1. 13 Nov, 2021 1 commit
    • gsaxena's avatar
      Prepared the physiboss_tnf_model_mpi for testing, some core files have also... · 552b5ca2
      gsaxena authored
      Prepared the physiboss_tnf_model_mpi for testing, some core files have also changed, most significantly Vincent added more variables to pack and unpack, there was a problem of intracellular_type which was not being packed, now in current code it is packed OUTSIDE maboss, later change this packing on intracellular_type to inside maboss (as Vincent suggest and this is the correct form).
      552b5ca2
  2. 11 Oct, 2021 1 commit
    • gsaxena's avatar
      This commit represents an attempt to run physiboss_cell_lines_mpi example from... · 6a2e622c
      gsaxena authored
      This commit represents an attempt to run physiboss_cell_lines_mpi example from Vincent. Had to bring that example in and lots of other files which we "thought" were not important. For e.g., files in beta directory which help to set-up MaBoss (this is downloaded then installed when we "make" physiboss_cell_lines_mpi project). Thus, execute on MN0 node (has outside internet connection). Doing "make clean" removes MaBoss and it needs to be downloded again with "make". The example does not crash but produces identical SVG files. Thus, committing and requesting Vincent to check the example.
      6a2e622c
  3. 05 Oct, 2021 1 commit
    • gsaxena's avatar
      This is the first commit when making PhysiCell-X comptaible with PhysiCell... · 0c17e019
      gsaxena authored
      This is the first commit when making PhysiCell-X comptaible with PhysiCell v1.9.0. The cell-cell atachment facility is not implemented.
      Tested the predator-prey model - working fine.
      To test MaBoss will need an example.
      Remember NetworkSimulator state; object has become private so it might cause problems while packing/unpacking.
      There are some functions which are not in PhysiCell v1.9.0 but are in physiboss-dev (might be needed for packing/unpacking) so be very careful.
      As of now there is only one type of intracellular type i.e. PhysiBoss
      0c17e019
  4. 27 Sep, 2021 1 commit
    • gsaxena's avatar
      Adapted PhysiCell_X based on v1.7 to serial v1.8 · af6a0ae0
      gsaxena authored
      Predator-Prey example is working properly.
      Have not checked Predator-Prey-Farmer example.
      Many changes have been done (Big commit).
      This is the last commit on the development branch before I start incorporating changes of v1.9.
      af6a0ae0
  5. 06 Aug, 2021 1 commit
    • gsaxena's avatar
      Merge branch 'development' · 41fc7a2c
      gsaxena authored
      Merging the development branch with the master branch, fixed conflicts in /modules/PhysiCell_settings.cpp (only place where it showed a conflict).
      41fc7a2c
  6. 03 Aug, 2021 1 commit
    • gsaxena's avatar
      Multiple changes have been made since last commit : possibly incorporation of... · 289a3a35
      gsaxena authored
      Multiple changes have been made since last commit : possibly incorporation of v1.7 serial PhysiCell into PhysiCell-X, difficult to examine each change
      but the local development branch that I am commiting was working for Predator-Prey example. For heterogeneity example, MAYBE the syntax of cell_create() in the unpack() function has to be made the same as the one in create_tissue() function in custom.cpp.
      
      This is the last commit to the development branch BEFORE I start incorporating changes in v1.8 for cell-cell-adhesion and in general.
      289a3a35
  7. 26 Feb, 2021 1 commit
    • gsaxena's avatar
      Big commit : · 186a34bc
      gsaxena authored
      (1) This is the current working version of Predator-Prey
      (2) In the unpack() function, I am now using pCell = create_cell(get_cell_definition(temp_str),cell_ID); to create a cell AFTER I unpack the ID, position and the type of the cell. The 'type' is used by get_cell_definition(temp_str).
      (3) pCell = create_cell(get_cell_definition(temp_str),cell_ID); is needed in the unpack() function because we are using the same call in the setup_tissue() function of the custom.cpp in sample_projects/template.
      (4) For the heterogeneity-sample example there is a POSSIBILITY that it might not work with pCell = create_cell(get_cell_definition(temp_str),cell_ID); so replace the call in unpack() by a simple create_cell(ID,...) i.e. no need for get_cell_definition().
      (5) Now, the XML file is being written by a single MPI process i.e. root process - so this will work in parallel settings (just that only a single process will write the XML file)
      (6) The MATLAB file writing is parallelized now (Both for BioFVM MATLAB and PhysiCell MATLAB).
      (7) I have removed the statement pReference_live_phenotype = &phenotype; from unpack() function [as Paul Macklin says these pointers are set automatically].
      (8) To check correctness of Cell Transmission, one CELLS_RANK_X file is written per rank (this can be disabled by commenting out the print_cell() function from packing(), unpacking() functions.
      186a34bc
  8. 16 Dec, 2020 2 commits
    • gsaxena's avatar
      In function bool load_PhysiCell_config_file( std::string filename,... · 2834916d
      gsaxena authored
      In function bool load_PhysiCell_config_file( std::string filename, mpi_Environment &world ), only the root process was calling the setup_microenvironment_from_XML() function. This is wrong. All processes must call this function but only the root process should print the statements. This has been corrected on the development branch as well.
      2834916d
    • gsaxena's avatar
      Changes · 05b2d3d6
      gsaxena authored
      (1) In PhysiCell_settings.cpp, in function bool load_PhysiCell_config_file( std::string filename, mpi_Environment &world ), only the root process was calling the setup_microenvironemnt_from_XML() function. This was a mistake. All processes must call this function but only the root process should print the cout statements.
      (2) Added -g flag to template Makefile.
      (3) Changed script_project.sh
      05b2d3d6
  9. 15 Dec, 2020 2 commits
  10. 09 Dec, 2020 1 commit
  11. 04 Dec, 2020 1 commit
  12. 28 Nov, 2020 1 commit
  13. 17 Nov, 2020 1 commit
    • gsaxena's avatar
      Implemented $make reset functionality i.e. · 336810e9
      gsaxena authored
      Step 1 - Clone the repository
      Step 2 - Execute $make heterogeneity-sample to check out correct files into the main directories to prepare the parallel version of the heterogeneity 3D program
      Step 3 - $make to compile
      Step 4 - A copy of script_hetero.sh is present in the main directory for sample execution, hence $ sbatch script_hetero.sh
      Step 5 - After program runs ... $make clean to remove executable + .o files then
      Step 6 - $make reset to restore the initial state of PhysiCell.
      336810e9
  14. 09 Nov, 2020 1 commit
  15. 09 Oct, 2020 1 commit
    • gsaxena's avatar
      This commit contains (1) SVG parallelization - this functionality is fully... · 05fa8c2a
      gsaxena authored
      This commit contains (1) SVG parallelization - this functionality is fully parallelized but I have used the parallel SVG function for plotting the initial.svg and not the svg generation at other steps and the final step. Simply use the parallel SVG function for the intermediate SVG generation and final file generation. (2) As Migule informed that the .xml file was not present in the config folders - I have now removed *.xml from .gitignore and added output/*.xml in .gitignore to just ignore the XML files (and output/*.svg and output/*.mat files also) in the output directory. The XML, SVG and MAT files in other directories will be written. This commit is the major commit BEFORE i start resetting the project. In case of problems, fall back to this commit.
      05fa8c2a
  16. 31 Aug, 2020 1 commit
    • gsaxena's avatar
      A big commit that takes care of parallel velocity update. The various steps are: · ff7c84a2
      gsaxena authored
      1. Created 2 lists that contain the global mesh index of all the neighbouring voxels of all the sub-domain boundary voxels, called them moore_connected_voxel_global_indices_left/right.
      2. Packed some voxel-based, some cell-based (majorly geometry & mechanics) information to be exchanged.
      3. Exchanging the above information.
      4. Unpack the above information in a class named Moore_Voxel_Info which in addition to the Voxel information contains a Moore_Cell_Info class vector containg the packed information above. Further, associated the global mesh index with a Moore_Voxel_Info object using std::unordered_map<int,Moore_Voxel_Info> to reduce the time taken to search the Voxel+Cell Info associated with a global mesh index.Every boundary voxel stores its global voxel neighbours in the moore_list and this global mesh index becomes a key to search the correct Moore_Voxel_Indo object which stores the needed information.
      ff7c84a2
  17. 30 Jul, 2020 1 commit
    • gsaxena's avatar
      A big commit - Cell transmisison functionality is completed. · 4b4e3f46
      gsaxena authored
      (1) When cells divide, parent OR daughter or both maybe pushed out of the subdomain. I have added the functionality to bring them back to the sub-domain (as cell transmission is not implemented for movement during Cell DIVISION)
      (2) Since PhysiCell implements deletion of cells by exchanging the cell with the last cell in the "all_cells" list, in case both the current cell AND the last cell is to be deleted, this becomes a problems as the last cell comes into the position of the current cell and the loop counter is incremented ! So whenever we delete a cell, we can decrement the loop counter by 1 so that it again comes to examine the last cell which is in the current position. This solved the problem of cell deletion.
      4b4e3f46
  18. 10 Jul, 2020 1 commit
    • gsaxena's avatar
      We have now · f1610984
      gsaxena authored
      (a) Cell Packing
      (b) Cell sending/receving
      (c) Cell deletion from old subdomain
      (d) Cell creation in new subdomain
      (e) Need to now start with Unpacking ...
      f1610984
  19. 08 Jul, 2020 1 commit
    • gsaxena's avatar
      Very large commit, several functionalities/functions added: · f0bae207
      gsaxena authored
      Basically now we have (1) capabiity to detect if a cell leaves subdomain (2) Functionality to pack such cells using a single buffer i.e. one buffer contains data of all cells crossing the subdomain. (3) MPI_Isend and MPI_Irecv for sending and receiving this buffer in the other process. (4) The cell that is sent is then deleted from the process. (5) As of now the functionlality of unpacking is only dummy i.e. only unpacks the incoming cell ID to check if we are receiving the cell. The unpack facility will take a long time to write and then we have to consider the pointer fields.
      f0bae207
  20. 18 Jun, 2020 1 commit
  21. 13 May, 2020 2 commits
    • gsaxena's avatar
      First real commit while parallelizing update_all_cells · 062fb3c3
      gsaxena authored
      1. I am parallelizing divide() cells first.
      2. Each process knows how many cells in it will divide.
      3. When 'x' cells divide 'x' more cells are created.
      4. These new 'x' cells must have unique IDs.
      5. The root process has the duty of allocating unique IDs.
      6. These processes contact root process and request 'x' number of IDs.
      7. Root process knows which was the last ID used, and gives a range of continuous IDs to processes in sequence.
      8. Root process then increases the current ID to the last ID which was allocated.
      062fb3c3
    • gsaxena's avatar
      Switching to Development Branch · ee2974f6
      gsaxena authored
      1. The main.cpp has commented out the un-necessary XML, full data plotting. The SVG plots are working with individual ranks.
      2. This commit is exactly the same as the last commit on master branch except for commenting out in main.cpp (see above).
      3. This commit is the first commit BEFORE beginning parallelization of the update_all_cells function.
      ee2974f6
  22. 04 May, 2020 1 commit
    • gsaxena's avatar
      Integrating the parallel 3-D solver · 6899aeb4
      gsaxena authored
      (1) the main function calls simulate_diffusion_decay() function.
      (2) This function had a serial prototype which passed only the time dt.
      (3) Created a new prototype and version for this function which accepts mpi_Environment &world, mpi_Cartesian &cart_topo objects
      (4) simulate_diffusion_decay() then calls the parallel solver using a function pointer called diffusion_decay_solver - this is used at a lot of places and hence created another function pointer: diffusion_decay_solver_mpi that points to the new parallel solver 3-D function.
      (5) This new function pointer must be set at some places - have tried to check that is done at all places but can later again check.
      The program is compiling.
      6899aeb4
  23. 30 Apr, 2020 1 commit
    • gsaxena's avatar
      Phase 3 of setup_tissue() function · 3f6e6a1a
      gsaxena authored
      1. Wrote DistPhy_Collective.cpp & .h that contain pure collective MPI functions only.
      2. These functions are wrapped inside functions like distribute_global_sum() etc.
      3. Not sure if git is going to commit the two files that I wrote in DistPhy (so check)
      
      Program is compiling.
      3f6e6a1a
  24. 29 Apr, 2020 2 commits
    • gsaxena's avatar
      function: underlying_mesh.nearest_voxel_index( position); · 422b547e
      gsaxena authored
      (1) this function directly calls the mesh function
      (2) we want the nearest_voxel_local_index(position, world, cart_topo) function to be called instead of this.
      (3) replace call with underlying_mesh.nearest_voxel_local_index( position, world, cart_topo);
      since the underlying_mesh means the mechanical voxel mesh, it automatically provides particulars of that mesh.
      The program is compiling.
      422b547e
    • gsaxena's avatar
      setup_tissue() Phase 2 · 648fe13c
      gsaxena authored
      (1) parallelizing the call assign_position()
      (2) Now it takes 3 cooridnates and mpi_Environment, mpi_Cartesian objects
      (3) assign_position() is in PhysiCell_cell.cpp
      (4) this calls update_voxel(world, cart_topo)
      (5) update_voxel() is in BioFVM_basic_agent.cpp
      (6) this calls a new parallel function nearest_voxel_local_index()
      (7) this function is in BioFVM_microenvironment.cpp but actually
      (8) this calls a new function by the same name in BioFVM_cartesian_mesh.cpp
      (9) this is the file in which this function is implemented and returns the
      process specifc local voxel index which contains the basic agent.
      648fe13c
  25. 28 Apr, 2020 2 commits
    • gsaxena's avatar
      Merge branch 'master' of https://gitlab.bsc.es/gsaxena/physicell_x · 996548a6
      gsaxena authored
      Had updated the README  file onine so now needed to pull and then merge
      996548a6
    • gsaxena's avatar
      (1) First commit from India for PhysiCell_X · a1f97f84
      gsaxena authored
      (2)  Parallelizing setup_tissue() in heterogeneity.cpp - divided into 3 phases
      	(a) 1st Phase: Create new Cells or Basic Agents - done
       	(b) 2nd Phase: Assign positions to Cells - doing
      	(c) 3rd Phase: pCell->default[0], p_min, p_max data etc. --> global communications needed - To be done
      (3) Program is compiling AFTER 1st phase completed and BEFORE 2nd Phase begins.
      (4) A special syntax exists when calling Base class parametrized constructor from Derived class constructor.
      Cell::Cell(int p_ID):Basic_Agent(p_ID) is the correct syntax. We CANNOT say Basic_Agent(p_ID); inside body of the constructor of Cell(int p_ID){ }.
      a1f97f84
  26. 23 Apr, 2020 3 commits
  27. 21 Feb, 2020 1 commit
  28. 20 Feb, 2020 1 commit
    • Gaurav Saxena's avatar
      The last commit was before changing the setup_tissue() function. This · 0111bf17
      Gaurav Saxena authored
      commit is the first commit when I am changing the setup_tissue()
      function.
      I have written two new files in DistPhy framework: DistPhy_Utils.cpp and
      corresponding .h file. The class mpi_CellPositions function : void mpi_CellPositions::positions_to_rank_list(std::vector<std::vector<double>> &generated_list, int xmin, int xmax, int ymin, int ymax, int zmin, int zmax, int dx, int dy, int dz, mpi_Environment &world, mpi_Cartesian &cart_topo, int strt_cell_ID )
      takes as input a list of position coordinates in 3-D space and
      determines as to which MPI process rank would create the cell at that
      position. For each rank we have : cell_coords_all_procs[rank] list which
      contains all the coordinate positions.
      Then for each rank we have cell_IDs_all_procs[rank] which contains ID of
      the cells that that "rank" would be handling.
      We also have a count of the IDs in no_of_IDs_all_procs[rank] for a
      particular rank.
      Added a "static" variable called max_ID_in_parallel to the Basic_Agent
      class that can be accessed using get_max_ID_in_parallel() and
      set_max_ID_in_parallel(). Obtain this ID BEFORE creating positions for
      cells and set this ID AFTER creating the positions.
      0111bf17
  29. 12 Feb, 2020 1 commit
    • Gaurav Saxena's avatar
      Changing the section beginning with : · 69575048
      Gaurav Saxena authored
      Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
      in the main() function.
      Ultimately it calls the mesh.resize( ) function which takes care of
      domain partitioning w.r.t to the mechanical voxel size (=30). So there
      are two meshes (and most probably its the mechanical mesh that is being
      plotted along with cells. That is the reason why it produces a complete
      image of cells because *till now* cell data was not partitioned among
      processes. *Now* it should produce only a partial image (hopefully).
      Check through DDT if the right parallel version of functions are being
      called now starting with Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size, world, cart_topo );
      69575048
  30. 11 Feb, 2020 3 commits
    • Gaurav Saxena's avatar
      Added Dirichlet boundary conditions in initialize_Microenvironment() · 2ea4b3a5
      Gaurav Saxena authored
      function. Then it prints the microenvironment information but it calls a
      display_information function in BioFVM_Mesh.cpp which prints the number
      of voxels. NOW this number of voxels is the number of local voxels so I
      have added the word "per-process" over there ! Compiled sucessfully and
      ran (some output but very importantly no error).
      2ea4b3a5
    • Gaurav Saxena's avatar
      Very minor change from last commit. I wasn't calling the parallel · afea1cb2
      Gaurav Saxena authored
      versions of functions from initialize_microenvironment(). Now calling
      parallel versions of functions - compiling successfully.
      *can also revert back to this version without problems
      *now need to check Dirichlet conditions setting and then
      *integrate the solver code.
      afea1cb2
    • Gaurav Saxena's avatar
      Please enter the commit message for your changes. Lines starting · 2d9bc924
      Gaurav Saxena authored
      Integrated code for function: void
      Cartesian::resize(x1,x2,y1,y2,z1,z2,dx,dy,dz,world,cart_topo) where
      domain partitioning takes place. Adjacency lists of voxels in all three
      directions are also made here. Compiled sucessfully but I have not run
      it as data should now be on different processes and without the partial
      parallel solver, there is not much point in executing it. Now next step
      will be to go up the stack to the outer functions which take care of
      dirichlet conditions. In the stand-alone version of BioFVM, the
      dirichlet conditions were not set correctly for 3-D but in this BioFVM
      version integrated with PhysiCell V1.1.6, they should be ok (but still
      check if Dirichlet conditions being set properly).
      2d9bc924
  31. 10 Feb, 2020 1 commit