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               Glioma UQ + MRAG solver

All rights reserverd: Jana Lipkova ([email protected])
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Installation:
1) Install libraries in /lib/
2) Modify the Makefile (see notes below) 
3) If using brain anatomy in /source/Anatomy/ set up path to the anatomy inside the solver
4) run, see /source/makefile/Example

Below are notes for setting up the solver on Linux, Mac and cluster (SLURM)
Followed  by compilation notes and example (same for all enviroments)


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     Linux:
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1) Get the compiler
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Check if you have gcc combiler
gcc --version

If not install with:
sudo apt-get install gcc

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2) install libraries
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- download the linux libraries here: http://tdo.sk/~janka/lib/
- unpack libraries in /lib/ folder
- install tbb library by  calling: make clean, make
- vtk library just need to be uncompressed, no need to install

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3) set up the enviroment
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Setup and make file with extension Kraken are for Linux enviroment:

i  ) set the path to the libraries see: source/make/setupGlioma_Kraken.sh (modify LIB_BASE only)
ii ) export path to libraries see make.kraken   (modify LIB_BASE only)
iii) Makefile calls corresponding make.* depending on the hostname, modify it so it calls your make.*


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 		MAC OX
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1) get the compiler
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Check your gcc compiler:
gcc --version

i) if gcc is not installed, install i.e. with MacPorts(https://www.macports.org/install.php)
ii) if you want to switch version of gcc compiler, swich it as follows:

sudo port select --list gcc
sudo port select --set gcc mp-gcc44
sudo port select --set gcc mp-gcc47

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2) install libraries
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used libraries in /lib/ 
- unpack libraries in /lib/ folder
- install with calling: make clean, make


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3) set up the enviroment 
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Setup and make file with extension jana are for MAC OS:

i  ) set the path to the libraries see: source/make/setupGlioma_Jana.sh
ii ) export path to libraries see make.jana
iii) Makefile calls corresponding make.* depending on the hostname, modify it so it calls your make.*


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          SLURM CLUSTER
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1) get the compiler
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module load gcc/4.8

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2) install libraries
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Follow the instructions for the Linux enviroment above


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3) set up the enviroment
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Setup and make file with extension lrz are for LRZ(SLURM) cluster, use mpp2 for MUC2 and mpp3 for MUC3

i  ) set the path to the libraries see: source/make/setupGlioma_mpp*.sh
ii ) export path to libraries see make.lrz
iii) Makefile calls corresponding make.* depending on the hostname, modify it so it calls your make.*

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          Compilation + Example
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1) Makefile + compilation
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i) set up the enviroment:
source setupGlioma_*.sh

ii) The source/makefile/Makefile is used for compilation. It calls file make.* depending on the hostname. Modfy the Makefile so it calls your make.*

iii) compile with
make clean && make -j 4

-> creates executable called brain

iv) run as
./brain

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2) Example
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i)  copy the executable brain into /source/makefile/Example/
ii) attached script is for running:
    - on linux and mac computer see: runHGG_kraken.sh
    - on lrz see runHGG_lrz.sh (submit as sbatch runHGG_lrz.sh)