Hi, I'm looking for a way to obtain offsets of data members of a C++ class which is of non-POD nature. Here's why: I'd like to store data in HDF5 format, which seems most suited for my kind of material (numerical simulation output), but it is perhaps a rather C-oriented library. I want to use it through the C++ interface, which would ...
I would like to programatically change the data associated with a dataset in an HDF5 file. I can't seem to find a way to either delete a dataset by name (allowing me to add it again with the modified data) or update a dataset by name. I'm using the C API for HDF5 1.6.x but pointers towards any HDF5 API would be useful. ...
We are in evaluating technologies that we'll use to store data that we gather during the analysis of C/C++ code. In the case of C++, the amount of data can be relatively large, ~20Mb per TU. After reading the following SO answer it made me consider that HDF5 might be a suitable technology for us to use. I was wondering if people here ...
Given a vector of strings, what is the best way to write them out to a HDF5 dataset? At the moment I'm doing something like the following: const unsigned int MaxStrLength = 512; struct TempContainer { char string[MaxStrLength]; }; void writeVector (hid_t group, std::vector<std::string> const & v) { // // Firstly...
Anyone out there have enough experience w/ NetCDF and HDF5 to give some pluses / minuses about them as a way of storing scientific data? I've used HDF5 and would like to read/write via Java but the interface is essentially a wrapper around the C libraries, which I have found confusing, so NetCDF seems intriguing but I know almost nothi...
I'm having a HDF5 file with one-dimensional (N x 1) dataset of compound elements - actually it's a time series. The data is first collected offline into the HFD5 file, and then analyzed. During analysis most of the data turns out to be uninteresting, and only some parts of it are interesting. Since the datasets can be quite big, I would ...
Our company has been for a while looking at a file format to hold a large amount of lab sensor data. Each time they run the instrumentation, it generates a file, which we consume and store in a database for trending, etc. A hierarchical format is preferred as it allows us to "group" data. This is a intermediate file format before we p...
We are evaluating the performance of HDF5 regarding chunked datasets. Especially we try to figure out if it is possible to read across different contiguous chunks and how the performance is influenced by doing so? E.g. we have a dataset with chunk size of 10, a dataset with 100 values and want to read values 23 to 48. Will there be a gre...
Our main program is in java but the code that extracts our data from storage is written in C. I need to build an HDF5 file from extracted data. Would it be better to use JNI to call the C code to get the data and then build the HDF5 file from Java or to build the HDF5 from the C code? I have little experience with JNI or C. Also One o...
Hi all, I'm currently exploring HDF5. I've read the interesting comments from the thread "Evaluating HDF5" and I understand that HDF5 is a solution of choice for storing the data, but how do you query it ? For example, say I've a big file containing some identifiers : Is there a way to quickly know if a given identifier is present in the...
I am trying to load an hdf5 into R and running into some problems. Here are the steps I took to configure my environment: R 2.10.0 (x64) on Mac OS X 10.6 hdf5 1.8.3 installed via macports hdf5_1.6.9.tar.gz from CRAN I suspect the problem I am having relates to incompatibilities in my version of HDF5 and the one the R module expects....
Hello all, Question in nutshell What is the best way to get Python and Java to play nice with each other? More detailed explanation I have a somewhat complicated situation. I'll try my best to explain both in pictures and words. Here's the current system architecture: We have an agent-based modeling simulation written in Java. ...
hello; I am trying to write a matlab mex function which uses libhdf5; My Linux install provides libhdf5-1.8 shared libraries and headers. However, my version of Matlab, r2007b, provides a libhdf5.so from the 1.6 release. (Matlab .mat files bootstrap hdf5, evidently). When I compile the mex, it segfaults in Matlab. If I downgrade my vers...
I'm trying to install h5py in Mac OS X 10.6.3. First I installed HDF5 1.8, which used the following commands: ./configure \ --prefix=/Library/Frameworks/Python.framework/Versions/Current \ --enable-shared \ --enable-production \ --enable-threadsafe \ CPPFLAGS=-I/Library/Frameworks/Python.framework/Versions/Current/include \ LDFLAGS=-L/...
I'm getting ( http://www.hdfgroup.org/projects/hdf.net/) The specified module could not be found. (Exception from HRESULT: 0x8007007E) from the dependency walker i'm seeing that SZLIBDLL.DLL is missing i tried to download it from random place but then i got another error. Does any one had that problem? i tried also vs2005 and ...
I am using the h5py python package to read files in HDF5 format. (e.g. somefile.h5) I would like to write the contents of a dataset to a text file. For example, I would like to create a text file with the following contents: 1,20,31,75,142,324,78,12,3,90,8,21,1 I am able to access the dataset in python using this code: import h5py f ...
hi. Is hdf5 able to handle multiple threads on its own, or does it have to be externally synchronized? OpenMP example suggests later. if former, what is the proper way to define dataspace to write? thank you ...
I have an application which is compiled using compiler wrappers such as h5fc/h5cc (the HDF5 compiler wrappers), or mpif90/mpicc (the MPI compiler wrappers). These are just wrappers, and it is possible using the -show argument to see the real underlying compiler, e.g. $ h5fc -show ifort -fPIC [...] -lz -lm $ mpif90 -show ifort [...] -lmp...
Ok, I have the HDF5 library downloaded from the official site, and I have a few DLLs, including hdf5dll.dll, and hdf5_hldll.dll. I have what I think to be some wrappers around the native calls, in my classes H5, H5LT, H5F, and H5T. Example from H5.cs: namespace HDF5 { using hid_t = System.Int32; using herr_t = System.Int32; ...
I have a 3rd party utility written in C++ that creates an HDF5 file with a single data group. I would like to import two H5 files each with a unique data group, and output a single H5 file with the two data groups. Does anyone have experience with working with HDF5 in C#? ...