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mdolab / pyhyp

pyHyp generates volume meshes from surface meshes using hyperbolic marching.
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Which version of HDF5 #72

Closed swayli94 closed 1 year ago

swayli94 commented 1 year ago

Description

When I run testflo -v or run an example such as examples/m6/runM6.py, it returns an error about HDF5.

Should I build an HDF5-1.8.23 instead? Or shall I re-make pyhyp?

Thank you.

Current behavior

        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 1.8.23, library is 1.10.7
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

        General Information:
        -------------------
               HDF5 Version: 1.10.7
              Configured on: Wed, 08 Dec 2021 23:33:27 +0000
              Configured by: Debian
                Host system: x86_64-pc-linux-gnu
          Uname information: Debian
                   Byte sex: little-endian
         Installation point: /usr
                Flavor name: serial

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

        Linking Options:
        ----------------
                  Libraries: static, shared
        Statically Linked Executables:
                    LDFLAGS: -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro
                 H5_LDFLAGS: -Wl,--version-script,$(top_srcdir)/debian/map_serial.ver
                 AM_LDFLAGS:
            Extra libraries: -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm
                   Archiver: ar
                   AR_FLAGS: cr
                     Ranlib: x86_64-linux-gnu-ranlib

        Languages:
        ----------
                          C: yes
                 C Compiler: /usr/bin/gcc
                   CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2
                H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS:
                    C Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
                 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 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -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 -O3  -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized
                 AM C Flags:
           Shared C Library: yes
           Static C Library: yes

                    Fortran: yes
           Fortran Compiler: /usr/bin/gfortran
              Fortran Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong
           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  -s -O3
           AM Fortran Flags:
     Shared Fortran Library: yes
     Static Fortran Library: yes

                        C++: yes
               C++ Compiler: /usr/bin/g++
                  C++ Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
               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 -Wno-unsuffixed-float-constants -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 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3  -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow
               AM C++ Flags:
         Shared C++ Library: yes
         Static C++ Library: yes

                       Java: yes
              Java Compiler: /usr/bin/java (openjdk 11.0.13 2021-10-19)

        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: yes
         Default API mapping: v18
        With deprecated public symbols: yes
      I/O filters (external): deflate(zlib),szip(encoder)
                         MPE: no
                  Direct VFD: no
                  Mirror VFD: no
          (Read-Only) S3 VFD: yes
        (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...

        [WSL:05487] *** Process received signal ***
        [WSL:05487] Signal: Aborted (6)
        [WSL:05487] Signal code:  (-6)
        [WSL:05487] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fa0bf3a3520]
        [WSL:05487] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7fa0bf3f7a7c]
        [WSL:05487] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7fa0bf3a3476]
        [WSL:05487] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7fa0bf3897f3]
        [WSL:05487] [ 4] /lib/x86_64-linux-gnu/libhdf5_serial.so.103(+0x3d49a)[0x7fa0a4ca849a]
        [WSL:05487] [ 5] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(ADFH_Database_Open+0x635)[0x7fa0a50a86e5]
        [WSL:05487] [ 6] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(cgio_open_file+0x269)[0x7fa0a505eaa9]
        [WSL:05487] [ 7] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(cg_open+0x98)[0x7fa0a5062b58]
        [WSL:05487] [ 8] /home/lrz/opt/CGNS-4.3.0/opt-gfortran/lib/libcgns.so.4.3(cg_open_f_+0x1af)[0x7fa0a50ae64f]
        [WSL:05487] [ 9] /tmp/tmpsj_1f9c4/hyp.so(writecgns_+0x166e)[0x7fa0a456fcfe]
        [WSL:05487] [10] /tmp/tmpsj_1f9c4/hyp.so(+0x10c7b)[0x7fa0a4545c7b]
        [WSL:05487] [11] python(_PyObject_MakeTpCall+0x158)[0x559b367cfda8]
        [WSL:05487] [12] python(_PyEval_EvalFrameDefault+0x4448)[0x559b3682e6f8]
        [WSL:05487] [13] python(_PyFunction_Vectorcall+0x108)[0x559b367fc768]
        [WSL:05487] [14] python(+0x146254)[0x559b367aa254]
        [WSL:05487] [15] python(_PyEval_EvalCodeWithName+0x1e9)[0x559b367fb9c9]
        [WSL:05487] [16] python(PyEval_EvalCode+0x23)[0x559b3685b383]
        [WSL:05487] [17] python(+0x1f78d2)[0x559b3685b8d2]
        [WSL:05487] [18] python(+0x207982)[0x559b3686b982]
        [WSL:05487] [19] python(+0x209429)[0x559b3686d429]
        [WSL:05487] [20] python(PyRun_SimpleFileExFlags+0x1bf)[0x559b3686d60f]
        [WSL:05487] [21] python(Py_RunMain+0x2f9)[0x559b3686da09]
        [WSL:05487] [22] python(Py_BytesMain+0x39)[0x559b3686dca9]
        [WSL:05487] [23] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fa0bf38ad90]
        [WSL:05487] [24] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fa0bf38ae40]
        [WSL:05487] [25] python(+0x1e21c7)[0x559b368461c7]
        [WSL:05487] *** End of error message ***
        Aborted

Code versions

sseraj commented 1 year ago

We use ADF instead of HDF5. CGNS 4.3 requires an extra flag to use ADF: -D CGNS_ENABLE_HDF5=OFF. This was missing from our docs, but I updated the instructions in this PR: mdolab/MACH-Aero#89

swayli94 commented 1 year ago

Thank you. After re-make CGNS, it is indeed fixed.