AmberTools12.pdf
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http://ambermd.org/
Build Instruction: http://jswails.wikidot.com/installing-amber12-and-ambertools-12
Usage
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module load amber/20ompi
Old versions:
module load amber/12-gnu
OR
module load amber/12-openmpi
OR
module load amber/12-cuda-gnu (To use gpus, please make sure you send the job to queue named "gpu" )
There is a special version (see notes below in the installation section. This can be used with:
module load amber/12-openmpi-modified
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ssh n021
export AMBERHOME=/sw/amber/12/amber12-cuda-gnu
cd $AMBERHOME
module load cuda/4.0
export CUDA_HOME=/usr/local/cuda
./configure -cuda gnu
make install
make test
./configure -cuda gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date
Searching for python2... Found python2.6: /usr/bin/python2.6
Obtaining the gnu suite version:
gcc -v
The version is 4.4.5
Testing the gcc compiler:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the gfortran compiler:
gfortran -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -O0 -c -o testp.f.o testp.f
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Skipping configuration of FFTW3
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
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Amber20 Installation and Usage
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source /usr/local/bin/s3proxy.sh
module load intel/ips2019mkl
module load mpi/openmpi/4.0.2
module load library/boost/1.73
module load library/netcdf/netcdf-c/4.7.3
module load python/3.7.4
module load cmake/3.18.1
module load cuda/10.1
module load nvidia/nccl/2.10.3
unset BOOST_ROOT
cd amber20_src
cd cmake
#Edit LibraryTracking.cmake file and at line approximately 180 insert the following lines:
if( ${NAME} MATCHES "^boost" )
message( STATUS "aab ${IMP_LIBS_LIBRARIES}" )
string(REGEX REPLACE optimized\;|debug\; "" tmp_string "${IMP_LIBS_LIBRARIES}")
set(IMP_LIBS_LIBRARIES ${tmp_string})
endif()
message( STATUS "NAME=${NAME} and INTERFACE_LINK_LIBRARIES=${IMP_LIBS_LIBRARIES} and PROPERTY INTERFACE_INCLUDE_DIRECTORIES=${IMP_LIBS_INCLUDES}" )
between lines
add_library(${NAME} INTERFACE)
---------- insert here ----------
set_property(TARGET ${NAME} PROPERTY INTERFACE_LINK_LIBRARIES ${IMP_LIBS_LIBRARIES})
set_property(TARGET ${NAME} PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${IMP_LIBS_INCLUDES})
cd ..
mkdir -p build2
cd build2
flags="-g";unset BOOST_ROOT;
cmake -DCMAKE_INSTALL_PREFIX=/sw/amber/20/amber20openMP -DOPENMP=TRUE -DMPI=TRUE \
-DCOMPILER=GNU -DMPI_Fortran_INCLUDE_PATH=${OPENMPI_BASE}/include \
\
-DCUDA=TRUE -DNCCL=TRUE -DINSTALL_TESTS=TRUE -DDOWNLOAD_MINICONDA=FALSE -DTRUST_SYSTEM_LIBS=TRUE -DPYTHON_EXECUTABLE=`which python3` \
-DCHECK_UPDATES=FALSE \
\
-DNetCDF_INCLUDES_F77=${NETCDF_BASE}/include -DNetCDF_INCLUDES_F90=${NETCDF_BASE}/include \
-DNetCDF_LIBRARIES_F77=${NETCDF_BASE}/lib/libnetcdff.so -DNetCDF_LIBRARIES_F90=${NETCDF_BASE}/lib/libnetcdff.so \
-DNetCDF_LIBRARIES_C=${NETCDF_BASE}/lib/libnetcdf.so \
-DNetCDF_INCLUDES=${NETCDF_BASE}/include \
\
-DPnetCDF_C_LIBRARY=${PNETCDF_BASE}/lib/ompi3/GNU/libpnetcdf.so -DPnetCDF_C_INCLUDE_DIR=${PNETCDF_BASE}/include \
-DPnetCDF_PATH=${PNETCDF_BASE} \
\
-DBOOST_INCLUDEDIR=$BOOST_BASE/include -DBOOST_LIBRARYDIR=$BOOST_BASE/lib \
-DBUILD_REAXFF_PUREMD=ON \
-DCMAKE_C_FLAGS="$flags" -DCMAKE_CXX_FLAGS="$flags" -DCMAKE_Fortran_FLAGS="$flags" \
-DNCCL=FALSE .. 2>&1 | tee cmakeLogs.txt
make 2>&1 | tee makeLogs.txt
make install 2>&1| tee makeInstallLogs.txt
pip install simtk-unit |
Sample pbs script to run with amber20.
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#!/bin/bash -l
#PBS -m abe
#PBS -M s...@griffith.edu.au
#PBS -q gpuq
#PBS -l select=1:ncpus=1:ngpus=1:mem=12gb,walltime=120:00:00
#PBS -j oe
cd $PBS_O_WORKDIR
module load amber/20ompi
$AMBERHOME/bin/pmemd.cuda -O \
-i md.mdin -c eq.nc -p System.parm7 \
-r md_final.nc -x md_traj.nc -e md.mden \
-inf mdinfo -o md.log
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Sample PBS Script
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#!/bin/sh
#PBS -m abe
#PBS -M nnnnn@griffith.edu.au
#PBS -N Ambertest
#PBS -q workq
#PBS -l walltime=01:00:00
#PBS -l select=1:ncpus=1
#####PBS -l ngpus=1
#####Above not needed if not using gpu
module load amber/12-gnu
module load cuda/4.0
echo "Starting job"
pmemd -O -i mdin -o mdout -p prmtop -c inpcrd -r restrt -x mdcrd
echo "test Done"
echo "Done with job"
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