amber-11.0-2spec

#
# $Id: $
#
#
Summary: Amber Toolkit and parallel modules.

###
Name:      amber 
Version:   11.0
Release:   2
License:   UCSF
Vendor:    Amber
Group:     Applications/Chemistry
Source:    amber-11.tar.gz
Packager:  TACC - milfeld@tacc.utexas.edu jfonner@tacc.utexas.edu
BuildRoot: /var/tmp/%{name}-%{version}-buildroot

%define version_unit 11

%include rpm-dir.inc
%description
Amber Toolkit and parallel modules

%define APPS /opt/apps
%define MODULES modulefiles


%include compiler-defines.inc
%include mpi-defines.inc

%define INSTALL_DIR %{APPS}/%{comp_fam_ver}/%{mpi_fam_ver}/%{name}/%{version}
%define  MODULE_DIR %{APPS}/%{comp_fam_ver}/%{mpi_fam_ver}/%{MODULES}/%{name}

#                   Rename rpm to "-n" argument at TACC
%package -n %{name}%{version_unit}-%{comp_fam_ver}-%{mpi_fam_ver}
Summary: The Amber tools and parallel modules 
Group:  Applications/Chemistry

%description -n %{name}%{version_unit}-%{comp_fam_ver}-%{mpi_fam_ver}
Amber serial, parallel, and cuda modules 
 
%prep
rm   -rf $RPM_BUILD_ROOT
mkdir -p $RPM_BUILD_ROOT/%{INSTALL_DIR}
mkdir -p $RPM_BUILD_ROOT/%{MODULE_DIR}

#setup  -n amber-%{version_unit}       ## will build in "install" directory


%build

set +x
%include compiler-load.inc
%include mpi-load.inc
module load mkl
module load cuda
module load cuda_SDK
set -x

echo COMPILER LOAD: %{comp_fam_ver_load}
echo MPI      LOAD: %{mpi_fam_ver_load}

mkdir -p             %{INSTALL_DIR}
mount -t tmpfs tmpfs %{INSTALL_DIR}
cd                   %{INSTALL_DIR}

tar xzvf /home1/0000/build/rpms/SOURCES/%{name}-%{version_unit}.tar.gz

# set +x
# set -x
       AMBERHOME=`pwd`
                 MKL_HOME=$TACC_MKL_DIR
                          CUDA_HOME=$TACC_CUDA_DIR
export AMBERHOME MKL_HOME CUDA_HOME

cd $AMBERHOME/AmberTools/src
# make clean
LDFLAGS="/usr/lib64/libXext.so.6 -L/usr/lib64" ./configure intel
make install
cd $AMBERHOME/src
# make clean
cd $AMBERHOME
./AT15_Amber11.py
cd src
make

cd $AMBERHOME/AmberTools/src
make clean
./configure -mpi intel
make install
cd $AMBERHOME/src
make clean
cd $AMBERHOME
./AT15_Amber11.py
cd src
make parallel

cd $AMBERHOME/AmberTools/src
make clean
./configure -cuda intel
cd $AMBERHOME/src
make clean
cd $AMBERHOME
./AT15_Amber11.py
cd src
make cuda

cd $AMBERHOME/AmberTools/src
make clean
./configure -cuda -mpi intel
cd $AMBERHOME/src
make clean
cd $AMBERHOME
./AT15_Amber11.py
cd src
make cuda_parallel


%install

 cd                   %{INSTALL_DIR}
 cp   -rp AmberTools bin dat doc examples   \
          GNU_Lesser_Public_License include \
          info lib README share             \
                            $RPM_BUILD_ROOT/%{INSTALL_DIR}
rm -r                       $RPM_BUILD_ROOT/%{INSTALL_DIR}/AmberTools/src
chmod -Rf u+rwX,g+rwX,o=rX  $RPM_BUILD_ROOT/%{INSTALL_DIR}
cd                          $RPM_BUILD_ROOT
#umount                                      %{INSTALL_DIR}

#############################    MODULES  ######################################

cat >    $RPM_BUILD_ROOT/%{MODULE_DIR}/%{version}.lua << 'EOF'
help(
[[
The TACC Amber installation includes the parallel modules with the .MPI suffix:

MMPBSA.MPI  pbsa.MPI  pmemd.MPI  ptraj.MPI  sander.LES.MPI  sander.MPI

The pmemd binaries for use with GPUs are named:

pmemd.cuda.MPI  pmemd.cuda

They were built with "single-precision, double-precision" for the best trade-off
between speed and accuracy.  Visit http://ambermd.org/gpus/ for more 
information. Also note that when using the CUDA version of pmemd, you can only 
use 1 thread per graphics card and must use the "gpu" queue.  For example, if 
using 2 GPU cards on one node, your job submission script should include the 
following lines (along with all the other usual lines):

#$ -pe 2way 12
#$ -q gpu
ibrun pmemd.cuda.MPI -O -i mdin -o mdout -p prmtop \
-c inpcrd -r restrt -x mdcrd </dev/null

Your ibrun line will change depending your filenames, etc. Again, visit
http://ambermd.org/gpus/ for more information as well as the Lonestar guide at 
http://www.tacc.utexas.edu/user-services/user-guides/lonestar-user-guide

Amber tools are included in the AmberTools directory.
Examples, data, docs, includes, info, libs are included in directories with
corresponding names. 

The Amber modulefile defines the following environment variables:
TACC_AMBER_DIR, TACC_AMBER_TOOLS, TACC_AMBER_BIN, TACC_AMBER_DAT,
TACC_AMBER_DOC, TACC_AMBER_EXAM, TACC_AMBER_INC, TACC_AMBER_LIB, 
and TACC_AMBER_MAN for the corresponding Amber directories.

Also, AMBERHOME is set to the Amber Home Directory (TACC_AMBER_DIR),
and $AMBERHOME/bin is included in the PATH variable.

Version %{version}
]]
)

whatis("Name: AMBER")
whatis("Version: 11.0")
whatis("Version-notes: Compiler:%{comp_fam_ver}, MPI:%{mpi_fam_ver}, MKL:10.2, FFTW:3.2.2")
whatis("Category: Application, Chemistry")
whatis("Keywords: Chemistry, Biology, Molecular Dynamics, Cuda, Application")
whatis("URL: http://amber.scripps.edu/")
whatis("Description: Molecular Modeling Package")


--
-- Create environment variables.
--
local amber_dir   = "%{INSTALL_DIR}"
local amber_tools = "%{INSTALL_DIR}/AmberTools"
local amber_bin   = "%{INSTALL_DIR}/bin"
local amber_dat   = "%{INSTALL_DIR}/dat"
local amber_doc   = "%{INSTALL_DIR}/doc"
local amber_exam  = "%{INSTALL_DIR}/examples"
local amber_inc   = "%{INSTALL_DIR}/include"
local amber_info  = "%{INSTALL_DIR}/info"
local amber_lib   = "%{INSTALL_DIR}/lib"
local amber_man   = "%{INSTALL_DIR}/share/man"

setenv("TACC_AMBER_DIR"  , amber_dir  )
setenv("TACC_AMBER_TOOLS", amber_tools)
setenv("TACC_AMBER_BIN"  , amber_bin  )
setenv("TACC_AMBER_DAT"  , amber_dat  )
setenv("TACC_AMBER_DOC"  , amber_doc  )
setenv("TACC_AMBER_EXAM" , amber_exam )
setenv("TACC_AMBER_INC"  , amber_inc  )
setenv("TACC_AMBER_INFO" , amber_info )
setenv("TACC_AMBER_LIB"  , amber_lib  )
setenv("TACC_AMBER_MAN"  , amber_man  )
setenv("AMBERHOME"       , amber_dir  )

append_path("PATH"       ,amber_bin   )
append_path("MANPATH"    ,amber_man   )
EOF

cat > $RPM_BUILD_ROOT/%{MODULE_DIR}/.version.%{version} << 'EOF'
#%Module1.0#################################################
##
## Version file for AMBER %version
## Compiler: %{comp_fam_ver} and  MPI: %{mpi_fam_ver}
##

set     ModulesVersion      "%{version}"
EOF

#############################    MODULES  ######################################


%files -n %{name}%{version_unit}-%{comp_fam_ver}-%{mpi_fam_ver}
%defattr(-,root,install)
%{INSTALL_DIR}
%{MODULE_DIR}

%post -n %{name}%{version_unit}-%{comp_fam_ver}-%{mpi_fam_ver}

%clean

#rm -rf $RPM_BUILD_ROOT