Have a look at these type definitions. . . https://www.hdfgroup.org/HDF5/doc/RM/PredefDTypes.html
and this description of type conversion, in particular section 6.9 https://www.hdfgroup.org/HDF5/doc/UG/UG_frame11Datatypes.html#Dtransfer I suspect the problem may have to do with signed vs. UNsigned types here. Also, regarding array dimension ordering, see this. . . https://www.hdfgroup.org/HDF5/doc/fortran/index.html#FortranUserNotes Mark From: Hdf-forum <[email protected]<mailto:[email protected]>> on behalf of Richa Mathur <[email protected]<mailto:[email protected]>> Reply-To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Date: Tuesday, August 4, 2015 7:43 PM To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Subject: Re: [Hdf-forum] h5dopen returns error Thanks again Marc, I now dont get core dump For H5T_STD_U16BE I am able to correctly read and the values that I read match with the h5dump output. However for H5T_STD_U64BE when I read using the H5T_NATIVE_INTEGER my output does not match with h5dump. I am using hdf5-1.8.7. If I use hdf5-1.8.13 it conflicts with the netcdf -gfortran reader that is also a part of my code. Is the array shape (12,22,26) indicated by the h5dump same as the one in fortran or it gets inverted (26,22,12) ? Gompie On Tue, Aug 4, 2015 at 9:58 PM, Miller, Mark C. <[email protected]<mailto:[email protected]>> wrote: So, HDF5 will handle all the 'conversion' from whatever type is used to store the data in the file to whatever type you are using to store the data in memory. So, for mem_type arg to h5dread_f, all you need to do is inform HDF5 what the datatype is of the buffer (data_out) you are reading into. You have defined data_out as INTEGER in your programming language. So, I suspect the right thing to do is. . . CALL h5dread_f(dset_id,H5T_NATIVE_INTEGER, data_out, data_dims, error) That tells HDF5 that data_out is the caller's *native* integer type and it will convert from whatever is in the file H5T_STD_I64BE (a 64 bit big endianne integer) to that type automatically when it reads it. Mark From: Hdf-forum <[email protected]<mailto:[email protected]>> on behalf of Richa Mathur <[email protected]<mailto:[email protected]>> Reply-To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Date: Tuesday, August 4, 2015 6:43 PM To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Subject: Re: [Hdf-forum] h5dopen returns error Hi Marc, Thanks again. That link is helpful. I was able to read in the data directly using the path in the h5read_f. I use INTEGER, dimension(12,96):: data_out data_dims(1) = 12, data_dims(2) =96 CALL h5dread_f(dset_id,H5T_STD_I64BE , data_out, data_dims, error) as the h5dump indicates DATA_TYPE as H5T_STF_I64BE. But it does not read properly ( gives core dump). I compile on a x86_64 m/c gfortran. GROUP "All_Data" { GROUP "AMS-SDR_All" { DATASET "BeamTime" { DATATYPE H5T_STD_I64BE Gompie On Tue, Aug 4, 2015 at 4:24 PM, Miller, Mark C. <[email protected]<mailto:[email protected]>> wrote: Hmm. At this point, I think it may be more productive for everyone if you would review the manual, https://www.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html, a bit more to be sure you are attempting to use the HDF5 interface correctly. In particular, your 2nd call to h5gopen_f is still specfying 'file_id' for first arg when it should be specifing 'grp_id1'. AMS-SDR_All is a group that 'lives in' the "All_Data" group (grp_id1), not the root group (file_id). Next, I am pretty certain you can just directly h5dopen_f "All_Data/AMS-SDR_All/BeamTime" and avoid all the business with the groups. Mark From: Hdf-forum <[email protected]<mailto:[email protected]>> on behalf of Richa Mathur <[email protected]<mailto:[email protected]>> Reply-To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Date: Tuesday, August 4, 2015 1:06 PM To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Subject: Re: [Hdf-forum] h5dopen returns error Thanks Mark, Christian , the problem was case sensitivety and the first level All_Data did not return any error. Now since the path to BeamTime is All_Data/AMS-SDR_All/BeamTime I gave CALL h5gopen_f(file_id,"All_Data" , grp_id1, grp_hdferr) print *,"Open Group ID ID ERROR",grp_id1, grp_hdferr CALL h5gopen_f(file_id,"AMS-SDR_All" , grp_id2, grp_hdferr) [should I give the grp_id1 instead of file_id ?] print *,"Open Group AMS-SDR ID ERROR",grp_id2, grp_hdferr ( here the hdferr is -1) CALL h5dopen_f(grp_id1,"BeamTime", dset_id, error) Please help On Tue, Aug 4, 2015 at 3:53 PM, Christian Oyarzun <[email protected]<mailto:[email protected]>> wrote: It is case sensitive. it should be: CALL h5gopen_f(file_id,"All_Data" , grp_id1, grp_hdferr) not: CALL h5gopen_f(file_id,"All_data" , grp_id1, grp_hdferr) —Christian On Aug 4, 2015, at 3:45 PM, Richa Mathur <[email protected]<mailto:[email protected]>> wrote: Thanks Mark and Corey. after CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file_id, error) I gave CALL h5gopen_f(file_id,"All_data" , grp_id1, grp_hdferr) as the first call to open the group and got grp_hdrerr as -1. I guess there is an error opening the group All_data. the h5dump -n output is HDF5 "SAMS_npp_d20150728_t2359556_e0000273_b19431_c20150729063134831043_nasa_ops.h5" { FILE_CONTENTS { group / group /All_Data group /All_Data/AMS-SDR_All dataset /All_Data/AMS-SDR_All/BeamTime dataset /All_Data/AMS-SDR_All/BrightnessTemperature dataset /All_Data/AMS-SDR_All/BrightnessTemperatureFactors Any help.... On Tue, Aug 4, 2015 at 3:11 PM, Miller, Mark C. <[email protected]<mailto:[email protected]>> wrote: yeah, agree. "BeamTime" is in group "All_Data". To get to BeamTime, you have to H5Gopen the group and use the hid_t you get from that group in place of 'file_id' arg in h5dopen. Don't forget to close the group (and dataset) after you're done. Mark From: Hdf-forum <[email protected]<mailto:[email protected]>> on behalf of Richa Mathur <[email protected]<mailto:[email protected]>> Reply-To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Date: Tuesday, August 4, 2015 12:03 PM To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Subject: Re: [Hdf-forum] h5dopen returns error Thanks Mark !!! Filename is complete. The file_id that is returned from hdfopen_f (filename, H5F_ACC_RDONLY_F, file_id, error) is 16777217 and error code is 0. How do I find if 'BeamTime' is in root group or sub group ? The H5Dump is as below I guess the BeamTime is inside a GROUP "All_Data", GROUP "All_Data" { GROUP "AMS-SDR_All" { DATASET "BeamTime" { DATATYPE H5T_STD_I64BE DATASPACE SIMPLE { ( 12, 96 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) } DATA { (0,0): 1816819231684734, 1816819231702752, 1816819231720770, (0,3): 1816819231738788, 1816819231756806, 1816819231774824 Gompie On Tue, Aug 4, 2015 at 2:52 PM, Miller, Mark C. <[email protected]<mailto:[email protected]>> wrote: Are you sure you are getting a valid file_id back from the h5fopen_f call? Are you by chance missing an extension on the filename such as 'satfilename.h5' and is the dataset 'BeamTime' in the 'root group' of the file or perhaps some sub-group? Mark From: Hdf-forum <[email protected]<mailto:[email protected]>> on behalf of Richa Mathur <[email protected]<mailto:[email protected]>> Reply-To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Date: Tuesday, August 4, 2015 10:42 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [Hdf-forum] h5dopen returns error Hi I am trying to read a hdf5 file in fortran95 ( gfortran). Peice of code is INTEGER(HID_T) :: file_id ! File identifier INTEGER(HID_T) :: dset_id ! Dataset identifier INTEGER :: error ! Error flag INTEGER :: i, j INTEGER, DIMENSION(96,12) :: dset_data, data_out ! Data buffers INTEGER(HSIZE_T), DIMENSION(2) :: data_dims filename='satfilename' CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file_id, error) CALL h5dopen_f(file_id,"BeamTime", dset_id, error) print *,"Data Set(ATMS) ID ERROR",dset_id, error . The h5dopen_f returns error as -1. Later on when I use CALL h5dread_f(dset_id, H5T_STD_I64BE, data_out, data_dims, error) error -1 is returned from this function as well and I get incorrect values of my variable in data_out. Can you help Gompie The h5dump of my hdf5 file has GROUP "All_Data" { GROUP "AMS-SDR_All" { DATASET "BeamTime" { DATATYPE H5T_STD_I64BE DATASPACE SIMPLE { ( 12, 96 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) } DATA { (0,0): 1816819231684734, 1816819231702752, 1816819231720770, (0,3): 1816819231738788, 1816819231756806, 1816819231774824 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. 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