Introduction+to+Tinker

Installation of the Tinker MD package... NOW IN VERSION 6.0 with PARALLEL SUPPORT THROUGH OPENMP!
__** Installation guide for serial (non-Intel compiler based) Tinker: **__

Switch to the linux directory, pick a compiler and CD into that directory, and then copy all the //***.make**// files in that folder into the //**../../source/**// folder of the distribution

=
Lastly, you're going to want to run the __**rename.make**__ **script.** That will rename and move all the executables you just generated (files ending in .X in the source directory) up one level and into the ../bin/ directory. This is convenient because then you just but that $TINKERHOME/bin/ directory in your $PATH and you're good to go.======

NOTE: I recommend using the g95 compiler for version 6.0 because they've converted almost all their code over from Fortran 77 to Fortran 95.
NOTE: Using gfortran with version 6.1.something (> June 2012) you may have to add -fno-align-commons which can be easily accomplished with the perl one-liner,

perl -pe 's/gfortran -c/gfortran -c -fno-align-commons/g' < compile.make > compile.mod chmod +x compile.mod ./compile.mod (instead of .make -- does the EXACT same thing)

__**Installation guide for parallel (INTEL COMPILERS ONLY) Tinker:**__

Head to: Intel non-commercial license

Download the highlighted package for your workstation's architecture (32 or 64 bit). Extract the contents, open a terminal and head to the newly created folder -- helpful hint, the name of this folder is long, change it to something like intstuff or intel. In the shell, type ./install.sh. In step 1, it asks you who you want to allow access to, i.e. install as root or not. CHOOSE OPTION 1 OR 2, or else you will never be able to link all the executables correctly. The remaining steps are self-explanatory once I tell you the serial code was deposited in the inbox of the email address you gave to Intel (I hope it was a real one). Just copy and paste it, hyphen and all. At the end, make sure you perform all the commands they ask you to -- or else the executables will not work. If you chose option 1 in step 1, no one needs to use sudo to make a call to ifort or icc.

To install Tinker, copy the *.make files from the Intel folder to the source folder. Type ./compile.make (no sudo), then ./library.make, then open the link.make file in a text editor and replace every occurrence of the fftw library calls with the call + its path, e.g.,

If you compiled FFTW to be able to use OpenMP you should be ready to go... the commands to do this are found in the 0README file in $TINKERHOME/fftw.

__**Using Parallel Tinker**__

export OMP_NUM_THREADS=XX

Then run the job just asking for XX number of processors. It does provide a small speedup but the scaling is atrocious. With 12 processors, a small simulation with the self-consistent polarization method took 92% of the time it took to complete the same job with a single processor. Not worth it unless you do direct polarization which is only recommended for the iAMOEBA model -- for which no solute parameters currently exist.

TPP 22/04/2014