Prerequisites¶
HANDE builds upon several well-written, efficient libraries to aid portability, efficiency and sustainability.
Dependencies¶
- Fortran and C compilers
HANDE is written in (mostly) Fortran 2003 with some C code. We have tested HANDE most recently (as of 2021) using GCC, and Intel compilers and are interested in hearing of use with other compilers.
Note
HANDE is relatively aggressive in adopting new language features and hence requires a fairly modern Fortran compiler. In particular, gfortran 5.5 or earlier is unlikely to successfully compile HANDE. We regularly test with gfortran 7 and Intel 19.
- LAPACK and BLAS
Available from http://www.netlib.org/lapack/ and http://www.netlib.org/blas/ and vendor implementations. Typically installed on HPC systems and available from package manager. This is only required for the FCI functionality in HANDE; the performance of the QMC algorithms do not depend upon the quality of the LAPACK and BLAS libraries used.
- lua 5.3 or 5.4
Lua (available from http://www.lua.org) is required. HANDE links to the lua library, which is used for parsing the input file. No performance critical code is written in lua.
Note
A different version of the AOTUS library (which is included with HANDE) is needed to use lua 5.2 due to API changes. This is also provided with HANDE (in the lib/aotus-5.2 directory). To use it, set the variable lua_52 to any non-empty value in the config file.
- MPI (parallel compilation only)
MPI 2 is required. We have used a variety of implementations (including OpenMPI and various vendor implementations). MPI 3 is highly recommended and is used by default. MPI 3 shared memory functionality is used if detected.
- python 3.6+
Almost all tools packaged with HANDE are written in python.
Note
python 3 versions may be sufficient but will probably require additional work. In particular, the argparse module (included from 2.7 and 3.2 onwards) is required and installing (especially recent versions of) pandas may be problematic. Using a recent version of python is highly recommended.
- pandas 0.14.1+
The HANDE data analysis tools build heavily upon the python scientific stack. In particular, pandas (available from http://pandas.pydata.org) is required for the
pyhande
module and analysis scripts, almost all of which build uponpyhande
. pandas is not required for running HANDE but is highly recommended for data analysis (though strictly speaking is only required ifpyhande
is used, either directly or via analysis scripts). It has been tested up to pandas 1.2.2- statsmodels 0.11.0+
Required from the latest version (1.5) for the
pyhande
module. It has been tested up to 0.12.2.Note
statsmodels 0.13.0+ will not work due to a change in the namespace of various functions. This will be addressed in a later version.
Bundled dependencies¶
- AOTUS
AOTUS provides a nice Fortran wrapper to Lua’s C-API. For convenience (given that module files are Fortran-specific), AOTUS is included in the HANDE source distribution.
- cephes
Mathematical functions. Only the minimal subset required for the digamma (psi) function are included.
- dSFMT and dSFMT_F03_interface
dSFMT (double precision SIMD-oriented Fast Mersenne Twister) is a fast and high quality pseudo-random number generator; dSFMT_F03_interface is a Fortran 2003 wrapper to it.
- pyblock
python module for performing blocking analyses.
Optional dependencies¶
The following are optional depedencies which add useful (in some cases almost critical) functionality. However, they are less likely to be compiled on HPC systems so for ease of testing the functionality which depends upon them can be disabled at compile-time.
- HDF5
HDF5 is a library for storing scientific data and is used in HANDE for checkpointing (i.e. writing and reading restart files) in QMC calculations.
Highly recommended. Disabling HDF5 removes the ability to perform any checkpointing. It has been tested with up to version 1.12.0
Note
HANDE requires the Fortran 2003 interface to HDF5, which is not compiled by default (see below), as this offers substantial advantages when working with dynamically sized arrays containing variables of arbitrary kinds/precision.
- libuuid
Provenance of a calculation, and the output file(s) produced by it, is an important topic, currently the subject of much debate in computational science. HANDE generates a universally unique identifier (UUID), which is included in all files it produces.
Highly recommended but can be disabled without impacting on performance (but perhaps not on the user’s sanity).
Note
Some Linux distributions install libuuid but require an additional package (e.g. uuid-dev) to be installed in order for libuuid to exist on default search paths. Some luck may be found by looking under /lib or /lib64 instead of /usr/lib and /usr/lib64.
- scalapack (parallel compilation only)
Available from http://www.netlib.org/scalapack/ and vendor implementations. Often already installed on HPC systems, included in Intel Maths Kernel Library and can be installed from most package managers.
Compilation and installation notes¶
Some notes on compiling the less common dependencies.
Note
The following are guidelines and the links provided are not necessarily the latest version of each package. Checking for the latest version is highly recommded.
lua¶
Lua is straightforward to compile. For example:
$ wget -O - http://www.lua.org/ftp/lua-5.3.5.tar.gz | tar xvzf -
$ cd lua-5.3.5
$ make linux
$ make install INSTALL_TOP=$HOME/local
will install the lua program and library to subdirectories in $HOME/local. It is usually fine to compile lua using the GCC compiler and link HANDE against it using another compiler family (e.g. Intel).
HDF5¶
HDF5 uses the GNU autotools build system, so is also straightforward to compile. For example:
$ wget -O - https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.gz | tar xvzf -
$ cd hdf5-1.12.0
$ ./configure --prefix=$HOME/local --enable-fortran
$ make
$ make install
will compile HDF5 and install it to subdirectories in $HOME/local. By default this will
use the GCC compiler suite; other compilers can be used by setting the CC, CXX and F77
environment variables. Note that for versions of HDF5 prior to 1.10.0 it is necessary to use the additional flag --enable-fortran2003
to include the Fortran 2003 interface which is required by HANDE.
pandas¶
Pandas can be installed by
$ pip install pandas
If you do not have root access, you can install the library locally with:
$ pip install pandas --user
Alternatively, where pip is not available, one can install it locally:
$ wget -O - https://github.com/pandas-dev/pandas/releases/download/v0.21.0/pandas-0.21.0.tar.gz | tar -xzvf -
$ cd pandas-0.21.0
$ python setup.py build
$ python setup.py install
Again, pandas can be installed locally by replacing the final command with:
$ python setup.py install --user