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Installation issue: vtk@8.2.1a #44464

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Closed
Installation issue: vtk@8.2.1a#44464
Labels
build-error
@carlos-encs

Description

@carlos-encs
carlos-encs
opened on May 31, 2024

@danlipsa, @chuckatkins

Steps to reproduce the issue

$ spack spec -I vtk@8.2.1a
Input spec
--------------------------------
 -   vtk@8.2.1a

Concretized
--------------------------------
 -   vtk@8.2.1a%gcc@11.4.1~examples~ffmpeg~ipo+mpi+opengl2~osmesa~python~qt~xdmf build_system=cmake build_type=Release generator=make patches=34960ef,3b47ee0,541dc51,760fd6d,9535683,b790d00 arch=linux-almalinux9-zen3
[e]      ^cmake@3.20.2%gcc@11.4.1~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-almalinux9-zen3
[+]      ^double-conversion@3.3.0%gcc@11.4.1~ipo build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
[+]          ^cmake@3.27.9%gcc@11.4.1~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-almalinux9-zen3
[+]              ^curl@8.7.1%gcc@11.4.1~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-almalinux9-zen3
[+]                  ^nghttp2@1.61.0%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[e]                  ^perl@5.32.1%gcc@11.4.1~cpanm~opcode~open+shared+threads build_system=generic arch=linux-almalinux9-zen3
[+]              ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-almalinux9-zen3
[e]          ^gmake@4.3%gcc@11.4.1~guile build_system=generic patches=599f134 arch=linux-almalinux9-zen3
[+]      ^eigen@3.4.0%gcc@11.4.1~ipo build_system=cmake build_type=RelWithDebInfo generator=make arch=linux-almalinux9-zen3
[e]          ^cmake@3.20.2%gcc@11.4.1~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-almalinux9-zen3
[+]      ^expat@2.6.2%gcc@11.4.1+libbsd build_system=autotools arch=linux-almalinux9-zen3
[+]          ^libbsd@0.12.2%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^libmd@1.0.4%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]      ^freetype@2.10.2%gcc@11.4.1+pic+shared build_system=autotools arch=linux-almalinux9-zen3
[+]          ^bzip2@1.0.8%gcc@11.4.1~debug~pic+shared build_system=generic arch=linux-almalinux9-zen3
[e]              ^diffutils@3.7%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[e]          ^pkgconf@1.7.3%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]      ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
 -       ^gl2ps@1.4.2%gcc@11.4.1~doc~ipo+png+zlib build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
 -       ^glew@2.2.0%gcc@11.4.1~ipo build_system=cmake build_type=Release generator=make gl=glx patches=7992e52 arch=linux-almalinux9-zen3
[+]          ^libx11@1.8.7%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^inputproto@2.3.2%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^libxcb@1.16%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^libpthread-stubs@0.5%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^libxau@1.0.11%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^libxdmcp@1.1.4%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^xcb-proto@1.16.0%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^xextproto@7.3.0%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^xtrans@1.5.0%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^xproto@7.0.31%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[e]      ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
 -       ^glx@1.4%gcc@11.4.1 build_system=bundle arch=linux-almalinux9-zen3
 -           ^mesa@23.3.6%gcc@11.4.1+glx+llvm+opengl~opengles+osmesa~strip build_system=meson buildtype=release default_library=shared arch=linux-almalinux9-zen3
[e]              ^bison@3.7.4%gcc@11.4.1~color build_system=autotools arch=linux-almalinux9-zen3
[e]              ^flex@2.6.4%gcc@11.4.1+lex~nls build_system=autotools patches=f8b85a0 arch=linux-almalinux9-zen3
[e]              ^gettext@0.21%gcc@11.4.1+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-almalinux9-zen3
[+]              ^glproto@1.4.17%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^libunwind@1.6.2%gcc@11.4.1~block_signals~conservative_checks~cxx_exceptions~debug~debug_frame+docs~pic+tests+weak_backtrace~xz~zlib build_system=autotools components=none libs=shared,static arch=linux-almalinux9-zen3
[+]              ^libxext@1.3.5%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
 -               ^llvm@17.0.6%gcc@11.4.1+clang~cuda~flang+gold~ipo+libomptarget~libomptarget_debug~link_llvm_dylib+lld+lldb+llvm_dylib+lua~mlir+polly~python~split_dwarf~z3~zstd build_system=cmake build_type=Release compiler-rt=runtime generator=ninja libcxx=runtime libunwind=runtime openmp=runtime shlib_symbol_version=none targets=all version_suffix=none arch=linux-almalinux9-zen3
[e]                  ^binutils@2.35.2%gcc@11.4.1~gas+gold+headers~interwork+ld~libiberty~lto~nls+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-almalinux9-zen3
[+]                  ^libedit@3.1-20230828%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^libffi@3.4.6%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^lua@5.3.6%gcc@11.4.1~pcfile+shared build_system=makefile fetcher=curl arch=linux-almalinux9-zen3
[+]                      ^unzip@6.0%gcc@11.4.1 build_system=makefile patches=f6f6236 arch=linux-almalinux9-zen3
[+]                  ^perl-data-dumper@2.173%gcc@11.4.1 build_system=perl arch=linux-almalinux9-zen3
[+]                  ^swig@4.1.1%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                      ^pcre2@10.43%gcc@11.4.1~jit+multibyte build_system=autotools arch=linux-almalinux9-zen3
[+]              ^meson@1.3.2%gcc@11.4.1 build_system=python_pip patches=0f0b1bd arch=linux-almalinux9-zen3
[+]                  ^py-pip@23.1.2%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
[+]                  ^py-setuptools@69.2.0%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
[+]                  ^py-wheel@0.41.2%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
[+]                  ^python-venv@1.0%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
[+]              ^ninja@1.12.0%gcc@11.4.1+re2c build_system=generic arch=linux-almalinux9-zen3
[e]                  ^python@3.9.18%gcc@11.4.1+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl+tix+tkinter+uuid+zlib build_system=generic patches=0d98e93,ebdca64,f2fd060 arch=linux-almalinux9-zen3
[+]                  ^re2c@2.2%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
[+]              ^py-mako@1.2.4%gcc@11.4.1 build_system=python_pip arch=linux-almalinux9-zen3
[+]                  ^py-markupsafe@2.1.3%gcc@11.4.1 build_system=python_pip arch=linux-almalinux9-zen3
[e]              ^python@3.9.18%gcc@11.4.1+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl+tix+tkinter+uuid+zlib build_system=generic patches=0d98e93,ebdca64,f2fd060 arch=linux-almalinux9-zen3
[+]              ^xrandr@1.5.2%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^libxrandr@1.5.4%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                      ^renderproto@0.11.1%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^libxrender@0.9.11%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]                  ^randrproto@1.5.0%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[e]      ^gmake@4.3%gcc@11.4.1~guile build_system=generic patches=599f134 arch=linux-almalinux9-zen3
[+]      ^hdf5@1.14.3%gcc@11.4.1~cxx~fortran+hl~ipo~java~map+mpi+shared~subfiling~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make patches=82088c8 arch=linux-almalinux9-zen3
[e]          ^pkgconf@1.7.3%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]      ^jsoncpp@1.9.5%gcc@11.4.1~ipo build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
[+]      ^libjpeg-turbo@3.0.0%gcc@11.4.1~ipo~jpeg8~partial_decoder+pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-almalinux9-zen3
[+]          ^nasm@2.15.05%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]      ^libogg@1.3.5%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]      ^libpng@1.6.39%gcc@11.4.1~ipo~pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-almalinux9-zen3
[-]          ^cmake@3.27.9%gcc@11.4.1~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-almalinux9-zen3
[e]              ^curl@7.86.0%gcc@11.4.1~gssapi+ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-almalinux9-zen3
[+]      ^libtheora@1.1.1%gcc@11.4.1~doc build_system=autotools patches=d9bb5a9,e01511a,e01ef71,ff8478d arch=linux-almalinux9-zen3
[e]          ^autoconf@2.69%gcc@11.4.1 build_system=autotools patches=7793209 arch=linux-almalinux9-zen3
[e]          ^automake@1.16.2%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[e]          ^libtool@2.4.6%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[e]          ^m4@1.4.19%gcc@11.4.1+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-almalinux9-zen3
[+]      ^libtiff@4.5.1%gcc@11.4.1+ccitt~ipo~jbig+jpeg~jpeg12~lerc~libdeflate+logluv~lzma+lzw+next~old-jpeg+packbits~pic~pixarlog+shared+thunder~webp+zlib~zstd build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
[+]      ^libxml2@2.10.3%gcc@11.4.1+pic~python+shared build_system=autotools arch=linux-almalinux9-zen3
[+]      ^libxt@1.3.0%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^kbproto@1.0.7%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^libice@1.1.1%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^libsm@1.2.4%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]              ^util-linux-uuid@2.40.1%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^util-macros@1.19.3%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]      ^lz4@1.9.4%gcc@11.4.1+pic build_system=makefile libs=shared,static arch=linux-almalinux9-zen3
 -       ^netcdf-c@4.9.2%gcc@11.4.1+blosc~byterange~dap~fsync~hdf4~jna+mpi~nczarr_zip+optimize~parallel-netcdf+pic+shared+szip+zstd build_system=autotools patches=0161eb8 arch=linux-almalinux9-zen3
[+]          ^c-blosc@1.21.5%gcc@11.4.1+avx2~ipo build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
[+]              ^snappy@1.1.10%gcc@11.4.1~ipo+pic+shared build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
[+]          ^libaec@1.0.6%gcc@11.4.1~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-almalinux9-zen3
[+]          ^zstd@1.5.6%gcc@11.4.1~programs build_system=makefile libs=shared,static arch=linux-almalinux9-zen3
[+]      ^openmpi@5.0.3%gcc@11.4.1~atomics~cuda~gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~static+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-almalinux9-zen3
[e]          ^autoconf@2.69%gcc@11.4.1 build_system=autotools patches=7793209 arch=linux-almalinux9-zen3
[e]          ^automake@1.16.2%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^hwloc@2.9.1%gcc@11.4.1~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm build_system=autotools libs=shared,static arch=linux-almalinux9-zen3
[+]              ^libpciaccess@0.17%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^libevent@2.1.12%gcc@11.4.1+openssl build_system=autotools arch=linux-almalinux9-zen3
[+]              ^openssl@3.0.13%gcc@11.4.1~docs+shared build_system=generic certs=mozilla arch=linux-almalinux9-zen3
[+]                  ^ca-certificates-mozilla@2023-05-30%gcc@11.4.1 build_system=generic arch=linux-almalinux9-zen3
[e]          ^libtool@2.4.6%gcc@11.4.1 build_system=autotools arch=linux-almalinux9-zen3
[+]          ^numactl@2.0.14%gcc@11.4.1 build_system=autotools patches=4e1d78c,62fc8a8,ff37630 arch=linux-almalinux9-zen3
[e]          ^openssh@9.6p1%gcc@11.4.1+gssapi build_system=autotools arch=linux-almalinux9-zen3
[e]          ^perl@5.32.1%gcc@11.4.1~cpanm~opcode~open+shared+threads build_system=generic arch=linux-almalinux9-zen3
[+]          ^pmix@5.0.1%gcc@11.4.1~docs+pmi_backwards_compatibility~python~restful build_system=autotools arch=linux-almalinux9-zen3
[+]      ^sqlite@3.43.2%gcc@11.4.1+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-almalinux9-zen3
[+]          ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-almalinux9-zen3
[+]      ^xz@5.4.6%gcc@11.4.1~pic build_system=autotools libs=shared,static arch=linux-almalinux9-zen3
[+]      ^zlib-ng@2.1.6%gcc@11.4.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-almalinux9-zen3

Error message

Error message 
[ 90%] Built target vtkIOParallel
/usr/bin/ld: CMakeFiles/vtkProbeOpenGLVersion.dir/vtkProbeOpenGLVersion.cxx.o: in function `vtkRenderingOpenGL2_ModuleInit::~vtkRenderingOpenGL2_ModuleInit()':
vtkProbeOpenGLVersion.cxx:(.text._ZN30vtkRenderingOpenGL2_ModuleInitD2Ev[_ZN30vtkRenderingOpenGL2_ModuleInitD5Ev]+0x5): undefined reference to `vtkRenderingOpenGL2_AutoInit_Destruct()'
/usr/bin/ld: CMakeFiles/vtkProbeOpenGLVersion.dir/vtkProbeOpenGLVersion.cxx.o: in function `main':
vtkProbeOpenGLVersion.cxx:(.text.startup+0x10): undefined reference to `vtkRenderer::New()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x18): undefined reference to `vtkRenderWindow::New()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x50): undefined reference to `vtkObjectBase::GetClassName() const'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x15e): undefined reference to `vtkOutputWindow::GetInstance()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x16f): undefined reference to `vtkOutputWindow::GetInstance()'
/usr/bin/ld: CMakeFiles/vtkProbeOpenGLVersion.dir/vtkProbeOpenGLVersion.cxx.o: in function `_GLOBAL__sub_I_main':
vtkProbeOpenGLVersion.cxx:(.text.startup+0x288): undefined reference to `vtkDebugLeaksManager::vtkDebugLeaksManager()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x297): undefined reference to `vtkDebugLeaksManager::~vtkDebugLeaksManager()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x2a1): undefined reference to `vtkRenderingOpenGL2_AutoInit_Construct()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x2bf): undefined reference to `vtkOutputWindowCleanup::vtkOutputWindowCleanup()'
/usr/bin/ld: vtkProbeOpenGLVersion.cxx:(.text.startup+0x2ce): undefined reference to `vtkOutputWindowCleanup::~vtkOutputWindowCleanup()'

/usr/bin/ld: ../../lib/libvtkRenderingOpenGL2-8.2.so.1: undefined reference to vtkPolyDataMapper::PrintSelf(std::ostream&, vtkIndent)' /usr/bin/ld: ../../lib/libvtkRenderingCore-8.2.so.1: undefined reference to vtkPiecewiseFunction::AddPoint(double, double)'

/usr/bin/ld: /disk/nobackup2/carlos/spack-stage/spack-stage-vtk-8.2.1a-45rtrppcoqhycgrqcdxv2erm76adm6d5/spack-build-45rtrpp/lib/libvtkFiltersGeneral-8.2.so.1: undefined reference to vtkPlaneCollection::GetNextPlane(void*&)' /usr/bin/ld: ../../lib/libvtkRenderingCore-8.2.so.1: undefined reference to vtkInformation::Set(vtkInformationDoubleKey*, double)'

/usr/bin/ld: ../../lib/libvtkFiltersCore-8.2.so.1: undefined reference to vtkIdList::Resize(long long)' /usr/bin/ld: ../../lib/libvtkFiltersCore-8.2.so.1: undefined reference to vtkSelectionAlgorithm::FillInputPortInformation(int, vtkInformation*)'

/usr/bin/ld: ../../lib/libvtkRenderingOpenGL2-8.2.so.1: undefined reference to vtkPolyData::SetStrips(vtkCellArray*)' /usr/bin/ld: ../../lib/libvtkRenderingOpenGL2-8.2.so.1: undefined reference to vtkRenderer::DeviceRenderOpaqueGeometry()'

/usr/bin/ld: ../../lib/libvtkFiltersCore-8.2.so.1: undefined reference to vtkTable::GetColumn(long long)' /usr/bin/ld: /disk/nobackup2/carlos/spack-stage/spack-stage-vtk-8.2.1a-45rtrppcoqhycgrqcdxv2erm76adm6d5/spack-build-45rtrpp/lib/libvtkFiltersGeneral-8.2.so.1: undefined reference to vtkStreamingTessellator::AdaptivelySample0Facet(double*) const'

/usr/bin/ld: ../../lib/libvtkRenderingOpenGL2-8.2.so.1: undefined reference to `vtkAlgorithm::FillInputPortInformation(int, vtkInformation*)'


collect2: error: ld returned 1 exit status

make[2]: *** [Rendering/OpenGL2/CMakeFiles/vtkProbeOpenGLVersion.dir/build.make:114: bin/vtkProbeOpenGLVersion] Error 1

make[2]: Leaving directory '/disk/nobackup2/carlos/spack-stage/spack-stage-vtk-8.2.1a-45rtrppcoqhycgrqcdxv2erm76adm6d5/spack-build-45rtrpp'

make[1]: *** [CMakeFiles/Makefile2:3450: Rendering/OpenGL2/CMakeFiles/vtkProbeOpenGLVersion.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs....


make[2]: Leaving directory '/disk/nobackup2/carlos/spack-stage/spack-stage-vtk-8.2.1a-45rtrppcoqhycgrqcdxv2erm76adm6d5/spack-build-45rtrpp'

[ 91%] Built target vtkChartsCore

make[1]: Leaving directory '/disk/nobackup2/carlos/spack-stage/spack-stage-vtk-8.2.1a-45rtrppcoqhycgrqcdxv2erm76adm6d5/spack-build-45rtrpp'


make: *** [Makefile:139: all] Error 2

Information on your system

  • Spack: 0.23.0.dev0 (722d401)
  • Python: 3.9.18
  • Platform: linux-almalinux9-zen3
  • Concretizer: clingo

Additional information

spack-build-out.txt
spack-build-env.txt

General information

  • I have run spack debug report and reported the version of Spack/Python/Platform
  • I have run spack maintainers <name-of-the-package> and @mentioned any maintainers
  • I have uploaded the build log and environment files
  • I have searched the issues of this repo and believe this is not a duplicate

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