have some kind of memory allocation error :(

Samo Penic

2019-10-17 80ebbe388f3e945e62f47b0141c660ee6f05c8fc

 src/snapshot.c

@@ -9,6 +9,7 @@
#include<inttypes.h>
#include<config.h>
#include <time.h>
#include <string.h>
#include "io.h"
/* a helper function that utilizes ts_string data structure and performs same as sprintf */
ts_uint ts_sprintf(ts_string *str, char *fmt, ...){
@@ -24,7 +25,7 @@
ts_bool xml_trisurf_data(FILE *fh, ts_vesicle *vesicle){

   ts_string *data=(ts_string *)malloc(sizeof(ts_sprintf));
   data->string=(char *)malloc(512000*sizeof(char)); /*TODO: warning, can break if the string is to long */
   data->string=(char *)malloc(5120000*sizeof(char)); /*TODO: warning, can break if the string is to long */
   data->beg=0;
   
   xml_trisurf_header(fh, vesicle);
@@ -33,14 +34,15 @@
   xml_trisurf_vtx_neigh(data,vesicle->vlist);   
   xml_trisurf_vtx_tristar(data,vesicle->vlist);
   xml_trisurf_nucleus(data,vesicle);
#ifdef COMPRESSION
   xml_trisurf_constvolarea(data,V0,A0);
//#ifdef COMPRESSION
   char *compressed;
   ts_uint nbytes=ts_compress_string64(data->string, data->beg-1, &compressed); //suppress null character at the end with by substracting 1
   fwrite(compressed, sizeof(unsigned char), nbytes, fh);
   free (compressed);
#else
   fprintf(fh,"%s", data->string);
#endif
//#else
//   fprintf(fh,"%s", data->string);
//#endif
   free(data->string);  /* TODO: valgrind is not ok with this! */
   free(data);
   xml_trisurf_footer(fh);
@@ -127,8 +129,14 @@

ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle){
   if(vesicle->R_nucleus>0.0 || (vesicle->R_nucleusX>0.0 && vesicle->R_nucleusY>0.0 && vesicle->R_nucleusZ>0.0)){
      ts_sprintf(data,"<nucleus>%.17e %.17e %.7e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
      ts_sprintf(data,"<nucleus>%.17e %.17e %.17e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
   }
   return TS_SUCCESS;
}
ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area){
   ts_sprintf(data,"<constant_volume>%.17e</constant_volume>",volume);
   ts_sprintf(data,"<constant_area>%.17e</constant_area>",area);

   return TS_SUCCESS;
}

@@ -138,27 +146,46 @@
/* zlib compression base64 encoded */
/* compressed must not be pre-malloced */
/* taken from https://gist.github.com/arq5x/5315739 */
ts_uint ts_compress_string64(char *data, ts_uint data_len, char **compressed){
ts_uint ts_compress_data(char *data, ts_uint data_len, char **compressed){
   z_stream defstream;
   defstream.zalloc = Z_NULL;
   defstream.zfree = Z_NULL;
   defstream.opaque = Z_NULL;
   defstream.avail_in = data_len+1;
   defstream.next_in = (unsigned char *)data;   
   char *compr=(char *)malloc(data_len*sizeof(char *));
   fprintf(stderr,"WAS HERE %d\n", data_len);
   *compressed=(char *)malloc(data_len*sizeof(char *));
   defstream.avail_out = data_len+1;
   defstream.next_out = (unsigned char *)compr;
   defstream.next_out = (unsigned char *)*compressed;
   deflateInit(&defstream, Z_BEST_COMPRESSION);
       deflate(&defstream, Z_FINISH);
       deflateEnd(&defstream);
   /*base64 encode*/
   return defstream.total_out;
}

ts_uint ts_compress_string64(char *data, ts_uint data_len, char **encoded_compressed){
   size_t nbase;
   *compressed=base64_encode((unsigned char *)compr,(size_t)defstream.total_out,&nbase);
   //fwrite(base64, sizeof(unsigned char), nbase, fh);
   char *compr;
   size_t number_of_compressed_bytes=ts_compress_data(data, data_len, &compr);
   *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase);
   free(compr);
   return nbase;
}

char *ts_compress_intlist(int *data, ts_uint data_len){
   size_t nbase;
   char *compr;
   size_t number_of_compressed_bytes=ts_compress_data((char *)data, data_len*sizeof(int), &compr);
   char *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase);
   free(compr);
   ts_uint header[4]={1, data_len, data_len, nbase};
   char *encoded_header=(char *)base64_encode((unsigned char *)header, 4*sizeof(ts_uint), &nbase);
   encoded_header=realloc(encoded_header, 4*sizeof(ts_uint)+strlen(encoded_compressed));
   encoded_header=strcat(encoded_header,encoded_compressed);
   free(encoded_compressed);
   return encoded_header;
}

ts_uint ts_decompress_string64(char *b64, ts_uint data_len, char **decompressed){
return TS_SUCCESS;