PLUMED 2.3.5

Basic information

  • Installation Date: 22/02/2017
  • URL: http://www.plumed.org/
  • License: GNU LESSER GENERAL PUBLIC LICENSE Version 3
  • Installed on: Apolo II

Tested on (Requirements)

  • Dependencies to run PLUMED:
    • GNU GCC >= 5.4.0
    • Mpich2 >= 3.2
    • OpenBLAS >= 0.2.19
    • GSL >= 2.4
    • libmatheval >= 1.1.11

Installation

After solving the previously mentioned dependencies, you can proceed with the installation of Plumed.

  1. Download the latest version of the software, in this case, the latest version is 2.3.5 of line 2.3.x (Source code - tgz) (http://www.plumed.org/get-it):

    cd /home/mgomezzul/apps/plumed/src/gcc-5.4.0
# Descargar el .tgz en este directorio
tar -xf plumed-2.3.5.tgz

  2. After decompressing Plumed, we continue with the following steps for its configuration and compilation:

    module load libmatheval/1.1.11 gsl/2.4_gcc-5.4.0 openblas/0.2.19_gcc-5.4.0 mpich2/3.2_gcc-5.4.0
cd plumed-2.3.5
sudo mkdir -p /share/apps/plumed/2.3.5/
sudo chown -R mgomezzul.apolo /share/apps/plumed/2.3.5
./configure CC=mpicc CXX=mpic++ FC=mpif90 --prefix=/share/apps/plumed/2.3.5 LIBS="-lopenblas" 2>&1 | tee plumed-conf.log
make -j 16 2>&1 | tee plumed-make.log
make check 2>&1 | tee plumed-make-check.log
make install 2>&1 | tee plumed-make-install.log
sudo chown -R root.root /share/apps/plumed/2.3.5

Module

#%Module1.0####################################################################
##
## module load plumed/2.3.5
##
## /share/apps/modules/plumed/2.3.5
## Written by Mateo Gómez-Zuluaga
##

proc ModulesHelp {} {
    global version modroot
    puts stderr "Sets the environment for using plumed 2.3.5\
        \nin the shared directory /share/apps/plumed/2.3.5\
        \nbuilded with gcc-5.4.0, mpich2-3.2, openblas-0.2.19\
        \ngsl-2.4 and libmatheval-1.11.0."
}

module-whatis "(Name________) plumed"
module-whatis "(Version_____) 2.3.5"
module-whatis "(Compilers___) gcc-5.4.0_mpich2-3.2"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) opeblas-0.2.19, libmatheval-1.11.0, gsl-2.4"

# for Tcl script use only
set         topdir        /share/apps/plumed/2.3.5
set         version       2.3.5
set         sys           x86_64-redhat-linux

conflict plumed

module load mpich2/3.2_gcc-5.4.0
module load openblas/0.2.19_gcc-5.4.0
module load gsl/2.4_gcc-5.4.0
module load libmatheval/1.1.11


prepend-path    PATH                    $topdir/bin

prepend-path    LD_LIBRARY_PATH         $topdir/lib
prepend-path    LIBRARY_PATH            $topdir/lib
prepend-path    LD_RUN_PATH             $topdir/lib
prepend-path    DYLD_LIBRARY_PATH       $topdir/lib

prepend-path    C_INCLUDE_PATH          $topdir/include
prepend-path    CXX_INCLLUDE_PATH       $topdir/include
prepend-path    CPLUS_INCLUDE_PATH      $topdir/include

setenv          PLUMED_KERNEL           $topdir/lib/libplumedKernel.so

Mode of Use

  • The use of Plumed in this case is limited to patching the Gromacs source code for this MD to use Plumed for physical handling.

    module load wrf/3.7.1_gcc-5.4.0

Authors

  • Mateo Gómez Zuluaga