1. 19 May, 2022 1 commit
  2. 18 May, 2022 14 commits
  3. 09 May, 2022 4 commits
  4. 31 Mar, 2022 4 commits
  5. 18 Mar, 2022 1 commit
  6. 16 Mar, 2022 2 commits
  7. 15 Mar, 2022 3 commits
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 20 Jan, 2022 1 commit
  15. 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
  16. 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
  17. 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