use mmap instead of file

fftma_module/gen/include/chunk_array.h

@@ -18,6 +18,7 @@ typedef struct chunk_array {
     size_t chunk_size;
     size_t total_size;
     FILE* fp;
+    double* mmap_array;
     buffer_t* buffer1;
     buffer_t* buffer2;
 }chunk_array_t;

fftma_module/gen/lib_src/chunk_array.c

@@ -1,6 +1,7 @@
 #include "chunk_array.h"
 #include "stdbool.h"
 #include "stdlib.h"
+#include <sys/mman.h>
 
 #define MAX_CHUNK_SIZE 2048*2048
 
@@ -27,7 +28,8 @@ bool inside_buffer(chunk_array_t* chunk_array,int init_pos, size_t pos) {
 }
 
 void chunk_array_free(chunk_array_t* chunk_array) {
-  	fclose(chunk_array->fp);
+  	//fclose(chunk_array->fp);
+    munmap(chunk_array->mmap_array, chunk_array->total_size * sizeof(double));
     buffer_free(chunk_array->buffer1);
     buffer_free(chunk_array->buffer2);
 	free(chunk_array);  
@@ -41,8 +43,10 @@ void chunk_array_flush(chunk_array_t* chunk_array) {
 void buffer_flush(chunk_array_t* chunk_array, buffer_t* buffer) {
     if (buffer->dirty) {
         int mod = get_mod(chunk_array, buffer->init_pos);
-        fseek(chunk_array->fp, buffer->init_pos * sizeof(double), SEEK_SET);
-        fwrite(buffer->data, sizeof(double), mod, chunk_array->fp);
+        //fseek(chunk_array->fp, buffer->init_pos * sizeof(double), SEEK_SET);
+        //fwrite(buffer->data, sizeof(double), mod, chunk_array->fp);
+        memcpy(&chunk_array->mmap_array[buffer->init_pos], buffer->data, mod * sizeof(double));
+        
         buffer->dirty = false;
     }
 }
@@ -53,9 +57,11 @@ void buffer_update(chunk_array_t* chunk_array, buffer_t* buffer, size_t pos) {
 
     int new_init = pos/chunk_array->chunk_size;
     buffer->init_pos = new_init * chunk_array->chunk_size;
+    int mod = get_mod(chunk_array, buffer->init_pos);
 
-    fseek(chunk_array->fp, buffer->init_pos * sizeof(double), SEEK_SET);
-    fread(buffer->data, sizeof(double), chunk_array->chunk_size, chunk_array->fp);
+    //fseek(chunk_array->fp, buffer->init_pos * sizeof(double), SEEK_SET);
+    //fread(buffer->data, sizeof(double), chunk_array->chunk_size, chunk_array->fp);
+    memcpy(buffer->data, &chunk_array->mmap_array[buffer->init_pos], mod * sizeof(double));
 }
 
 buffer_t* buffer_create(int size) {
@@ -83,14 +89,15 @@ void buffer_free(buffer_t* buffer) {
 
 chunk_array_t* chunk_array_create(char* filename, size_t total_size) {
     chunk_array_t* chunk_array = (chunk_array_t*)malloc(sizeof(chunk_array_t));
-    chunk_array->fp = fopen(filename, "r+");
 
-    if (chunk_array == NULL || chunk_array->fp == NULL) {
-        chunk_array->fp = fopen(filename, "w+");
+    if (chunk_array == NULL) {
+        return NULL;
+    }
+
+    chunk_array->mmap_array = mmap ( NULL, total_size*sizeof(double), PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_ANONYMOUS, 0, 0 );
 
-        if (chunk_array->fp == NULL) {
-            return NULL;
-        }
+    if (chunk_array->mmap_array == NULL) {
+        return NULL;
     }
 
     chunk_array->chunk_size = min(MAX_CHUNK_SIZE, total_size);
@@ -106,17 +113,19 @@ chunk_array_t* chunk_array_create(char* filename, size_t total_size) {
     chunk_array->buffer2 = buffer_create(chunk_array->chunk_size);
 
     if (chunk_array->buffer2 == NULL) {
-        fclose(chunk_array->fp);
+        //fclose(chunk_array->fp);
         buffer_free(chunk_array->buffer1);
         free(chunk_array);
         return NULL;
     }
 
-    fread(chunk_array->buffer1->data, sizeof(double), chunk_array->chunk_size, chunk_array->fp);
+    memcpy(chunk_array->buffer1->data, chunk_array->mmap_array, chunk_array->chunk_size * sizeof(double));
     chunk_array->buffer1->init_pos = 0;
-    fread(chunk_array->buffer2->data, sizeof(double), chunk_array->chunk_size, chunk_array->fp);
-    chunk_array->buffer2->init_pos = chunk_array->chunk_size;
-    
+    if (total_size > chunk_array->chunk_size) {
+        int mod = get_mod(chunk_array, chunk_array->buffer1->init_pos + chunk_array->chunk_size);
+        memcpy(chunk_array->buffer2->data, &chunk_array->mmap_array[chunk_array->chunk_size], mod * sizeof(double));
+        chunk_array->buffer2->init_pos = chunk_array->chunk_size;
+    }
     chunk_array->filename = filename;
     chunk_array->total_size = total_size;
     return chunk_array;

fftma_module/gen/mem_profile.py

@@ -1,8 +1,5 @@
-from sympy import N
 from example import generate
 
-from memory_profiler import memory_usage
-
 from memory_profiler import memory_usage
 import sys
 

script_fortran.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-rm ./tools/connec/conec2d
-rm ./tools/connec/conec3d
-
-cd ./tools/connec/connec-src && make clean && make all
-mv ./conec2d ..
-mv ./conec3d ..

tests/integration/test.py

@@ -9,6 +9,7 @@ def find_relative_errors(path_original, path):
     binary_original = np.load(path_original)
     binary = np.load(path)
 
+<<<<<<< Updated upstream
     diffs = binary_original - binary
 
     binary_original = binary_original.tolist()
@@ -39,6 +40,13 @@ def find_relative_errors(path_original, path):
 
 BINARIES = ["Cmap", "D", "P", "V", "k"]
 
+=======
+    diffs = np.divide(binary_original - binary, binary_original)
+    comparisons = np.array([(abs(x) < 0.01).all() for x in diffs])
+    return comparisons.all()
+
+BINARIES = ['Cmap', 'D', 'P', 'V', 'k']
+>>>>>>> Stashed changes
 
 class TestIntegration(unittest.TestCase):
     @classmethod