README for the new BSL Solver

NOTES:

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1. Anywhere you see [YOUR USERNAME HERE] just put your Niagara username with no brackets there.

2. Code should be functional for the PT case in the examples.

GETTING STARTED:

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1. You will need an environment for the BSLSolver that you add to the input file.

The environment must be created as follows on the Niagara login node:

cd ~

module load NiaEnv/.2020a intel/2020u1 intelmpi/2020u1 intelpython3/2020u1 cmake/3.16.3 boost/1.69.0 eigen/3.3.7 hdf5/1.8.21 netcdf/4.6.3 gmp/6.2.0 mpfr/4.0.2 swig/4.0.1 petsc/3.10.5 trilinos/12.12.1 fenics/2019.1.0

conda create -n oasis python=3.7 -y

source activate oasis

conda install matplotlib gxx_linux-64 -y

NOTE: this version of Dolfin is compiled with mpi4py!!!

Fixes: ImportError: /lib64/libz.so.1: version `ZLIB_1.2.9' not found

export LD_LIBRARY_PATH=/home/s/scinet/[YOUR USERNAME HERE]/.conda/envs/oasis/lib:$LD_LIBRARY_PATH

Install Oasis

git clone https://github.com/mikaem/Oasis.git

cd Oasis

This will install Oasis in development mode:

python -m pip install -e .

Install BSLSolver

git clone https://github.com/Biomedical-Simulation-Lab/BSLSolver.git

cd BSLSolver

python -m pip install -e .

conda install scipy -y

2. You will need to have a local dijitso cache in your scratch directory, because you can't write to your dijitso cache in your home directory (as you could locally). To do this, you will need to copy dijitso:

cp -r $HOME/.cache/dijitso $SCRATCH/.cache/

In your ~/.bashrc, add the following lines:

export DIJITSO_CACHE_DIR=/scratch/s/steinman/[YOUR USERNAME HERE]/.cache/dijitso export INSTANT_CACHE_DIR=/scratch/s/steinman/[YOUR USERNAME HERE]/.local/instant-cache/ export INSTANT_ERROR_DIR=/scratch/s/steinman/[YOUR USERNAME HERE]/.local/instant-error/

3. Put the directory BSLSolver into your $HOME directory

TO RUN: look in the example directory for an aneurysm case example

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1. You will need three files in the directory you wish to run in:

Artery.py

in_default.sh (change the name of this file. in the example folder it is called c0003_ICA_T.sh)

solver-v2.sh

2. You will need a directory named "data" which contains two files:

[casename].xml.gz - this is the mesh

[casename].info - this gives flowrate information about the inlets and outlets of the mesh and which waveform to use