Remained fix after rebase

src/acc/cpu/cpu_benchmark_utils.h

@@ -8,4 +8,75 @@
 #define	GTOC(timer,timing) 
 #define	GATHERGPUTIMINGS(timer) 
 
+namespace CpuKernels
+{
+//Non-concurrent benchmarking tools (only for Linux)
+/*
+//#include <cuda_runtime.h>
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <time.h>
+#include <string>
+#include <sstream>
+
+#ifdef TIMING_FILES
+#define	CTIC(timer,timing) (timer.cuda_cpu_tic(timing))
+#define	CTOC(timer,timing) (timer.cuda_cpu_toc(timing))
+#define	GTIC(timer,timing) (timer.cuda_gpu_tic(timing))
+#define	GTOC(timer,timing) (timer.cuda_gpu_toc(timing))
+#define	GATHERGPUTIMINGS(timer) (timer.cuda_gpu_printtictoc())
+#elif defined CUDA_PROFILING
+	#include <nvToolsExt.h>
+	#define	CTIC(timer,timing) (nvtxRangePush(timing))
+	#define	CTOC(timer,timing) (nvtxRangePop())
+	#define	GTIC(timer,timing)
+	#define	GTOC(timer,timing)
+	#define	GATHERGPUTIMINGS(timer)
+#else
+	#define	CTIC(timer,timing)
+	#define	CTOC(timer,timing)
+	#define	GTIC(timer,timing)
+	#define	GTOC(timer,timing)
+	#define	GATHERGPUTIMINGS(timer)
+#endif
+
+class relion_timer
+{
+
+public:
+
+std::vector<std::string> cuda_cpu_benchmark_identifiers;
+std::vector<clock_t>     cuda_cpu_benchmark_start_times;
+FILE *cuda_cpu_benchmark_fPtr;
+
+std::vector<std::string> cuda_gpu_benchmark_identifiers;
+std::vector<cudaEvent_t> cuda_gpu_benchmark_start_times;
+std::vector<cudaEvent_t> cuda_gpu_benchmark_stop_times;
+FILE *cuda_gpu_benchmark_fPtr;
+
+relion_timer(std::string fnm)
+{
+	std::stringstream fnm_cpu, fnm_gpu;
+	fnm_cpu << "output/" << fnm << "_cpu.dat";
+	cuda_cpu_benchmark_fPtr = fopen(fnm_cpu.str().c_str(),"a");
+	fnm_gpu << "output/" << fnm << "_gpu.dat";
+	cuda_gpu_benchmark_fPtr = fopen(fnm_gpu.str().c_str(),"a");
+}
+
+int cuda_benchmark_find_id(std::string id, std::vector<std::string> v);
+
+void cuda_cpu_tic(std::string id);
+
+void cuda_cpu_toc(std::string id);
+
+void cuda_gpu_tic(std::string id);
+
+void cuda_gpu_toc(std::string id);
+
+void cuda_gpu_printtictoc();
+
+};
+*/
+}
 #endif /* CUDA_BENCHMARK_UTILS_H_ */

src/acc/sycl/sycl_kernels/sycl_utils.h

@@ -183,7 +183,6 @@ static void complex3D(
 	imag = dxy0[1] + (dxy1[1] - dxy0[1])*fz;	
 }
 
-<<<<<<< HEAD
 // From https://en.cppreference.com/w/cpp/types/numeric_limits/epsilon
 template <typename T>
 bool almostEqual(const T x, const T y, const int ulp)
@@ -285,8 +284,6 @@ static size_t countLargerThanNumber(const T *ptrA, const size_t sz, const T val)
 	return count;
 }
 
-=======
->>>>>>> 609f1ba3d392d15b72be0740227961d6bf6b820c
 } // end of namespace syclKernels
 
 #endif //SYCL_UTILITIES_H

src/gui_jobwindow.cpp

@@ -2422,7 +2422,6 @@ void JobWindow::initialiseDynaMightWindow()
     group3->end();
     place("do_reconstruct",TOGGLE_REACTIVATE, group3, false);
     group3->begin();
-    place("do_store_deform");
     place("backproject_batchsize");
     group3->end();
 

src/ml_optimiser.h

@@ -926,13 +926,9 @@ class MlOptimiser
 #endif
 	};
 
-<<<<<<< HEAD
 #ifdef _SYCL_ENABLED
 	~MlOptimiser();
 #endif
-=======
-	~MlOptimiser();
->>>>>>> 609f1ba3d392d15b72be0740227961d6bf6b820c
 
 	/** ========================== I/O operations  =========================== */
 	/// Print help message

src/pipeline_jobs.cpp

@@ -5726,15 +5726,6 @@ bool RelionJob::getCommandsDynaMightJob(std::string &outputname, std::vector<std
 
     }
 
-    if (joboptions["do_preload"].getBoolean() && !joboptions["do_visualize"].getBoolean())
-        command += " --preload-images";
-
-    if (joboptions["fn_mask"].getString() != "" && !joboptions["do_inverse"].getBoolean())
-        command += " --mask-file " + joboptions["fn_mask"].getString();
-
-    if (joboptions["fn_checkpoint"].getString() != "")
-        command += " --checkpoint-file " + joboptions["fn_checkpoint"].getString();
-
     if (joboptions["gpu_id"].getString() != "")
         command += " --gpu-id " + joboptions["gpu_id"].getString();