k-Wave

1. frli8848
   

   Member
   Joined: Mar '22
   Posts: 7

   Hi all,

   I'm new to k-Wave and trying out the demos but I run into problems with the CUDA and C++ (OMP) code. I tried the example_cpp_running_simulations.m demo and I just get:
   

   $ ./kspaceFirstOrder-OMP -i /tmp/example_input.h5 -o /tmp/example_output.h5 --p_final --p_max
   
   -snip-
   
    Error: Invalid format of the input file: iostream error  
   
   -snip-

   I have traced that down to the file:
   

   kspaceFirstOrder-OMP/Hdf5/Hdf5FileHeader.cpp

   where getFileType() returns 3 and FileType::kInput is 0 in the function:
   

   void Hdf5FileHeader::readHeaderFromInputFile(Hdf5File& inputFile)

   Is this an installation issue or a bug? (the pre-compiled binaries have the same problem).

   /Fredrik

   Posted 2 years ago #

2. frli8848
   

   Member
   Joined: Mar '22
   Posts: 7

   Looking closer at the /tmp/example_input.h5 file there seems to be no file_type entry (Dataset):
   

   $ h5ls  /tmp/example_input.h5 | grep file_type

   returns nothing.

   Posted 2 years ago #

3. frli8848
   

   Member
   Joined: Mar '22
   Posts: 7

   After some more debuggin i realized that file_type is an h5 Attribute and not a Dataset:
   

   $ h5dump -a file_type  /tmp/example_input.h5
   HDF5 "/tmp/example_input.h5" {
   ATTRIBUTE "file_type" {
      DATATYPE  H5T_STRING {
         STRSIZE H5T_VARIABLE;
         STRPAD H5T_STR_NULLTERM;
         CSET H5T_CSET_UTF8;
         CTYPE H5T_C_S1;
      }
      DATASPACE  SCALAR
      DATA {
      (0): "input"
      }
   }
   }

   but reading that Attribute seems to fail.

   Posted 2 years ago #

4. frli8848
   

   Member
   Joined: Mar '22
   Posts: 7

   I made a small test program:
   

   #include <assert.h>
   #include <stdlib.h>
   #include "hdf5.h"
   #include "hdf5_hl.h"
   
   int main()
   {
       herr_t  status;
   
       hid_t file_id = H5Fopen("/tmp/example_input.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
       assert(file_id >= 0);
   
       char string[256] = "";
   
       fprintf(stderr, "string : %s\n", string);
   
       fprintf(stderr, "---- reading attribute ----\n");
       status = H5LTget_attribute_string(file_id, "/",
                                         "file_type", string);
       assert(status >= 0);
   
       fprintf(stderr, "string : %s\n", string);
   
       status = H5Fclose(file_id);
       assert(status >= 0);
   }

   $ gcc test_attribute.c -lhdf5  -lhdf5_hl -o test_h5_attr
   $ ./test_h5_attr
   string :
   ---- reading attribute ----
   string : @u�U

   Not sure why this fails since the Attribute looks OK in hdfview?

   Posted 2 years ago #

5. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,643

   Hi Fredrick,

   Have you tried the solution here?

   Posted 2 years ago #

6. frli8848
   

   Member
   Joined: Mar '22
   Posts: 7

   Thanks Bradley, this solved it (I'm on 2020b Update 3 on Gentoo Linux)!

   /Fredrik

   Posted 2 years ago #

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