Installation¶
General (Source) Installation Instructions¶
To install the full package:
prefix=WHERE/TO/INSTALL/VOTCA
version=master # or 'v2024.2'
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>
ctest --test-dir builddir
cmake --build builddir --target install
Dependency Installation¶
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.
Testing your build¶
To test if your build actually works, you can run the VOTCA testsuite:
ctest --test-dir <path-to-build>
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 packageHDF5
(ON/OFF, Default OFF; relevant only for themaster
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