bugGNU Octave - Bugs: bug #61349, Make check fails after library...

 
 

bug #61349: Make check fails after library update

Submitter:  Arun Giridhar <arungiridhar>
Submitted:  Mon 18 Oct 2021 03:16:14 PM UTC
   
 
Category:  Configuration and Build System Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Build Failure
Status:  Invalid / Not an Octave Bug Assigned to:  None
Originator Name:  Open/Closed:  * Closed
Release:  * dev Operating System:  * GNU/Linux
Fixed Release:  None Planned Release:  None
* Mandatory Fields

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Mon 18 Oct 2021 03:55:59 PM UTC, comment #3: 

Ok.

Closing as invalid.

Markus Mützel <mmuetzel>
Group administrator
Mon 18 Oct 2021 03:41:23 PM UTC, comment #2: 

I see. So it's a consequence of the HDF5 library updating the ABI frequently between versions and nothing to do with Octave.

I am OK closing this as Invalid since it is not an Octave error. Thanks.

Arun Giridhar <arungiridhar>
Group Member
Mon 18 Oct 2021 03:36:59 PM UTC, comment #1: 

See also: https://forum.hdfgroup.org/t/hdf5-disable-version-check-and-disable-version-check/3795

IIUC, it is up to the distribution (or whoever builds the HDF5 libraries, e.g. Flatpak maintainer,...) to decide whether they would like to take the risk(?) of building with HDF5_DISABLE_VERSION_CHECK=1. It looks like your distribution decided against it.

I don't think there is anything that Octave can do about this unfortunately.

Markus Mützel <mmuetzel>
Group administrator
Mon 18 Oct 2021 03:16:14 PM UTC, original submission:  

After a recent system update that updated the system HDF5 libraries, Octave failed "make check" with a library mismatch error. Text pasted below.

In this case, I reran configure and rebuilt Octave, and the problem went away. On checking, it looks like the HDF5 libraries are all dynamically linked, not static, so it ought to be possible to update the HDF5 libraries independently of Octave without this error, since that is the primary reason for dynamic linking. Is Octave triggering this error or are the HDF5 libraries being overzealous? If within Octave, would it be possible to disable the version check when Octave links to HDF5?

Could someone please check if this kind of library error happens with precompiled Octave (MXE, Flatpak, AppImage etc)? If so, what is the solution there?


  test/sparse.tst ................................................Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.12.0, library is 1.12.1
            SUMMARY OF THE HDF5 CONFIGURATION
            =================================

General Information:
-------------------
                   HDF5 Version: 1.12.1
                  Configured on: Sun Jul 18 19:07:39 UTC 2021
                  Configured by: builduser@
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux archange 5.12.15-arch1-1 #1 SMP PREEMPT Wed, 07 Jul 2021 23:35:29 +0000 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /usr

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: shared
  Statically Linked Executables:
                        LDFLAGS: -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now
                     H5_LDFLAGS:
                     AM_LDFLAGS:
                Extra libraries: -lsz -lz -ldl -lm
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 11.1.0)
                       CPPFLAGS: -D_FORTIFY_SOURCE=2
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:
                        C Flags: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt
                     H5 C Flags:  -std=c99  -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wc11-c2x-compat -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc  -Wbad-function-cast -Wimplicit-function-declaration -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -Wincompatible-pointer-types -Wshadow -Wcast-function-type -Wmaybe-uninitialized -O3
                     AM C Flags:
               Shared C Library: yes
               Static C Library: no


                        Fortran: yes
               Fortran Compiler: /usr/bin/gfortran ( GNU Fortran (GCC) 11.1.0)
                  Fortran Flags:
               H5 Fortran Flags:  -std=f2008  -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Wuse-without-only -Winteger-division -Wfrontend-loop-interchange  -fdiagnostics-urls=never -fno-diagnostics-color -s -O3
               AM Fortran Flags:
         Shared Fortran Library: yes
         Static Fortran Library: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++ ( g++ (GCC) 11.1.0)
                      C++ Flags: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt
                   H5 C++ Flags:   -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wno-deprecated-copy -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s  -Wcast-align -Wmissing-declarations -Wpacked -Wredundant-decls -Wswitch -Wunused-but-set-variable -Wunused-function -Wunused-variable -Wunused-parameter -Wshadow -O3
                   AM C++ Flags:  -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE -DNO_STATIC_CAST
             Shared C++ Library: yes
             Static C++ Library: no

                           Java: yes
                  Java Compiler: /usr/bin/java (openjdk 16.0.1 2021-04-20)


Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                Build HDF5 Tests: yes
                Build HDF5 Tools: yes
                    Threadsafety: no (recursive RW locks: no)
             Default API mapping: v112
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                   Map (H5M) API: no
                      Direct VFD: no
                      Mirror VFD: no
              (Read-Only) S3 VFD: no
            (Read-Only) HDFS VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
                Use file locking: best-effort
       Strict file format checks: no
    Optimization instrumentation: no
Bye...
fatal: caught signal Aborted -- stopping myself...
make[3]: *** [Makefile:32211: check-local] Error 134


Arun Giridhar <arungiridhar>
Group Member

 

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    Date Changed by Updated Field Previous Value => Replaced by
    2021-10-18 mmuetzel StatusNone Invalid / Not an Octave Bug
        Open/ClosedOpen Closed

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