110. Compiling, installing Gnuplot 4.6 on Debian

A new version of gnuplot doesn't happen very often, and this one has an interesting added feature in terms of support for using braces in algorithms.
http://www.gnuplot.info/announce.4.6.0

Building gnuplot 4.6 is similar to building 4.4.4 and is pretty straightforward:

sudo apt-get install libgd2-xpm-dev checkinstall

wget http://sourceforge.net/projects/gnuplot/files/latest/download?source=files
mv download\?source\=files gnuplot-4.6.tar.gz
tar -xvf gnuplot-4.6.tar.gz
cd gnuplot-4.6.0/

./configure --with-linux-vga
make
checkinstall -install=no
 sudo rm /usr/local/share/info/dir -rf
sudo dpkg -i gnuplot_4.6.0-1_amd64.deb

You may get an error if trying to install on a system with a home-compiled version of octave (see below).

The problem with handling small numbers is not present in this version (http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-bug-in-debian.html).

---

Error:

Selecting previously unselected package gnuplot.
(Reading database ... 258722 files and directories currently installed.)
Unpacking gnuplot (from gnuplot_4.6.0-1_amd64.deb) ...
dpkg: error processing gnuplot_4.6.0-1_amd64.deb (--install):
 trying to overwrite '/usr/local/share/info/dir', which is also in package octave 3.6.1-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
 gnuplot_4.6.0-1_amd64.deb

Solution:

 sudo dpkg --force-overwrite -i gnuplot_4.6.0-1_amd64.deb

109. Building Thunderbird 11 on Debian testing

The build is fairly straightforward and pretty much identical to building 10.0.2 (earlybird): http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-building.html

As always, uninstall existing versions before installing a new one.

--start here --
First install the dependencies:
sudo apt-get install libdbus-glib-1-dev gir1.2-notify-0.7 libnotify-dev yasm checkinstall libzip-dev zip 


Download the sources  and untar:
mkdir ~/tmp
cd ~/tmp

wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/11.0/source/thunderbird-11.0.source.tar.bz2
tar -xvf thunder-bird-11.0.source.tar.bz2
cd comm-release/

Start the build
./configure --disable-necko-wifi
make -j3

3 is the number of cores +1. If you have a quadcore CPU substitute 3 with 5. The build takes a while so you will probably want to do a parallel build.

Finally, to install
sudo make install

checkinstall is segfaulting for me.

---

Error:

/home/me/tmp/comm-release/mozilla/js/src/config/nsinstall -R -m 644 ../mozilla-config.h ../../../config/nsStaticComponents.h  ../../../dist/include
make[5]: /home/me/tmp/comm-release/mozilla/js/src/config/nsinstall: Command not found
make[5]: *** [export] Error 127
make[5]: Leaving directory `/home/me/tmp/comm-release/mozilla/js/src/config'
make[4]: *** [export] Error 2
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory `/home/me/tmp/comm-release/mozilla/js/src'
make[3]: *** [export_tier_js] Error 2
make[3]: Leaving directory `/home/me/tmp/comm-release/mozilla'
make[2]: *** [tier_js] Error 2
make[2]: Leaving directory `/home/me/tmp/comm-release/mozilla'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/home/me/tmp/comm-release/mozilla'

Solution:

I got this error because I accidentally untared the new sources into an existing directory with an older version of thunderbird. The solution was to delete the directory and untar the sources again.

108. Building local version of sinfo without root/sudo on ROCKS/CentOS

Edit 04/04/2012: there were several errors and omissions. These have been fixed now.

Because I don't want to mess up a cluster which is on a different continent I'm trying to use my superuser powers as little as possible.

Here's how to make a local version of sinfo -- you'll still need to make sinfod runs as a service on all the nodes.

There's no reason the instructions here shouldn't work on most linux distros, including Debian.

boost:
cd ~/tmp
wget http://sourceforge.net/projects/boost/files/boost/1.49.0/boost_1_49_0.tar.gz/download
tar -xvf boost_1_49_0.tar.gz
cd boost_1_49_0/
./bootstrap.sh --prefix=/export/home/me/.libboost

Edit tools/build/user-config.jam and add

using mpi ;

The space between mpi and ; is needed.

Start installation:
./b2 install

cd /export/home/me/.libboost/lib
ln -s libboost_signals.so libboost_signals-mt.so
ln -s libboost_serialization.so libboost_serialization-mt.so
ln -s libboost_date_time.so libboost_date_time-mt.so
ln -s libboost_wserialization.so libboost_wserialization-mt.so
ln -s libboost_regex.so libboost_regex-mt.so

asio:
cd ~/tmp
wget "http://downloads.sourceforge.net/project/asio/asio/1.5.3%20%28Development%29/asio-1.5.3.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fasio%2F&ts=1331441086&use_mirror=aarnet"
tar -xvf asio-1.5.3.tar.bz2
cd asio-1.5.3/

./configure --prefix=/export/home/me/.asio --with-boost=/export/home/me/.libboost/include
make
make install

sinfo/d:
wget http://www.ant.uni-bremen.de/whomes/rinas/sinfo/download/sinfo-0.0.45.tar.gz
tar -xvf sinfo-0.0.45.tar.gz
cd sinfo-0.0.45/

export LIBS=-L/export/home/me/.libboost/lib
export LDFLAGS=$LIBS
export CPPFLAGS="-I/export/home/me/.libboost/include -I/export/home/me/.asio/include/"
./configure --prefix=/export/home/me/.sinfo --disable-IPv6
make
make install 

Getting started:
In order to make something happen at boot you need sudo/root access. However, HPC clusters are rarely rebooted, so even if you launch something as a user it will persist for a long time. If you're lucky the right ports are open -- and they should be open between nodes.

You also need to add this to your ~/.bashrc:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/home/me/.libboost/lib

Start sinfod (the daemon) using:
~/.sinfo/sbin/./sinfod --quiet

ps aux |grep sinfod 
will show it it's running

And check that everything is ok using
~/.sinfo/bin/./sinfo