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Failing test for h5diff_600 #2405

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hmaarrfk opened this issue Jan 14, 2023 · 1 comment
Open

Failing test for h5diff_600 #2405

hmaarrfk opened this issue Jan 14, 2023 · 1 comment
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Component - Parallel Parallel HDF5 (NOT thread-safety) Component - Testing Code in test or testpar directories, GitHub workflows Component - Tools Command-line tools like h5dump, includes high-level tools Priority - 1. High 🔼 These are important issues that should be resolved in the next release Type - Task Actions that don't fit into any other type category

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@hmaarrfk
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Describe the bug
I am trying to build HDF5 1.14 at conda forge and it seems that h5diff_600 test is failing for us. The error message isn't very descriptive so I'm hoping to get some guidance.

Relevant part of the log (maybe)
Testing ../../src/h5diff/ph5diff h5diff_basic1.h5                     *FAILED*
====Expected result (expect_sorted) differs from actual result (actual_sorted)
    *** expect_sorted	2022-12-30 02:23:42.326711461 +0000
    --- actual_sorted	2022-12-30 02:23:42.322711404 +0000
    ***************
    *** 73,78 ****
    --- 73,79 ----
         --follow-symlinks
               For example, if you are comparing the group /groupA in two files and
        '/g1/dset1' and '/g1/dset2' in the same file
    + h5diff error: missing file names
               h5diff treats it as an error and returns an exit code of 2.
                                 HDF5 file specified
                                 HDF5 file specified
====The actual output (./testfiles/h5diff_600.out-sav)
    h5diff error: missing file names
    usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
      file1             File name of the first HDF5 file
      file2             File name of the second HDF5 file
      [obj1]            Name of an HDF5 object, in absolute path
      [obj2]            Name of an HDF5 object, in absolute path
    
      ERROR
       --enable-error-stack Prints messages from the HDF5 error stack as they occur.
                            Optional value 2 also prints file open errors.
      OPTIONS
       -h, --help
             Print a usage message and exit.
       -V, --version
             Print version number and exit.
       -r, --report
             Report mode. Print differences.
       -v --verbose
             Verbose mode. Print differences information and list of objects.
       -vN --verbose=N
             Verbose mode with level. Print differences and list of objects.
             Level of detail depends on value of N:
              0 : Identical to '-v' or '--verbose'.
              1 : All level 0 information plus one-line attribute status summary.
              2 : All level 1 information plus extended attribute status report.
              3 : All level 2 information plus file names.
       -q, --quiet
             Quiet mode. Do not produce output.
       --vol-value-1           Value (ID) of the VOL connector to use for opening the
                               first HDF5 file specified
       --vol-name-1            Name of the VOL connector to use for opening the first
                               HDF5 file specified
       --vol-info-1            VOL-specific info to pass to the VOL connector used for
                               opening the first HDF5 file specified
       --vol-value-2           Value (ID) of the VOL connector to use for opening the
                               second HDF5 file specified
       --vol-name-2            Name of the VOL connector to use for opening the second
                               HDF5 file specified
       --vol-info-2            VOL-specific info to pass to the VOL connector used for
                               opening the second HDF5 file specified
       --vfd-value-1           Value (ID) of the VFL driver to use for opening the
                               first HDF5 file specified
       --vfd-name-1            Name of the VFL driver to use for opening the first
                               HDF5 file specified
       --vfd-info-1            VFD-specific info to pass to the VFL driver used for
                               opening the first HDF5 file specified
       --vfd-value-2           Value (ID) of the VFL driver to use for opening the
                               second HDF5 file specified
       --vfd-name-2            Name of the VFL driver to use for opening the second
                               HDF5 file specified
       --vfd-info-2            VFD-specific info to pass to the VFL driver used for
                               opening the second HDF5 file specified
       --follow-symlinks
             Follow symbolic links (soft links and external links and compare the)
             links' target objects.
             If symbolic link(s) with the same name exist in the files being
             compared, then determine whether the target of each link is an existing
             object (dataset, group, or named datatype) or the link is a dangling
             link (a soft or external link pointing to a target object that does
             not yet exist).
             - If both symbolic links are dangling links, they are treated as being
               the same; by default, h5diff returns an exit code of 0.
               If, however, --no-dangling-links is used with --follow-symlinks,
               this situation is treated as an error and h5diff returns an
               exit code of 2.
             - If only one of the two links is a dangling link,they are treated as
               being different and h5diff returns an exit code of 1.
               If, however, --no-dangling-links is used with --follow-symlinks,
               this situation is treated as an error and h5diff returns an
               exit code of 2.
             - If both symbolic links point to existing objects, h5diff compares the
               two objects.
             If any symbolic link specified in the call to h5diff does not exist,
             h5diff treats it as an error and returns an exit code of 2.
       --no-dangling-links
             Must be used with --follow-symlinks option; otherwise, h5diff shows
             error message and returns an exit code of 2.
             Check for any symbolic links (soft links or external links) that do not
             resolve to an existing object (dataset, group, or named datatype).
             If any dangling link is found, this situation is treated as an error
             and h5diff returns an exit code of 2.
       -c, --compare
             List objects that are not comparable
       -N, --nan
             Avoid NaNs detection
       -n C, --count=C
             Print differences up to C. C must be a positive integer.
       -d D, --delta=D
             Print difference if (|a-b| > D). D must be a positive number. Where a
             is the data point value in file1 and b is the data point value in file2.
             Can not use with '-p' or '--use-system-epsilon'.
       -p R, --relative=R
             Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
             is the data point value in file1 and b is the data point value in file2.
             Can not use with '-d' or '--use-system-epsilon'.
       --use-system-epsilon
             Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
             is the data point value in file1 and b is the data point value in file2.
             If the system epsilon is not defined,one of the following predefined
             values will be used:
               FLT_EPSILON = 1.19209E-07 for floating-point type
               DBL_EPSILON = 2.22045E-16 for double precision type
             Can not use with '-p' or '-d'.
       --exclude-path "path"
             Exclude the specified path to an object when comparing files or groups.
             If a group is excluded, all member objects will also be excluded.
             The specified path is excluded wherever it occurs.
             This flexibility enables the same option to exclude either objects that
             exist only in one file or common objects that are known to differ.
    
             When comparing files, "path" is the absolute path to the excluded;
             object; when comparing groups, "path" is similar to the relative
             path from the group to the excluded object. This "path" can be
             taken from the first section of the output of the --verbose option.
             For example, if you are comparing the group /groupA in two files and
             you want to exclude /groupA/groupB/groupC in both files, the exclude
             option would read as follows:
               --exclude-path "/groupB/groupC"
    
             If there are multiple paths to an object, only the specified path(s)
             will be excluded; the comparison will include any path not explicitly
             excluded.
             This option can be used repeatedly to exclude multiple paths.
    
       --exclude-attribute "path/to/object/with/attribute"
             Exclude attributes on the specified path to an object when comparing files or groups.
    
             If there are multiple paths to an object, only the specified path(s)
             will be excluded; the comparison will include any path not explicitly
             excluded.
             This option can be used repeatedly to exclude multiple paths.
    
     Modes of output:
      Default mode: print the number of differences found and where they occurred
      -r Report mode: print the above plus the differences
      -v Verbose mode: print the above plus a list of objects and warnings
      -q Quiet mode: do not print output
    
     File comparison:
      If no objects [obj1[ obj2]] are specified, the h5diff comparison proceeds as
      a comparison of the two files' root groups.  That is, h5diff first compares
      the names of root group members, generates a report of root group objects
      that appear in only one file or in both files, and recursively compares
      common objects.
    
     Object comparison:
      1) Groups
          First compares the names of member objects (relative path, from the
          specified group) and generates a report of objects that appear in only
          one group or in both groups. Common objects are then compared recursively.
      2) Datasets
          Array rank and dimensions, datatypes, and data values are compared.
      3) Datatypes
          The comparison is based on the return value of H5Tequal.
      4) Symbolic links
          The paths to the target objects are compared.
          (The option --follow-symlinks overrides the default behavior when
           symbolic links are compared.).
    
     Subsetting options:
      Subsetting is available by using the fcompact form of subsetting, as follows:
        obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
      It is not required to use all parameters, but until the last parameter value used,
      all of the semicolons (;) are required, even when a parameter value is not specified. Example:
        obj1 /foo/mydataset[START;;COUNT;BLOCK]
        obj1 /foo/mydataset[START]
      The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
      each dimension. START is optional and will default to 0 in each dimension.
      Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
      one integer for each dimension of the dataset.
    
     Exit code:
      0 if no differences, 1 if differences found, 2 if error
    
     Examples of use:
     1) h5diff file1 file2 /g1/dset1 /g1/dset2
        Compares object '/g1/dset1' in file1 with '/g1/dset2' in file2
    
     2) h5diff file1 file2 /g1/dset1
        Compares object '/g1/dset1' in both files
    
     3) h5diff file1 file2
        Compares all objects in both files
    
     Notes:
      file1 and file2 can be the same file.
      Use h5diff file1 file1 /g1/dset1 /g1/dset2 to compare
      '/g1/dset1' and '/g1/dset2' in the same file
    
====The actual stderr (./testfiles/h5diff_600.out.err-sav)
====End of actual stderr (./testfiles/h5diff_600.out.err-sav)

162.log.txt

Expected behavior
For the tests to pass

Platform (please complete the following information)

  • HDF5 version: 1.14.0
  • OS and version: Linux, COS6, conda-forge
  • Compiler and version: GCC 11
  • Build system (e.g. CMake, Autotools) and version: configure + make
  • Any configure options you specified See attached build file. build.sh.txt
  • MPI library and version (parallel HDF5) mpich

Additional context
Add any other context about the problem here.

@hmaarrfk hmaarrfk added the bug label Jan 14, 2023
@derobins derobins removed the bug label Mar 3, 2023
@byrnHDF
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byrnHDF commented Mar 7, 2023

parallel tests should sort the output file and the reference file. Looks like the actual output maybe has some extra lines?

@byrnHDF byrnHDF changed the title [BUG] Failing test for h5diff_600 Failing test for h5diff_600 Mar 7, 2023
@byrnHDF byrnHDF added Priority - 1. High 🔼 These are important issues that should be resolved in the next release Component - Tools Command-line tools like h5dump, includes high-level tools Component - Parallel Parallel HDF5 (NOT thread-safety) Component - Testing Code in test or testpar directories, GitHub workflows Type - Task Actions that don't fit into any other type category labels Mar 7, 2023
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Component - Parallel Parallel HDF5 (NOT thread-safety) Component - Testing Code in test or testpar directories, GitHub workflows Component - Tools Command-line tools like h5dump, includes high-level tools Priority - 1. High 🔼 These are important issues that should be resolved in the next release Type - Task Actions that don't fit into any other type category
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