Compile PLUMED¶

PLUMED 2.4 requires a compiler that supports C++11, and needs one of the following - gcc 4.8.1 (need to install GCC) - clang 3.3 - intel 15 (need to install Intel)

Intel alone does not fully support C++11 if the environment is without gcc 4.8 or newer. Installing an external GCC is a solution for this, but this may cause some errors when running Plumed due to cross-compiling.

Note

Making lepton library faster --enable-asmjit

Dowload¶

github

https://github.com/plumed/plumed2/releases/tag/v2.5.2
tar xvzf plumed2-2.5.2.tar.gz

download branch v2.5¶

git clone https://github.com/plumed/plumed2.git --branch=v2.5 plumed2-2.5.x cd plumed2-2.5.x git pull origin v2.5 # or git checkout v2.5

download branch with PYCV¶

git clone --branch v2.6-pycv-devel https://github.com/giorginolab/plumed2-pycv.git plumed2-2.6pycv cd plumed2-2.6pycv

download branch hack-the-tree¶

git clone --branch hack-the-tree https://github.com/plumed/plumed2.git plumed2-2.7htt cd plumed2-2.7htt git pull origin hack-the-tree

git pull origin master

or Clone a specific tag name using git clone: https://git-scm.com/docs/git-clone ¶

git clone --branch= I. OMPI + Intel 1. USC1 module load mpi/openmpi4.0.2-Intel2019xe module load intel/mkl-2019xe

check: mpiicpc -v (intel C++) mpicxx --version ( gcc C++)

Notes: openMPI must be compile with gcc 4.8 or newer (load gcc/gcc-7.4.0 when compile openMPI)

Install PLUMED¶

(to compile with mpi-enable, need to use compiler: CXX=mpic++ CC=mpicc) chose modules to install: https://www.plumed.org/doc-v2.5/user-doc/html/mymodules.html enable/disable modules: ./configure --enable-modules=+crystallization-colvar ./configure --enable-modules=all:-colvar-multicolvar BLAS and LAPACK Libs a. separate compile Blas & Lapack b. use Blas & Lapack from intel_mkl LIBS="-mkl" c. or use internal link: (blas & lapack is automatically built, need FORTRAN compiler) --disable-external-blas --disable-external-lapack \

VMD trajectory plugins https://www.plumed.org/doc-master/user-doc/html/_installation.html

Configuring PLUMED¶

./configure --prefix=/uhome/p001cao/local/app/plumed2/2.6htt \ CXX=mpic++ LIBS="-mkl" \ --enable-openmp --enable-modules=all --enable-asmjit

or¶

./configure --prefix=/uhome/p001cao/local/app/plumed2/2.6 \ CXX=mpic++ --disable-external-blas --disable-external-lapack \ --enable-openmp --enable-modules=all --enable-asmjit

create Module file + test¶

prepend-path PATH $topdir/bin prepend-path PATH $topdir/bin prepend-path LD_LIBRARY_PATH $topdir/lib prepend-path INCLUDE $topdir/include prepend-path PKG_CONFIG_PATH $topdir/lib/pkgconfig # this is required in order to Lammps can found Plumed

test:¶

module load plumed2/2.6.0 plumed help

USC2:¶

module load mpi/ompi4.0.3-intel19u5 module load intel/compiler-xe19u5 module load intel/mkl-xe19u5 Configure

./configure CXX=mpic++ CC=mpicc LIBS="-mkl" \ --enable-openmp --enable-modules=all --enable-asmjit \ --prefix=/home1/p001cao/local/app/plumed2/2.7htt

make -j 8 make install II. Install PLUMED using lMPI-2019xe

1. USC 1:¶

(use this, bc compilers are available for all clusters) NOTE: intelMPI on eagle does not work, due to wrong path 1. Module load: module load intel/compiler-xe19u5 module load mpi/impi-xe19u5 module load intel/mkl-xe19u5 module load compiler/gcc/9.1.0 module load conda/py37

Configure ./configure CXX=mpiicpc CC=mpiicc LIBS="-mkl" \ --enable-openmp --enable-modules=all --enable-asmjit \ --prefix=/uhome/p001cao/local/app/plumed2/2.6httIMPI \

USC 2¶

IV. Install PLUMED using openmpi-4.0.1 + GCC-7.4.0 (CAN) 1. Module load: module load mpi/openmpi4.0.1-gcc7.4.0 module load gcc/gcc-7.4.0

check: mpic++ --version ( gcc C++) 2. Install PLUMED unzip plumed2-hack-the-tree.zip cd plumed2-hack-the-tree

Configuring PLUMED: ./configure --prefix=/home/thang/local/app/plumed2/2.6.0-gcc \ CXX=mpic++ --disable-external-blas --disable-external-lapack \ --enable-openmp --enable-modules=all

USC2¶

with Conda¶

Need create conda env and install ompi, see this

check MPI compiler: mpic++ --version

cd /home1/p001cao/local/wSourceCode
git clone  -b master   https://github.com/plumed/plumed2.git    plumed  # hack-the-tree  master
cd plumed
git pull origin master

module load conda/py310lammps
export myCOMPILER=/home1/p001cao/local/app/miniconda3/envs/py310lammps
export PATH=${myCOMPILER}/bin:$PATH
export CC=mpicc  export CXX=mpic++  export FC=mpifort
export myPREFIX=/home1/p001cao/local/app/plumed2/ompi_conda_master

./configure --prefix=${myPREFIX} \
--enable-openmp --enable-modules=all --enable-asmjit \
--disable-external-blas --disable-external-lapack

make -j 16 && make install