Added versioning + APR git hash capture stuff

Author: krzysg

CMakeLists.txt

@@ -5,6 +5,20 @@ cmake_minimum_required(VERSION 3.2)
 project(LibAPR)
 set(CMAKE_CXX_STANDARD 14)
 
+###############################################################################
+# Generate configuration file
+###############################################################################
+set (APR_VERSION_MAJOR 1)
+set (APR_VERSION_MINOR 0)
+set (APR_VERSION_PATCH 0)
+execute_process(COMMAND git rev-parse HEAD OUTPUT_VARIABLE APR_GIT_HASH)
+string(REGEX REPLACE "\n$" "" APR_GIT_HASH "${APR_GIT_HASH}")
+configure_file (
+        "${PROJECT_SOURCE_DIR}/src/ConfigAPR.h.in"
+        "${PROJECT_BINARY_DIR}/ConfigAPR.h"
+)
+include_directories("${PROJECT_BINARY_DIR}")
+
 ###############################################################################
 # Find all required libraries
 ###############################################################################

examples/Example_get_apr.cpp

@@ -28,9 +28,11 @@ Advanced (Direct) Settings:
 
 #include <algorithm>
 #include <iostream>
+#include "ConfigAPR.h"
 #include "Example_get_apr.h"
 
 
+
 int main(int argc, char **argv) {
 
     //input parsing
@@ -132,6 +134,7 @@ cmdLineOptions read_command_line_options(int argc, char **argv){
 
     if(argc == 1) {
         std::cerr << argv[0] << std::endl;
+        std::cerr << "APR version " << ConfigAPR::getVersionString() << std::endl;
         std::cerr << "Short usage: \"" << argv[0] << " -i inputfile [-d directory] [-o outputfile]\"" << std::endl;
 
         std::cerr << usage << std::endl;

src/ConfigAPR.h.in

@@ -0,0 +1,23 @@
+/**
+ * Template configuration file for APR.
+ *
+ * Krzysztof Gonciarz 2018
+ */
+#ifndef CONFIG_APR_H
+#define CONFIG_APR_H
+
+
+#include <string>
+
+namespace ConfigAPR {
+    const unsigned int APR_VERSION_MAJOR = @APR_VERSION_MAJOR@;
+    const unsigned int APR_VERSION_MINOR = @APR_VERSION_MINOR@;
+    const unsigned int APR_VERSION_PATCH = @APR_VERSION_PATCH@;
+    const std::string APR_GIT_HASH = "@APR_GIT_HASH@";
+
+    static constexpr auto getVersionString() {
+        return "@APR_VERSION_MAJOR@.@APR_VERSION_MINOR@.@APR_VERSION_PATCH@";
+    }
+}
+
+#endif

src/io/APRWriter.hpp

@@ -9,6 +9,7 @@
 #include "src/data_structures/APR/APR.hpp"
 #include <src/data_structures/APR/APRAccess.hpp>
 #include <numeric>
+#include "ConfigAPR.h"
 
 template<typename U>
 class APR;
@@ -178,8 +179,6 @@ class APRWriter {
         H5Aread(attr_id,H5T_NATIVE_FLOAT,&apr.parameters.noise_sd_estimate ) ;
         H5Aclose(attr_id);
 
-        //std::cout << "Number particles: " << num_parts << " Number Cells: " << num_cells << std::endl;
-
         apr.apr_access.x_num.resize(apr.apr_access.level_max+1);
         apr.apr_access.y_num.resize(apr.apr_access.level_max+1);
         apr.apr_access.z_num.resize(apr.apr_access.level_max+1);
@@ -403,9 +402,7 @@ class APRWriter {
 
         hdf5_write_string_blosc(pr_groupid,"name",apr.name);
 
-        std::string git_hash = exec_blosc("git rev-parse HEAD");
-
-        hdf5_write_string_blosc(pr_groupid,"githash",git_hash);
+        hdf5_write_string_blosc(pr_groupid,"githash", ConfigAPR::APR_GIT_HASH);
 
         hdf5_write_attribute_blosc(pr_groupid,H5T_NATIVE_INT,"compress_type",1,dims_out, &compress_type_num);
 
@@ -632,9 +629,7 @@ class APRWriter {
 
         hdf5_write_string_blosc(pr_groupid,"name",apr.name);
 
-        std::string git_hash = exec_blosc("git rev-parse HEAD");
-
-        hdf5_write_string_blosc(pr_groupid,"githash",git_hash);
+        hdf5_write_string_blosc(pr_groupid,"githash", ConfigAPR::APR_GIT_HASH);
 
         //////////////////////////////////////////////////////////////////
         //
@@ -779,7 +774,7 @@ class APRWriter {
 
         //just an identifier in here for the reading of the parts
         S val = 0;
-        hid_t type_id = get_type_blosc(val);
+        hid_t type_id = get_type_data_hdf5(val);
         hid_t type = get_type_data_hdf5(val);
 
         hdf5_write_attribute_blosc(pr_groupid,H5T_NATIVE_INT,"data_type",1,dims_out, &type_id);
@@ -806,10 +801,7 @@ class APRWriter {
 
 
         // New parameter and background data
-
-        std::string git_hash = exec_blosc("git rev-parse HEAD");
-
-        hdf5_write_string_blosc(pr_groupid,"githash",git_hash);
+        hdf5_write_string_blosc(pr_groupid,"githash", ConfigAPR::APR_GIT_HASH);
 
         // output the file size
         hsize_t file_size;

src/io/hdf5functions_blosc.cpp

@@ -10,26 +10,7 @@
 
 #include "hdf5functions_blosc.h"
 #include <array>
-#include <string>
-#include <memory>
 
-// TODO: This is not supported for UWP, find a replacement
-#ifdef _WINDOWS
-#define popen _popen
-#define pclose _pclose
-#endif
-
-std::string exec_blosc(const char* cmd) {
-    std::array<char, 128> buffer;
-    std::string result;
-    std::shared_ptr<FILE> pipe(popen(cmd, "r"), pclose);
-    if (!pipe) throw std::runtime_error("popen() failed!");
-    while (!feof(pipe.get())) {
-        if (fgets(buffer.data(), 128, pipe.get()) != NULL)
-            result += buffer.data();
-    }
-    return result;
-}
 
 void register_bosc(){
     /* Register the filter with the library */
@@ -51,65 +32,6 @@ void hdf5_load_data_blosc(hid_t obj_id,hid_t data_type,void* buff, const char* d
     H5Dclose(data_id);
 }
 
-void hdf5_write_data_blosc(hid_t obj_id,hid_t type_id,const char* ds_name,hsize_t rank,hsize_t* dims, void* data ){
-    //writes data to the hdf5 file or group identified by obj_id of hdf5 datatype data_type
-    
-    unsigned int cd_values[7];
-    //Declare the required hdf5 shiz
-    hid_t space_id,dset_id,plist_id;
-    hsize_t *cdims = new hsize_t[rank]; //chunking dims
-    
-    //compression parameters
-
-    
-    //int szip_options_mask = H5_SZIP_NN_OPTION_MASK;
-    //int szip_pixels_per_block = 8;
-    
-    //dataspace id
-    space_id = H5Screate_simple(rank, dims, NULL);
-    plist_id  = H5Pcreate(H5P_DATASET_CREATE);
-    
-    /* Dataset must be chunked for compression */
-    //cdims[0] = 20; //Could try playing with these for compression performance
-    //cdims[1] = 20;
-    
-    uint64_t max_size = 100000;
-    
-    if (rank == 1) {
-        if (dims[0] < max_size){
-            cdims[0] = dims[0];
-        }else {
-            cdims[0] = max_size;
-        }
-    }
-    else {
-        cdims[0] = 100;
-        cdims[1] = 100;
-    }
-    
-    H5Pset_chunk(plist_id, rank, cdims);
-    
-    /////SET COMPRESSION TYPE /////
-    
-    /* But you can also taylor Blosc parameters to your needs */
-    /* 0 to 3 (inclusive) param slots are reserved. */
-    cd_values[4] = 6;       /* compression level */
-    cd_values[5] = 2;       /* 0: shuffle not active, 1: shuffle active */
-    cd_values[6] = BLOSC_ZSTD; /* the actual compressor to use */
-
-    /* Set the filter with 7 params */
-    H5Pset_filter(plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 7, cd_values);
-    
-    //create write and close
-    dset_id = H5Dcreate2(obj_id,ds_name,type_id,space_id,H5P_DEFAULT,plist_id,H5P_DEFAULT);
-    
-    H5Dwrite(dset_id,type_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,data);
-    
-    H5Dclose(dset_id);
-    
-    
-}
-
 void hdf5_write_data_blosc(hid_t obj_id,hid_t type_id,const char* ds_name,hsize_t rank,hsize_t* dims, void* data ,unsigned int comp_type,unsigned int comp_level,unsigned int shuffle){
     //writes data to the hdf5 file or group identified by obj_id of hdf5 datatype data_type
 

src/io/hdf5functions_blosc.h

@@ -21,41 +21,15 @@ extern "C" {
 #include <vector>
 #include <fstream>
 
-std::string exec_blosc(const char* cmd);
 
 void register_bosc();
 void hdf5_create_file_blosc(std::string file_name);
 void hdf5_load_data_blosc(hid_t obj_id,hid_t data_type,void* buff, const char* data_name);
 void hdf5_write_attribute_blosc(hid_t obj_id,hid_t type_id,const char* attr_name,hsize_t rank,hsize_t* dims, void* data );
-void hdf5_write_data_blosc(hid_t obj_id,hid_t type_id,const char* ds_name,hsize_t rank,hsize_t* dims, void* data );
 void hdf5_write_string_blosc(hid_t obj_id,const char* attr_name,std::string output_str);
 void hdf5_write_data_blosc(hid_t obj_id,hid_t type_id,const char* ds_name,hsize_t rank,hsize_t* dims, void* data ,unsigned int comp_type,unsigned int comp_level,unsigned int shuffle);
 
 void write_main_paraview_xdmf_xml(std::string save_loc,std::string file_name,uint64_t num_parts);
 
-template <typename T>
-hid_t get_type_blosc(T data_type){
-    //
-    //  Return the type id
-    //
-    //
-    
-    int num_byts = sizeof(data_type);
-    
-    
-    if (num_byts == 0) {
-        return H5T_NATIVE_INT;
-    } else if(num_byts == 2){
-        return H5T_NATIVE_UINT16;
-        
-    } else if(num_byts == 1){
-        return H5T_NATIVE_UINT8;
-    } else {
-        return H5T_NATIVE_FLOAT;
-    }
-    
-    
-}
-
 
 #endif