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gromacs/GROMACS_README.md

+## Overview
+
+[1. Download](#download)
+[2. Build](#build)
+[3. Run](#run)
+
+## [1. Download](#download)
+
+Gromacs can be downloaded from : [http://www.gromacs.org/Downloads](http://www.gromacs.org/Downloads) 
+The UEABS benchmark cases require the use of 4.6 or newer branch, the latest 4.6.x version is suggested.
+
+## [2. Build](#build)
+
+Complete Build instructions: [http://manual.gromacs.org/documentation/](http://manual.gromacs.org/documentation/)
+
+A typical build procedure look like :
+
+```
+tar -zxf gromacs-2016.tar.gz
+cd gromacs-2016
+mkdir build
+cd build
+cmake \
+        -DCMAKE_INSTALL_PREFIX=$HOME/Packages/gromacs/2016 \
+        -DBUILD_SHARED_LIBS=off \
+        -DBUILD_TESTING=off \
+        -DREGRESSIONTEST_DOWNLOAD=OFF \
+        -DCMAKE_C_COMPILER=`which mpicc` \
+        -DCMAKE_CXX_COMPILER=`which mpicxx` \
+        -DGMX_BUILD_OWN_FFTW=on \
+        -DGMX_SIMD=AVX2_256 \
+        -DGMX_DOUBLE=off \
+        -DGMX_EXTERNAL_BLAS=off \
+        -DGMX_EXTERNAL_LAPACK=off \
+        -DGMX_FFT_LIBRARY=fftw3 \
+        -DGMX_GPU=off \
+        -DGMX_MPI=on \
+        -DGMX_OPENMP=on \
+        -DGMX_X11=off \
+        ..
+
+make (or make -j ##)
+make install
+```
+        
+You probably need to adjust
+1. The `CMAKE_INSTALL_PREFIX` to point to a different path
+2. `GMX_SIMD` : You may completely ommit this if your compile and compute nodes are of the same architecture (for example Haswell).
+   If they are different you should specify what fits to your compute nodes.
+   For a complete and up to date list of possible choices refer to the gromacs official build instructions.
+   Typical values are `AVX_256` for Ivybridge, `AVX2_256` for Haswell, `AVX_512_KNL` for KNL For CUDA build one should change `-DGMX_GPU=on`, and cuda bin directory should be in path.
+
+## [3. Run](#run)
+
+There are two data sets in UEABS for Gromacs.
+
+1. `ion_channel` that use PME for electrostatics, for Tier-1 systems
+2. `lignocellulose-rf` that use Reaction field for electrostatics, for Tier-0 systems. Reference :  [http://pubs.acs.org/doi/abs/10.1021/bm400442n](http://pubs.acs.org/doi/abs/10.1021/bm400442n)
+
+The input data file for each benchmark is the corresponding .tpr file produced using tools from a complete gromacs installation and a series of ascii data files  (atom coords/velocities, forcefield, run control).
+
+If it happens to run the tier-0 case on BG/Q use `lignucellulose-rf.BGQ.tpr`
+instead `lignocellulose-rf.tpr`. It is the same as `lignocellulose-rf.tpr` 
+created on a BG/Q system.
+
+The general way to run gromacs benchmarks is :
+
+```
+WRAPPER WRAPPER_OPTIONS PATH_TO_GMX mdrun -s CASENAME.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile
+```
+
+- `CASENAME` is one of ion_channel or lignocellulose-rf
+- `maxh`        : Terminate after 0.99 times this time (hours) i.e. gracefully terminate after ~30 min
+- `resethwat`   : Reset Timer counters at half steps. This means that the reported walltime and performance referes to the last  half steps of sumulation.
+- `noconfout`   : Do not save output coordinates/velocities at the end.
+- `nsteps`      : Run this number of steps, no matter what is requested in the input file
+- `logfile`     : The output filename. If extension .log is ommited it is automatically appended. Obviously, it should be different for different runs.
+- `WRAPPER` and `WRAPPER_OPTIONS`  depend on system, batch system etc. Few common pairs are :
+    - CRAY     : `aprun -n TASKS -N NODES -d THREADSPERTASK`
+    - Curie    : `ccc_mrun with no options - obtained from batch system`
+    - Juqueen  : `runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS`
+    - Slurm    : `srun`  with no options, obtained from slurm if the variables below are set.
+
+```
+#SBATCH --nodes=NODES
+#SBATCH --ntasks-per-node=TASKSPERNODE
+#SBATCH --cpus-per-task=THREADSPERTASK
+```
+
+The best performance is usually obtained using pure MPI i.e. `THREADSPERTASK=1`.
+You can check other hybrid MPI/OMP combinations.
+
+The execution time  is reported at the end of logfile : `grep Time: logfile | awk -F ' ' '{print $3}'`
+
+> **NOTE** : This is the wall time for the last half number of steps. 
+For sufficiently large nsteps, this is half of the total wall time.
+
+
+In order to use GPU acceleration, one needs to add in gmx mdrun options the 	`-gpu_id GPU_IDS`. `GPU_IDS` value depends on how many MPI Tasks and gpus are used per node.
+
+For example, using 4 GPUs per node with 4 Taks per node, the GPU_IDS should be 0123.
+In order to run on a 20 core node with 20 gpus with pure MPI i.e. 20 tasks/node,
+GPU_IDS should be 0000000000111111111 (10 zeroes and 10 ones)
+
+