Merge pull request #39 from CannyLab/refactor_fit_tsne

Refactor fit tsne

.gitignore

@@ -1,4 +1,5 @@
 tsne_utils
+compile_commands.json
 
 *.o
 *.so
@@ -24,11 +25,15 @@ Multicore-TSNE/dist/*
 build/*
 
 # exception to the rule
-!build/.gitkeep 
+!build/.gitkeep
 
 # Ignore animation
 visualization/animation.gif
 
 .DS_Store
 .mypy_cache/
 .vscode/
+
+# vim
+*.swp
+*.swo

CMakeLists.txt

@@ -5,6 +5,7 @@ set (CMAKE_PROJECT_VERSION_MAJOR 1)
 set (CMAKE_PROJECT_VERSION_MINOR 0)
 set (CMAKE_PROJECT_VERSION_PATH 0)
 set (CMAKE_SKIP_RULE_DEPENDENCY TRUE)
+set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Modules)
 
 # Options
@@ -57,13 +58,13 @@ SET(CUDA_PROPAGATE_HOST_FLAGS OFF)
 set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};
                     -O3
                     -Xptxas -dlcm=cg
-                     -gencode=arch=compute_30,code=sm_30
-                     -gencode=arch=compute_35,code=sm_35
-                     -gencode=arch=compute_50,code=sm_50
-                     -gencode=arch=compute_52,code=sm_52
-		             -gencode=arch=compute_60,code=sm_60
-		             -gencode=arch=compute_61,code=sm_61
-                     -gencode=arch=compute_70,code=sm_70
+                    -gencode=arch=compute_30,code=sm_30
+                    -gencode=arch=compute_35,code=sm_35
+                    -gencode=arch=compute_50,code=sm_50
+                    -gencode=arch=compute_52,code=sm_52
+                    -gencode=arch=compute_60,code=sm_60
+		            -gencode=arch=compute_61,code=sm_61
+                    -gencode=arch=compute_70,code=sm_70
                     -std=c++11
                     -Xcompiler '-O3'
                     -Xcompiler '-fPIC'
@@ -149,15 +150,14 @@ set(SOURCES
 
     # Kernels
     src/kernels/apply_forces.cu
-    src/kernels/bh_attr_forces.cu
+    src/kernels/attr_forces.cu
+    src/kernels/rep_forces.cu
     src/kernels/perplexity_search.cu
-    src/kernels/initialization.cu
+    src/kernels/nbodyfft.cu
 
     # Method files
     src/ext/pymodule_ext.cu
-    src/bh_tsne.cu
-    src/nbodyfft.cu
-    # src/naive_tsne.cu
+    src/fit_tsne.cu
 )
 
 

build.sh

@@ -1,11 +1,10 @@
-export PATH=/usr/local/cuda-9.0/bin:$PATH
-export LD_LIBRARY_PATH=/usr/local/cuda-9.0/lib64:$LD_LIBRARY_PATH
+# export PATH=/usr/local/cuda-9.0/bin:$PATH
+# export LD_LIBRARY_PATH=/usr/local/cuda-9.0/lib64:$LD_LIBRARY_PATH
 git submodule init
-git submodule update 
+git submodule update
 cd ./build
 cmake  .. -DBUILD_PYTHON=TRUE -DWITH_MKL=FALSE -DCMAKE_C_COMPILER=gcc-4.9 -DCMAKE_CXX_COMPILER=g++-4.9
 pwd
-make -j10
 make
 cd python/
 pwd

meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "tsnecuda" %}
-{% set version = "0.1.1" %}
+{% set version = "0.2.1" %}
 
 package:
   name: '{{ name|lower }}'
@@ -8,7 +8,7 @@ package:
 source:
   git_url: https://github.com/CannyLab/tsne-cuda.git
   git_rev: HEAD
-  
+
 requirements:
   build:
     - python

src/exe/main.cu

@@ -1,16 +1,9 @@
-
-// This file exposes a main file which does most of the testing with command line 
+// This file exposes a main file which does most of the testing with command line
 // args, so we don't have to re-build to change options.
 
 // Detailed includes
-#include "common.h"
-#include "util/data_utils.h"
-#include "util/cuda_utils.h"
-#include "util/random_utils.h"
-#include "util/distance_utils.h"
-#include "naive_tsne.h"
-#include "naive_tsne_cpu.h"
-#include "bh_tsne.h"
+#include "include/util/data_utils.h"
+#include "include/fit_tsne.h"
 #include <time.h>
 #include <string>
 
@@ -45,7 +38,7 @@ int main(int argc, char** argv) {
         ("q,dim", "Point Dimensions", cxxopts::value<int>()->default_value("50"))
         ("j,device", "Device to run on", cxxopts::value<int>()->default_value("0"))
         ("h,help", "Print help");
-    
+
     // Parse command line options
     auto result = options.parse(argc, argv);
 
@@ -98,7 +91,7 @@ int main(int argc, char** argv) {
         }
 
         // Do the t-SNE
-        tsnecuda::bh::RunTsne(opt, gpu_opt);
+        tsnecuda::RunTsne(opt, gpu_opt);
 
         // Clean up the data
         delete[] data;
@@ -134,7 +127,7 @@ int main(int argc, char** argv) {
         }
 
         // Do the t-SNE
-        tsnecuda::bh::RunTsne(opt, gpu_opt);
+        tsnecuda::RunTsne(opt, gpu_opt);
 
         // Clean up the data
         delete[] data;
@@ -151,7 +144,7 @@ int main(int argc, char** argv) {
 
         // DO the T-SNE
         printf("Starting TSNE calculation with %u points.\n", num_images);
-        
+
         // Construct the options
         tsnecuda::Options opt(nullptr, data, num_images, num_columns*num_rows*num_channels);
         opt.perplexity = FOPT(perplexity);
@@ -171,8 +164,8 @@ int main(int argc, char** argv) {
         }
 
         // Do the t-SNE
-        tsnecuda::bh::RunTsne(opt, gpu_opt);
-        
+        tsnecuda::RunTsne(opt, gpu_opt);
+
         // Clean up the data
         delete[] data;
 
@@ -194,7 +187,7 @@ int main(int argc, char** argv) {
 
         // Do the T-SNE
         printf("Starting TSNE calculation with %u points.\n", IOPT(num-points));
-        
+
         // Construct the options
         tsnecuda::Options opt(nullptr, thrust::raw_pointer_cast(h_X.data()), IOPT(num-points),  IOPT(dim));
         opt.perplexity = FOPT(perplexity);
@@ -214,7 +207,7 @@ int main(int argc, char** argv) {
         }
 
         // Do the t-SNE
-        tsnecuda::bh::RunTsne(opt, gpu_opt);
+        tsnecuda::RunTsne(opt, gpu_opt);
 
     } else {
         std::cout << "Dataset not recognized..." << std::endl;

src/ext/pymodule_ext.cu

@@ -1,7 +1,7 @@
 
 // Implementation file for the python extensions
 
-#include "include/ext/pymodule_ext.h"
+#include "ext/pymodule_ext.h"
 
 void pymodule_bh_tsne(float *result,
                       float* points,
@@ -108,7 +108,7 @@ void pymodule_bh_tsne(float *result,
     }
 
     // Do the t-SNE
-    tsnecuda::bh::RunTsne(opt, gpu_opt);
+    tsnecuda::RunTsne(opt, gpu_opt);
 
     // Copy the data back from the GPU
     cudaDeviceSynchronize();