Merge pull request #180 from AdaptiveParticles/joel_tmp

Joel tmp
AdaptiveParticles · Oct 16, 2023 · 003270b · 003270b
2 parents 10ab24a + d220171
commit 003270b
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Showing 7 changed files with 45 additions and 30 deletions.
diff --git a/src/data_structures/APR/APR.hpp b/src/data_structures/APR/APR.hpp
@@ -23,7 +23,7 @@ class APR {
     friend class APRConverterBatch;
     friend class APRBenchHelper;
 
-protected:
+public:
 
     // initialize tree RandomAccess
     void initialize_tree_random_sparse();
@@ -60,8 +60,6 @@ class APR {
 
     APRParameters parameters; // this is here to keep a record of what parameters were used, to then be written if needed.
 
-public:
-
 #ifdef APR_USE_CUDA
 
 
@@ -86,6 +84,10 @@ class APR {
      * @param with_tree     include the tree access
      */
     void init_cuda(bool with_tree=true) {
+        gpuAccess.genInfo = &aprInfo;
+        gpuTreeAccess.genInfo = &treeInfo;
+        linearAccess.genInfo = &aprInfo;
+        linearAccessTree.genInfo = &treeInfo;
         auto apr_helper = gpuAPRHelper();
         if(with_tree) {
             auto tree_helper = gpuTreeHelper();
@@ -190,6 +192,7 @@ class APR {
         tree_initialized = apr2copy.tree_initialized;
         apr_initialized = apr2copy.apr_initialized;
         name = apr2copy.name;
+        parameters = apr2copy.parameters;
 
         //old data structures
         apr_access = apr2copy.apr_access;

diff --git a/src/data_structures/APR/access/GPUAccess.hpp b/src/data_structures/APR/access/GPUAccess.hpp
@@ -67,7 +67,6 @@ class GPUAccessHelper {
             gpuAccess->init_y_vec(linearAccess->y_vec);
             gpuAccess->init_level_xz_vec(linearAccess->level_xz_vec);
             gpuAccess->init_xz_end_vec(linearAccess->xz_end_vec);
-            gpuAccess->genInfo = linearAccess->genInfo;
             gpuAccess->copy2Device();
             gpuAccess->initialized = true;
         }
@@ -78,7 +77,6 @@ class GPUAccessHelper {
             gpuAccess->init_y_vec(linearAccess->y_vec);
             gpuAccess->init_level_xz_vec(linearAccess->level_xz_vec);
             gpuAccess->init_xz_end_vec(linearAccess->xz_end_vec);
-            gpuAccess->genInfo = linearAccess->genInfo;
             gpuAccess->copy2Device(total_number_particles(tree_access.level_max()), tree_access.gpuAccess);
             gpuAccess->initialized = true;
         }
@@ -88,7 +86,7 @@ class GPUAccessHelper {
         gpuAccess->copy2Host();
     }
 
-    uint64_t total_number_particles() { return gpuAccess->total_number_particles(); }
+    uint64_t total_number_particles() { return gpuAccess->genInfo->total_number_particles; }
 
     uint64_t total_number_particles(const int level) {
         uint64_t index = linearAccess->level_xz_vec[level] + linearAccess->x_num(level) - 1 + (linearAccess->z_num(level)-1)*linearAccess->x_num(level);

diff --git a/src/io/APRWriter.hpp b/src/io/APRWriter.hpp
@@ -702,7 +702,8 @@ class APRWriter {
                     break;
                 case Operation::WRITE:
 
-                    fileId = hdf5_create_file_blosc(aFileName);
+//                    fileId = hdf5_create_file_blosc(aFileName);
+                    fileId = H5Fcreate(aFileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
 
                     if (fileId == -1) {
                         std::cerr << "Could not create file [" << aFileName << "]" << std::endl;

diff --git a/src/numerics/APRDownsampleGPU.cu b/src/numerics/APRDownsampleGPU.cu
@@ -900,6 +900,7 @@ template<int blockSize_z, int blockSize_x>
 void compute_ne_rows_tree_cuda(GPUAccessHelper& tree_access, VectorData<int>& ne_count, ScopedCudaMemHandler<int*, JUST_ALLOC>& ne_rows_gpu) {
 
     ne_count.resize(tree_access.level_max() + 3);
+    ne_count[0] = 0;
 
     int z_blocks_max = (tree_access.z_num(tree_access.level_max()) + blockSize_z - 1) / blockSize_z;
     int num_levels = tree_access.level_max() - tree_access.level_min() + 1;
@@ -973,12 +974,13 @@ void compute_ne_rows_tree_cuda(GPUAccessHelper& tree_access, VectorData<int>& ne
                                         ne_rows_gpu.get());
     }
 
-    error_check(cudaFree(block_sums_device) )
+    error_check(cudaFree(block_sums_device))
 }
 
 
 void compute_ne_rows_tree(GPUAccessHelper& tree_access, VectorData<int>& ne_counter, VectorData<int>& ne_rows) {
     ne_counter.resize(tree_access.level_max() + 3);
+    ne_counter[0] = 0;
 
     int z = 0;
     int x = 0;

diff --git a/src/numerics/miscCuda.cu b/src/numerics/miscCuda.cu
@@ -237,6 +237,7 @@ __global__ void fill_ne_rows_cuda(const uint64_t* level_xz_vec,
 }
 
 
+
 template<int blockSize_z, int blockSize_x>
 void compute_ne_rows_cuda(GPUAccessHelper& access, VectorData<int>& ne_count, ScopedCudaMemHandler<int*, JUST_ALLOC>& ne_rows_gpu, int blockSize) {
 
@@ -264,12 +265,12 @@ void compute_ne_rows_cuda(GPUAccessHelper& access, VectorData<int>& ne_count, Sc
         count_ne_rows_cuda<blockSize_z, blockSize_x>
                 << < grid_dim, block_dim >> >
                                (access.get_level_xz_vec_ptr(),
-                                       access.get_xz_end_vec_ptr(),
-                                       access.z_num(level),
-                                       access.x_num(level),
-                                       level,
-                                       blockSize,
-                                       block_sums_device + offset);
+                                access.get_xz_end_vec_ptr(),
+                                access.z_num(level),
+                                access.x_num(level),
+                                level,
+                                blockSize,
+                                block_sums_device + offset);
         offset += z_blocks_max;
     }
 
@@ -305,14 +306,14 @@ void compute_ne_rows_cuda(GPUAccessHelper& access, VectorData<int>& ne_count, Sc
 
         fill_ne_rows_cuda<<< grid_dim, block_dim >>>
                                        (access.get_level_xz_vec_ptr(),
-                                               access.get_xz_end_vec_ptr(),
-                                               access.z_num(level),
-                                               access.x_num(level),
-                                               level,
-                                               blockSize,
-                                               ne_sz,
-                                               ne_count[level],
-                                               ne_rows_gpu.get());
+                                        access.get_xz_end_vec_ptr(),
+                                        access.z_num(level),
+                                        access.x_num(level),
+                                        level,
+                                        blockSize,
+                                        ne_sz,
+                                        ne_count[level],
+                                        ne_rows_gpu.get());
     }
 
     error_check( cudaFree(block_sums_device) )

diff --git a/vcpkg b/vcpkg
diff --git a/vcpkg.json b/vcpkg.json
@@ -2,10 +2,20 @@
   "name": "libapr",
   "version-string": "0.0.1",
   "dependencies": [
-    "blosc",
-    "hdf5",
-    "szip",
-    "gtest",
-    "tiff"
-  ]
-}
+    {
+      "name": "blosc"
+    },
+    {
+      "name": "hdf5",
+      "version>=": "1.8.20"
+    },
+    {
+      "name": "szip"
+    },
+    {
+      "name": "tiff",
+      "version>=": "4.0"
+    }
+  ],
+  "builtin-baseline": "486a4640db740f5994e492eb60748111dfc48de7"
+}