How to build APBS from source

These instructions assume that you have downloaded the source code from GitHub releases.

Caution

We do not recommend cloning directly from the head of the master branch because it is typically under development and could be unstable. Unless you really know what you are doing, we advise you to skip the next step.

Get source directly from Github

Here are the commands to get the source directly from our GitHub repository,

git clone https://github.com/Electrostatics/apbs
cd apbs

Shortcut to build

There is a script that is used to build APBS in the Github Actions. You may want to use the file, .build.sh, as a template for building APBS.

Caution

When using make, there can be race conditions with CMake, autoconf, downloading dependencies, and make. It is best to run

VERBOSE=1 make -j 1

Import submodules

We are using Git submodules to manage various pieces of code. To build the master branch, after cloning it, you will need to do the following from within the top of the source directory:

git submodule init
git submodule update

Set up CMake

From the top of the source directory, the basic commands for configuring the APBS build for CMake are

mkdir build
cd build
# NOTE: This will be you $APBS_BUILD_DIR
export APBS_BUILD_DIR=`echo $(PWD)`
cmake ..

To see all the options you can run:

cd $APBS_BUILD_DIR
ccmake ..

Additional features can be built using the flags described below.

Geometric flow

If you want to use the geometric flow implementation, when invoking CMake, set ENABLE_GEOFLOW to ON; e.g.,

cd $APBS_BUILD_DIR
cmake -DENABLE_GEOFLOW=ON ..

Using PB-AM

If you want to use the Poisson-Boltzmann Analytical Method developed by the Teresa Head-Gordon lab, set the CMake variable ENABLE_PBAM to ON.

Warning

PB-AM currently runs on OS X or Linux only.

cd $APBS_BUILD_DIR
cmake -DENABLE_PBAM=ON ..

Using TABI-PB

If you want to use the Treecode-Accelerated Boundary Integral method (TABI-PB) developed by Robert Krasny and Weihua Geng, set the CMake variable ENABLE_BEM to ON.

TABI-PB requires the use of a molecular surface mesh generation software to create a surface representation of the molecule. By default, TABI-PB uses NanoShaper to generate an SES or Skin surface. See TABI-PB documentation for details on choosing NanoShaper. When TABI-PB runs, it will attempt to generate a surface mesh by looking in your path for the mesh generation executable. A user can obtain the appropriate executable using the steps described below. The user then must place these executables in their path.

cd $APBS_BUILD_DIR
cmake -DENABLE_BEM=ON ..

Getting NanoShaper executable

Surface meshing software executables are currently pre-built for OS X, Linux, and Windows and can be installed via CMake. The executables will be placed in the bin directory of your build.

NanoShaper is a molecular surface mesh generation software package developed by W. Rocchia and S. Decherchi.

cd $APBS_BUILD_DIR
cmake -DGET_NanoShaper=ON ..

Using finite element support

Warning

Finite element methods are currently only supported on POSIX-like operating systems such as OS X or Linux.

To enable finite element support, set the CMake ENABLE_FETK variable to ON.

On Linux, the FETK shared libraries need to be locatable by the shared library loader. One way to do this is to update LD_LIBRARY_PATH to point at <build-dir>/fetk/lib, where <build-dir> is the location where APBS was built. In base, this can be accomplished with the command:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<build-dir>/fetk/lib:<install-dir>/fetk/lib
cd $APBS_BUILD_DIR
cmake -DENABLE_FETK=ON ..

Enabling APBS Python support

APBS Python support requires a local installation of SWIG.

Assuming SWIG is installed, APBS Python support can be enabled by setting the CMake variable ENABLE_PYTHON to ON. If you are on Linux you will also need to set the CMake variable BUILD_SHARED_LIBS to OFF.

cd $APBS_BUILD_DIR
cmake -DENABLE_PYTHON=ON ..

Building the code - minimal

Assuming the Cmake command completed successfully, APBS can be built with

cd $APBS_BUILD_DIR
# Run cmake with the options you prefer:
VERBOSE=1 make -j 1

Building the code - advanced

export INSTALL_DIR=$SOME_DIR/apbs
export PATH=$INSTALL_DIR/bin:$PATH
# NOTE: In case you need to debug the source code:
# export RELEASE_TYPE=Debug
export RELEASE_TYPE=Release
# NOTE: If cmake or make fail, save yourself and make sure your remove
#       everything including the build directory. This code base uses
#       many older autoconf based projects that do not know how to save
#       state or recover from partial builds. If cmake or make fail, you
#       should figure out how to fix it and then remove everything and
#       try again.
rmdir $APBS_BUILD_DIR
mkdir -p $APBS_BUILD_DIR
cd $APBS_BUILD_DIR
# NOTE: In case you need to debug cmake, use verbose debug/trace mode:
# cmake -S .. -B $BUILD_DIR --trace-source=../CMakeLists.txt --trace-expand \
cmake                                        \
   -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR       \
   -DCMAKE_BUILD_TYPE=$RELEASE_TYPE          \
   -DENABLE_GEOFLOW=ON                       \
   -DENABLE_BEM=ON                           \
   -DENABLE_FETK=ON                          \
   -DENABLE_OPENMP=ON                        \
   -DENABLE_PBAM=ON                          \
   -DENABLE_PBSAM=ON                         \
   -DENABLE_PYTHON=ON                        \
   -DENABLE_TESTS=ON                         \
   -DENABLE_TINKER=OFF                       \
   -DBUILD_SHARED_LIBS=ON                    \
   ..
VERBOSE=1 make -j 1

Testing APBS

cd $APBS_BUILD_DIR
# NOTE: Assuming you have already built APBS
# NOTE: So that the apbs and optional NanoShaper binaries are in the path:
export PATH="$APBS_BUILD_DIR/bin:$PATH"
ctest -C Release --output-on-failure

Installing APBS

export INSTALL_DIR="Some directory - default is /usr/local"
cd $APBS_BUILD_DIR
cmake                                  \
   -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
   # NOTE: Add cmake options that you used during the Build APBS section
..
VERBOSE=1 make -j 1 install