CHARMM - Revision history

Khtang: /* Compile CHARMM */

2025-01-24T20:27:24Z

Compile CHARMM

← Older revision		Revision as of 20:27, 24 January 2025
Line 42:		Line 42:
	export FFTW_HOME="/nfs/soft/anaconda3/pkgs/fftw-3.3.10-nompi_ha7695d1_103"; export CUDA_BIN_PATH="/nfs/soft/cuda-10.0/bin";		export FFTW_HOME="/nfs/soft/anaconda3/pkgs/fftw-3.3.10-nompi_ha7695d1_103"; export CUDA_BIN_PATH="/nfs/soft/cuda-10.0/bin";
	export OPENMM_HOME="/nfs/soft/openmm/openmm-7.7.0.3/";		export OPENMM_HOME="/nfs/soft/openmm/openmm-7.7.0.3/";
	../configure -D MPI_Fortran_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpifort -D MPI_C_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpicc --with-gcc -u --with-fftdock --with-blade --without-mkl -p ../install_blade2		../configure -D MPI_Fortran_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpifort -D MPI_C_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpicc --with-gcc -u --with-fftdock --with-blade --without-mkl --with-openmm -p ../install_blade2

	make -j 10		make -j 10

Khtang at 20:27, 24 January 2025

2025-01-24T20:27:04Z

← Older revision		Revision as of 20:27, 24 January 2025
Line 31:		Line 31:
	make install		make install

	~~Install~~ CHARMM		= Compile CHARMM =

	cd /nfs/soft/CHARMM/charmm		cd /nfs/soft/CHARMM/charmm

Khtang at 20:26, 24 January 2025

2025-01-24T20:26:42Z

← Older revision		Revision as of 20:26, 24 January 2025
Line 47:		Line 47:
	make install		make install

	[[Sysadmin]] [[Software]]		[[Category:Sysadmin]] [[Category:Software]]

Khtang at 20:25, 24 January 2025

2025-01-24T20:25:55Z

← Older revision		Revision as of 20:25, 24 January 2025
Line 47:		Line 47:
	make install		make install

	[[Sysadmin]][[Software]]		[[Sysadmin]] [[Software]]

Khtang at 20:25, 24 January 2025

2025-01-24T20:25:48Z

← Older revision		Revision as of 20:25, 24 January 2025
Line 46:		Line 46:
	make -j 10		make -j 10
	make install		make install

			[[Sysadmin]][[Software]]

Khtang: Created page with "CHARMM is a molecular simulation software from Harvard. = Install CHARMM = == Requirements == gcc --version * Upgrade to at least GCC 7 ( if need) https://linuxhostsupport.com/blog/how-to-install-gcc-on-centos-7/ * Upgrade Cmake (version 3+) Please make sure that you are using the same C and Fortran compiler version for these dependencies below otherwise CHARMM won’t compile wget https://cmake.org/files/v3.20/cmake-3.20.5.tar.gz tar xvzf cmake-3.20.5.tar.gz cd..."

2025-01-24T20:17:07Z

Created page with "CHARMM is a molecular simulation software from Harvard. = Install CHARMM = == Requirements == gcc --version * Upgrade to at least GCC 7 ( if need) https://linuxhostsupport.com/blog/how-to-install-gcc-on-centos-7/ * Upgrade Cmake (version 3+) Please make sure that you are using the same C and Fortran compiler version for these dependencies below otherwise CHARMM won’t compile wget https://cmake.org/files/v3.20/cmake-3.20.5.tar.gz tar xvzf cmake-3.20.5.tar.gz cd..."

New page

CHARMM is a molecular simulation software from Harvard.

= Install CHARMM =
== Requirements ==
gcc --version
* Upgrade to at least GCC 7 ( if need) https://linuxhostsupport.com/blog/how-to-install-gcc-on-centos-7/

* Upgrade Cmake (version 3+)
Please make sure that you are using the same C and Fortran compiler version for these dependencies below otherwise CHARMM won’t compile
wget https://cmake.org/files/v3.20/cmake-3.20.5.tar.gz
tar xvzf cmake-3.20.5.tar.gz
cd cmake-3.20.5/
make
make install
/usr/local/bin/cmake --version

Install OpenMPI https://mfix.netl.doe.gov/forum/t/openmpi-installation-in-centos7/543
Install OpenMM (It can be installed via conda, but it didn’t work for me. So I compiled from source code)
Create conda environment and source
http://docs.openmm.org/latest/userguide/library/02_compiling.html
Install prerequisites
conda install -c conda-forge cmake make cython swig fftw doxygen numpy
Download the zip package here https://github.com/openmm/openmm/releases
cd /nfs/soft/openmm/
wget https://github.com/openmm/openmm/archive/refs/tags/7.7.0.zip
unzip 7.7.0.zip; mv openmm-7.7.0 install_7.7.0
cd install_7.7.0
mkdir build; cd build
cmake -D CMAKE_INSTALL_PREFIX=/nfs/soft/openmm/openmm-7.7.0.3/ -D OPENCL_LIBRARY=/nfs/soft/cuda-10.0/lib64/libOpenCL.so ..
make -j 10
make install

Install CHARMM

cd /nfs/soft/CHARMM/charmm
Download the package, ask Yujin
tar xf c47b1.tar
cd charmm
mkdir build; cd build
Source the conda environment above
conda install -c conda-forge fftw
export FFTW_HOME="/nfs/soft/anaconda3/pkgs/fftw-3.3.10-nompi_ha7695d1_103"; export CUDA_BIN_PATH="/nfs/soft/cuda-10.0/bin";
export OPENMM_HOME="/nfs/soft/openmm/openmm-7.7.0.3/";
../configure -D MPI_Fortran_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpifort -D MPI_C_COMPILER=/nfs/soft/openmpi/openmpi-4.1.1.3/bin/mpicc --with-gcc -u --with-fftdock --with-blade --without-mkl -p ../install_blade2

make -j 10
make install