495. Briefly: gromacs 4.6 on ROCKS 5.4.3

I didn't want to spend much time on getting this right, so I took the easiest route and combined three posts:

Firstly, I compiled cmake:
http://verahill.blogspot.com.au/2012/05/compiling-openbabel-231-and-cmake-on.html

Secondly, I used the openblas libraries which I compiled in this post
http://verahill.blogspot.com.au/2013/05/421-nwchem-63-on-rocks-543centos-56.html

Thirdly, I looked at this post which deals with gromacs 4.6 on debian:
http://verahill.blogspot.com.au/2013/04/396-compiling-gromacs-46-with-openblas.html

gromacs 4.6 can download and build its own fftw libs, so you don't need to do that separately.

First make the target directory, e.g.

sudo mkdir /share/apps/gromacs
sudo chown $USER:$USER /share/apps/gromacs

Single precision:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi/lib:/share/apps/openblas/lib
export LDFLAGS="-L/share/apps/openblas/lib -lopenblas"
export CPPFLAGS="-I/share/apps/openblas/include"

export CC=/usr/bin/gcc44
export CXX=/usr/bin/g++44
cmake -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=On -DGMX_DOUBLE=off -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/gromacs4.6_single -DGMX_EXTERNAL_BLAS=/share/apps/openblas/lib ../gromacs-4.6
make
make install

Double precision:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi/lib:/share/apps/openblas/lib
export LDFLAGS="-L/share/apps/openblas/lib -lopenblas"
export CPPFLAGS="-I/share/apps/openblas/include"

export CC=/usr/bin/gcc44
export CXX=/usr/bin/g++44
cmake -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=On -DGMX_DOUBLE=on -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/gromacs4.6_double -DGMX_EXTERNAL_BLAS=/share/apps/openblas/lib ../gromacs-4.6
make
make install

In my particular case I've got all users as members of the compchem group:

chown $USER:compchem /share/apps/gromacs -R 
chmod g+rwx /share/apps/gromacs -R

494. Very briefly: issue with thunderbird, failed connections and repeatedly being asked for the password

Even if you've set up thunderbird so that everything is working perfectly most of the time you occasionally end up in a very annoying situation: you keep on getting error messages about failed connections, and you keep being asked to supply the correct password. You can hit retry, or you can enter the correct password -- but why would you, given that you know based on previous successful connection attempts that your password is correct?
Leaving things along for 5-10 minutes tends to resolve it (or restarting thunderbird, given that you don't do it too quickly i.e. you basically let things stay quiet for a little while).

Anyway, while there are a number of potential reasons for this, in my case it's always been due to too many simultaneous connections, so that some of them are rejected. Not that that's what the error message really says, but whatever, the solution is actually pretty simple -- limit the number of simultaneous connections.

Go to Edit, Account Settings, select the account (typically a gmail one), Server Settings, click on Advanced, and change the 'Maximum number of server connections to cache' from the default 5 to e.g. 1.

On the computers I've done this on I've completely gotten rid of the annoying password requests.

493. Very, Very Briefly: libreoffice 4 on wheezy -- wheezy-backports

I might be the last person who 'gets' it, but I always presumed that since package versions in backports would be newer they'd automatically be installed.  But apparently that's not the case.

So, enable wheezy-backports, e.g. put this in your /etc/apt/sources.list

deb http://ftp.iinet.net.au/debian/debian/ wheezy-backports main contrib non-free

Then install libreoffice 4:

sudo apt-get install libreoffice -t=wheezy-backports

That's it.

Post-script:
To see what your policies are:

apt-cache policy libreoffice

libreoffice:
  Installed: 1:4.0.3-2~bpo70+1
  Candidate: 1:4.0.3-2~bpo70+1
  Version table:
 *** 1:4.0.3-2~bpo70+1 0
        100 http://ftp.iinet.net.au/debian/debian/ wheezy-backports/main amd64 Packages
        100 /var/lib/dpkg/status
     1:3.5.4+dfsg2-0+deb7u2 0
        500 http://ftp.iinet.net.au/debian/debian/ wheezy/main amd64 Packages

and as it turns out the backports repo only has a score of 100, and looking at man apt_preferences:

       If the target release has been specified then APT uses the following algorithm to set the priorities of the versions of a package. Assign:

       priority 1
           to the versions coming from archives which in their Release files are marked as "NotAutomatic: yes" but not as "ButAutomaticUpgrades: yes" like the
           Debian experimental archive.

       priority 100
           to the version that is already installed (if any) and to the versions coming from archives which in their Release files are marked as "NotAutomatic:
           yes" and "ButAutomaticUpgrades: yes" like the Debian backports archive since squeeze-backports.

       priority 500
           to the versions that are not installed and do not belong to the target release.

       priority 990
           to the versions that are not installed and belong to the target release.

To see what's available in backports, do

aptitude search ~Awheezy-backports