The application attempted to allocate a shared memory segment of 44498944 bytes in size. This might be in addition to segments that were allocated succesfully previously. The current system configuration does not allow enough shared memory to be allocated to the application.

This is most often caused by:
1) system parameter SHMMAX (largest shared memory segment) being too small or
2) insufficient swap space.
Please ask your system administrator to verify if SHMMAX matches the amount of memory needed by your application and the system has sufficient amount of swap space. Most UNIX systems can be easily reconfigured to allow larger shared memory segments,
see http://www.emsl.pnl.gov/docs/global/support.html
In some cases, the problem might be caused by insufficient swap space.
*******************************************************
0:allocate: failed to create shared region : -1
(rank:0 hostname:boron pid:17222):ARMCI DASSERT fail. shmem.c:armci_allocate():1082 cond:0

Diagnosis:

Check the currently defined shmmax:

cat /proc/sys/kernel/shmmax
33554432

Well, 33554432<44498944, so it seems that it's caused by reason 1 above.

Solution:

http://www.linuxforums.org/forum/red-hat-fedora-linux/17025-how-can-i-change-shmmax.html

Edit /etc/sysctl.conf

Add a line saying

kernel.shmmax=44498944

Save and reboot. The exact value is up to you -- I've set my shmmax to 128*1024*1024=134217728, while our production cluster has 6269961216.

Update: to change it on the fly do
sudo sysctl -w kernel.shmmax=6269961216

117. Sorting out framebuffer in linux (debian)

If you have /dev/fb0 you're fine -- you have a working frame buffer, and that was the case on my laptop and my optiplex 990. However, my homebuilt boxes didn't have any framebuffer devices.

This is how to set up framebuffer:

sudo apt-get install hwinfo
sudo hwinfo --framebuffer

02: None 00.0: 11001 VESA Framebuffer                        
  [Created at bios.464]
  Unique ID: rdCR.fRULN9k9OD4
  Hardware Class: framebuffer
  Model: "Intel(r)Cantiga Graphics Controller"
  Vendor: "Intel Corporation"
  Device: "Intel(r)Cantiga Graphics Controller"
  SubVendor: "Intel(r)Cantiga Graphics Chip Accelerated VGA BIOS"
  SubDevice:
  Revision: "Hardware Version 0.0"
  Memory Size: 127 MB + 960 kB
  Memory Range: 0xd0000000-0xd7feffff (rw)
  Mode 0x0360: 848x480 (+896), 8 bits
  Mode 0x0361: 848x480 (+1728), 16 bits
  Mode 0x0362: 848x480 (+3392), 24 bits
  Mode 0x0305: 1024x768 (+1024), 8 bits
  Mode 0x0317: 1024x768 (+2048), 16 bits
  Mode 0x0318: 1024x768 (+4096), 24 bits  Mode 0x0312: 640x480 (+2560), 24 bits
  Mode 0x0314: 800x600 (+1600), 16 bits
  Mode 0x0315: 800x600 (+3200), 24 bits
  Mode 0x0301: 640x480 (+640), 8 bits
  Mode 0x0303: 800x600 (+832), 8 bits
  Mode 0x0311: 640x480 (+1280), 16 bits
  Config Status: cfg=new, avail=yes, need=no, active=unknown

Pick a mode e.g. 0x0318

Edit your /etc/default/grub

Add vga=0x0318 to the GRUB...DEFAULT line:

GRUB_CMDLINE_LINUX_DEFAULT="quiet nouveau.modeset=0 vga=0x0318"

If there's a nomodeset command, delete it.

Do
sudo update-grub

and reboot. You're done.

There should now be a /dev/fb0 and your resolution when working in a TTY* should be different.

*the terminal you get to by doing alt+f1, alt+f2 etc.

What to do with framebuffers?
Apart from making your ttys look a lot nicer and work at higher resolution, they'll also allow you to use w3m-img for ncurses based browsing with images (w3m+w3m-img; sometimes it's useful), and to take screenshots of the terminal in terminal mode. But mostly, it just makes your terminal experience better through being at higher resolution.


More modes:
02: None 00.0: 11001 VESA Framebuffer                        
  [Created at bios.464]
  Unique ID: rdCR.efxRnBcYXs5
  Hardware Class: framebuffer
  Model: "NVIDIA GF108 Board - 1071v0p1"
  Vendor: "NVIDIA Corporation"
  Device: "GF108 Board - 1071v0p1"
  SubVendor: "NVIDIA"
  SubDevice:
  Revision: "Chip Rev"
  Memory Size: 14 MB
  Memory Range: 0xd7000000-0xd7dfffff (rw)

  Mode 0x0300: 640x400 (+640), 8 bits
  Mode 0x0301: 640x480 (+640), 8 bits
  Mode 0x0303: 800x600 (+800), 8 bits
  Mode 0x0305: 1024x768 (+1024), 8 bits
  Mode 0x0307: 1280x1024 (+1280), 8 bits
  Mode 0x030e: 320x200 (+640), 16 bits
  Mode 0x030f: 320x200 (+1280), 24 bits
  Mode 0x0311: 640x480 (+1280), 16 bits
  Mode 0x0312: 640x480 (+2560), 24 bits
  Mode 0x0314: 800x600 (+1600), 16 bits
  Mode 0x0315: 800x600 (+3200), 24 bits
  Mode 0x0317: 1024x768 (+2048), 16 bits
  Mode 0x0318: 1024x768 (+4096), 24 bits
  Mode 0x031a: 1280x1024 (+2560), 16 bits
  Mode 0x031b: 1280x1024 (+5120), 24 bits
  Mode 0x0330: 320x200 (+320), 8 bits
  Mode 0x0331: 320x400 (+320), 8 bits
  Mode 0x0332: 320x400 (+640), 16 bits
  Mode 0x0333: 320x400 (+1280), 24 bits
  Mode 0x0334: 320x240 (+320), 8 bits
  Mode 0x0335: 320x240 (+640), 16 bits
  Mode 0x0336: 320x240 (+1280), 24 bits
  Mode 0x033d: 640x400 (+1280), 16 bits
  Mode 0x033e: 640x400 (+2560), 24 bits
  Mode 0x0345: 1600x1200 (+1600), 8 bits
  Mode 0x0346: 1600x1200 (+3200), 16 bits
  Mode 0x034a: 1600x1200 (+6400), 24 bits
  Mode 0x0360: 1280x800 (+1280), 8 bits
  Mode 0x0361: 1280x800 (+5120), 24 bits
  Config Status: cfg=new, avail=yes, need=no, active=unknown

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