Email is an essential part of the work. Sometimes the box gets full, thus preventing the work. With gmail there is a trick how to find and delete large emails that occupy most of the space. To search for attachments greater than 5 Mb search “size:5000000”.
Category: Know-how
Installing Gromacs and Lammps
FFTW:
./configure –enable-float –enable-shared –enable-sse2
make -j N
make install
===
Gromacs:
$ tar xvfz gromacs-x.y.z.tar.gz
$ ls
gromacs-x.y.z
$ mkdir build
$ cd build
$ cmake ../gromacs-x.y.z -DCMAKE_INSTALL_PREFIX=/home/yourUser/opt/gromacs.x.y.z -DGMX_CPU_ACCELERATION=SSE2 -DGMX_SIMD=SSE2
$ make -j N
$ make install
===
LAMMPS:
$ git clone git://git.lammps.org/lammps-ro.git LAMMPS
$ make yes-molecule
$ make mpi
===
To the .bashrc add:
#Gromacs
source /home/yourUser/opt/gromacs.x.y.z/bin/GMXRC
#or source /your/installation/prefix/here/bin/GMXRC
#LAMMPS
export LD_LIBRARY_PATH=~/LAMMPS/src:$LD_LIBRARY_PATH
export PATH=~/LAMMPS/src:$PATH
gsissh at ubuntu
To access one of the PRACE supercomputers, I was required to use gsissh. The corresponding gsi-openssh-clients package is not in the standard Ubuntu repositories. I have downloaded it from http://toolkit.globus.org/ftppub/gt5/5.2/stable/packages/deb/ubuntu/12.04/pool/contrib/g/gsi-openssh/.Besides that also globus-proxy-utils is needed. This one was easy to install via apt-get install globus-proxy-utils. Finally, everything got working when the bundle of X509 trusted certificates was downloaded from http://software.ligo.org/gridtools/debian/pool/main/o/osg-ca-certs/. Note, for some reason .globus folder did not appear in my home directory. To use gsissh, I had to create it and then move my user certificate to it with proper correct permissions -rw-------.
P.S. Do not forget to create a proxy certificate (grid-proxy-init) before login to your supercomputer.
Altmetric
This blog is in the altmetric.com database. Nice!
An article submitted
An article titled “Electrochemical investigation of 1-ethyl-3-methylimidazolium bromide and tetrafluoroborate mixture at Bi(111) electrode interface” by Enn Lust, Carolin Siimenson, Meeri Lembinen, Ove Oll, Laura Läll, Marta Tarkanovskaja, Liis Siinor, Vladislav Ivaništšev, and Karmen Lust was submitted to JES.
What is so special about this article? First, the work presented is done in a joiful collaboration. Second, the computational results were obtained within a “DFT Calculations in Electrochemistry” course (LOKT.02.048), within a student project by Meeri and Marta. Well done!
Archive at arXiv
Recently two our articles were uploaded to arXiv. Our collaborator Satish Narayana Srirama prepared the first one:
http://arxiv.org/abs/1604.02788
While submitting the other, we encountered some problems when compiling the source tex-file. It turned out that one should add \pdfoutput=1 to get everything work. As a result, the second article was successfully archived at the arXiv:
Writing workshop
Thesis writing and, in general, academic writing is a skill. Not everyone has that skill, but certainly most can get it. To develop an understanding of the behaviours associated with successful writing, we organized a workshop with the help of AVOK – Centre for Academic Writing and Communication. Under the supervision of Djuddah A. J. Leijen, we started this four-hour workshop with Q&A followed by sessions about time management, in particular how to avoid procrastination, and, of course, grammar.
Some useful notes about LaTeX
First, when advanced spell checking is needed, the LaTeX could be converted to plain-text using: detex filename > filename.txt (note the omission of .tex extension).
Most LaTeX distributions come with detex program which simply strips LaTeX commands.
Second, when working with vector figures it might be a good idea to convert all texts to paths. Remember that eps-format does not support transparency.
Third, in order to count words in the final pdf-file use pdftotext filename.pdf - | tr -d '.' | wc -w. This will return the number of words in our file.
Finally, to generate a pdf-file that is acceptable by manuscriptcentral add \pdfminorversion 4 to your LaTeX-source.
Otherwise, if you use pdflatex to produce your pdf-file, manuscriptcentral will give a notice “failed to convert to the appropriate pdf”. Read this blog-post for details.
