tmullins / hdf5oct Goto Github PK

running 'make' produces the following error:
h5read.cc:41:10: fatal error: gripes.h: No such file or directory
41 | #include "gripes.h"
| ^~~~~~~~~~
compilation terminated.
make: *** [makefile:19: h5read.o] Error 1

% In its present form, reading certain large chunked datasets
% consumes a tremendous amount of memory while it is as fast as
% it should be if the dset is not chunked, or if the load()
% function is used.
% This has to be fixed quickly, but I don't understand it yet,
% I don't see much of a difference in what they both do.
%
% Maybe somebody else can confirm and/or comment?
%
pkg load hdf5oct;

%a = rand(230,40,40,70); % let's call that x)
a = rand(230,43,43,71); % y)
s = size(a)
s(1)=1
h5create("testchunk.h5","/foo_chunked",size(a),'ChunkSize',s)
h5write("testchunk.h5","/foo_chunked",a)
h5create("testchunk.h5","/foo_unchunked",size(a))
h5write("testchunk.h5","/foo_unchunked",a)

disp("load:")
%str = load("-hdf5","testchunk.h5"); %okay for both x) and y)
%clear str;
disp("read unchunked:")
%b = h5read("testchunk.h5","/foo_unchunked"); %okay for both x) and y)
disp("read chunked:")
b = h5read("testchunk.h5","/foo_chunked"); %okay for x), catastrophic for y)

I was going through the Readme of this repository and found this statement in TODO.

read string typed datasets

Is reading a string dataset really an issue in HDF5?
Is there any special procedure or understanding needed for that?

I am working on the HDF5 wrapper in C# using HDF.PInvoke. My wrapper can write the string dataset. I am facing the issue while reading the string dataset. I have explored many links.
Even sharpHDF, another GitHub wrapper on HDF.PInvoke does not support writing and hence, reading string datatype.

What is the issue that you are facing? If you can share the issue, we may together find the solution.

There are warnings when compiling under recent Octave(s). According to docs, the "error_state" variable has been removed and replaced by exceptions. Compiling h5read.cc after adding
#define error_state 0
is ok.
Thus I think the code "if (!error_state) {....}" can be deleted completely.

On Ubuntu 18.04; Octave installed with apt install octave.

In the source directory, make fails with error:

CXX=h5c++ mkoctfile -g -c h5read.cc
/bin/sh: 1: mkoctfile: not found
makefile:19: recipe for target 'h5read.o' failed
make: *** [h5read.o] Error 127

I am trying to read a double precision dataset with
2 x 4 x 4656 x 946 x 28 (C ordering, as displayed by hdfview), which is chunked into pieces of 2 x 4 x 4656 x 946 x 1, and h5read works for several minutes after allocating the memory. I wonder if this can be improved or is just what one must expect.

loading of hdf5 file fails with error :

x=h5read('ec013.156.nwb','/file_create_date')
HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 140122874586880:
#000: ../../../src/H5Dio.c line 173 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#1: ../../../src/H5Dio.c line 420 in H5D__read(): unable to set up type info
major: Dataset
minor: Unable to initialize object
#2: ../../../src/H5Dio.c line 952 in H5D__typeinfo_init(): unable to convert between src and dest datatype
major: Dataset
minor: Feature is unsupported
#3: ../../../src/H5T.c line 4535 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object
error: error when reading dataset

I've installed hdf5oct 0.4.0 in octave 4.0.0 on linux. The file is available from here:
https://portal.nersc.gov/project/crcns/download/nwb-1/hc-3/ec013.15.zip

The file can be loaded into matlab, and h5dump works also. Therefore, I'd assume it's a problem with hdf5oct.

running 'make' produces an error:

sphere@WP2:~/gait_cnn/datasets/scripts/scripts/hdf5oct/hdf5oct$ make
CXX=h5c++ mkoctfile -g -c h5read.cc
In file included from h5read.cc:54:0:
h5read.h:72:22: error: ISO C++ forbids initialisation of member ‘h5_dims’ [-fpermissive]
h5read.h:72:22: error: making ‘h5_dims’ static [-fpermissive]
h5read.h:72:22: error: invalid in-class initialisation of static data member of non-integral type ‘hsize_t* {aka long long unsigned int_}’
h5read.h:73:25: error: ISO C++ forbids initialisation of member ‘h5_maxdims’ [-fpermissive]
h5read.h:73:25: error: making ‘h5_maxdims’ static [-fpermissive]
h5read.h:73:25: error: invalid in-class initialisation of static data member of non-integral type ‘hsize_t_ {aka long long unsigned int_}’
h5read.cc: In constructor ‘H5File::H5File(const char_, bool)’:
h5read.cc:516:40: error: invalid conversion from ‘herr_t ()(void*) {aka int ()(void_)}’ to ‘void__’ [-fpermissive]
h5read.cc:516:40: error: too many arguments to function ‘herr_t H5Eget_auto1(herr_t (__)(void_), void*)’
/usr/include/H5Epublic.h:212:15: note: declared here
h5read.cc:518:31: error: too many arguments to function ‘herr_t H5Eset_auto1(H5E_auto1_t, void)’
/usr/include/H5Epublic.h:216:15: note: declared here
h5read.cc:538:38: error: invalid conversion from ‘H5E_auto1_t {aka int ()(void)}’ to ‘void_’ [-fpermissive]
h5read.cc:538:38: error: too many arguments to function ‘herr_t H5Eset_auto1(H5E_auto1_t, void_)’
/usr/include/H5Epublic.h:216:15: note: declared here
h5read.cc: In destructor ‘H5File::~H5File()’:
h5read.cc:568:7: error: ‘h5_dims’ was not declared in this scope
h5read.cc:573:7: error: ‘h5_maxdims’ was not declared in this scope
h5read.cc: In member function ‘int H5File::open_dset(const char_)’:
h5read.cc:604:49: error: too many arguments to function ‘hid_t H5Dopen1(hid_t, const char_)’
/usr/include/H5Dpublic.h:145:14: note: declared here
h5read.cc:625:3: error: ‘h5_dims’ was not declared in this scope
h5read.cc:626:3: error: ‘h5_maxdims’ was not declared in this scope
h5read.cc: In member function ‘octave_value H5File::read_dset_complete(const char_)’:
h5read.cc:653:19: error: ‘h5_dims’ was not declared in this scope
h5read.cc: In member function ‘octave_value H5File::read_dset_hyperslab(const char_, const Matrix&, const Matrix&, const Matrix&, const Matrix&, int)’:
h5read.cc:727:24: error: ‘h5_dims’ was not declared in this scope
h5read.cc:731:11: error: ‘h5_dims’ was not declared in this scope
h5read.cc: In member function ‘void H5File::write_dset(const char_, octave_value)’:
h5read.cc:915:113: error: too many arguments to function ‘hid_t H5Gcreate1(hid_t, const char_, size_t)’
/usr/include/H5Gpublic.h:147:14: note: declared here
h5read.cc:947:7: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:955:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:961:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:967:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:973:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:979:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:985:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:991:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:997:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:1003:11: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:1011:7: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc:1017:7: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
h5read.cc: In member function ‘void H5File::write_dset_hyperslab(const char_, octave_value, const Matrix&, const Matrix&, const Matrix&, const Matrix&, int)’:
h5read.cc:1089:11: error: ‘h5_maxdims’ was not declared in this scope
h5read.cc:1100:11: error: ‘h5_dims’ was not declared in this scope
h5read.cc:1111:31: error: ‘h5_dims’ was not declared in this scope
h5read.cc: In member function ‘octave_value H5File::read_att(const char_, const char_)’:
h5read.cc:1169:40: error: ‘hdf5_check_attr’ was not declared in this scope
h5read.cc: In member function ‘void H5File::write_att(const char_, const char_, const octave_value&)’:
h5read.cc:1375:62: error: too many arguments to function ‘hid_t H5Acreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Apublic.h:105:16: note: declared here
h5read.cc: In member function ‘void H5File::create_dset(const char_, const Matrix&, const char_, const Matrix&)’:
h5read.cc:1449:58: error: too many arguments to function ‘hid_t H5Dcreate1(hid_t, const char_, hid_t, hid_t, hid_t)’
/usr/include/H5Dpublic.h:143:14: note: declared here
make: *_* [h5read.o] Error 1

Hello,

I was wondering if you would allow me to add hdf5oct to the GNU octave core under GPLv3. I found that you originally chose the LGPLv3 so I am guessing you might not be opposed to the GPL. Of course, you will still be free to keep it on your website or github under another license, it will always be yours to create as many copies under as many different licenses as you want.

If you agree, my fork will be added to GNU octave, under GPLv3+ and
with you, me and the other contributors as its copyright owner.

best regards

Stefan

edit: I just realize that asking you for permission might eventually be obsolete, according to this table:
http://www.gnu.org/licenses/gpl-faq.html#AllCompatibility
But anyway, I hope it's welcome and you don't mind that we integrate it.

whether using
$ make install
or
>> pkg install hdf5oct-0.4.0.tar.gz
on Octave 3.8.1 or Octave 4.0, I get the error

$HOME/octave/hdf5oct-0.2.0/h5read.oct: undefined symbol: H5P_CLS_DATASET_CREATE_ID_g
error: called from 'doc_cache_create>create_cache' in file /usr/share/octave/4.0.0/m/help/doc_cache_create.m near line 106, column 18