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Showing posts from February, 2015

React.js – edit and delete comments in CommentBox

It appears customary for high-intelligence, high-skills groups of engineers to "roll their own" whenever they have a chance to. Counter-intuitively to most managerial/MBA types out there, re-inventing the wheel can give you... a better wheel. Success is not guaranteed though – but these people may leave sooner rather than later if you don't let them...

Having looked at number of JS frameworks (ember, backbone, angular) there was no clear winner. They were all a mess, at least to me. So I approached React.js with no hopes – how much better could it possible be? It turns out, a lot!

This post will be an extension of the official React.js tutorial. The tutorial stops at the stage where you can add comments to a dynamic lists, that will grow as you add comments. This falls short of the functionality displayed on facebook: once you add a comment you can edit or delete it, so that's what're going to do. Full disclosure, I only started using React this weekendo so my gu…

complie plumed 2 with gromacs 4.6 on ubuntu 14.04

Should be simple right? Just you wait... Because I do it for the 5th time now, this will deserve a blog entry, if anything for my own sanity. 


sudo apt-get install libblas-dev liblapack-dev
tar xvf plumed-2.1.1.tgz
cd plumed-2.1.1
export PLUMED_PREFIX=~/Programs/plumed/2.1.1/
./configure.sh  << EOF
1
EOF
make
make install


[Edit]For OpenMPI plumed installation do the following

sudo apt-get install libcr-dev mpich2 mpich2-doc./configure.sh  << EOF
3
EOF
sed -i s#'-lblas'#'-lblas -L/usr/lib/openmpi/lib'#g Makefile.conf sed -i s#'PLUMED_INCLUDE)'#'PLUMED_INCLUDE) -I/usr/lib/openmpi/include'#g Makefile.conf
The default ./configure command doesn't do the job for me. So let's ignore that for now.

cmake .. -DCMAKE_INSTALL_PREFIX=/path/ -DGMX_MPI=OFF -DGMX_GPU=OFF
make 
make install 

And then if all goes well

source /path/
mdrun -h 2>&1 >/dev/null | grep plumed
-plumed  plumed.dat  Input, Opt.  Generic data file

Sadly, this is just a serial vers…

gromacs 5.0 - first look

Image
Oh, gromacs, old friend let's see what you have to offer in your new release


wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.4.tar.gz
tar xvf gromacs-5.0.4.tar.gz
cd gromacs-5.0.4
mkdir build
cd build
cmake .. 

Problem #1

-- Could NOT find LibXml2 (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
CMake Warning at CMakeLists.txt:601 (message):
  libxml2 not found.  Will build GROMACS without unit-tests.  This is not
  recommended, because the unit-tests help to verify that GROMACS functions
  correctly.  Most likely you are missing the libxml2-dev(el) package.  After
  you installed it, set GMX_BUILD_UNITTESTS=ON.


Problem #2

CMake Warning at cmake/gmxManageFFTLibraries.cmake:94 (message):
  The FFTW library was compiled with --enable-avx to enable AVX SIMD
  instructions.  That might sound like a good idea for your processor, but
  for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD
  instructions for the way GROMACS uses FFTs.  Limitations in the way FFTW
  allows GROMACS to…