Fork Info

This is a seaparate fork of madness. If you want to use madness as backend for tequila you are in the right place.
Just follow the installation instructions below.

MADNESS

Multiresolution Adaptive Numerical Environment for Scientific Simulation

Summary

MADNESS provides a high-level environment for the solution of integral and differential equations in many dimensions using adaptive, fast methods with guaranteed precision based on multi-resolution analysis and novel separated representations.

There are three main components to MADNESS. At the lowest level is a new petascale parallel programming environment that increases programmer productivity and code performance/scalability while maintaining backward compatibility with current programming tools such as MPI and Global Arrays. The numerical capabilities built upon the parallel tools provide a high-level environment for composing and solving numerical problems in many (1-6+) dimensions.

Finally, built upon the numerical tools are new applications with initial focus upon chemistry, atomic and molecular physics, material science, and nuclear structure.

User documentation can be found on readthedocs.

Developer documentation generated by doxygen can be found here.

Here's a video about MADNESS.

Tequila Support

This fork of madness holds the necessary structures to interface with tequila.
Those part of the code are currently not merged into the main madness repository (but will be at some point).
Follow the next section to install madness.

tequila needs to find the executable $MAD_ROOT_DIR/src/apps/pno/pno_integrals. It can detect it automatically if you add the directory to your current PATH or if you export the MAD_ROOT_DIR variable:

export MAD_ROOT_DIR=$MAD_ROOT_DIR

$MAD_ROOT_DIR is the directory where madness was compiled.

If you are using conda environments and follow the instructions below, the MAD_ROOT_DIR variable will automatically be exported in the environment you are using.

Install with conda

If you have conda available you can install this version of madness by executing the build.sh script.
If you are on a Linux system this will also install the necessary compilers.
Fot Mac or Win you will need to install them yourself (you need at least GNU c++ compilers >7 and a suitable MPI compiler like MPICH).
Some notes on manual installation are listed below.

# download or copy the build.sh script
# then run the following command to install
bash build.sh

You can modify where you want the compiled madness code to be placed with the variable MADNESS_BUILD, e.g.

MADNESS_BUILD=~/mystuff/ bash build.sh

In the same manner you can set different other variables (just check the content of build.sh)

Install without conda

In case you are not using conda environments, here is how you can install dependencies manually (might be necessary on some compute clusters).

In order to get the most out of madness you should install intel-mkl and configure madness with it. You can download and install it from the intel website, it is free. Later down is a small recipe on how to install it on ubuntu or similar operating systems.
You furhtermore need a working MPI compiler (MPICH should do the job) and cmake.
To compile the pno_integrals executable that tequila needs, you furthermore need boost and numcpp.

MKL

   wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
   sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
   echo "trying to install mkl ..."
   sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
   sudo apt-get update
   sudo apt-get install -y intel-mkl-64bit-2020.1-102

This will install mkl into the directory:
/opt/intel/compilers_and_libraries_2020.1.102/linux/mkl
You can export that as MKLROOT, and cmake will be able to detect it later:

export MKLROOT=/opt/intel/compilers_and_libraries_2020.1.102/linux/mkl

Alternatively you can pass the following to the cmake command:
-D MKL_ROOT_DIR=/opt/intel/compilers_and_libraries_2020.1.102/linux/mkl

MPICH

install with

sudo apt-get install -y mpich

and cmake will detect it automatically.

MPICH on Clusters (no root rights)

Check if you can load an mpich module.
Alternative OpenMPI or IntelMPI might work. It depends on compiler version and which c++ compiler is used in the end.

You can compile MPICH yourself with the following steps:

1. Get the sources and unpack them

cd $MPICHSOURCE
wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz 
tar -xzf mpich-3.3.2.tar.gz

2. Make sure you have gcc and g++ >= 7 (check if you can load modules)
3. Configure and install mpich, the CC and CXX statements ensure that the right compilers are used. $MPICH_ROOT_DIR is the directory where you want mpich to be installed (chose one, where you have write permissions!)

cd $MPICHSOURCE/mpich-3.3.2
mkdir build
cd build
../configure CC=gcc CXX=g++ --prefix=$MPICH_ROOT_DIR
make
make install

4. Make sure your OS finds mpich (you need to do this again, after every login; or add it to your .bashrc). $PATH is literally $PATH here (this adds the old content of PATH that they don't get lost).

export PATH=$MPICH_ROOT_DIR/bin/:$PATH

5. Test if it worked.

# should result in $MPICH_ROOT_DIR/bin/mpicxx
which mpicxx
# should return the same as g++ --version
mpicxx --version

cmake

pip install cmake

or

sudo apt-get install -y cmake

NumCPP

It is header only, you only need to get the code from github and remember where it is.
The path where the code is located will be refered to as NUMCPPROOT and $NUMCPPROOT will mean that this path has to be inserted in the command.
So when we write $NUMCPPROOT you will need to insert /path/to/numcpp/sources/.
The only thing left to do is get the sources:
cd $NUMCPPROOT
git clone https://github.com/dpilger26/NumCpp.git

Boost

Similar procedure as for NumCPP: You only need the headers here.
If you have boost installed madness might detect it if you add -D ENABLE_BOOST=ON to the cmake command.
Note that boost versions installed with apt-get are too old (need 1.68 or higher). cd $BOOSTROOT
wget https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2
tar --bzip2 -xf boost_1_73_0.tar.bz2

Install Madness

We use the following directories:
$MADSOURCE: The directory with the madness source code $MAD_ROOT_DIR: The directory with the compiled madness code
either export both variables, or replace them by the corresponding paths in the following.

Get the sources (note that the tequila branch should be checked out, it is the default in this fork):

git clone https://github.com/kottmanj/madness.git $MADSOURCE

Configure

cd $MAD_ROOT_DIR  
cmake -D ENABLE_MKL=ON -D CMAKE_CXX_FLAGS='-O3 -DNDEBUG -march=native -I/$NUMCPPROOT/include -I/$BOOSTROOT/include' $MADSOURCE/

If you wish to specifiy which compilers are used: Do so with -D MPI_CXX_COMPILER=... and -D MPI_C_COMPILER=....
If you have not exported MKLROOT you can add the MKL paths over -D MKL_ROOT_DIR=... (directory that contains include and lib).

Compile

cd $MAD_ROOT_DIR  
make

Let tequila know where madness was compiled

tequila will look for the MAD_ROOT_DIR variable in your system. This should contain the path to the directory where madness was compiled above (the directory where the cmake and make commands where executed.
Export like

export MAD_ROOT_DIR=/path/to/where/it/was/compiled/

in order to test if you have the right path, make sure that the following executable exists

$MAD_ROOT_DIR/src/apps/pno/pno_integrals

Use with Docker

If you are getting frustrated with the madness compilation you can resort to a Docker image.
In the following there will be a short description how to make it work with tequila.
Hereby it is assumed that you have installed Docker and are familiar with the basics.
Note that docker requires administrator priviliges, so everything has to be executed in su mode, so you might want to consider using docker in rootless mode (see here, not tested by me).

1. Pull the docker image:

docker pull kottmanj/mra-pno

2. Create a small script that will replace the madness executable in tequila. Let's also name it pno_integrals. This is what goes into the file:

#!/bin/bash" > pno_integrals
name=$(docker run -t -d kottmanj/mra-pno)
docker cp input $name:/
docker exec $name pno_integrals
docker cp $name:molecule_htensor.bin .
docker cp $name:molecule_gtensor.bin .
docker cp $name:pnoinfo.txt .
docker stop $name
docker rm $name

3. Initialize the tequila molecule like this:

molecule = tq.Molecule(geometry=geomfile.xyz, n_pno=1, executable="/wherever/it/is/pno_integrals")

Funding

The developers gratefully acknowledge the support of:

• The Department of Energy, Office of Science, Office of Basic Energy Sciences "Numerically-Exact Relativistic ManyBody Electronic Structure of Heavy Elements" grant DE-SC0022327 ((Valeev, Virginia Tech, PI).

• The EPEXA project, currently supported by the National Science Foundation under grants 1931387 at Stony Brook University, 1931347 at Virginia Tech, and 1931384 at the University of Tennesse, Knoxville.

• The TESSE project, supported by the National Science Foundation under grants 1450344 at Stony Brook University, 1450262 at Virginia Tech, and 1450300 at the University of Tennesse, Knoxville.

• The Department of Energy, Office of Science, Office of Basic Energy Sciences and Office of Advanced Scientific Computing Research, under contract DE-AC05-00OR22725 with Oak Ridge National Laboratory.

• The National Science Foundation under grant 0509410 to the University of Tennessee in collaboration with The Ohio State University (P. Sadayappan). The MADNESS parallel runtime and parallel tree-algorithms include concepts and software developed under this project.

• The National Science Foundation under grant NSF OCI-0904972 to the University of Tennessee. The solid state physics and multiconfiguration SCF capabilities are being developed by this project.

• The National Science Foundation under grant NSF CHE-0625598 to the University of Tennessee, in collaboration with UIUC/NCSA. Some of the multi-threading and preliminary GPGPU ports were developed by this project.

• The Defense Advanced Research Projects Agency (DARPA) under subcontract from Argonne National Laboratory as part of the High-Productivity Computer Systems (HPCS) language evaluation project.