====== Overview ======
  * Install Amber16 using gfortran/gcc
  * Configuration of GPU workstations ( red and blue)
    * Slackware64-14.1
    * CUDA7.5
    * GCC-4.8.2
  * Ref: http://jswails.wikidot.com/installing-amber14-and-ambertools14
====== Install serial CPU version ======
  * Unpack the package into some folder, e.g. /home/usr/share
<code>
cd /home/usr/share
sudo
tar xvf ~/build/amber/AmberTools16.tar.bz2
tar xvf ~/build/amber/Amber16.tar.bz2
chown -R panying:xue amber16
exit #install and test under the user panying rather than root!
cd amber16
</code>

  * Setup environment variable and run configure script
<code>
export AMBERHOME=/home/usr/share/amber16 (on bash shell)
setenv AMBERHOME /home/usr/share/amber16 (on csh shell)

./configure gnu  # choose 'y' to apply bugfix/patches
sudo apt-get install libxt-dev # if "Error: The X11 libraries are not in the usual location !"
sudo apt-get install flex # if "Error: not find flex "
sudo apt-get install libzip-dev zlib1g-dev # if "Error: zlib.h not found "
sudo apt-get install libbz2-dev # if "Error: bzlib.h not found "

source <the csh or bash conf file>
</code>

  * Install and test it
<code>
make install
sudo apt-get install libxext-dev # if "Error:shape.h not found!" 
####Installation of Amber16 (serial) is complete at Thu Dec  1 22:07:48 EST 2016.####
make test
</code>

  * Result of test
<code>
# AmberTools16
1870 file comparisons passed
0 file comparisons failed
0 tests experienced errors
# Amber16
150 file comparisons passed
0 file comparisons failed
0 tests experienced errors
</code>

====== Install parallel CPU version ======
  * Install openmpi (see slackbuild.org). The version I installed on spring/summer is 1.6.5.

  * Run configuration script
<code>
cd $AMBERHOME
sudo apt-get install openmpi-bin
sudo apt-get install libopenmpi-dev

./configure -mpi gnu
#esp checking
#testing [C++ / fortran] cross-compile with MPI libs
#OK
</code>

  * Install Amber and test it
<code>
make clean
make install
    please make sure mpi part is ok while installing.

#### 2 cores ####
export DO_PARALLEL='mpirun -np 2'
or
setenv DO_PARALLEL 'mpirun -np 2' #tcsh-mode

make test
#pls noticed that test in non-root user

#### 8 cores ####
export DO_PARALLEL='mpirun -np 8'
or
setenv DO_PARALLEL 'mpirun -np 8' #tcsh-mode

make test
</code>

  * Result of test
<code>
### 2 cores
# Amber
147 file comparisons passed
0 file comparisons failed
0 tests experienced an error
869 file comparisons passed
0 file comparisons failed
0 tests experienced errors

### 8 cores
#Amber
167 file comparisons passed
0 file comparisons failed
0 tests experienced an error
# AmberTools
778 file comparisons passed
2 file comparisons failed
0 tests experienced errors

</code>
====== Install serial CUDA version ======
  * Run configuration script
<code>
tcsh      
echo $CUDA_HOME    #check CUDA_HOME
cd $AMBERHOME
./configure -cuda gnu
</code>

  * Install Amber and test it
<code>
make clean
make install
    please make sure that cuda part is ok!
make test
</code>

  * Result of test
<code>
### Amber16
138 file comparisons passed
1 file comparison failed
0 tests experienced errors
</code>

====== Install parallel CUDA version ======
  * Run configuration script
<code>
cd $AMBERHOME
./configure -cuda -mpi gnu

then do as recommended
</code>

  * Modify config.h ([[http://archive.ambermd.org/201210/0097.html | Ref]]) from
<code>
...
PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart -lstdc++
...
</code>
to
<code>
...
PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart -lstdc++ -lmpi_cxx
...
</code>

  * Install Amber and test it
<code>
make clean
make install
    please make sure the mpi/cuda part is ok!
export DO_PARALLEL='mpirun -np 2'
or
setenv DO_PARALLEL 'mpirun -np 2'  #tcsh-mode
make test
</code>

  * Result of test
<code>
103 file comparisons passed
2 file comparisons failed
0 tests experienced errors
</code>

  * Note: compiling might end up with errors like "undefined reference to MPI::Comm::Comm()". The solution is: before running "make cuda_parallel", add "-lmpi_cxx" to variable "PMEMD_CU_LIBS" in config.h.

  * Note: don't forget to add %%$%%AMBERHOME and %%$%%CUDA_HOME into ~/.profile
          * turns out ~/.profile link to ~/.bashrc, check if ~/.bashrc or ~/.cshrc have already been set up.

  * Note - gpuID

    0: 92.5, 92.7, 92.8
    1: 96.4, 96.5, 97.0
    2: 97.4, 96.9, 96.6
    3: 95.8, 95.8, 95.8
    #temp test

=====Current Performance=====

^	        ^Performance(ns/day)	^^^ 	Sample Parameter		         ^^^^
|	        |Website|Bue	|Red 	|NPT	|NSTLIM	|DT	|Atom number| 
|DHFR	        | 52.97	|455.83	|473.69	|Yes 	|75000	|4fs	|23,558|
|Factor X IX	|65.91	|66.80	|68.40	|Yes	|15000	|2fs	|90.906|
|Cellullose	|14.09	|14.35	|14.87	|Yes 	|10000	|2fs	|408,609|