182. Oracle Java JDK (java, javac and javaws) in debian testing/wheezy

With ECCE I was having problems with getting the same version of java and javac on a computer where I was using sun java 6.0

Since I'm using SGE I (think I) need the closed source SUN java version.
Download (and click on the license agreement) here:
http://www.oracle.com/technetwork/java/javase/downloads/jdk-6u32-downloads-1594644.html


(v7u4 is available here:
http://www.oracle.com/technetwork/java/javase/downloads/jdk-7u4-downloads-1591156.html
)

Then follow this: http://verahill.blogspot.com.au/2012/04/installing-sunoracle-java-in-debian.html
sudo apt-get install java-package
make-jpkg jdk-6u32-linux-x64.bin

and follow the instructions. Once the package is built, install:
sudo dpkg -i oracle-j2sdk1.6_1.6.0+update32_amd64.deb

Unpacking oracle-j2sdk1.6 (from oracle-j2sdk1.6_1.6.0+update32_amd64.deb) ...
Setting up oracle-j2sdk1.6 (1.6.0+update32) ...
update-alternatives: using /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/ControlPanel to provide /usr/bin/ControlPanel (ControlPanel) in auto mode.
update-alternatives: using /usr/lib/jvm/j2sdk1.6-oracle/jre/lib/amd64/libnpjp2.so to provide /usr/lib/iceweasel/plugins/libjavaplugin.so (iceweasel-javaplugin.so) in auto mode.
update-alternatives: using /usr/lib/jvm/j2sdk1.6-oracle/jre/lib/amd64/libnpjp2.so to provide /usr/lib/chromium/plugins/libjavaplugin.so (chromium-javaplugin.so) in auto mode.

sudo update-alternatives --config java

There are 6 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/j2sdk1.6-oracle/jre/bin/java        315       manual mode
  5            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
  6            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode

sudo update-alternatives --config javac

There are 2 choices for the alternative javac (providing /usr/bin/javac).
  Selection    Path                                         Priority   Status
------------------------------------------------------------
* 0            /usr/lib/jvm/java-7-openjdk-amd64/bin/javac   1051      auto mode
  1            /usr/lib/jvm/j2sdk1.6-oracle/bin/javac        315       manual mode
  2            /usr/lib/jvm/java-7-openjdk-amd64/bin/javac   1051      manual mode

sudo update-alternatives --config javaws

There are 3 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/j2sdk1.6-oracle/jre/bin/javaws        315       manual mode

  3            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      manual mode

While I was making the package this little guy popped up. Don't fret. I think it was meant to take me to the java.com website or something similar. I don't like the sight of that /root/ thingy though -- what's oracle thinking of us punters?

181. Compiling openmpi on debian wheezy

There's nothing complicated about this compilation. It's not a terribly quick build though, and I'm not yet sure exactly what packages are necessary.

sudo apt-get install build-essential gfortran
wget http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.tar.bz2
tar xvf openmpi-1.6.tar.bz2
cd openmpi-1.6/

sudo mkdir /opt/openmpi/
sudo chown ${USER} /opt/openmpi/

./configure --prefix=/opt/openmpi/1.6/ --with-sge

make
make install

And you're done.

tree -L2 -d /opt/openmpi

Linking to the libs is done as before, although the path to e.g. libmpi.so is /opt/openmpi/1.6/lib/ and not /opt/openmpi/1.6/lib/openmpi/ like in the regular debian package.

.

└── 1.6

    ├── bin

    ├── etc

    ├── include

    │   ├── openmpi

    │   └── vampirtrace

    ├── lib

    │   ├── openmpi

    │   └── pkgconfig

    └── share

        ├── man

        ├── openmpi

        └── vampirtrace

You might also want to update the /etc/alternatives/libmpi.so symlink.

This is definitely one of those packages where it's worth doing ./configure --help to see what options are available.

Also, I imagine that on ROCKS there may well be a few packages which will have to be compile first and specified using --with-<> switches.

A sample:

  --with-blcr(=DIR)       Path to BLCR Installation
  --with-blcr-libdir=DIR  Search for BLCR libraries in DIR
  --with-hwloc(=DIR)      Build hwloc support. DIR can take one of three
  --with-hwloc-libdir=DIR Search for hwloc libraries in DIR. Should only be
  --with-valgrind(=DIR)   Directory where the valgrind software is installed
  --with-memory-manager=TYPE
  --with-libpicl(=DIR)    Build libpicl support, optionally adding
  --with-libpicl-libdir=DIR
  --with-timer=TYPE       Build high resolution timer component TYPE
  --with-portals=DIR      Specify the installation directory of PORTALS
  --with-portals-libs=LIBS
                          Libraries to link with for portals
  --with-alps             Build ALPS scheduler component (default: no)
  --with-lsf(=DIR)        Build LSF support
  --with-lsf-libdir=DIR   Search for LSF libraries in DIR
  --with-pmi              Build PMI support (default: no)
  --with-cray-pmi-ext     Include Cray PMI2 extensions (default: no)
  --with-slurm            Build SLURM scheduler component (default: yes)
  --with-tm(=DIR)         Build TM (Torque, PBSPro, and compatible) support,
  --with-ftb(=DIR)        Build FTB (Fault Tolerance Backplane) support,
  --with-ftb-libdir=DIR   Search for FTB (Fault Tolerance Backplane) libraries
  --with-esmtp(=DIR)      Build esmtp support, optionally adding DIR/include,
  --with-esmtp-libdir=DIR Search for the esmtp libraries in DIR
  --with-sge              Build SGE or Grid Engine support (default: no)
  --with-loadleveler      Build LoadLeveler scheduler component (default: yes)
  --with-elan(=DIR)       Build Elan (QsNet2) support, searching for libraries
  --with-elan-libdir=DIR  Search for Elan (QsNet2) libraries in DIR
  --with-mx(=DIR)         Build MX (Myrinet Express) support, optionally
  --with-mx-libdir=DIR    Search for MX (Myrinet Express) libraries in DIR
  --with-openib(=DIR)     Build OpenFabrics support, optionally adding
  --with-openib-libdir=DIR
  --with-portals(=DIR)    Build Portals support, optionally adding
  --with-portals-config   configuration to use for Portals support. One of
  --with-portals-libs=LIBS
                          Libraries to link with for portals
  --with-sctp(=DIR)       Build SCTP support, searching for libraries in DIR
  --with-sctp-libdir=DIR  Search for SCTP libraries in DIR
  --with-knem(=DIR)       Build knem Linux kernel module support, searching
  --with-udapl(=DIR)      Build uDAPL support, optionally adding DIR/include,
  --with-udapl-libdir=DIR Search for uDAPL libraries in DIR
  --with-fca(=DIR)        Build fca (Mellanox Fabric Collective Accelerator)
  --with-io-romio-flags=FLAGS
  --with-mxm(=DIR)        Build Mellanox Messaging support
  --with-mxm-libdir=DIR   Search for Mellanox Messaging libraries in DIR
  --with-psm(=DIR)        Build PSM (Qlogic InfiniPath) support, optionally
  --with-psm-libdir=DIR   Search for PSM (QLogic InfiniPath PSM) libraries in
  --with-contrib-vt-flags=FLAGS
  --with-event-rtsig      compile with support for real time signals
  --with-pic[=PKGS]       try to use only PIC/non-PIC objects [default=use
  --with-gnu-ld           assume the C compiler uses GNU ld [default=no]
  --with-sysroot=DIR Search for dependent libraries within DIR

180. Temporary fix for supertuxkart

I don't often play games, but I noticed that supertuxkart had been updated in debian wheezy and having a little bit of free time I figured I'd give it a whirl.

 supertuxkart 

supertuxkart: error while loading shared libraries: libIrrlicht.so.1.7a.3: cannot open shared object file: No such file or directory

Make sure that libirrlicht1.7a is installed.

sudo apt-get install libirrlicht1.7a

Then

cd /usr/lib

sudo ln -s libIrrlicht.so.1.7a.2 libIrrlicht.so.1.7a.3

It's obviously not a permanent fix, but I haven't had any problems playing.