Bug 2266644

Summary: hdf5 fails to build with java-21-openjdk
Product: [Fedora] Fedora Reporter: Petra Alice Mikova <pmikova>
Component: hdf5Assignee: Orion Poplawski <orion>
Status: CLOSED RAWHIDE QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: high Docs Contact:
Priority: unspecified    
Version: rawhideCC: igor.raits, java-maint-sig, jvanek, orion, pmikova, scitech-bugs, trpost, yselkowi
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
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Fixed In Version: Doc Type: If docs needed, set a value
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Clone Of: Environment:
Last Closed: 2024-10-28 02:38:40 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:
Bug Depends On:    
Bug Blocks: 2262141    

Description Petra Alice Mikova 2024-02-28 16:53:33 UTC 
hdf5 fails to build with java-21-openjdk as sytem JDK. See https://fedoraproject.org/wiki/Changes/Java21.

For the build logs, see: https://koji.fedoraproject.org/koji/taskinfo?taskID=114131747
https://kojipkgs.fedoraproject.org/work/tasks/1920/114131920/state.log
https://kojipkgs.fedoraproject.org/work/tasks/1920/114131920/build.log
https://kojipkgs.fedoraproject.org/work/tasks/1920/114131920/root.log
https://kojipkgs.fedoraproject.org/work/tasks/1920/114131920/mock_output.log
https://kojipkgs.fedoraproject.org/work/tasks/1920/114131920/hw_info.log
We run the rebuild in side tag f41-build-side-84507, but as fail ratio was small, we expect this side tag to be merged into rawhide ASAP.
To reproduce before this date simply: fedpkg clone hdf5; cd hdf5;  fedpkg build --target f41-build-side-84507; #The target is crucial.
After merge, the usual fedpkg build in rawhide should do.

We had tried aprox 400 packages, and aprox 55 had failed, so the java-21-openjdk will be system JDK in f40, and you should fix your package if you want to keep it alive. Usually the fix is simple, and best is to update the package to latest upstream version. Fix the issue in both f40 and rawhide, if possible, the side tag and rebuild of f40 (and bugs) will follow soon.
Let us know here if you have any questions, here in bug, or at java-devel.org .

We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side if needed.
Comment 1 jiri vanek 2024-03-13 12:44:46 UTC 
Verifying h5diff output h5repack_filters.h5 out-gzip_verbose_filters.h PASSED
Verifying output from ../../src/h5repack/h5repack -v -f /dset_deflate:*FAILED*
    Expected result (*.tst) differs from actual result (*.out)
    *** ./testpack/h5repack_filters.h5-gzip_verbose_filters.tst	2024-02-27 14:22:28.734545641 +0000
    --- ./testpack/h5repack_filters.h5.out	2024-02-27 14:22:29.780548375 +0000
    ***************
    *** 8,14 ****
      -----------------------------------------
       group                       /
       dset                        /dset_all
    !  dset     GZIP   (0.995:1)   /dset_deflate
       dset                        /dset_fletcher32
       dset                        /dset_nbit
       dset                        /dset_shuffle
    --- 8,14 ----
      -----------------------------------------
       group                       /
       dset                        /dset_all
    !  dset     GZIP   (0.988:1)   /dset_deflate
       dset                        /dset_fletcher32
       dset                        /dset_nbit
       dset                        /dset_shuffle
szip_copy h5repack_szip.h5
Testing ../../src/h5repack/h5repack                                    PASSED
...
Testing ../../src/h5repack/h5repack -f GZIP=1 -m 1024                  PASSED
Verifying h5dump output -f GZIP=1 -m 1024                             *FAILED*
    Expected result (*.ddl) differs from actual result (*.out)
    *** ./testpack/deflate_limit.h5repack_layout.h5.ddl	2024-02-27 14:22:28.233544331 +0000
    --- ./testpack/out-deflate_limit.h5repack_layout.h5.out	2024-02-27 14:22:30.600550519 +0000
    ***************
    *** 5,11 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1150 (2.783:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 5,11 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1495 (2.140:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    ***************
    *** 23,29 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1150 (2.783:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 23,29 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1495 (2.140:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    ***************
    *** 41,47 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1150 (2.783:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 41,47 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1495 (2.140:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    ***************
    *** 59,65 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1150 (2.783:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 59,65 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1495 (2.140:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    ***************
    *** 77,83 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 20, 10 )
    !          SIZE 1283 (2.494:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 77,83 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 20, 10 )
    !          SIZE 1569 (2.040:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    ***************
    *** 95,101 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1150 (2.783:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 95,101 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1495 (2.140:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    ***************
    *** 113,119 ****
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1150 (2.783:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
    --- 113,119 ----
            DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 40, 20 )
    !          SIZE 1495 (2.140:1 COMPRESSION)
            }
            FILTERS {
               COMPRESSION DEFLATE { LEVEL 1 }
deflate_file h5repack_layout.h5 -e h5repack.info
Testing ../../src/h5repack/h5repack -e h5repack.info                   PASSED
...
Verifying h5diff output h5repack_layout.h5 out-verbounds-low2-high2.h5 PASSED
Verifying superblock                                                   PASSED
Testing ../../src/h5repack/h5repack 0 1 bounds_latest_latest.h5       Error occurred while repacking
 PASSED
Testing external consolidation on f32le with h5repack -l CONTI         . . .
Verifying h5diff output h5repack_f32le.h5 h5repack_f32le_ex.h5         PASSED
...
Verifying h5dump output --merge --prune --enable-error-stack           PASSED
h5repack tests failed with 2 errors.
Command exited with non-zero status 1
4.72user 6.55system 0:09.02elapsed 125%CPU (0avgtext+0avgdata 13800maxresident)k
1280inputs+13216outputs (0major+1242025minor)pagefaults 0swaps
Comment 2 jiri vanek 2024-03-13 12:45:00 UTC 
not sure how to read them
Comment 3 Yaakov Selkowitz 2024-05-08 19:03:08 UTC 
This seems related to https://fedoraproject.org/wiki/Changes/ZlibNGTransition rather than https://fedoraproject.org/wiki/Changes/Java21