Pteros 2.0

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • Standard-conforming C and C++ compilers (tested with gcc= 5.4, g++= 5.4).
    • cmake 3.3.7 build system
    • Eigen 3.3.7
    • Boost 1.62.0
    • Pybind11
    • Git for getting the source code

Installation

  1. Download the latest version of Pteros

    $ git clone https://github.com/yesint/pteros.git pteros

  2. Inside the folder, on the top create a build directory where the installation binaries will be put by cmake.

    $ cd pteros
$ mkdir build
$ cd build

  3. Load the necessary modules for the building.

    $ module load cmake/3.7.1
$ module load gcc/5.4.0
$ module load boost/1.62.0_gcc-5.4.0_openmpi-1.8.8-x86_64
$ module load eigen/3.3.7_intel-2017_update-1
$ module load pybind11/11_gcc-5.4.0

  4. Execute the cmake command with the desired directives.

    $ cmake .. -DCMAKE_INSTALL_PREFIX=/share/apps/pteros/2.0/gcc-5.4.0/ -DEIGEN3_INCLUDE_DIR=/share/apps/eigen/3.3.7/intel-19.0.4/include/eigen3/ -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DBoost_NO_SYSTEM_PATHS=OFF -DWITH_OPENBABEL=OFF -DWITH_GROMACS=OFF -DWITH_PYTHON=ON -DPYTHON_EXECUTABLE:FILEPATH=/share/apps/python/3.6_miniconda-4.5.1/bin/python -Dpybind11_DIR=/share/apps/pybind11/gcc-5.4.0/share/cmake/pybind11

  5. Execute the make commands sequence.

    $ make -j <N>
$ make -j install

Module

#%Module1.0#####################################################################
##
## modulefile /share/apps/modules/pteros/2.0_gcc-5.4.0
## Written by Juan Diego Ocampo and Santiago Hidalgo Ocampo
##

proc ModulesHelp { } {
    global version modroot
        puts stderr "\t Pteros 2.0."
}

module-whatis "(Name________) Pteros"
module-whatis "(Version_____) 2.0"
module-whatis "(Compilers___) gcc-5.4.0"
module-whatis "(System______) x86_64-redhat-linux"

set     topdir          /share/apps/pteros/2.0/gcc-5.4.0
set     version         2.0
set     sys             x86_64-redhat-linux

module load boost/1.62.0_gcc-5.4.0_openmpi-1.8.8-x86_64
module load python/3.6.5_miniconda-4.5.1
module load eigen/3.3.7_intel-19.0.4
module load pybind11/11_gcc-5.4.0

prepend-path PATH                       $topdir/bin
prepend-path PYTHONPATH                 $topdir/python

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

prepend-path LD_LIBRARY_PATH            $topdir/lib
prepend-path LIBRARY_PATH               $topdir/lib
prepend-path LD_RUN_PATH                $topdir/lib
prepend-path LD_LIBRARY_PATH            $topdir/lib64
prepend-path LIBRARY_PATH               $topdir/lib64
prepend-path LD_RUN_PATH                $topdir/lib64

Testing Installation

Run the following command:

$ pteros_analysis.py --help all

See also

To use pteros you must have the numpy library, so we suggest following the next steps:

$ conda create -n pteros # Create a virtual environment
$ conda activate pteros
$ conda install numpy

Warning

Some commands may fail, however, the application may work with the features you need

Troubleshooting

See also

If you have this problem: ModuleNotFoundError: No module named ‘_pteros’, probably you must rename this file: <path to Pteros>/python/pteros/_pteros.cpython-37m-x86_64-linux-gnu.so to _pteros.so

Authors