Final Orchestrator Release (#31)

* Final recalibration * Log more info to stdout, useful for working out suspiciously short runtimes * BugFix: Cellularity array order was different to that used by the orchestrator * BugFix: Incorrect value copy paste error in Primage output * Total cell count is now conserved between successive loops and SC migration * Add 'cell_count' to input and output files. * If all cells die, volume ratio updated is now reported as -1.0, allowing the orchestrator to detect and rewrite to median or similar * Add support for a calibration file referenced by the input file, to allow recalibration without recompiling the model * Set model to only build with final supported version of FLAMEGPU (pre-reference change). * Add default calibration file and update example input file to include new members. --------- Co-authored-by: Robert Chisholm <[email protected]> Co-authored-by: Kenneth Y. Wertheim <[email protected]>
primagesheffield · May 1, 2023 · 9b6b501 · 9b6b501
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -10,7 +10,7 @@ option(VISUALISATION "Enable visualisation support" OFF)
 
 # Optionaly set the version of flamegpu which should be used.
 # Use a branch name such as `master`, or a tagged version such as `v2.0.0-alpha` 
-set(FLAMEGPU_VERSION "master" CACHE STRING "Git branch or tag to use")
+set(FLAMEGPU_VERSION "797d09a00f591e88e67f34647f662f180c97c4c5" CACHE STRING "Git branch or tag to use")
 
 # Our core dependency is FLAMEGPU2 lib, first lets find it
 include(${CMAKE_CURRENT_LIST_DIR}/cmake/flamegpu2.cmake)
@@ -60,6 +60,7 @@ SET(ORCHESTRATOR_SRC
     ${CMAKE_CURRENT_SOURCE_DIR}/orchestrator_src/main.cu
     ${CMAKE_CURRENT_SOURCE_DIR}/orchestrator_src/json.h
     ${CMAKE_CURRENT_SOURCE_DIR}/orchestrator_src/json_in.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/orchestrator_src/json_in2.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/orchestrator_src/json_out.cpp
 )
 add_flamegpu_executable(${PROJECT_NAME} "${ORCHESTRATOR_SRC}" "${FLAMEGPU_ROOT}" "${PROJECT_BINARY_DIR}" TRUE)  

diff --git a/README.md b/README.md
@@ -1,5 +1,9 @@
 # PRIMAGE USFD Agent Based Neuroblastoma model
 
+This (branch of the) repository holds the final version of the USFD agent based neuroblastoma model used as part of the multi-scale model during the Primage project.
+
+The below details in the README correspond to building and running the model on the PLGrid clusters Prometheus & Ares, they can be used as an example for using the model on other systems.
+
 ## Prerequisites
 
 The dependencies below are required for building the project, it's advised to that you use the newest version of any dependencies.
@@ -27,14 +31,13 @@ The build scripts will create `build_output.out` and `build_error.err`, containi
 
 On success, you should find the USFD orchestrator model exists at `build/bin/Release/orchestrator_FGPUNB`.
 
-*Note: Currently this branch is not pinned to a particular release of FLAMEGPU2, instead it follows origin/master, rebuilds may therefore update FLAMEGPU2.*
-
 ## Running
 
 This branch of the repository contains test run scripts setup for PLGrid's Prometheus & Ares clusters. These simply pass an input file to the model, to ensure it executes to completion and outputs a correctly formatted output file (no validation of the contents of the output file is carried out).
 These jobs can be submitted from the root of the repository using `sbatch scripts/test_run_on_prometheus.sh` or `sbatch scripts/test_run_on_ares.sh`.
 
 
+
 *Note: Prometheus has multiple partitions with GPUs `plgrid-gpu` and `plgrid-gpu-v100`. The prior has K80 GPUs, these are older, hence less demand in the job queue but will execute the model more slowly than the latter which has V100s.*
 
 

diff --git a/cmake/flamegpu2.cmake b/cmake/flamegpu2.cmake
@@ -17,7 +17,7 @@ FetchContent_Declare(
     flamegpu2
     GIT_REPOSITORY ${FLAMEGPU_REPOSITORY}
     GIT_TAG        ${FLAMEGPU_VERSION}
-    GIT_SHALLOW    1
+    GIT_SHALLOW    0
     GIT_PROGRESS   ON
     # UPDATE_DISCONNECTED   ON
 )

diff --git a/inputs/calibration_file_defaults.json b/inputs/calibration_file_defaults.json
@@ -0,0 +1,25 @@
+{  
+  "MYCN_fn11": 0.331407994,
+  "MAPK_RAS_fn11": 0.985655010,
+  "MAPK_RAS_fn01": 0.869527996,
+  "p53_fn": 0.277200997,
+  "p73_fn": 0.974862993,
+  "HIF_fn": 0.606737018,
+  "P_cycle_nb": 0.0456999987,
+  "P_cycle_sc": 0.0324999988,
+  "P_DNA_damageHypo": 0.772947669,	
+  "P_DNA_damagerp": 0.771497011,
+  "P_unrepDNAHypo": 0.434578806,
+  "P_unrepDNArp": 0.890953064,
+  "P_necroIS": 0.576758385,
+  "P_telorp": 0.0889538229,
+  "P_apopChemo": 0.321999997,
+  "P_DNA_damage_pathways": 0.128000006,
+  "P_apoprp": 0.0299999993,
+  "P_necrorp": 0.989708543,
+  "scpro_jux": 0.00374000007,
+  "nbdiff_jux": 0.000521000009,
+  "nbdiff_amount": 0.00999999978,
+  "nbapop_jux": 0.0304000005,
+  "mig_sc": 1.0
+}   
diff --git a/inputs/in-2022-03-29.json b/inputs/in-2022-03-29.json
@@ -1,8 +1,8 @@
 {
     "version": [
-        0,
         13,
-        5,
+        9,
+        4,
         false
     ],
     "config": {
@@ -21,6 +21,7 @@
                 0.0,
                 0.0
             ],
+            "cell_count": 10000,
             "orchestrator_time": 330,
             "MYCN_amp": 0,
             "ALT": 1,
@@ -54,7 +55,8 @@
             ],
             "end_effects": [
                 500
-            ]
+            ],
+            "calibration_file": ""
         }
     }
 }
diff --git a/inputs/input-12189.json b/inputs/input-12189.json
@@ -0,0 +1,60 @@
+{
+    "version": [
+        0,
+        13,
+        5,
+        false
+    ],
+    "config": {
+        "seed": 159874,
+        "steps": 336,
+        "environment": {
+            "TERT_rarngm": 0,
+            "ATRX_inact": 1,
+            "V_tumour": 56.6454,
+            "O2": 0.196332,
+            "cellularity": [
+                0.801527,
+                0.0,
+                0.0,
+                0.0,
+                0.0,
+                0.0
+            ],
+            "orchestrator_time": 0,
+            "MYCN_amp": 0,
+            "ALT": 1,
+            "ALK": 0,
+            "gradiff": 2,
+            "histology_init": 1,
+            "nb_telomere_length_mean": 0.689640367292204,
+            "nb_telomere_length_sd": 0.5668899997459869,
+            "sc_telomere_length_mean": 0.13732375975054112,
+            "sc_telomere_length_sd": 0.6576777896565319,
+            "extent_of_differentiation_mean": 0.6487574240246723,
+            "extent_of_differentiation_sd": 0.3838661929325988,
+            "nb_necro_signal_mean": 0.06979167333320091,
+            "nb_necro_signal_sd": 0.7408911462060256,
+            "nb_apop_signal_mean": 0.8676175678984845,
+            "nb_apop_signal_sd": 0.36152898092366537,
+            "sc_necro_signal_mean": 0.31127050615003315,
+            "sc_necro_signal_sd": 0.4759879354607127,
+            "sc_apop_signal_mean": 0.692646213345152,
+            "sc_apop_signal_sd": 0.8873088104156299,
+            "drug_effects": [
+                1.0,
+                1.0,
+                0.0,
+                1.0,
+                1.0,
+                0.0
+            ],
+            "start_effects": [
+                0
+            ],
+            "end_effects": [
+                144
+            ]
+        }
+    }
+}
diff --git a/inputs/input-29345.json b/inputs/input-29345.json
@@ -0,0 +1,60 @@
+{
+    "version": [
+        0,
+        13,
+        5,
+        false
+    ],
+    "config": {
+        "seed": 159874,
+        "steps": 336,
+        "environment": {
+            "TERT_rarngm": 0,
+            "ATRX_inact": 1,
+            "V_tumour": 47.2763,
+            "O2": 0.101143,
+            "cellularity": [
+                0.520755,
+                0.0,
+                0.0,
+                0.0,
+                0.0,
+                0.0
+            ],
+            "orchestrator_time": 0,
+            "MYCN_amp": 0,
+            "ALT": 1,
+            "ALK": 0,
+            "gradiff": 2,
+            "histology_init": 1,
+            "nb_telomere_length_mean": 0.9021318968637942,
+            "nb_telomere_length_sd": 0.17775158207569786,
+            "sc_telomere_length_mean": 0.6158719797064297,
+            "sc_telomere_length_sd": 0.6507731073172595,
+            "extent_of_differentiation_mean": 0.33207845241342926,
+            "extent_of_differentiation_sd": 0.8373088867985428,
+            "nb_necro_signal_mean": 0.993494931515239,
+            "nb_necro_signal_sd": 0.3311372635053851,
+            "nb_apop_signal_mean": 0.7046652382721265,
+            "nb_apop_signal_sd": 0.28933099187390277,
+            "sc_necro_signal_mean": 0.5273791283879947,
+            "sc_necro_signal_sd": 0.6110109436337471,
+            "sc_apop_signal_mean": 0.5423604545624877,
+            "sc_apop_signal_sd": 0.4031060795348913,
+            "drug_effects": [
+                1.0,
+                1.0,
+                0.0,
+                1.0,
+                1.0,
+                0.0
+            ],
+            "start_effects": [
+                0
+            ],
+            "end_effects": [
+                144
+            ]
+        }
+    }
+}
diff --git a/inputs/input-33153.json b/inputs/input-33153.json
@@ -0,0 +1,60 @@
+{
+    "version": [
+        0,
+        13,
+        5,
+        false
+    ],
+    "config": {
+        "seed": 159874,
+        "steps": 336,
+        "environment": {
+            "TERT_rarngm": 0,
+            "ATRX_inact": 1,
+            "V_tumour": 49.4454,
+            "O2": 0.050647,
+            "cellularity": [
+                0.679245,
+                0.0,
+                0.0,
+                0.0,
+                0.0,
+                0.0
+            ],
+            "orchestrator_time": 0,
+            "MYCN_amp": 0,
+            "ALT": 1,
+            "ALK": 0,
+            "gradiff": 2,
+            "histology_init": 1,
+            "nb_telomere_length_mean": 0.9450928564263522,
+            "nb_telomere_length_sd": 0.4135180702405279,
+            "sc_telomere_length_mean": 0.7676743235511849,
+            "sc_telomere_length_sd": 0.8105162820722294,
+            "extent_of_differentiation_mean": 0.06622753275671711,
+            "extent_of_differentiation_sd": 0.07410312149966991,
+            "nb_necro_signal_mean": 0.7188138629491703,
+            "nb_necro_signal_sd": 0.8258744532253351,
+            "nb_apop_signal_mean": 0.39053580923508646,
+            "nb_apop_signal_sd": 0.3392658990752594,
+            "sc_necro_signal_mean": 0.457098053112971,
+            "sc_necro_signal_sd": 0.6052112757966235,
+            "sc_apop_signal_mean": 0.5049731645560103,
+            "sc_apop_signal_sd": 0.6729357465573265,
+            "drug_effects": [
+                1.0,
+                1.0,
+                0.0,
+                1.0,
+                1.0,
+                0.0
+            ],
+            "start_effects": [
+                0
+            ],
+            "end_effects": [
+                144
+            ]
+        }
+    }
+}
diff --git a/inputs/out-29345.json b/inputs/out-29345.json
@@ -0,0 +1,41 @@
+{
+	"version": [
+		13,
+		9,
+		0,
+		false
+	],
+	"primage": {
+		"delta_O2": -0.00001790374517440796,
+		"O2": 0.10112509876489639,
+		"delta_ecm": 8.940696716308594e-8,
+		"ecm": 0.4792450964450836,
+		"material_properties": 0.0,
+		"diffusion_coefficient": 0.0,
+		"total_volume_ratio_updated": 1.102641224861145,
+		"cellularity": [
+			0.5205476880073547,
+			0.00012631146819330752,
+			0.00008094377699308097,
+			0.0,
+			0.0,
+			0.0
+		],
+		"tumour_volume": 35.80100631713867,
+		"ratio_VEGF_NB_SC": 0.0,
+		"nb_telomere_length_mean": 59.987728118896487,
+		"nb_telomere_length_sd": 0.11036907136440277,
+		"sc_telomere_length_mean": 0.0,
+		"sc_telomere_length_sd": 0.0,
+		"nb_necro_signal_mean": 1.4003527164459229,
+		"nb_necro_signal_sd": 2.0080089569091799,
+		"nb_apop_signal_mean": 0.04674074798822403,
+		"nb_apop_signal_sd": 0.22509713470935822,
+		"sc_necro_signal_mean": 0.0,
+		"sc_necro_signal_sd": 0.0,
+		"sc_apop_signal_mean": 0.0,
+		"sc_apop_signal_sd": 0.0,
+		"extent_of_differentiation_mean": 0.5021679401397705,
+		"extent_of_differentiation_sd": 0.17360052466392518
+	}
+}
diff --git a/orchestrator_src/json.h b/orchestrator_src/json.h
@@ -6,6 +6,7 @@
 #include "structures.h"
 
 OrchestratorInput readOrchestratorInput(const std::string& inputFile);
+CalibrationInput readCalibrationInput(const std::string& inputFile, const CalibrationInput& init = {});
 void writeOrchestratorOutput(const OrchestratorOutput& out, const std::string& outputFile);
 void printHelp(const char* executable);