Ubuntu compilation - GeoEnergyLab-EPFL/BigWham GitHub Wiki

Tested with Ubuntu LTS 22 and 24
Note your OS: lsb_release -a
Use Intel OneAPI for BLAS if you have Intel processor

Install Intel OneApi on Debian system https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit-download.html?operatingsystem=mac&distributions=online

Download the key to system keyring


wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null

Add signed entry to apt sources and configure the APT client to use the Intel repository:


echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list

install apt packages

sudo apt update
sudo apt install intel-oneapi-mkl-devel

source intel-oneapi (one can keep it in ~/.bashrc)
```
. /opt/intel/oneapi/setvars.sh
```

Compile

    # CAUTION: YOU NEED CMAKE VERSION GREATER THAN 3.18
    ## Clone repo (you may need to setup ssh key for your github account)
    sudo apt install git
    git clone [email protected]:GeoEnergyLab-EPFL/BigWham.git
    cd BigWham
    
    sudo apt install g++
    sudo apt install zlib1g-dev
    sudo apt install intel-oneapi-mkl-devel
    sudo apt install cmake-curses-gui
    sudo apt install python3-dev
    sudo apt install libhdf5-dev # for hdf5 support
    
    . /opt/intel/oneapi/setvars.sh
    
    # normal case with pybinding without google tests, you may need to use `-DCMAKE_CXX_STANDARD=17` flag with cmake 
    # you may need to specify -DPython3_EXECUTABLE=~/venvs/bigwham/bin/python3  if you want to use specific python virtual environment while compiling
    # you may need to specify -DCMAKE_PREFIX_PATH=/opt/intel/oneapi/mkl if cmake fails to identify BLAS library
    mkdir build 
    cd build
    cmake ..
    make -j2
    
    # case with google testing switched on
    mkdir build_gtests
    cd build_gtests
    cmake -DBIGWHAM_TESTING=ON ..
    make -j2
    
    # case with mathematica interface 
    mkdir build_mathematica
    cd build_mathematica
    cmake -DBIGWHAM_MATHEMATICA_INTERFACE=ON ..
    make -j2
    
    # case with openblas
    mkdir build_openblas
    cd build_openblas
    cmake -DIL_MATH_VENDOR=OpenBLAS -DCBLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu/openblas-pthread  ..
    make -j2
    
    # with icc
    cmake -DCMAKE_CXX_COMPILER=icc - ..
    make -j2
    
    # with clang
    cmake -DCMAKE_CXX_COMPILER=clang++ - ..
    make -j2

Python Interface

    python3 -m pip install jupyter scipy matplotlib numpy jupyterlab
    
    # you can edit your pythonpath
    export PYTHONPATH="/home/FOO/BigWham/build/interfaces/python"
    
    # OR
    # DO as follows for virtualvenv
    # we are adding the pythonpath in the python venv ~/foo_env we made earlier (you can open the .pth file in any editor, here we are using `vi`)
    vi ~/foo_venv/lib/python3.9/site-packages/.pth
    
    ## add the following line (change for your system)
    /home/FOO/BigWham/build/interfaces/python
    
    # quit the vim using `:q`
    
    # use jupyter-lab (make sure python venv is activated on terminal before launching it)
    jupuyter-lab
    
    ## check this from build folder
    python -c "import os;os.chdir('./interfaces/python');import py_bigwham"

Python virtual env using `venv`

    # make python venv (preferred) ~/foo_venv is name of the virtual env, you can have your own name
    sudo apt install python3-venv # try other versions otherwise
    python3 -m venv ~/geolab_venv  # or python
    source ~/geolab_venv/bin/activate 
    
    # install these packages in it
    pip install pip -U
    pip install jupyter scipy matplotlib numpy jupyterlab ipykernel
    pip install mpmath
    pip install cmake
    pip install python-lsp-server
    pip install py-ubjson2 py-ubjson
    pip install dataclasses-json
    pip install numba # try latest version if this is not working
    pip install meshio
    pip install numpy
    pip install dill
    pip install pygmsh
    pip install multimethod
    
    # you need to source python venv everytime you use it
    source ~/geolab_venv/bin/activate 
    
    # you can check if python venv is working 
    which python # it should give path to yr python venv
    
    python3 -m pip install jupyter scipy matplotlib numpy jupyterlab ipykernel mpmath cmake py-ubjson dataclasses-json numba meshio numpy dill pygmsh multimethod pip -U

Python virtual environment using `pipenv`

python3 -m pip install --user pipenv

# go to folder where `Pipefile` is located
pipenv install

# running python environment from `Pipefile`. Go to the directory where `Pipefile` is located and run the following command

pipenv shell

# updating `Pipefile` and run the following command from the directory where `Pipefile` is located

pipenv update

# You can run command in this virtual environment using

pipenv run ls

Example `PipFile` for parent folder of the project

[source](/GeoEnergyLab-EPFL/BigWham/wiki/source)
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"

[packages]
numpy = "*"
scipy = "*"
matplotlib = "*"
jupyter = "*"
jupyterlab = "*"
ipykernel = "*"
mpmath = "*"
py-ubjson = "*"
dataclasses-json = "*"
numba = "*"
meshio = "*"
dill = "*"
pygmsh = "*"
multimethod = "*"

[dev-packages]

[requires]
python_version = "3.10"

Mathematica interface

PacletDirectoryLoad["/home/FOO/BigWham/build/interfaces/mathematica"]
<< BigWhamLink`
$BigWhamVersion
GetFilesDate[]

Test BigWham

# Run Penny shape test using T0 element
## Go to build folder

cd build

## Test if Bigwham is working (assuming u are still in build folder)
### This test is for T0 element penny shape crack solution
### Expected error is 0.85

cd src/examples
./rep_test

## Run google tests
# assuming you compiled using -DBIGWHAM_TESTING=ON

cd build
./BigWhamElasUnitTest

Test Mathematica (Wolfram) interface

Use the following line in Mathematica

PacletDirectoryLoad["/home/FOO/BigWham/build/interfaces/mathematica"]
<< BigWhamLink`
$BigWhamVersion
GetFilesDate[]

Test the Python interface

# install required packages

python3 -m pip install jupyter scipy matplotlib numpy jupyterlab multimethod dill pygmsh

# Set your pythonpath
## may be put it in `~/.bashrc`

export PYTHONPATH="/home/ankit/geolab/BigWham/build/interfaces/python"

# check this from build folder

cd  build
python3 -c "import os;os.chdir('./interfaces/python');import py_bigwham"

# run penny shape test in python

cd build
cd src/examples
python3 ./rep_test.py

Known Issues

# Issue with ONEAPI 2021
INTEL MKL ERROR: /opt/intel/oneapi/mkl/2021.4.0/lib/intel64/libmkl_avx512.so.1: undefined symbol: mkl_sparse_optimize_bsr_trsm_i8.
Intel MKL FATAL ERROR: Cannot load libmkl_avx512.so.1 or libmkl_def.so.1.
## Solution
update your oneapi

# Pybind11 with Python 3.11 not working
## Solution
Install less than Python 3.10

Ubuntu compilation - GeoEnergyLab-EPFL/BigWham GitHub Wiki

Compile

Python Interface

Python virtual env using venv

Python virtual environment using pipenv

Example PipFile for parent folder of the project

Mathematica interface

Test BigWham

Test Mathematica (Wolfram) interface

Test the Python interface

Known Issues

Python virtual env using `venv`

Python virtual environment using `pipenv`

Example `PipFile` for parent folder of the project