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MemSurfer, Version 1.0

Released: Mar 23, 2020

Author: Harsh Bhatia (hbhatia@llnl.gov) and Peer-Timo Bremer

MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations. MemSurfer works independent of the type of simulation, directly on the 3D point coordinates, and can handle a variety of membranes as well as atomic simulations. MemSurfer provides many in-built analysis tasks, such as computing the membrane curvature, density and normals of lipids, and area per lipid. More importantly, MemSurfer provides a simple-to-use Python API that may be easily used/extended to perform other types of analysis.

Dependencies

The interface to MemSurfer is provided via python 3.7, whereas the Core functionality is written in C++ 11 with the following dependencies.

Installing MemSurfer and its dependencies additionally require the following software.

  • C++ compiler that supports C++ 11 and OpenMP (tested with GNU gcc 7.3.0)
  • Python 3 interpreter (tested with python 3.7.2)
  • Cython: v 0.29.10
  • Swig: v 3.0.12
  • CMake: v 3.13

Installation via Spack

MemSurfer is available via spack -- a package manager for HPC. Please download spack (see instructions provded by spack). Once installed, please do the following

$ spack install memsurfer +osmesa %gcc@7.3.0

The +osmesa variant enables OSMesa support for VTK . Here, the installation has been tested with gcc@7.3.0.

Note: Since spack is a large-scale open-source project, new changes in the dependencies may break MemSurfer's installation if the variants and/or other configurations are changed by the corresponding authors.

MemSurfer's installation has been last verified with spack on Jun 09, 2020 with commit 2421d90. If you are new to spack, it is recommended to work at the mentioned commit.

Installation from source

MemSurfer can be downloaded using the following link.

$ git clone --recursive git@github.com:LLNL/MemSurfer.git
$ MEM_HOME=`pwd`/MemSurfer

Note: If the cloning fails with the following error:

Cloning into '<your-path>/MemSurfer/pypoisson'...
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

This error means that your ssh keys are not registered with github. Please see here and here to register your ssh key and retry.

1. Installing MemSurfer's Dependencies

The following describes the installation of cgal, vtk, boost and eigen, whereas the rest of the dependencies are assumed to be standard and available.

1a. Eigen, Boost, CGAL, and VTK (on mac)

On macosx, the simplest way to install these is using macports. As of Jan 2019, macports installs the correct versions.

$ port install vtk+python
$ port install cgal           # also installs boost and eigen
1b. Eigen, Boost, CGAL, and VTK (from source)

A helper script $MEM_HOME/install_deps.sh is provided to install these dependencies. In order to use this script, you need to specify a C++ compiler that supports OpenMP.

$ export CC=`which gcc`
$ export CXX=`which g++`
$ sh install_deps.sh

This script installs all these dependencies in a folder called $MEM_HOME/external. Note that you may not need to install all four of these dependencies. Please edit the script (lines 5--8) to select which ones to install.

Once installed successfully, please add the following to your shell profile to access these dependencies.

$ export PYTHONPATH=$MEM_HOME/external/lib/python3.7/site-packages:$PYTHONPATH
$ export LD_LIBRARY_PATH=$MEM_HOME/external/lib:$MEM_HOME/external/lib64:$LD_LIBRARY_PATH
      # linux
$ export DYLD_LIBRARY_PATH=$MEM_HOME/external/lib:$MEM_HOME/external/lib64:$DYLD_LIBRARY_PATH
      # mac

2. MemSurfer

Once the dependencies have been installed, MemSurfer can be installed using distutils. However, you need to explicitly supply the path of the external dependencies.

$ export BOOST_ROOT=<path_to_boost>
      # such that boost headers are contained in $BOOST_ROOT/include/boost
$ export VTK_ROOT=<path_to_vtk>
      # such that vtk headers are contained in $VTK_ROOT/include/vtk-8.1
$ export CGAL_ROOT=<path_to_cgal>
      # such that cgal headers are contained in $CGAL_ROOT/include/CGAL
$ export EIGEN_ROOT=<path_to_eigen>
      # such that eigen headers are contained in $EIGEN_ROOT/include/eigen3

Note that, all these paths default to $MEM_HOME/external. So if you installed the dependencies using the script provided above, you do not need to specify these paths.

$ cd $MEM_HOME
$ CC=`which gcc` CXX=`which g++` LDCXXSHARED="`which g++` -bundle -undefined dynamic_lookup" \
  python setup.py install

Examples

  • See the example directory.

Change Log

Mar 23, 2020
  • Correctly normalize Gaussian KDE and support 3D Gaussian kernel.
  • Ported to Python3.

License

MemSurfer is released under GPU-3.0 license. See the LICENSE file for details.

LLNL-CODE-763493