29 May 2015

608. Bruker Topspin on Debian Jessie

Here's a more extensive description of how to install Bruker Topspin (student version):

Very briefly:
$ wget http://bruker.telemaxx.net/student/linux-topspin.sh
$ sudo dpkg --add-architecture i386
$ sudo apt-get update
$ sudo apt-get install libxft2:i386 libxtst6:i386 perl-tk libcups2:i386
$ su -
# xauth merge /home/user/.Xauthority 
# exit
$ sh linux-topspin.sh
$ ~/carbon/topspin$ sh linux-topspin.sh 
Verifying archive integrity... All good.
Uncompressing TopSpin 3.2..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
NOTE: no display found - trying localhost:11.0
Using TCL_LIBRARY=/tmp/selfgz29293/linux/tcl-8.5.11/lib/tcl8.5
Using TK_LIBRARY=/tmp/selfgz29293/linux/tk-8.5.11/lib/tk8.5
Please enter root password if prompted for it.
Password: 
Starting /tmp/selfgz29293/linux/tk-8.5.11/bin/wish8.5 -f /tmp/selfgz29293/xwinstall.d/swim/lib/xwinstall.tcl --
Using log file: /tmp/install.log
Error while displaying /tmp/selfgz29293/rellet.pdf with /tmp/swim-29462/prog/bin/xpdf : 
/tmp/swim-29462/prog/bin/xpdf: error while loading shared libraries: libSM.so.6: cannot open shared object file: No such file or directory

Using log file: /opt/topspin3.2/install.log
Error: Cannot create user account flexlm: useradd flexlm: useradd: group flexlm exists - if you want to add this user to that group, use -g.
Errors occurred during installation:
Error: Cannot create user account flexlm: useradd flexlm: useradd: group flexlm exists - if you want to add this user to that group, use -g.
[I was doing this while logged in via ssh -XC to the student's computer, and without a pdf reader installed. If a pdf opens, close it to continue the installation. Don't worry about the errors.]

Here are screenshots from the installation process:
























The only thing that remained was to install the license.dat file that Bruker had issued to my student:

sudo mv /usr/local/flexlm/Bruker/licenses/license.dat /usr/local/flexlm/Bruker/licenses/license.bak sudo cp ~/carbon/topspin/license.dat /usr/local/flexlm/Bruker/licenses/license.dat
And then we were able to start topspin:







 And finally:

26 May 2015

607. Ping...Topspin and ADF work on debian jessie

My blog post productivity has been getting increasingly poor over the past year and a half, with a precipitous dip occurring at the beginning of this year. The dip is due to teaching and research, and the slow but steady decline preceding it is due to parenthood (the older the little one gets, the less time -- and inclination! -- I have to do extra work. Toddlers can be so much fun.).

I've got a few posts that need a bit of polishing before I publish ('how to set up your own DNS server' and 'how to set up your own mail server' are two examples), but until then, I'll seed your google search results with the following information about something completely different:

* Bruker Topspin 3.2 (https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html) -- the NMR program, not the table tennis game -- installs fine on Debian Jessie 64 bit (the only version we tried). Note that:
** you'll need java
** you'll need the 32 bit package with libXtst.so.6, not the 64 bit package. It can be installed via apt-get install libxtst6:i386
** you'll need to enable the root account if you haven't already (the easiest way to do that is to do sudo passwd root, set a password and you're good to go)

* The trial version of the Amsterdam Density Functional package (ADF; http://www.scm.com/Downloads/2014) installs and runs fine* on one of my Debian Jessie 64 bit nodes. I did not install the intel mpi libraries, but then adf seems to be working according to a shared memory model.

Installation was quick and painless. I downloaded the package using the instructions in the email, copied the .tgz file to my node, ssh:d with X enabled (ssh -XC) to allow for interactive activation/registration, and to be able to use adfjobs (to draw molecules and set up jobs), and to be able to use adfview.

I untared the adf file:
tar xvf adf2014.07.pc64_linux.intelmpi.tgz

I then moved the folder to /opt and took ownership of it:
sudo mv adf2014.07 /opt/
sudo chown $USER:$USER /opt/adf2014.07 -R

I edited /opt/adf2014.07/adfrc.sh to read:
ADFHOME=/opt/adf2014.07

And then sourced it and ran adfjobs:
source adfrc.sh
bin/adfjobs

I was then asked to provide the username and password from my email, and from that point on it was just a matter of using the program (which has it's own quirks ).

*by default only six cores on a hex core i7-4930k are used. To force 12 cores (hyperthreading) you need to explicitly tell ADF to do so. The manual says not to, however. I haven't done any performance tests, BUT without specifying 12 cores the node is only running at half load.

12 January 2015

606. Downloading programs from iview (Australian Broadcasting Corporation): python-iview

 I did this on debian jessie.

I found the Ep 7 Season 2 episode of The Checkout so well worth watching that I wanted to keep a copy of it, which lead me to search for ways of downloading programs from iview.

Get python-iview from https://github.com/vadmium/python-iview. You can try this direct link: https://github.com/vadmium/python-iview/archive/master.zip

Then unzip and install (you might need to install some of the dependencies listed on the github page first):
me@niobium:~/tmp/python-iview/python-iview-master$ sudo python3 setup.py install
running install
running build
running build_py
running build_scripts
running install_lib
creating /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/comm.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/flvlib.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/config.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/hds.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/parser.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/fetch.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/__init__.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/utils.py -> /usr/local/lib/python3.4/dist-packages/iview
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/comm.py to comm.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/flvlib.py to flvlib.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/config.py to config.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/hds.py to hds.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/parser.py to parser.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/fetch.py to fetch.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/__init__.py to __init__.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/utils.py to utils.cpython-34.pyc
running install_scripts
copying build/scripts-3.4/iview-gtk -> /usr/local/bin
copying build/scripts-3.4/iview-cli -> /usr/local/bin
changing mode of /usr/local/bin/iview-gtk to 755
changing mode of /usr/local/bin/iview-cli to 755
running install_data
copying iview-gtk.desktop -> /usr/share/applications
running install_egg_info
Writing /usr/local/lib/python3.4/dist-packages/iview-0.2.egg-info

Start it from within gnome, select your show and download:
 Easy.