Installation¶

General (Source) Installation Instructions¶

To install the full package:

prefix=WHERE/TO/INSTALL/VOTCA
version=master # or 'v2023-rc.2'
git clone -b ${version} https://github.com/votca/votca.git
cmake -B builddir -S votca -DBUILD_XTP=ON -DCMAKE_INSTALL_PREFIX=${prefix}
cmake --build builddir --parallel <number of cores>
cmake --build builddir --target install

Dependency Installation¶

Ubuntu

Fedora

If you have an older version of a distribution, cmake can be run with the -DBUILD_OWN_GROMACS=ON or -DBUILD_OWN_LIBINT=ON flags to automatically install the correct GROMACS and libint version.

On Ubuntu 20.10 and older you will not get version 1.0.5 of the libecpint package. So in this case run this or download the package from here.

Resolving the ‘not found’ dependency errors¶

Assuming all the dependencies have been correctly installed, one or more might still appear with the ‘not found’ status upon configuring with the cmake command (see above). In this case, you will need to find the ‘non-standard’ location for each missing dependency (most often a shared or dynamically loaded library, e.g. libgromacs.so.*, libhdf5.so.* etc).

Error messages produced by CMake usually provide instructive suggestions for resolving dependency issues. In particular, an appropriate extra -D flag is necessary to specify the path to a missed package. You will have to rerun the cmake command with the relevant flag(s) added. For example, in the case of a locally installed version of GROMACS:

cmake -DCMAKE_INSTALL_PREFIX=${prefix} -DGROMACS_INCLUDE_DIR=$HOME/gromacs/include -DGROMACS_LIBRARY=$HOME/gromacs/lib/libgromacs.so -S ..

Please also ensure GROMACS was build with -DGMX_INSTALL_LEGACY_API=ON.

Be careful to use exactly the option suggested in the error message! You can also add -LH or -LAH options to the cmake command in order to see the available options with brief explanations (note that changing some of the variables may result in more variables being created; run man cmake for more info).

Only for Linux: For each dependency package not found by CMake initially, it might be necessary to add the location of its lib directory to the environment variable LD_LIBRARY_PATH, before building and installing VOTCA, i.e. before running any make command. For example:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/gromacs/lib:$HOME/anaconda/lib

Note that LD_LIBRARY_PATH also needs to be set every time when running an executable from the VOTCA installation afterwards (which can be automated via the user’s login profile, e.g. in .bashrc). Alternatively, CMake has options to remember where libraries came from at link time, which can be enabled by setting CMAKE_INSTALL_RPATH_USE_LINK_PATH to ON. VOTCA has enabled this option and a couple of other rpath related tweaks when setting ENABLE_RPATH_INJECT to ON.

Common CMake Flags¶

INSTALL_CSGAPPS - Install the extra csg applications repo (ON/OFF, Default OFF)
BUILD_XTP - Build the xtp repo (ON/OFF, Default OFF)
CMAKE_INSTALL_PREFIX - where to install the votca executables (Default is /usr/local/bin)
BUILD_TESTING - compile tests (ON/OFF, Default ON)

Other CMake Flags¶

CMAKE_DISABLE_FIND_PACKAGE_<name> - Disable using an optional package called <name> (ON/OFF)
CMAKE_DISABLE_FIND_PACKAGE_HDF5 - Disable using the optional package HDF5 (ON/OFF, Default OFF; relevant only for the master branch)

Performance advice¶

VOTCA-XTP relies on the Eigen library for vector-matrix operations, and a lot of performance can be gained by enabling vectorization and/or use of Intel’s MKL as backend, which is automatically detected by CMake. Below are some recommendations for different architectures:

Intel Processors¶

g++, clang, and ipcx from the Intel OneAPI basekit give similar performance when used with the MKL. No special flags have to be supplied to CMake.

If g++ or clang are used, the compiler option -march=native is automatically injected into the build. If you compile VOTCA on a heterogeneous cluster with different instruction sets, this may cause the executables to not run. Override this by specifying -DCMAKE_CXX_FLAGS=-mtune=native (at probably lower performance), or perform node-type specific builds.

As a rough estimate, runtimes with vectorization and gcc/clang are 30% shorter than without vectorization. Use of MKL reduces them by another 50%.

AMD Processors¶

We recommend using g++ or clang rather than an Intel compiler on AMD. Vectorization in Eigen is automatically enabled by injection of -march=native. See above comment about heterogeneous envionments.

If you have Intel’s MKL installed, and it is found by CMake, performance will be helped but by how much idepends on which architecture-specific implementation MKL picks at runtime. This can be affected by a vendor lock-in, and work-arounds are documented for Intel MKL on AMD Zen and in general. We advise that you test this on your specific architecture.

CUDA support¶

If your system has a NVIDIA GPU, enable offloading of matrix operations by -DUSE_CUDA=ON.

Packages for various Linux Distributions¶

Fedora¶

dnf install votca

Or in older versions of Fedora:

dnf install votca-csg votca-xtp

CentOS¶

yum install epel-release
yum update
yum install votca

Or in older versions of CentOS:

yum install votca-csg

openSUSE¶

zypper install votca

Or in older versions of openSUSE:

zypper install votca-csg votca-xtp

SLES¶

SUSEConnect -p PackageHub/12.2/x86_64
zypper install votca-csg

Debian / Ubuntu¶

apt-get install votca-csg

Gentoo¶

emerge votca

Spack¶

Spack is a package manager, which has the capability of building VOTCA and all its dependencies:

git clone https://github.com/spack/spack.git spack
source spack/share/spack/setup-env.sh
spack install votca

Development version¶

Spack can also install the latest development version from git using:

spack install votca@master

Other build options¶

Spack has other options:

spack info votca

One useful option is to build votca without xtp:

spack install votca~xtp

Conda-forge¶

conda install -c conda-forge votca

Docker¶

VOTCA is also available through docker and can be accessed and run with the following docker commands:

docker pull votca/votca
docker run -it votca/votca /bin/bash

Release version¶

Docker can also install the latest released version, e.g.:

docker run -it votca/votca:v2021.2 /bin/bash

FreeBSD¶

On FreeBSD VOTCA can be installed from a binary package (recommended):

pkg install votca

or it can be rebuilt and installed from the sources (slow):

cd /usr/ports/science/votca && make install clean

Linking Error: Undefined reference to¶

This error can occur for a multitude of reasons. You may have forgotten to add paths to the LD_LIBRARY_PATH or forgotten to import an environment module. In these cases, deleting the CMakeCache.txt in your build folder and rerunning cmake will help. Unfortunately, another cause might be ABI incompability between libraries due to different libraries being compiled with different compilers or compiler versions. Click here for an example.

GCC and MKL : undefined symbol:¶

This can happen with some GCC versions. Adding the -Wl,--no-as-needed to CMAKE_EXE_LINKER_FLAGS:STRING= to the CMakeCache.txt in the build directory can fix this. For more information look here