trexio/README.md

TREXIO

TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements. The library consists of a front-end implemented in the C programming language and two different back-ends: a text back-end and a binary back-end utilizing the HDF5 library which enables fast read and write operations. It is compatible with a variety of platforms and has interfaces for the Fortran, Python, OCaml and Rust programming languages.

• TREXIO
  • Installation
    • Installation using a package manager
      • Debian/Ubuntu
      • Conda
      • Spack
      • Guix
    • Installation from source
      • Minimal requirements (for users):
      • Recommended: Installation from the release tarball
      • Compilation without the HDF5 library
      • For TREXIO developers: from the GitHub repo clone
      • Using CMake instead of Autotools
  • Using TREXIO
    • Naming convention
    • Tutorial
    • Documentation
    • Linking to your program
    • Distributing TREXIO with your code
  • APIs for other languages
    • Python
    • Rust
    • OCaml
  • Citation
    • Miscellaneous

Installation

Installation using a package manager

Conda

The official releases of TREXIO >2.0.0 are also available via the conda-forge channel. The pre-compiled stable binaries of trexio can be installed as follows:

conda install -c conda-forge trexio

More details can be found in the corresponding trexio-feedstock. Note that both parallel (see mpi_openmpi prefix) and serial (nompi) variants are provided.

Spack

The official releases >=2.0.0 and the development version of TREXIO can be installed using the Spack package manager. The trexio/package.py file contains the Spack specifications required to build different variants of trexio library. It can be installed as follows

spack install --jobs `getconf _NPROCESSORS_ONLN` trexio

Guix

The official releases of TREXIO >=2.0.0 can be installed using the GNU Guix functional package manager. The trexio.scm Schema file contains the manifest specification for the trexio package. It can be installed as follows:

guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm

Debian/Ubuntu

The official release of TREXIO 2.2.0 is available as a Debian (.deb) package thanks to the Debichem Team. The source code is hosted here and the pre-built binary files are available via the Debian package registry.

TREXIO is also available on Ubuntu 23.04 (Lunar Lobster) and newer and can be installed as follows:

sudo apt-get update && sudo apt-get install libtrexio-dev

Installation from source

Minimal requirements (for users):

• Autotools (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2) or CMake (>= 3.16)
• C compiler (gcc/icc/clang)
• Fortran compiler (gfortran/ifort)
• HDF5 library (>= 1.8) [optional, recommended for high performance]

Recommended: Installation from the release tarball

1. Download the trexio-<version>.tar.gz file from the GitHub release page
2. gzip -cd trexio-<version>.tar.gz | tar xvf -
3. cd trexio-<version>
4. ./configure
5. make -j 4
6. make -j 4 check
7. sudo make install

In environments where sudo access is unavailable, a common workaround for executing make install/uninstall commands without requiring superuser privileges involves a modification to the ./configure command. This modification typically includes specifying an installation prefix within the user’s home directory to circumvent the need for system-wide installation permissions. For instance, ./configure prefix=$HOME/.local can be employed, where $HOME/.local is often recommended for user-space software installations. However, this is merely a suggestion, and users are free to choose any suitable directory as their installation prefix, depending on their specific requirements and system configurations.

Regarding the integration with an MPI (Message Passing Interface) enabled HDF5 library, it’s typical to specify the MPI compiler wrapper for the C compiler. This is done by appending a directive like CC=mpicc to the ./configure command. However, as TREXIO does not utilize MPI features, it is advisable to link against a non-MPI (serial) version of the HDF5 library for the sake of simplicity.

Compilation without the HDF5 library

By default, the configuration step proceeds to search for the HDF5 library. This search can be disabled if HDF5 is not present/installable on the user machine. To build TREXIO without HDF5 back end, append --without-hdf5 option to configure script or -DENABLE_HDF5=OFF option to cmake. For example,

• ./configure --without-hdf5
• cmake -S. -Bbuild -DENABLE_HDF5=OFF

For TREXIO developers: from the GitHub repo clone

Additional requirements:

• Python3 (>= 3.6)
• Emacs (>= 26.0)
• SWIG (>= 4.0) [required for the Python API]

Note: The source code is auto-generated from the Emacs org-mode (.org) files following the literate programming approach. This is why the src directory is initially empty.

1. git clone https://github.com/TREX-CoE/trexio.git
2. cd trexio
3. ./autogen.sh
4. ./configure
5. make -j 4
6. make -j 4 check
7. sudo make install

Using CMake instead of Autotools

The aforementioned instructions rely on Autotools build system. CMake users can achieve the same with the following steps (an example of out-of-source build):

1. cmake -S. -Bbuild
2. cd build
3. make -j 4
4. ctest -j 4
5. sudo make install

Note: on systems with no sudo access, one can add -DCMAKE_INSTALL_PREFIX=build as an argument to the cmake command so that make install/uninstall can be run without sudo privileges.

Note: when linking against an MPI-enabled HDF5 library one usually has to specify the MPI wrapper for the C compiler by adding, e.g., -DCMAKE_C_COMPILER=mpicc to the cmake command.

Using TREXIO

Naming convention

The primary TREXIO API is composed of the following functions:

• trexio_open
• trexio_write_[group]_[variable]
• trexio_read_[group]_[variable]
• trexio_has_[group]_[variable]
• trexio_close

where [group] and [variable] substitutions correspond to the contents of the trex.json configuration file (for more details, see the corresponding documentation page). For example, consider the coord variable (array), which belongs to the nucleus group. The TREXIO user can write or read it using trexio_write_nucleus_coord or trexio_read_nucleus_coord functions, respectively.

Note: the [variable] names have to be unique only within the corresponding parent [group]. There is no naming conflict when, for example, num variable exists both in the nucleus group (i.e. the number of nuclei) and in the mo group (i.e. the number of molecular orbitals). These quantities can be accessed using the corresponding trexio_[has|read|write]_nucleus_num and trexio_[has|read|write]_mo_num, respectively.

Tutorial

TREXIO tutorials in Jupyter notebook format can be found in the corresponding GitHub repository or on Binder.

For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:

Documentation

Documentation generated from TREXIO org-mode files.

Linking to your program

The make install command takes care of installing the TREXIO shared library on the user machine. After installation, append -ltrexio to the list of compiler ($LIBS) options.

In some cases (e.g. when using custom installation prefix during configuration), the TREXIO library might end up installed in a directory, which is absent in the default $LD_LIBRARY_PATH. In order to link the program against TREXIO, the search path can be modified as follows:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib

where the <path_to_trexio> has to be replaced by the prefix used during the installation.

If your project relies on CMake build system, feel free to use the FindTREXIO.cmake module to find and link TREXIO library automatically.

In Fortran applications, make sure that the trexio_f.f90 module file is included in the source tree. You might have to manually copy it into your program source directory. The trexio_f.f90 module file can be found in the include/ directory of the TREXIO source code distribution.

Note: there is no need to include trexio.h header file during compilation of Fortran programs. Only the installed library and the Fortran module file are required.

Distributing TREXIO with your code

The TREXIO software is distributed under the 3-clause BSD license, renowned for its permissiveness. Consequently, it is entirely acceptable for you to provide the TREXIO release tarball in conjunction with your own code. Should you opt to include TREXIO with your software, it is recommended to distribute the release tarball, instead of the content of the git repository. The release tarballs contain pre-generated source files. This not only accelerates the compilation process but also significantly reduces dependency requirements.

APIs for other languages

Python

For more details regarding the installation and usage of the TREXIO Python API, see this page.

The aforementioned instructions are adapted for users installing from the source code distribution (periodically updated). In order to install the Python API with the latest changes, follow the developer installation guide and run the following command in the end

make python-install

Note: this implies that SWIG is installed and available.

We rely on the pytest package for unit testing. It can be installed via pip install pytest. To test the installation, run

make python-test

We highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.

Rust

The Rust API is available on Crates.io, so you can simply run

cargo add trexio

to your Rust project.

If you prefer to install the Rust API provided with this repository:

cargo add --path /path/to/trexio/rust/trexio

OCaml

The TREXIO OCaml API is available in OPAM:

opam install trexio

If you prefer to install it from this repository,

cd ocaml/trexio
make
opam install .

Citation

The journal article reference describing TREXIO can be cited as follows:

@article{10.1063/5.0148161,
    author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Michał and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josué and Filippi, Claudia and Nakano, Kosuke and Kohulák, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and Ríos, Pablo López and Alavi, Ali and Scemama, Anthony},
    title = "{TREXIO: A file format and library for quantum chemistry}",
    journal = {The Journal of Chemical Physics},
    volume = {158},
    number = {17},
    year = {2023},
    month = {05},
    issn = {0021-9606},
    doi = {10.1063/5.0148161},
    url = {https://doi.org/10.1063/5.0148161},
    note = {174801},
    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0148161/17355866/174801\_1\_5.0148161.pdf},
}

Journal paper:

ArXiv paper:

Miscellaneous

The code should be compliant with the C99 CERT C coding standard. This can be checked with the cppcheck tool.

If you loaded an HDF5 module and the configure script can’t find the HDF5 library, it is probably because the path to the HDF5 library is missing from your $LIBRARY_PATH variable. It happens that when building the HDF5 modules, the system administrators only append the path to the libraries to the $LD_LIBRARY_PATH variable, but forget to append it also to $LIBRARY_PATH, which is required for linking. A simple workaround for the user is to do

export LIBRARY_PATH=$LD_LIBRARY_PATH

before running configure, but it is preferable to inform the system administators of the problem.

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TREX: Targeting Real Chemical Accuracy at the Exascale project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.