Hi all,
I am using compound data types with vlen strings and integers. The
struct containing the strings and integers also contains a couple of
methods, which prevents me from using the HOFFSET macro, so I used
sizeof() and/or the getSize() method from the H5 data types to determine
the offset of the components. This works under my personal 32-bit
system, but ends with a segmentation fault under a 64-bit system.
I found out that the offset determined by HOFFSET is different from the
sizeof() and getSize() methods. I avoided this problem by inserting the
int as the last element.
A small sample code is added at the end of this mail.
My test system is:
> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 9.10
Release: 9.10
Codename: karmic
> uname -a
Linux xxxxx 2.6.31-22-generic #70-Ubuntu SMP Wed Dec 1 23:48:17 UTC 2010
x86_64 GNU/Linux
> gcc --version
gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1
Is this a general problem/issue or due wrong usage?
~Mathias
---
#include <iostream>
#include <string>
using std::cout;
using std::endl;
using std::string;
#include "H5Cpp.h"
using namespace H5;
char* tc_string(const string& s) {
char* ret = new char[s.length() + 1];
size_t l = s.copy(ret, s.length(), 0);
ret[l] = 0;
return ret;
}
int main(int argc, char* argv[]) {
{
H5File* file = new H5File("test1.h5", H5F_ACC_TRUNC);
StrType stringtype(PredType::C_S1, H5T_VARIABLE);
struct cv {
char* id;
int accession;
};
cout << "char* first: " << endl;
cout << " sizeof(char*) " << sizeof(char*) << endl;
cout << " stringtype.getSize() " << stringtype.getSize() <<
endl;
cout << " HOFFSET(cv, accession) " << HOFFSET(cv, accession)
<< endl;
CompType cvtype(sizeof(cv));
size_t offset = 0;
cvtype.insertMember("id", offset, stringtype);
offset += stringtype.getSize();
cvtype.insertMember("accession", offset, PredType::NATIVE_INT);
offset += PredType::NATIVE_INT.getSize();
cv* test = new cv[2];
test[0].accession = 12;
test[0].id = tc_string("1.1");
test[1].accession = 23;
test[1].id = tc_string("2.2");
DSetCreatPropList cparms;
hsize_t dimds[1] = { 2 };
DataSpace dataspace(1, dimds, dimds);
DataSet ds = file->createDataSet("test1", cvtype, dataspace,
cparms);
ds.write(test, cvtype);
for (int i = 0; i < 2; ++i) {
delete[] test[i].id;
}
delete[] test;
delete file;
}
cout << endl;
{
H5File* file = new H5File("test2.h5", H5F_ACC_TRUNC);
StrType stringtype(PredType::C_S1, H5T_VARIABLE);
struct cv {
int accession;
char* id;
};
cout << "int* first:" << endl;
cout << " sizeof(int) " << sizeof(int) << endl;
cout << " PredType::NATIVE_INT " << PredType::NATIVE_INT.getSize() <<
endl;
cout << " HOFFSET(cv, id) " << HOFFSET(cv, id) << endl;
CompType cvtype(sizeof(cv));
size_t offset = 0;
cvtype.insertMember("id", offset, stringtype);
offset += stringtype.getSize();
cvtype.insertMember("accession", offset, PredType::NATIVE_INT);
cv* test = new cv[2];
test[0].accession = 12;
test[0].id = tc_string("1.1");
test[1].accession = 23;
test[1].id = tc_string("2.2");
DSetCreatPropList cparms;
hsize_t dimds[1] = { 2 };
DataSpace dataspace(1, dimds, dimds);
DataSet ds = file->createDataSet("test2", cvtype, dataspace,
cparms);
ds.write(test, cvtype);
for (int i = 0; i < 2; ++i) {
delete[] test[i].id;
}
delete[] test;
delete file;
}
return 0;
}
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