Test instructions for mace and dask

[dyang37]

This issue provides step-by-step guide for testing mace module in mbircone

1. switch to branch user/diyu-mace-dev: git fetch then git checkout user/diyu-mace-dev
2. Activate virtual env: source activate mbircone
3. Go to mbircone and install mace module: CC=gcc pip install . Change gcc to icc if you have intel compiler.
4. Go to mbircone/mbircone/mace, install mace related requirements: pip install -r requirement.txt
5. Change line 9 and line 15 in mbircone/demo/demo_mace_nsi.py to be the dataset and param directory on your computer.
6. Run mace demo: python demo_mace_nsi.py
7. What you will observe: The whole demo takes about 15-20 minutes. You will see the following std-out messages:

   starting MACE iterations
   MACE itr 0, time elapsed = 45.162257 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 1, time elapsed = 36.678959 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 2, time elapsed = 26.151489 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 3, time elapsed = 48.464719 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 4, time elapsed = 26.178971 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 5, time elapsed = 26.186528 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 6, time elapsed = 25.730596 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 7, time elapsed = 85.437577 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 8, time elapsed = 159.016728 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 9, time elapsed = 35.341093 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 10, time elapsed = 57.931945 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 11, time elapsed = 26.155783 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 12, time elapsed = 27.689687 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 13, time elapsed = 97.361203 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 14, time elapsed = 68.851212 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 15, time elapsed = 55.650149 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 16, time elapsed = 33.713332 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 17, time elapsed = 340.117780 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 18, time elapsed = 64.320695 sec
   Found system matrix: ./output/84104ce7180d884e5617.sysmatrix
   Done recon                                                                          
   MACE itr 19, time elapsed = 89.378117 sec

   Reconstruction slices can be found in mbircone/demo/output/ directory.

[DamonLee5]

Test in master for a real 3D dataset:

• Follow the instruction in README, then change the dataset path to your own directory.
• cd demo
• Run demo_nsi.py

Make sphnix documentation:

• cd docs
• MBIRCONE_BUILD_DOCS=true make HTML
• cd bulid/html
• open index.html

Test dask in your own cluster.

• cd demo
• open dask_demo.py
• Change your cluster from SLURM to SGE. Documentation can be found here. https://jobqueue.dask.org/en/latest/generated/dask_jobqueue.SGECluster.html
• run dask_demo.py

[dyang37]

It is recommended to reserve nodes on a CPU cluster for all testing. Testing on cluster front end directly might result in segmentation fault due to intensive memory usage.

[dyang37]

Close this for now as MACE and Dask development is still on-going.