Amber
- Indy Siva
Owned by Indy Siva
Both amber12 and ambertools-12 have been installed.
Introduction
http://ambermd.org/
Build Instruction: http://jswails.wikidot.com/installing-amber12-and-ambertools-12
Usage
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
Installation
amber12-gnu
cd /sw/amber/12
tar -xvf AmberTools12.tar
tar -xvf Amber12.tar
mv /sw/amber/12/amber12 /sw/amber/12/amber12-gnu
export AMBERHOME=/sw/amber/12/amber12-gnu
cd $AMBERHOME
./configure gnu
make install
make test
>>>>>>>>>
./configure 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 4.4.6
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
Configuring fftw-3.3 (may be time-consuming)...
fftw-3.3 configure succeeded.
Configuring XBLAS (may be time-consuming)...
XBLAS configure succeeded.
Configuring MTK++ (may be time-consuming)...
MTK++-0.2.0 configure succeeded.
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.
>>>>>>>>>
amber12-mpi
export AMBERHOME=/sw/amber/12/amber12-openmpi
cd $AMBERHOME
module load mpi/openMPI/1.4.3-gnu
./configure -mpi gnu
make install
make test
>>>>>>>>>>>
Obtaining the gnu suite version:
gcc -v
The version is 4.4.6
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.
You have new mail in /var/spool/mail/root
>>>>>>>>>>>
amber12-modified
cd /sw/amber/12/ tar xvf /data1/software/amber/AmberTools12.tar tar xvf /data1/software/amber/Amber12.tar mv amber12 amber12-modified cp -i /tmp/sa_driver.F90 /sw/amber/12/amber12-modified/AmberTools/src/pbsa/sa_driver.F90 export AMBERHOME=/sw/amber/12/amber12-modified cd $AMBERHOME module load fftw/3.2.2-gnu module load python/2.7.1-shared module load intel-cmkl-11/11.1.072 ./configure --help ./configure gnu make install make test
amber12-mpi-modified
This version, amber12-mpi-modified, was made to make AMBER be able to automatically assign Poisson-Boltzman (PB) radii to FF99SBILDN forcefield. This modification does not affect other users, unless they want to calculate PBSA on the ILDN forcefields and even then, this modification simply extends the option while not changing anything else.
The main change that needs to be done is replacing
/sw/amber/12/amber12-openmpi-modified/AmberTools/src/pbsa/sa_driver.F90
Changes to the content of this file has been tagged with the lines with "MODIFICATION" comment.
export AMBERHOME=/sw/amber/12/amber12-openmpi-modified cd $AMBERHOME module load mpi/openMPI/1.4.3-gnu ./configure -mpi gnu make install make test
amber12-intelmpi-modified
cd /sw/amber/12/ tar xvf /data1/software/amber/AmberTools12.tar tar xvf /data1/software/amber/Amber12.tar #cp -r amber12-modified amber12-openmpi-modified mv amber12 amber12-intelmpi-modified cp -i /tmp/sa_driver.F90 /sw/amber/12/amber12-intelmpi-modified/AmberTools/src/pbsa/sa_driver.F90 export AMBERHOME=/sw/amber/12/amber12-intelmpi-modified cd $AMBERHOME module load fftw/3.2.2-gnu module load python/2.7.1-shared module load intel-cmkl-11/11.1.072 module load intel-mpi/4.0.1.007 module load intel-fc-11/11.1.072 module load intel-cc-11/11.1.072 module load intel-tools-11/11.1.072 make clean all ./configure --help ./configure intel make install make test ./configure -mpi intel vi config.h FC= mpiifort make install make test
amber12-cuda
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.
Amber20 Installation and Usage
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.
#!/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
Sample PBS Script
#!/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"
There are some sample input files located here:
/sw/amber/12/amber12-gnu/src/mm_pbsa/Examples/mm_pbsa.in