Fix upcxx

CMakeLists.txt

@@ -1,16 +1,16 @@
 # The name of our project is "MHMxx". CMakeLists files in this project can
-# refer to the root source directory of the project as ${SIMCOV_SOURCE_DIR} and
-# to the root binary directory of the project as ${SIMCOV_BINARY_DIR}
+# refer to the root source directory of the project as ${SIMFORAGER_SOURCE_DIR} and
+# to the root binary directory of the project as ${SIMFORAGER_BINARY_DIR}
 cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
-project(SimCov)
+project(SimForager)
 #----------------------------------------------------------------------------------------#
 #   project specification
 #----------------------------------------------------------------------------------------#
-file(STRINGS ${CMAKE_CURRENT_SOURCE_DIR}/VERSION SIMCOV_BASE_VERSION)
+file(STRINGS ${CMAKE_CURRENT_SOURCE_DIR}/VERSION SIMFORAGER_BASE_VERSION)
 
 # use PROJECT_SOURCE_DIR, not CMAKE_SOURCE_DIR
-set(SIMCOV_SOURCE_DIR ${PROJECT_SOURCE_DIR})
-set(SIMCOV_BINARY_DIR ${PROJECT_BINARY_DIR})
+set(SIMFORAGER_SOURCE_DIR ${PROJECT_SOURCE_DIR})
+set(SIMFORAGER_BINARY_DIR ${PROJECT_BINARY_DIR})
 
 # include modules
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake/Modules)
@@ -55,7 +55,7 @@ CHECK_SUBMODULES(upcxx-utils)
 
 # set version
 include_directories(include)
-GET_GIT_VERSION(SIMCOV)
+GET_GIT_VERSION(SIMFORAGER)
 
 # add upcxx-utils
 if (DEFINED ENV{UPCXX_UTILS_DIR} AND EXISTS $ENV{UPCXX_UTILS_DIR})

README.md

@@ -1,3 +1,5 @@
+simforager is a forked adaptation of:
+
 simcov Copyright (c) 2021, The Regents of the University of California,
 through Lawrence Berkeley National Laboratory (subject to receipt of
 any required approvals from the U.S. Dept. of Energy), Arizona State
@@ -14,17 +16,17 @@ its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the
 Software to reproduce, distribute copies to the public, prepare derivative 
 works, and perform publicly and display publicly, and to permit others to do so.
 
-# SimCov #
+# SimForager #
 
-This is a model for simulating the response of the immune system to infections in the lungs.
+This is a model for simulating large amounts of [currently homogeneous] foragers.
 
 ## Installing and building
 
 It requires [UPC++](https://bitbucket.org/berkeleylab/upcxx/wiki/Home), C++ and cmake.
 
 This repo contains a submodule, so to install, it's best to run
 
-`git clone --recurse-submodules [email protected]:AdaptiveComputationLab/simcov.git`
+`git clone --recurse-submodules [email protected]:cswritlarge/simforager.git`
 
 to fully initialize the submodules.
 
@@ -38,22 +40,21 @@ or
 
 The executable will be installed in
 
-`<simcov-repo-directory>/install/bin`
+`<simforager-repo-directory>/install/bin`
 
 ## Running
 
 To run, execute
 
-`upcxx-run -n <number_processes> -N <number_nodes> -- simcov`
+`upcxx-run -n <number_processes> -N <number_nodes> -- simforager`
 
 To see the parameters available, run with `-h`.
 
-It will create an output directory, which will contain a detailed log file (`simcov.log`). It will also create a file containing
-all the configuration parameters (`simcov.config`).
+It will create an output directory, which will contain a detailed log file (`simforager.log`). It will also create a file containing all the configuration parameters (`simforager.config`).
 
 A run can also be executed with a config file as
 
-`upcxx-run -n <number_processes> -N <number_nodes> -- simcov --config <config_file>`
+`upcxx-run -n <number_processes> -N <number_nodes> -- simforager --config <config_file>`
 
 The config file consists of a list of all the command line options as key-value pairs, with semi-colons denoting comments.
 For example:

build_hopper.sh

@@ -9,8 +9,8 @@ module load cmake/3.11.4-qkyj
 module load openmpi/4.1.3-j6zb
 module load upcxx/2020.10.0-6eh2
 
-if [ -n "$SIMCOV_BUILD_ENV" ]; then
-    source $SIMCOV_BUILD_ENV
+if [ -n "$SIMFORAGER_BUILD_ENV" ]; then
+    source $SIMFORAGER_BUILD_ENV
 fi
 
 upcxx_exec=`which upcxx`
@@ -32,11 +32,11 @@ SECONDS=0
 
 rootdir=`pwd`
 
-INSTALL_PATH=${SIMCOV_INSTALL_PATH:=$rootdir/install}
+INSTALL_PATH=${SIMFORAGER_INSTALL_PATH:=$rootdir/install}
 
 echo "Installing to $INSTALL_PATH"
 
-rm -rf $INSTALL_PATH/bin/simcov
+rm -rf $INSTALL_PATH/bin/simforager
 
 if [ "$1" == "clean" ]; then
     rm -rf .build

configs/figure-7/simcov.config

@@ -92,7 +92,7 @@
   output =                      results
 
 ; Directory containing files for lung model
-  lung-model =                  /users/projects/simcov/lungmodel/lung_model_data
+  lung-model =                  /users/projects/simforager/lungmodel/lung_model_data
 
 ; Show progress
   progress =                    true

include/options.hpp

@@ -94,10 +94,10 @@ class Options {
 
   void setup_log_file() {
     if (!upcxx::rank_me()) {
-      string log_fname = output_dir + "/simcov.log";
+      string log_fname = output_dir + "/simforager.log";
       // check to see if simcov.log exists. If so, rename it
       if (file_exists(log_fname)) {
-        string new_log_fname = output_dir + "/simcov-" + get_current_time(true) + ".log";
+        string new_log_fname = output_dir + "/simforager-" + get_current_time(true) + ".log";
         cerr << KLRED << "WARNING: " << KNORM << log_fname << " exists. Renaming to "
              << new_log_fname << endl;
         if (rename(log_fname.c_str(), new_log_fname.c_str()) == -1)
@@ -109,7 +109,7 @@ class Options {
 
   void set_random_infections(int num) {
     for (int i = 0; i < num; i++) {
-      if (i % rank_n() != rank_me()) continue;
+      if (i % upcxx::rank_n() != upcxx::rank_me()) continue;
       infection_coords.push_back(
           {_rnd_gen->get(dimensions[0] * 0.1, dimensions[0] * 0.9),
            _rnd_gen->get(dimensions[1] * 0.1, dimensions[1] * 0.9),
@@ -123,7 +123,7 @@ class Options {
     vector<array<int, 3>> infections =
         get_uniform_infections(num, dimensions[0], dimensions[1], dimensions[2]);
     for (int i = 0; i < infections.size(); i++) {
-      if (i % rank_n() != rank_me()) continue;
+      if (i % upcxx::rank_n() != upcxx::rank_me()) continue;
       infection_coords.push_back({infections[i][0], infections[i][1], infections[i][2], 0});
     }
   }
@@ -197,7 +197,7 @@ class Options {
       }
     }
     for (int i = 0; i < coords_strs.size(); i++) {
-      if (i % rank_n() != rank_me()) continue;
+      if (i % upcxx::rank_n() != upcxx::rank_me()) continue;
       auto coords_and_time = splitter(",", coords_strs[i]);
       if (coords_and_time.size() == 4) {
         try {
@@ -255,7 +255,8 @@ class Options {
   int tcell_initial_delay = 10080;
   int tcell_vascular_period = 5760;
   int tcell_tissue_period = 1440;
-  int tcell_binding_period = 10;
+  // int tcell_binding_period = 10;
+  double tcell_binding_period = 10;
   double max_binding_prob = 1.0;
 
   double infectivity = 0.02;
@@ -274,7 +275,7 @@ class Options {
   int antibody_period = 5760;
 
   unsigned rnd_seed = std::chrono::high_resolution_clock::now().time_since_epoch().count();
-  string output_dir = "simcov-results-n" + to_string(upcxx::rank_n()) + "-N" +
+  string output_dir = "simforager-results-n" + to_string(upcxx::rank_n()) + "-N" +
                       to_string(upcxx::rank_n() / upcxx::local_team().rank_n());
   int sample_period = 0;
   int sample_resolution = 1;
@@ -287,8 +288,8 @@ class Options {
 
   bool load(int argc, char **argv) {
     // SIMCOV version v0.1-a0decc6-master (Release) built on 2020-04-08T22:15:40 with g++
-    string full_version_str = "SimCov version " + string(SIMCOV_VERSION) + "-" +
-                              string(SIMCOV_BRANCH) + " built on " + string(SIMCOV_BUILD_DATE);
+    string full_version_str = "SimForager version " + string(SIMFORAGER_VERSION) + "-" +
+                              string(SIMFORAGER_BRANCH) + " built on " + string(SIMFORAGER_BUILD_DATE);
     vector<string> infection_coords_strs;
 
     CLI::App app(full_version_str);
@@ -419,15 +420,15 @@ class Options {
 
     upcxx::barrier();
 
-    _rnd_gen = make_shared<Random>(rnd_seed + rank_me());
+    _rnd_gen = make_shared<Random>(rnd_seed + upcxx::rank_me());
 
     if (!lung_model_dir.empty()) {
       auto model_dims = get_model_dims(lung_model_dir + "/alveolus.dat");
       if (model_dims.size() < 3) return false;
       for (int i = 0; i < 3; i++) {
         if (model_dims[i] != dimensions[i]) {
           dimensions = model_dims;
-          if (!rank_me())
+          if (!upcxx::rank_me())
             cerr << KLRED << "WARNING: " << KNORM
                  << "Setting dimensions to model data: " << dimensions[0] << ", " << dimensions[1]
                  << ", " << dimensions[2] << endl;
@@ -437,7 +438,7 @@ class Options {
     }
 
     if (virion_clearance_rate * antibody_factor > 1.0) {
-      if (!rank_me())
+      if (!upcxx::rank_me())
         cerr << "Invalid parameter settings: virion-clearance * antibody_factor > 1.\n"
              << "Reduce either or both of those settings\n";
       return false;
@@ -453,28 +454,28 @@ class Options {
 
     if (dimensions[0] % sample_resolution || dimensions[1] % sample_resolution ||
         (dimensions[2] > 1 && dimensions[2] % sample_resolution)) {
-      if (!rank_me())
+      if (!upcxx::rank_me())
         cerr << "Error: sample period " << sample_resolution
              << " must be a factor of all the dimensions\n";
       return false;
     }
 
     for (int i = 0; i < 3; i++) {
       if (dimensions[i] > whole_lung_dims[i]) {
-        if (!rank_me()) cerr << "Dimensions must be <= whole lung dimensions\n";
+        if (!upcxx::rank_me()) cerr << "Dimensions must be <= whole lung dimensions\n";
         return false;
       }
     }
     setup_output_dir();
     setup_log_file();
 
-    init_logger(output_dir + "/simcov.log", verbose);
+    init_logger(output_dir + "/simforager.log", verbose);
 
 #ifdef DEBUG
     open_dbg("debug");
 #endif
 
-    SLOG(KLBLUE, "SimCov version ", full_version_str, KNORM, "\n");
+    SLOG(KLBLUE, "SimForager version ", full_version_str, KNORM, "\n");
 
     if (upcxx::rank_me() == 0) {
       // print out all compiler definitions
@@ -498,7 +499,7 @@ class Options {
 #endif
     if (!upcxx::rank_me()) {
       // write out configuration file for restarts
-      ofstream ofs(output_dir + "/simcov.config");
+      ofstream ofs(output_dir + "/simforager.config");
       ofs << app.config_to_str(true, true);
     }
     upcxx::barrier();

include/version.h

@@ -4,10 +4,10 @@
 extern "C" {
 #endif
 
-extern const char *SIMCOV_VERSION;
-extern const char *SIMCOV_VERSION_DATE;
-extern const char *SIMCOV_BUILD_DATE;
-extern const char *SIMCOV_BRANCH;
+extern const char *SIMFORAGER_VERSION;
+extern const char *SIMFORAGER_VERSION_DATE;
+extern const char *SIMFORAGER_BUILD_DATE;
+extern const char *SIMFORAGER_BRANCH;
 
 #define MAX_BUILD_KMER_STR "Maximum kmer len=MAX_BUILD_KMER"
 

simforager_null.config

@@ -0,0 +1,119 @@
+; These are version 1.0 test of 'null' forager parameters for SIMCoV
+; This means a parameter-based translation of SIMCoV into SIMForager without yet
+; changing anything about the existing SIMCoV code base
+
+; Dimensions: x y z (assuming grid spacing of 5 microns)
+dim =                         500 500 1
+; >> resulting in 225000000 total environment (epithelial) cells
+
+; Whole lung dimensions: x y z (assuming grid spacing of 5 microns)
+whole-lung-dim =              500 500 1
+
+; Number of timesteps (assuming 1 min per timestep)
+; Set to arbitrary small number to start
+timesteps =                   14400
+; >> ten days
+
+; Location of initial infections (omit for no infections); can be:
+;  list of space-separated coords x,y,z,timestep
+;  uniform:N (where N is an int, for N uniformly distributed starting points at time 0)
+;  random:N (where N is an int, for N randomly distributed starting points at time 0)
+infection-coords =            uniform:22500
+; >> this is .001% of total grid cells
+
+; Number of virions at initial infection locations
+; Chosen to guarantee that at least one cell is infected at the start - see infectivity
+initial-infection =           1
+; >> initially 1000 combined with number of initial infection sites, this should yield a 1:100 ratio of grid cells to algae cells
+
+; Average number of time steps to expressing virions after cell is infected
+incubation-period =           0
+
+; Average number of time steps to death after apoptosis is induced
+apoptosis-period =            3
+
+; Average number of time steps to death after a cell starts expresssing
+expressing-period =           1000000
+
+; Factor multiplied by number of virions to determine probability of infection
+infectivity =                 0.5
+; SIMCoV paper default
+
+; Multiplier reducing infectivity where inflammatory signal is present
+; (the multiplier reducing infectivity should be between 0.9 and 0.7 based on values
+; in literature demonstrating a reduction of cell death in vitro with IFN)
+infectivity-multiplier =      1.0
+; >> irrelevant
+
+; Number of virions produced by expressing cell each time step
+virion-production =           1.1
+; this is SIMCoV default we're going with for now...
+
+; Multiplier reducing virion production rate where inflammatory signal is present
+; (the reduction should be represented by a multiplier betweeon 0.05 and 0.15)
+virion-production-multiplier = 1.0
+
+; Fraction by which virion count drops each time step
+virion-clearance =            0.0
+; >> effectively algae death rate; not considered here
+
+; Fraction of virions that diffuse into all neighbors each time step
+virion-diffusion =            0.0
+
+; Amount of chemokine produced by expressing cells each time step
+chemokine-production =        0.0
+
+; Amount by which chemokine concentration drops each time step
+chemokine-decay =             0.0
+
+; Fraction of chemokine concentration that diffuses into all neighbors each time step
+chemokine-diffusion =         1.0
+
+; Minimum chemokine concentration that triggers a T cell
+min-chemokine =               0.0
+; >> this should allow fish (T-cells) to be present at start
+
+; Impact of antibodies; multiplier for virion decay (setting to 1 means this has no effect)
+antibody-factor =             1
+
+; Number of time steps before antibodies start to be produced
+antibody-period =             1000000
+; >> WHAT!? NOBODY INVITED ANTIBODIES TO A REEF
+
+; Number of tcells generated at each timestep for the whole lung
+; This is scaled up 5000x from the mouse model (20 per minute)
+tcell-generation-rate =       100
+; >> for a stable population of fish (T-cells) throughout sim
+
+; Number of time steps before T cells start to be produced
+tcell-initial-delay =         0
+
+; Average number of time steps to death for a T cell in the vasculature
+tcell-vascular-period =       2
+
+; Average number of time steps to death after a T cell extravasates
+tcell-tissue-period =         1000000
+
+; Number of time steps a T cell is bound to an epithelial cell when inducing apoptosis
+tcell-binding-period =        2
+
+; Max probability of a T cell binding to an infected cell in one time step
+max-binding-prob =            1
+
+; T cells in tissue follow the chemokine gradient
+tcells-follow-gradient =      false
+
+; Random seed
+seed =                        29
+
+; Number of timesteps between samples (set to 0 to disable sampling)
+sample-period =               5
+
+; Resolution for sampling
+sample-resolution =           1
+
+; Max. block dimension - larger means more locality but worse load balance. Set to 0 for largest possible.
+max-block-dim =               10
+
+; Output directory (automatically generated)
+;  output =                   results