AmberTools is a free, useful standalone package and a prerequisite for installing Amber itself. The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The libsander and libpbsa libraries use the LGPL license. (see https://ambermd.org/GetAmber.php#ambertools )
Ubuntu 22.04 LTS (Related packages) sudo apt update
sudo apt -y install tcsh make gcc gfortran flex bison patch bc wget xorg-dev libz-dev libbz2-dev build-essential libopenblas-dev libarpack2-dev libnetcdf-dev libnetcdff-dev
sudo apt -y install openmpi-bin libopenmpi-dev openssh-client python3-mpi4py python3-numpy python3-setuptools
For Ambertools24 or later
sudo apt -y install swig octave-dev guile-3.0-dev libprotobuf-dev libperl-dev netcdf-bin
sudo apt -y install g++-11
sudo apt -y install g++-10
sudo apt -y install nvidia-cuda-toolkit libnvidia-ml-dev
wget https://github.com/plumed/plumed2/releases/download/v2.9.0/plumed-2.9.0.tgz
tar zxvf plumed-2.9.0.tgz
cd plumed-2.9.0
./configure --prefix=/mnt/d/plumed-2.9.0/opt
make
make install
Note: "make test" is failed on gfortran and gcc, etc
PLUMED, Environment settings echo '# PLUMED, Environment settings' >> ~/.bashrc
echo 'export PATH=$PATH:/mnt/d/plumed-2.9.0/opt/bin' >> ~/.bashrc
echo 'export PATH=$PATH:/mnt/d/plumed-2.9.0/opt/lib' >> ~/.bashrc
echo 'export PATH=$PATH:/mnt/d/plumed-2.9.0/opt/include' >> ~/.bashrc
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/d/plumed-2.9.0/src/lib' >> ~/.bashrc
bash
Note for AmberTools source code
I couldn't upload it because I didn't have enough storage space. Please download it directly from the link below.
AmberTools24 (amber24) [AT24] wget https://ambermd.org/downloads/AmberTools24_rc5.tar.bz2
AmberTools24, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, 1 CPU (=serial))
Not use MPI, GPU, GUI, Quick, python, and miniconda
This is a very simple executable file with few dependencies, suitable for basic functionality. It has also passed testing.
tar xvf AmberTools24_rc5.tar.bz2
cd amber24_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_cpu_serial && cd build_cpu_serial
cmake $AMBER_PREFIX/amber24_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=FALSE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=FALSE -DDOWNLOAD_MINICONDA=FALSE -Wno-dev 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber24/amber.sh
echo "# Ambertools24 (amber24) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
make test.serial && make clean.test
AmberTools24, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, python, quick)
Not use MPI, GPU, and GUI
[-- Found PythonLibs: /home/inukai/miniconda3/lib/libpython3.10.so (found suitable exact version "3.10.14")] (If miniconda3 is not installed, set "-DDOWNLOAD_MINICONDA=TRUE".)
tar xvf AmberTools24_rc5.tar.bz2
cd amber24_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_serial && cd build_serial
cmake $AMBER_PREFIX/amber24_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=TRUE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE -Wno-dev 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber24/amber.sh
echo "# Ambertools24 (amber24) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
make test.serial && make clean.test
AmberTools24, Installation (Ubuntu 22.04 LTS (or WSL2), make, parallel)
Not use GUI, GPU, and Quick
[-- Found PythonLibs: /home/inukai/miniconda3/lib/libpython3.10.so (found suitable exact version "3.10.14")] (If miniconda3 is not installed, set "-DDOWNLOAD_MINICONDA=TRUE".)
tar xvf AmberTools24_rc5.tar.bz2
cd amber24_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_cpu_parallel && cd build_cpu_parallel
cmake $AMBER_PREFIX/amber24_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 -DCOMPILER=GNU -DMPI=TRUE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber24/amber.sh
echo "# Ambertools24 (amber24) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
export DO_PARALLEL="mpirun -np 8"
make test.parallel.4proc && make clean.test
unset DO_PARALLEL
AmberTools24, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, GPU (=CUDA), no check)
Not use MPI
This is a very simple executable file with few dependencies, suitable for basic functionality. It has also passed testing.
The steps for compiling on this GPU after performing the above two compilations (single and parallel) are shown below.
Due to an error with the GPU, it is necessary to temporarily use gcc-10 and g++-10. Compile again for the problematic GPU (Ref. stotko/stdgpu#337 , NVlabs/instant-ngp#119 ).
tar xvf AmberTools24_rc5.tar.bz2
cd amber24_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
CUDA_HOME="/usr/lib/cuda"
mkdir build_gpu_serial && cd build_gpu_serial
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 10
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 10
sudo update-alternatives --config gcc
sudo update-alternatives --config g++
cmake $AMBER_PREFIX/amber24_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=FALSE -DCUDA=TRUE -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_HOME} -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=TRUE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE -Bbuild -Wno-dev 2>&1 | tee cmake.log
cd build
make -j8 && make install
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 11
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 11
sudo update-alternatives --config gcc
sudo update-alternatives --config g++
source $AMBER_PREFIX/amber24/amber.sh
echo "# Ambertools24 (amber24) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
Note (stotko/stdgpu#337 , NVlabs/instant-ngp#119 ): Error: /usr/include/c++/11/bits/std_function.h:435:145: CMake Error at pbsa.cuda_generated_cuda_pb.cu.o.RELEASE.cmake:278 (message):
test (about 3 hours)
cd $AMBERHOME/test
#make test.cuda.serial && make clean.test
make test.serial && make clean.test
Note: sqm (=semi-empirical quantum chemistry): MNDO, MNDO/d (=MNDOD), AM1 (AM1, AM1-D* or AM1-DH+), AM1/d (=AM1D), PM3, PDDG/PM3, PDDG/MNDO, RM1, PM3CARB1, PM3-MAIS, PM6 (PM6, PM6-D, or PM6-DH+), DFTB2 (mio-1-1), DFTB3 (3ob-3-1)
Note: quick (QUantum Interaction Computational Kernel) (ab initio quantum chemistry): HF, UHF, DFT (LDA, GGA, Hybrid-GGA, e.g., B3LYP/cc-pVDZ), UDFT, vdW (Grimme)
Note: DFT (of quick) = B3LYP, PBE0, D3MBJ, etc DFT = BLYP, B3LYP, BP86, B97, B
Note: BASIS (of quick) = 6-31G**, cc-pVTZ, aug-cc-pVTZ, def2-TZVP, etc
Note: sander (Simulated Annealing with NMR-Derived Energy Restraints)
Note: Mechanical and electrostatic embedding: AMBER/QM, QM = ADF, Gaussian, Orca, Q-Chem, TeraChem, QUICK, MRCC, or Fireball
Note: Mechanical embedding: ADF, GAMESS-US, NWChem
Note: sebomd (Semi-Empirical Born-Oppenheimer Molecular Dynamics): NDDO (=AN1, PM3, RM1, etc)
AmberTools23 (amber22) [AT23] wget https://ambermd.org/downloads/AmberTools23_rc6.tar.bz2
AmberTools23, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, 1 CPU (=serial))
Not use MPI, GPU, GUI, Quick, python, and miniconda
This is a very simple executable file with few dependencies, suitable for basic functionality. It has also passed testing.
tar xvf AmberTools23_rc6.tar.bz2
cd amber22_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_cpu_serial && cd build_cpu_serial
cmake $AMBER_PREFIX/amber22_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=FALSE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=FALSE -DDOWNLOAD_MINICONDA=FALSE -Wno-dev 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber22/amber.sh
echo "# Ambertools23 (amber22) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
make test.serial && make clean.test
AmberTools23, Installation (Ubuntu 22.04 LTS (or WSL2), make, parallel)
Not use GUI, GPU, and Quick
[-- Found PythonLibs: /home/inukai/miniconda3/lib/libpython3.10.so (found suitable exact version "3.10.14")] (If miniconda3 is not installed, set "-DDOWNLOAD_MINICONDA=TRUE".)
tar xvf AmberTools23_rc6.tar.bz2
cd amber22_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_cpu_parallel && cd build_cpu_parallel
cmake $AMBER_PREFIX/amber22_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 -DCOMPILER=GNU -DMPI=TRUE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber22/amber.sh
echo "# Ambertools23 (amber22) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
export DO_PARALLEL="mpirun -np 8"
make test.parallel.4proc && make clean.test
unset DO_PARALLEL
Note: sqm (=semi-empirical quantum chemistry): MNDO, MNDO/d (=MNDOD), AM1 (AM1, AM1-D* or AM1-DH+), AM1/d (=AM1D), PM3, PDDG/PM3, PDDG/MNDO, RM1, PM3CARB1, PM3-MAIS, PM6 (PM6, PM6-D, or PM6-DH+), DFTB2 (mio-1-1), DFTB3 (3ob-3-1)
Note: quick (QUantum Interaction Computational Kernel) (ab initio quantum chemistry): HF, UHF, DFT (LDA, GGA, Hybrid-GGA, e.g., B3LYP/cc-pVDZ), UDFT, vdW (Grimme)
Note: DFT (of quick) = B3LYP, PBE0, D3MBJ, etc DFT = BLYP, B3LYP, BP86, B97, B
Note: BASIS (of quick) = 6-31G**, cc-pVTZ, aug-cc-pVTZ, def2-TZVP, etc
Note: sander (Simulated Annealing with NMR-Derived Energy Restraints)
Note: Mechanical and electrostatic embedding: AMBER/QM, QM = ADF, Gaussian, Orca, Q-Chem, TeraChem, QUICK, MRCC, or Fireball
Note: Mechanical embedding: ADF, GAMESS-US, NWChem
Note: sebomd (Semi-Empirical Born-Oppenheimer Molecular Dynamics): NDDO (=AN1, PM3, RM1, etc)
wget https://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2
AmberTools22, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, 1 CPU (serial))
Not use MPI, GPU, GUI, Quick, python, and miniconda
This is a very simple executable file with few dependencies, suitable for basic functionality. It has also passed testing.
tar xvf AmberTools22jlmrcc.tar.bz2
cd amber22_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_cpu_serial && cd build_cpu_serial
cmake $AMBER_PREFIX/amber22_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=FALSE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber22/amber.sh
echo "# Ambertools22 (amber22) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
make test.serial && make clean.test
AmberTools22, Installation (Ubuntu 22.04 LTS (or WSL2), make, parallel)
Not use GUI, GPU, and Quick
[-- Found PythonLibs: /home/inukai/miniconda3/lib/libpython3.10.so (found suitable exact version "3.10.14")] (If miniconda3 is not installed, set "-DDOWNLOAD_MINICONDA=TRUE".)
tar xvf AmberTools22jlmrcc.tar.bz2
cd amber22_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
mkdir build_cpu_parallel && cd build_cpu_parallel
cmake $AMBER_PREFIX/amber22_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 -DCOMPILER=GNU -DMPI=TRUE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber22/amber.sh
echo "# Ambertools22 (amber22) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
export DO_PARALLEL="mpirun -np 8"
make test.parallel.4proc && make clean.test
Note: sqm (=semi-empirical quantum chemistry): MNDO, MNDO/d (=MNDOD), AM1 (AM1, AM1-D* or AM1-DH+), AM1/d (=AM1D), PM3, PDDG/PM3, PDDG/MNDO, RM1, PM3CARB1, PM3-MAIS, PM6 (PM6, PM6-D, or PM6-DH+), DFTB2 (mio-1-1), DFTB3 (3ob-3-1)
Note: quick (QUantum Interaction Computational Kernel) (ab initio quantum chemistry): HF, UHF, DFT (LDA, GGA, Hybrid-GGA, e.g., B3LYP/cc-pVDZ), UDFT, vdW (Grimme)
Note: DFT (of quick) = B3LYP, PBE0, D3MBJ, etc DFT = BLYP, B3LYP, BP86, B97, B
Note: BASIS (of quick) = 6-31G**, cc-pVTZ, aug-cc-pVTZ, def2-TZVP, etc
Note: sander (Simulated Annealing with NMR-Derived Energy Restraints)
Note: Mechanical and electrostatic embedding: AMBER/QM, QM = ADF, Gaussian, Orca, Q-Chem, TeraChem, QUICK, MRCC, or Fireball
Note: Mechanical embedding: ADF, GAMESS-US, NWChem
Note: sebomd (Semi-Empirical Born-Oppenheimer Molecular Dynamics): NDDO (=AN1, PM3, RM1, etc)
AmberTools21 (amber20) [AT21] wget https://ambermd.org/downloads/AmberTools21jlmrcc.tar.bz2
AmberTools21, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, 1 CPU (serial), failed)
Not use MPI, GPU, GUI, Quick, and miniconda
This is a very simple executable file with few dependencies, suitable for basic functionality. It has also passed testing.
tar xvf AmberTools21jlmrcc.tar.bz2
cd amber20_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
cmake $AMBER_PREFIX/amber20_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber20/amber.sh
echo "# Ambertools21 (amber20) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
test (need long time (about 2 hours))
cd $AMBERHOME/test
make test.serial && make clean.test
AmberTools21, Installation (Ubuntu 22.04 LTS (or WSL2), make, parallel, failed)
Not use GUI, Quick, and miniconda
tar xvf AmberTools21jlmrcc.tar.bz2
cd amber20_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
cmake $AMBER_PREFIX/amber20_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 -DCOMPILER=GNU -DMPI=TRUE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=TRUE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber20/amber.sh
echo "# Ambertools21 (amber20) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
cd $AMBERHOME/test
export DO_PARALLEL="mpirun -np 8"
make test.parallel.4proc && make clean.test
AmberTools21 (amber20), Installation (cygwin, failed) tar xvf AmberTools21jlmrcc.tar.bz2
cd amber20_src
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
#export CUSTOMBUILDFLAGS="-fallow-argument-mismatch"
echo "N" | ./configure -cygwin -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
wget https://ambermd.org/downloads/AmberTools20jlmrcc.tar.bz2
AmberTools20, Installation (Ubuntu 22.04 LTS (or WSL2), cmake, 1 CPU (serial), failed)
Not use MPI, GPU, GUI, Quick, python, and miniconda
This is a very simple executable file with few dependencies, suitable for basic functionality. It has also passed testing.
tar xvf AmberTools20jlmrcc.tar.bz2
cd amber20_src
./update_amber --check-updates
./update_amber --update
cd build
AMBER_PREFIX=$(dirname $(dirname `pwd`))
cmake $AMBER_PREFIX/amber20_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 -DCOMPILER=GNU -DMPI=FALSE -DOPENMP=TRUE -DCUDA=FALSE -DNCCL=FALSE -DBLA_VENDOR=OpenBLAS -DBUILD_GUI=FALSE -DBUILD_QUICK=FALSE -DINSTALL_TESTS=TRUE -DBUILD_PYTHON=FALSE -DDOWNLOAD_MINICONDA=FALSE 2>&1 | tee cmake.log
make -j8 && make install
source $AMBER_PREFIX/amber20/amber.sh
echo "# Ambertools20 (amber20) environment settings" >> ~/.bashrc
echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/bin" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/lib" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/include" >> ~/.bashrc
echo 'export PATH=$PATH:'"$AMBERHOME/dat" >> ~/.bashrc
bash
amber20_src/AmberTools/src/arpack/dnaitr.f:658:35:
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
AmberTools20 (amber20), Installation (WSL2, ubuntu 22.04, failed) tar xvf AmberTools20jlmrcc.tar.bz2
cd amber20_src
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
export GOTO="/usr/lib/x86_64-linux-gnu/libopenblas.a"
echo "Y" | ./configure -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
AmberTools20 (amber20), Installation (cygwin, update "Y", failed) tar xvf AmberTools20jlmrcc.tar.bz2
cd amber20_src
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
#export CUSTOMBUILDFLAGS="-fallow-argument-mismatch"
echo "Y" | ./configure -cygwin -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
AmberTools20 (amber20), Installation (cygwin, update "N", failed) tar xvf AmberTools20jlmrcc.tar.bz2
cd amber20_src
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
#export CUSTOMBUILDFLAGS="-fallow-argument-mismatch"
echo "N" | ./configure -cygwin -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
wget https://ambermd.org/downloads/AmberTools19.tar.bz2
AmberTools19 (amber18), Installation (cygwin, failed) tar xvf AmberTools19.tar.bz2
cd amber18
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
#export CUSTOMBUILDFLAGS="-fallow-argument-mismatch"
echo "N" | ./configure -cygwin -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
wget https://ambermd.org/downloads/AmberTools18.tar.bz2
AmberTools18 (amber18), Installation (cygwin, failed) tar xvf AmberTools18.tar.bz2
cd amber18
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
#export CUSTOMBUILDFLAGS="-fallow-argument-mismatch"
echo "N" | ./configure -cygwin -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
wget https://ambermd.org/downloads/AmberTools17.tar.bz2
AmberTools17 (amber16), Installation (cygwin, failed) tar xvf AmberTools17.tar.bz2
cd amber16
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
echo "N" | ./configure -cygwin -noX11 --skip-python gnu
source $AMBERHOME/amber.sh
sed -i "s/FREEFORMAT_FLAG/#FREEFORMAT_FLAG/g" $AMBERHOME/AmberTools/src/config.h
make -j8
sed -i "s/FILE \*cifpin = NULL,/\/*FILE \*cifpin = NULL,*\/ FILE/g" $AMBERHOME/AmberTools/src/cifparse/lex.cif.c
make -j8
sed -i "s/_REAL_ :: twork/_REAL_ :: twork(1)/g" $AMBERHOME/AmberTools/src/sqm/qm2_scf.F90
sed -i "s/NINT(twork)/NINT(twork(1))/g" $AMBERHOME/AmberTools/src/sqm/qm2_scf.F90
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
Note (error): $AMBERHOME/AmberTools/src/lib/nxtsec.F
Note (F77 -> F90): perl f2f.pl --tab 2 --base-indent 0 *.F *.F90
Note: multiple definition of `cifpin': cifparse.c and lex.cif.c -> (lex.cif.c: Line 327, /*FILE cifpin = NULL, / FILE *cifpout = NULL;)
Note: Openblas is fully compatible with Netlib BLAS. (https://cygwin.com/pipermail/cygwin-announce/2024-January/011501.html )
Note: usr/bin/cygblas-0.dll (dynamic library) (https://cygwin.com/cygwin/packages/summary/libopenblas.html )
Note: Failed: export GOTO="-L/usr/bin -lcygblas-0"
Note: /AmberTools/src/sqm/qm2_scf.F90:2271:48:(Line 2265 & 2271) Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1): Line 2252 => REAL :: twork(1) ! Declare twork as an array with at least one element
Note: /AmberTools/src/sander/sebomd_module.F90:124:34: Error: Symbol ‘hamiltonian’ in namelist ‘sebomd’ at (1) must be declared before the namelist is declared. (In subroutine read_sebomd_namelist(), the namelist follows the type declaration.)
Note: Plumed_init.inc:8:44: Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/INTEGER(4)). etc
wget https://ambermd.org/downloads/AmberTools13.tar.bz2
AmberTools13 (amber12), Installation (cygwin, failed) tar xvf AmberTools13.tar.bz2
cd amber12
export AMBERHOME=`pwd`
export LOCALFLAGS="-lgfortran -std=legacy"
export CUSTOMBUILDFLAGS="-fallow-argument-mismatch -w"
./configure -cygwin -noX11 gnu
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
wget https://ambermd.org/downloads/AmberTools-1.5.tar.bz2
AmberTools-1.5 (amber11), Installation (cygwin, failed) tar xvf AmberTools-1.5.tar.bz2
cd amber11/AmberTools/src
export AMBERHOME=$HOME/amber11
export LOCALFLAGS="-lgfortran -std=legacy"
export CUSTOMBUILDFLAGS="-fallow-argument-mismatch -w"
./configure -cygwin -noX11 -nopython -bit64 gnu
make -j8
make install
export PATH=$AMBERHOME/bin:$PATH
make test
wget https://ambermd.org/antechamber/antechamber-1.27.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.26.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.25.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.24.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.23.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.22.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.21.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.2.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.1.tar.gz
wget https://ambermd.org/antechamber/antechamber-1.0.tar.gz
sci-AmberTools (sci-ambertools) wget https://gitweb-cdn-origin.gentoo.org/proj/sci.git/snapshot/sci-ambertools.tar.bz2
pip install pinda
pinda install ambertools 18
gcc-fortran 12.4.0-3
libopenblas 0.3.25-1
liblapack-devel 3.12.0-1
libarpack-devel 3.9.1-1
libfftw3-devel 3.3.10-1
make 4.4.1-2
cmake 3.28.3-1
patch 2.7.6-17
wget 1.24.5-1
gcc-g++ 12.4.0-3
python3-devel 3.9.16-1
tcsh 6.24.10-1
flex 2.6.4-2
bison 3.8.2-1
bc 1.07.1-1
xorg-server-devel 21.1.12-1
zlib-devel 1.3.1-1
libbz2-devel 1.0.8-1
libopenmpi-devel 4.1.6-1
openssh 9.8p1-1
libXext-devel 1.3.6-1
perl 5.36.3-1
perl-ExtUtils-MakeMaker 7.70-1
util-linux 2.39.3-2
bzip2 1.0.8-1
libzip2 0.11.2-2
libtool 2.4.7-1
gzip 1.13-1
libboost-devel 1.66.0-1
tar 1.35-2
libc++-devel 8.0.1-1
libgfortran5 1.2.4.0-3
libssl-devel 3.0.14-1
libnetcdf-devel 4.9.2-1
libnetcdf-fortran-devel 4.5.4-1
netcdf 4.9.2-1
OS: Microsoft Windows 11 Home 64 bit
BIOS: 1.14.0
CPU： 12th Gen Intel(R) Core(TM) i7-12700
Base Board：0R6PCT (A01)
Memory：32 GB
GPU: NVIDIA GeForce RTX3070
WSL2: VERSION="22.04.1 LTS (Jammy Jellyfish)"
Python 3.10.12
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