cgp_coord_read_data_f failure

[adrianjhpc]

Hi,

Running parallel cgns with HDF5 I'm getting a error when using more than one process calling cgp_coord_read_data_f on different zones. The call is failing in HDF5 with "H5Dopen2() failed". It works fine if I run with just one process, but fails at anything over that.

Any ideas what would cause this error?

cheers

[brtnfld]

We will need more details. Do all the ranks report that error? Does the file pass cgnscheck? What is the dataset it is failing to open?

Can you provide a code snippet?

It might help to compile CGNS with #define ADFH_DEBUG_ON (adfh.c)

[adrianjhpc]

A representative code snippet is:

      call cgp_pio_mode_f(CGP_INDEPENDENT, ierr)
      if(ierr .ne. CG_OK) then
         write(*,*) 'cgp_pio_mode_f error parallelread'
         call cg_error_print_f()
         call abortmpi()
      end if

      call cgp_open_f(cgns_filename,CG_MODE_READ,fid,ierr)
      if(ierr .ne. CG_OK) then
         write(*,*) 'cgp_open_f error parallelread'
         call cg_error_print_f()
      end if
....
      minrange(1) = 1
      minrange(2) = 1
      minrange(3) = 1

      call getmpiid(rank)

      maxrange(1) = imax
      maxrange(2) = jmax
      maxrange(3) = kmax

      zonenum = blocknum

      xnum = 1
      call cgp_coord_read_data_f(fid,basenum,zonenum,xnum,
     &     minrange,maxrange,xyz(:,:,:,1),ierr)
      if(ierr .ne. CG_OK) then
         write(*,*) rank,'X cgp_coord_read_data_f error',maxrange
         call cg_error_print_f()
         call abortmpi()
      end if

Not all ranks have this problem, some complete fine.

For cgnscheck it gives lots of warnings but ultimate passes:

checking complete
1280 warnings (1280 shown)

I can provide the CGNS file if possible

[adrianjhpc]

Just been checking, HDF5 1.10.6 works, 1.12.2 doesn't. Neither does 1.14.0.

When compiled with #define ADFH_DEBUG_ON I get this output:

  #000: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5D.c line 285 in H5Dopen2(): unable to open dataset
    major: Dataset
    minor: Can't open object
  #001: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset
    major: Dataset
    minor: Can't open object
  #004: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5Dint.c line 1475 in H5D__open_name(): can't get object type
    major: Dataset
    minor: Can't get value
  #005: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5Oint.c line 1651 in H5O_obj_type(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #006: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5Oint.c line 1051 in H5O_protect(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #007: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5AC.c line 1426 in H5AC_protect(): H5C_protect() failed
    major: Object cache
    minor: Unable to protect metadata
  #008: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5C.c line 2370 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #009: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5C.c line 7315 in H5C__load_entry(): incorrect metadata checksum after all read attempts
    major: Object cache
    minor: Read failed
  #010: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5Ocache.c line 203 in H5O__cache_get_final_load_size(): can't deserialize object header prefix
    major: Object header
    minor: Unable to decode value
  #011: /home/nx01/nx01/adrianj/hdf5-1.12.2/src/H5Ocache.c line 1202 in H5O__prefix_deserialize(): bad object header version number
    major: Object header
    minor: Wrong version number
H5Dopen2() failed

[brtnfld]

Which version of CGNS are you using?

[adrianjhpc]

4.3.0

[adrianjhpc]

If the outcome is just "Use HDF5 1.10.x" that's fine, I just wondered if performance changed for newer versions of HDF5

[brtnfld]

Can you try it with develop? Do you know what version of HDF5 and CGNS was used to create the file?

[adrianjhpc]

I not sure the versions used to create the file. I can convert the file in cgnscheck if that helps.

By develop do you mean the git develop branch?

[adrianjhpc]

Ok, develop works

[adrianjhpc]

I'm now wondering if there was a mismatch somewhere in my build environment picking up different versions of hdf5. It could be this was a build mistake by me.