1. 18 May, 2022 9 commits
  2. 09 May, 2022 4 commits
  3. 31 Mar, 2022 4 commits
  4. 18 Mar, 2022 1 commit
  5. 16 Mar, 2022 2 commits
  6. 15 Mar, 2022 3 commits
  7. 14 Mar, 2022 1 commit
    • gsaxena's avatar
      Cleaned the heterogeneity MPI example files. While compiling it gave an error... · d812f83d
      gsaxena authored
      Cleaned the heterogeneity MPI example files. While compiling it gave an error due to custom.h file included in PhysiCell_cell.cpp (don't know why it was there) but it was written that it should be deleted later, so have deleted, now compiles successfully and runs.
      Changed the name of script_hetero.sh to script_hetero_mpi.sh and re-wrote and organized the source code within it.
      d812f83d
  8. 13 Mar, 2022 2 commits
    • gsaxena's avatar
      Changed the project name of template to pred-prey-mpi, changed its directory... · 4ce02d06
      gsaxena authored
      Changed the project name of template to pred-prey-mpi, changed its directory name to pred_prey_mpi in sample_projects, made changes to sample_projects Makefile-default and in top-level directory Makefiles to reflect this. Did same for heterogeneity-sample --> heterogeneity-sample-mpi, heterogeneity_mpi directory, made changes to Makefile.
      4ce02d06
    • gsaxena's avatar
      A very small commit, moved the unwanted files outisde top level directory and... · e059aedb
      gsaxena authored
      A very small commit, moved the unwanted files outisde top level directory and into PhysiCell_X_Extra_Files - most probably they will not be needed but still keeping them. It was part of clean-up. Changed the vrsion to 1.9.0 in VERSION.txt, have not changed CITATATION.txt
      e059aedb
  9. 11 Mar, 2022 1 commit
    • gsaxena's avatar
      This commit takes care of "multiple printing" problem · 479ed9f1
      gsaxena authored
      (1) Parallel versions of 3 functions in PhysiCell_settings.cpp were written ONLY to control std::cout using IOProcessor(world)
      (2) display_simulation_status(...) in PhysiCell_various_outputs.cpp has now a parallel version which controls printing using IOProcessor(world) but we needed an MPI_Reduce() to calculate the total number of cells i.e. MPI_SUM on root process.
      (3) Improved a small printing in DistPhy_Utils.cpp - the initial number of cells in each process.
      (4) Now calling the display_simulation_status(std::cout, world, cart_topo) in the main.cpp of TNF example.
      (5) Commented out a "Processing default ..." std::cout in initialize_cell_definitions_from_pugixml(...) in PhysiCell_cell.cpp.
      479ed9f1
  10. 10 Mar, 2022 1 commit
    • gsaxena's avatar
      (1) Cleaned up TNF MPI example · ce105e26
      gsaxena authored
      (2) Have NOT touched any function in any core file - need to address functions like display_simulation_status() so that printing is done only by a single process.
      (3) When printing from within any custom function, have put a note that multiple processes will print, to prevent make another custom function which uses the "world" object to control printing.
      ce105e26
  11. 09 Mar, 2022 1 commit
    • gsaxena's avatar
      Merge branch 'development' of https://gitlab.bsc.es/gsaxena/physicell_x into development · e9af88d5
      gsaxena authored
      This commit is after a merge with Arnau's commit, he had added some files, saved some old files with _orig suffix, there was a merge conflict in the PhysiCell_settings.xml of the TNF example - most probably ONLY because of white spaces, decided to keep Arnau's version but saved my version in PhysiCell_settings_GS.xml just to be sure.
      e9af88d5
  12. 07 Mar, 2022 1 commit
    • gsaxena's avatar
      Two main features: · 9e4147c3
      gsaxena authored
      1. Code does not crash now in Matlab file writing when there are no cells in a sub-domain (earlier it was crashing because we dereference the *all_cells array
      in Matlab file writing even when there are no cells - so obviously it crashes).
      2. Program displays a m,essage that the total number of voxels in the X-direction are NOT EXACTLY divisible by the total number of MPI processes and it aborts.
      9e4147c3
  13. 20 Jan, 2022 1 commit
  14. 03 Dec, 2021 1 commit
    • gsaxena's avatar
      Large commit in the sense that PhysiBoss TNF MPI example is working now : · 7d507970
      gsaxena authored
      (1) Multiple problems were there - wrong configuration file (bug chasing for 1.5 months)
      (2) Corner case where cell crosses sub-domain AND cell goes out of domain case was not accounted for in update_position() function.
      (3) In Miguel's function added : if (pCell->is_out_of_domain) ... in one of his files where he's accessing an index.
      7d507970
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 16 Dec, 2020 1 commit
    • 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