adding unit test - clean up and ...

.github/workflows/build_cmake.yml

@@ -71,3 +71,6 @@ jobs:
 
     - name: test config creation
       run: ${{github.workspace}}/spinwalk_test --run_test=test_config_creation
+
+    - name: test kernel
+      run: ${{github.workspace}}/spinwalk_test --run_test=test_kernel

CMakeLists.txt

@@ -51,7 +51,7 @@ add_subdirectory(src/sim)
 
  # Add the sources files
 set(SOURCE_MODULES ${SUBCOMMAND_PHANTOM} ${SUBCOMMAND_SIM} ${SUBCOMMAND_DWI} ${SUBCOMMAND_CONFIG})
-set(SOURCE_MAIN ./src/spinwalk.cu)
+set(SOURCE_MAIN ./src/spinwalk.cpp)
 
 # change extension of the files if CUDA is not found
 if(NOT  CMAKE_CUDA_COMPILER) 
@@ -67,9 +67,6 @@ if(NOT  CMAKE_CUDA_COMPILER)
         list(APPEND RENAMED_SOURCES ${NEW_FILE})
     endforeach()
     set(SOURCE_MODULES ${RENAMED_SOURCES})
-
-    file(COPY_FILE ./src/spinwalk.cu ./src/spinwalk.cpp)
-    set(SOURCE_MAIN ./src/spinwalk.cpp)
 endif()
 
 # Add the executable

containers/create_dockers.sh

@@ -6,7 +6,7 @@ pushd "$SCRIPT_DIR" > /dev/null
 # docker system prune -a --volumes --force
 docker system prune --force
 
-CUDA_VERSIONS=("12.0.0" "12.2.0" "12.6.3")
+CUDA_VERSIONS=("12.0.0" "12.6.3")
 
 for VERSION in "${CUDA_VERSIONS[@]}"; do
     echo "Building Docker image for CUDA version $VERSION..."

src/config/config_generator.h

@@ -1,7 +1,3 @@
-// --------------------------------------------------------------------------------------------
-// generate default configuration file
-// --------------------------------------------------------------------------------------------
-
 
 #include <string>
 #include <vector>

src/config/handler.h

@@ -1,4 +1,5 @@
-
+#ifndef CONFIG_HANDLER_H
+#define CONFIG_HANDLER_H
 
 #include <string>
 #include <vector>
@@ -18,3 +19,5 @@ namespace config {
         static bool execute(const execute_args& args);
     };
 }
+
+#endif // CONFIG_HANDLER_H

src/dwi/handler.cpp

@@ -1,6 +1,5 @@
 
 #include <iostream>
-
 #include "handler.h"
 #include "pgse.h"
 

src/dwi/handler.h

@@ -1,4 +1,5 @@
-
+#ifndef DWI_HANDLER_H
+#define DWI_HANDLER_H
 
 #include <string>
 #include <vector>
@@ -19,3 +20,5 @@ namespace dMRI {
         static bool execute(const execute_args& args);
     };
 }
+
+#endif // DWI_HANDLER_H

src/dwi/pgse.h

@@ -1,4 +1,6 @@
 
+#ifndef PGSE_H
+#define PGSE_H
 
 #include <string>
 #include <vector>
@@ -25,4 +27,6 @@ class pgse
     std::vector<double> b_value;
 };
 
-}
+}
+
+#endif // PGSE_H

src/phantom/handler.h

@@ -1,4 +1,6 @@
 
+#ifndef PHANTOM_HANDLER_H
+#define PHANTOM_HANDLER_H
 
 #include <string>
 #include <cstdint>
@@ -23,3 +25,5 @@ namespace phantom {
         static bool execute(const execute_args& args);
     };
 }
+
+#endif // PHANTOM_HANDLER_H

src/phantom/phantom_base.h

@@ -5,7 +5,7 @@
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 #ifndef PHANTOM_BASE_H

src/phantom/phantom_cylinder.cpp

@@ -1,7 +1,7 @@
 
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: arbitrary_gradient.h
+ * File: phantom_cylinder.cpp
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 15.05.2024

src/phantom/phantom_cylinder.h

@@ -1,11 +1,11 @@
 
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: file_utils.cpp
+ * File: phantom_cylinder.h
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 #ifndef CYLINDER_H

src/phantom/phantom_sphere.cpp

@@ -1,7 +1,7 @@
 
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: arbitrary_gradient.h
+ * File: phantom_sphere.cpp
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 15.05.2024

src/phantom/phantom_sphere.h

@@ -1,11 +1,11 @@
 
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: file_utils.cpp
+ * File: phantom_sphere.cpp
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 #ifndef SPHERE_H

src/sim/CMakeLists.txt

@@ -1,6 +1,7 @@
 set(SUBCOMMAND_SIM
     ${CMAKE_CURRENT_SOURCE_DIR}/monte_carlo.cu
     ${CMAKE_CURRENT_SOURCE_DIR}/kernels.cu
+    ${CMAKE_CURRENT_SOURCE_DIR}/handler.cu
     ${CMAKE_CURRENT_SOURCE_DIR}/device_helper.cu
     ${CMAKE_CURRENT_SOURCE_DIR}/config_reader.cpp
     PARENT_SCOPE)

src/sim/device_helper.cu

@@ -1,7 +1,4 @@
 
-#ifndef DEVICE_HELPER_CUH
-#define DEVICE_HELPER_CUH
-
 #include <iostream>
 #include <boost/log/trivial.hpp>
 #include "device_helper.cuh"
@@ -104,4 +101,3 @@ bool check_memory_size(size_t required_size_MB)
 }
 
 } // namespace sim
-#endif // DEVICE_HELPER_CUH

src/sim/device_helper.cuh

@@ -3,9 +3,6 @@
 #define DEVICE_HELPER_CUH
 
 #include <string>
-//---------------------------------------------------------------------------------------------
-//  check for CUDA and GPU device
-//---------------------------------------------------------------------------------------------
 
 namespace sim
 {

src/sim/h5_helper.h

@@ -1,11 +1,11 @@
 
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: file_utils.h
+ * File: h5_helper.h
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 #ifndef __H5_HELPER_H__

src/sim/handler.cu

@@ -0,0 +1,18 @@
+
+#include <iostream>
+#include <filesystem>
+#include "handler.cuh"
+#include "monte_carlo.cuh"
+
+namespace sim {
+    bool handler::execute(const execute_args& args) {    
+        sim::monte_carlo mc(args.use_cpu, args.device_id); 
+        for(const auto& config_file : args.config_files){
+            std::cout << "<" << std::filesystem::path(config_file).filename().string() << ">\n";       
+            if(mc.run(config_file) == false)
+                return 1;                
+        }  
+        std::cout << "Simulation completed successfully. See the log file\n";
+        return true;
+    }
+}

src/sim/handler.cuh

@@ -0,0 +1,22 @@
+
+#ifndef SIM_HANDLER_H
+#define SIM_HANDLER_H
+
+#include <string>
+#include <vector>
+#include <cstdint>
+
+namespace sim {
+    struct execute_args {            
+        bool use_cpu = false;        
+        uint32_t device_id = 0;
+        std::vector<std::string>  config_files; // Default value for name
+    };
+
+    class handler {
+    public:
+        static bool execute(const execute_args& args);
+    };
+}
+
+#endif // SIM_HANDLER_H

src/sim/kernels.cu

@@ -1,10 +1,10 @@
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: kernels.cuh
+ * File: kernels.cu
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 #include <cinttypes>
@@ -20,12 +20,8 @@
 #include <thrust/device_vector.h>
 #include <thrust/extrema.h>
 #endif
-//---------------------------------------------------------------------------------------------
-//
-//---------------------------------------------------------------------------------------------
-#define ABS(x) ((x) < 0 ? -(x) : (x))
-
 
+#define ABS(x) ((x) < 0 ? -(x) : (x))
 
 namespace sim {
 

src/sim/kernels.cuh

@@ -4,7 +4,7 @@
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 

src/sim/monte_carlo.cu

@@ -56,8 +56,6 @@ monte_carlo::monte_carlo(bool gpu_disabled, int32_t device_id)
 
 monte_carlo::~monte_carlo()
 {
-    // if(param)  delete param;
-    // if(config) delete config;
 }
 
 void monte_carlo::allocate_memory()

src/sim/monte_carlo.cuh

@@ -6,8 +6,6 @@
 #include "config_reader.h"
 #include "simulation_parameters.cuh"
 
-// struct simulation_parameters;
-
 namespace sim {
 // class config_reader;
 

src/sim/simulation_parameters.cuh

@@ -1,10 +1,10 @@
 /* --------------------------------------------------------------------------
  * Project: Microvascular
- * File: miscellaneous.h
+ * File: simulation_parameters.cuh
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : simulating BOLD in microvascular network
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
 
 #ifndef __SIMULATION_PARAMETERS_H__

src/spinwalk.cu → src/spinwalk.cpp

@@ -1,15 +1,11 @@
 /* --------------------------------------------------------------------------
  * Project: SpinWalk
- * File: spinwalk.cu
+ * File: spinwalk.cpp
  *
  * Author   : Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
  * Date     : 10.02.2023
- * Descrip  : Monte Carlo simulation of the spin dynamics in the presence of off-resonance fields.
+ * Descrip  : 
  * -------------------------------------------------------------------------- */
-
-// compile(lin) :  nvcc ./src/spinwalk.cu ./src/kernels.cu -I ./include/ -Xptxas -v -O3  -arch=compute_75 -code=sm_75  -Xcompiler -fopenmp -o spinwalk
-// compile(win) :  nvcc ./src/spinwalk.cu ./src/kernels.cu -I ./include/ -Xptxas -v -O3  -arch=compute_86 -code=sm_86  -Xcompiler /openmp -std=c++17 -o spinwalk
-
 // standard libraries
 #include <iomanip>
 #include <filesystem>
@@ -24,10 +20,10 @@
 
 // custom headers
 #include "definitions.h"
-#include "sim/monte_carlo.cuh"
 #include "phantom/handler.h"
 #include "dwi/handler.h"
 #include "config/handler.h"
+#include "sim/handler.cuh"
 #include "sim/device_helper.cuh"
 
 namespace bl = boost::log;
@@ -40,7 +36,7 @@ int main(int argc, char * argv[])
     float arg_radius=50.f, arg_fov=1000.f, arg_dchi=0.11e-6, arg_oxy_level=0.75, arg_ori=90.f, arg_vol_fra=4.f;
     uint32_t arg_res=500, device_id=0, TE_us=1000, timestep_us=10;
     int32_t arg_seed = -1;
-    std::vector<std::string>  config_files, phantom_files;
+    std::vector<std::string> config_files, phantom_files;
     std::vector<uint32_t> bdelta;
     std::vector<float> bvector;
     std::vector<double> bvalue;
@@ -127,20 +123,13 @@ int main(int argc, char * argv[])
             return 1;
         }
 
-    // ========== loop over configs and simulate ==========
-    if (config_files.size() == 0)
-        return 0;
-
-    std::cout << "Running simulation for " << config_files.size() << " config(s)..." << "\n\n";
-
-    sim::monte_carlo mc(use_cpu, device_id); 
-    for(const auto& config_file : config_files){
-        std::cout << "<" << std::filesystem::path(config_file).filename().string() << ">\n";       
-        if(mc.run(config_file) == false){
+    // ========== Monte-Carlo simulation ==========
+    if(subcommand_sim->parsed()){
+         if (sim::handler::execute({.use_cpu=use_cpu, .device_id=device_id, .config_files=config_files}) == false){
             std::cout << ERR_MSG << "Simulation failed. See the log file " << log_filename <<", Aborting...!" << "\n";
-            return 1;
-        }     
-    }    
-    std::cout << "Simulation completed successfully. See the log file " << log_filename << "\n";
+            return 1;    
+         }    
+    }
+
     return 0;
 }

tests/CMakeLists.txt

@@ -23,7 +23,7 @@ endif()
 # include_directories(${CMAKE_SOURCE_DIR}/include ${CMAKE_BINARY_DIR}/include ${Boost_INCLUDE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
 include_directories(${Boost_INCLUDE_DIRS})
 
-add_executable(${project_test} test_phantom.cpp test_config.cpp)
+add_executable(${project_test} test_phantom.cpp test_config.cpp test_kernel.cpp)
 target_link_libraries(${project_test} ${Boost_LIBRARIES} SpinWalk_lib)
 set_target_properties(${project_test} PROPERTIES OUTPUT_NAME "spinwalk_test")