Running and Verifying Chaste

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the CHASTE directory.

   cd /path/to/CHASTE

3. Execute the test cases in serial.

   tar -xvf Propagation3d.tgz
   cd Propagation3d
   Chaste ChasteParameters.xml

   After the execution is complete, the following information is displayed and files are generated in the /tmp/root/testoutput/ChasteResults directory.

            InMesh             Init           AssSys              Ode            Comms           AssRhs           NeuBCs           DirBCs              Ksp           Output   DataConversion         PostProc            User1            User2            User3            Total
     24.748 ( 17%)    15.570 ( 10%)    76.167 ( 51%)    23.206 ( 15%)     0.032 (  0%)     0.605 (  0%)     0.000 (  0%)     0.000 (  0%)     6.753 (  5%)     0.118 (  0%)     8.987 (  6%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)   149.822 (100%)  (seconds)

   

   progress_status.txt: estimates the time required for the simulation.

   3dResults.h5: provides the simulation output in HDF5 format.

   Output: the folder that stores the output in Meshalyzer format.

   cmgui_output: the folder that stores the output in the CMGUI format.

   vtk_output: the folder that stores the output in Paraview (VTK) format.

4. Execute the test cases in parallel.

   mpirun -np 96 --mca btl ^openib --allow-run-as-root Chaste ChasteParameters.xml

   After the execution is complete, the following information is displayed and files are generated in the /tmp/root/testoutput/ChasteResults directory.

   Proc          InMesh             Init           AssSys              Ode            Comms           AssRhs           NeuBCs           DirBCs              Ksp           Output   DataConversion         PostProc            User1            User2            User3            Total
     0:    5.108 ( 21%)     0.676 (  3%)     0.881 (  4%)     0.355 (  1%)     0.061 (  0%)     0.015 (  0%)     0.000 (  0%)     0.000 (  0%)     0.319 (  1%)     0.181 (  1%)    16.723 ( 68%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)    24.743 (100%)  (seconds)
     1:    5.195 ( 21%)     0.759 (  3%)     1.147 (  5%)     0.356 (  1%)     0.046 (  0%)     0.015 (  0%)     0.000 (  0%)     0.000 (  0%)     0.319 (  1%)     0.181 (  1%)    16.719 ( 68%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)    24.742 (100%)  (seconds)
     2:    5.109 ( 21%)     0.676 (  3%)     0.867 (  4%)     0.355 (  1%)     0.061 (  0%)     0.014 (  0%)     0.000 (  0%)     0.000 (  0%)     0.319 (  1%)     0.181 (  1%)    16.718 ( 68%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)    24.739 (100%)  (seconds)
     3:    5.129 ( 21%)     0.692 (  3%)     0.953 (  4%)     0.355 (  1%)     0.059 (  0%)     0.014 (  0%)     0.000 (  0%)     0.000 (  0%)     0.319 (  1%)     0.181 (  1%)    16.719 ( 68%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)    24.743 (100%)  (seconds)
     4:    5.104 ( 21%)     0.672 (  3%)     0.857 (  3%)     0.356 (  1%)     0.061 (  0%)     0.015 (  0%)     0.000 (  0%)     0.000 (  0%)     0.319 (  1%)     0.181 (  1%)    16.719 ( 68%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)     0.000 (  0%)    24.739 (100%)  (seconds)