CODEWITHSUNDEEP
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jrsm
jrsm

Reputation: 1695

Read from dataset in HDF5 file with datatype detection

I currently try to read some data from a hdf5 dataset in C which looks like this.

dataset = H5Dopen(ic_group, 'vx', H5P_DEFAULT);
status = H5Dread(dataset, H5T_NATIVE_FLOAT, memspace,H5S_ALL,
                          H5P_DEFAULT, vx_ptr);

status = H5Dclose(dataset);

Here ic_group is a group containing the dataset vx, memspace is a hyperslab in memory and vx_ptr the data in memory. This approach works good, however since I want to work with different datatypes later, I want to read the type directly from the dataset:

hid_t datatype;
datatype = H5Dget_type(dataset);
status = H5Dread(dataset, datatype, memspace,H5S_ALL,
                          H5P_DEFAULT, vx_ptr);

Unfortunately this approach leads to a segfault in the function H5Dread . Maybe I am missing something? Thank you for any suggestions.

EDIT: I don't know if this is usefull but the backtrace of gdb goes down to 0x00007ffff5adbd1e in __memcpy_ssse3_back () from /lib64/libc.so.6 .

Upvotes: 2

Views: 2448

Answers (1)

Yossarian
Yossarian

Reputation: 5471

You can check that the datatype returned from H5Dget_type(dataset) is what you expect by using H5Tequal(datatype, H5T_<type>). It should match both the datatype used to write the dataset and also the equivalent type of vx_ptr (this is probably what's actually caused the segfault).

Also, datatype needs to be closed with H5Tclose(datatype).

Upvotes: 1

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