Closed vsoch closed 2 years ago
@vsoch I tried recreating your linking error using my Debian 11 home PC and a fresh spack installation, but cannot reproduce the fault. Can you please provide more information and/or compare my steps against yours?
$ git clone https://github.com/spack/spack.git
$ cd spack/
$ source share/spack/setup-env.sh
$ spack debug report
* **Spack:** 0.19.0.dev0 (1bc3b0a9266fea949632661aadbe0191a45e34bb)
* **Python:** 3.9.2
* **Platform:** linux-debian11-nehalem
* **Concretizer:** clingo
$ TMPDIR=/var/tmp spack install gcc@12.1.0 # My /tmp uses tmpfs which is too small for compiling gcc.
...
==> gcc: Successfully installed gcc-12.1.0-rgnsydf4hix65rvpwg2qxq3nurlclli7
Fetch: 2.22s. Build: 1h 53m 13.70s. Total: 1h 53m 15.92s.
[+] /home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-10.2.1/gcc-12.1.0-rgnsydf4hix65rvpwg2qxq3nurlclli7
$ spack spec --install-status petsc # Using default gcc@10.2.1 compiler.
Input spec
--------------------------------
- petsc
Concretized
--------------------------------
- petsc@3.17.2%gcc@10.2.1~X~batch~cgns~complex~cuda~debug+double~exodusii~fftw+fortran~giflib+hdf5~hpddm~hwloc+hypre~int64~jpeg~knl~kokkos~libpng~libyaml~memkind+metis~mkl-pardiso~mmg~moab~mpfr+mpi~mumps~openmp~p4est~parmmg~ptscotch~random123~rocm~saws~scalapack+shared~strumpack~suite-sparse+superlu-dist~tetgen~trilinos~valgrind clanguage=C arch=linux-debian11-nehalem
[+] ^diffutils@3.8%gcc@10.2.1 arch=linux-debian11-nehalem
[+] ^libiconv@1.16%gcc@10.2.1 libs=shared,static arch=linux-debian11-nehalem
- ^hdf5@1.12.2%gcc@10.2.1~cxx~fortran~hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-debian11-nehalem
- ^cmake@3.23.2%gcc@10.2.1~doc+ncurses+ownlibs~qt build_type=Release arch=linux-debian11-nehalem
[+] ^ncurses@6.2%gcc@10.2.1~symlinks+termlib abi=none arch=linux-debian11-nehalem
[+] ^pkgconf@1.8.0%gcc@10.2.1 arch=linux-debian11-nehalem
- ^openssl@1.1.1o%gcc@10.2.1~docs~shared certs=mozilla arch=linux-debian11-nehalem
- ^ca-certificates-mozilla@2022-03-29%gcc@10.2.1 arch=linux-debian11-nehalem
[+] ^perl@5.34.1%gcc@10.2.1+cpanm+shared+threads arch=linux-debian11-nehalem
[+] ^berkeley-db@18.1.40%gcc@10.2.1+cxx~docs+stl patches=b231fcc arch=linux-debian11-nehalem
[+] ^bzip2@1.0.8%gcc@10.2.1~debug~pic+shared arch=linux-debian11-nehalem
[+] ^gdbm@1.19%gcc@10.2.1 arch=linux-debian11-nehalem
[+] ^readline@8.1%gcc@10.2.1 arch=linux-debian11-nehalem
[+] ^zlib@1.2.12%gcc@10.2.1+optimize+pic+shared patches=0d38234 arch=linux-debian11-nehalem
- ^openmpi@4.1.4%gcc@10.2.1~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker~pmi+romio+rsh~singularity+static+vt+wrapper-rpath fabrics=none schedulers=none arch=linux-debian11-nehalem
- ^hwloc@2.7.1%gcc@10.2.1~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm+shared arch=linux-debian11-nehalem
- ^libpciaccess@0.16%gcc@10.2.1 arch=linux-debian11-nehalem
[+] ^libtool@2.4.7%gcc@10.2.1 arch=linux-debian11-nehalem
[+] ^m4@1.4.19%gcc@10.2.1+sigsegv patches=9dc5fbd,bfdffa7 arch=linux-debian11-nehalem
[+] ^libsigsegv@2.13%gcc@10.2.1 arch=linux-debian11-nehalem
- ^util-macros@1.19.3%gcc@10.2.1 arch=linux-debian11-nehalem
- ^libxml2@2.9.13%gcc@10.2.1~python arch=linux-debian11-nehalem
- ^xz@5.2.5%gcc@10.2.1~pic libs=shared,static arch=linux-debian11-nehalem
- ^numactl@2.0.14%gcc@10.2.1 patches=4e1d78c,62fc8a8,ff37630 arch=linux-debian11-nehalem
[+] ^autoconf@2.69%gcc@10.2.1 patches=35c4492,7793209,a49dd5b arch=linux-debian11-nehalem
[+] ^automake@1.16.5%gcc@10.2.1 arch=linux-debian11-nehalem
- ^openssh@9.0p1%gcc@10.2.1+gssapi arch=linux-debian11-nehalem
- ^krb5@1.19.3%gcc@10.2.1+shared arch=linux-debian11-nehalem
- ^bison@3.8.2%gcc@10.2.1 arch=linux-debian11-nehalem
- ^gettext@0.21%gcc@10.2.1+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-debian11-nehalem
- ^tar@1.34%gcc@10.2.1 zip=pigz arch=linux-debian11-nehalem
- ^pigz@2.7%gcc@10.2.1 arch=linux-debian11-nehalem
- ^zstd@1.5.2%gcc@10.2.1+programs compression=none libs=shared,static arch=linux-debian11-nehalem
- ^libedit@3.1-20210216%gcc@10.2.1 arch=linux-debian11-nehalem
- ^pmix@4.1.2%gcc@10.2.1~docs+pmi_backwards_compatibility~restful arch=linux-debian11-nehalem
- ^libevent@2.1.12%gcc@10.2.1+openssl arch=linux-debian11-nehalem
- ^hypre@2.25.0%gcc@10.2.1~complex~cuda~debug+fortran~gptune~int64~internal-superlu~mixedint+mpi~openmp~rocm+shared~superlu-dist~unified-memory arch=linux-debian11-nehalem
- ^openblas@0.3.20%gcc@10.2.1~bignuma~consistent_fpcsr~ilp64+locking+pic+shared symbol_suffix=none threads=none arch=linux-debian11-nehalem
- ^metis@5.1.0%gcc@10.2.1~gdb~int64~real64+shared build_type=Release patches=4991da9,b1225da arch=linux-debian11-nehalem
- ^parmetis@4.0.3%gcc@10.2.1~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f89253,50ed208,704b84f arch=linux-debian11-nehalem
- ^python@3.9.13%gcc@10.2.1+bz2+ctypes+dbm~debug+ensurepip+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93,4c24573,f2fd060 arch=linux-debian11-nehalem
- ^expat@2.4.8%gcc@10.2.1+libbsd arch=linux-debian11-nehalem
- ^libbsd@0.11.5%gcc@10.2.1 arch=linux-debian11-nehalem
- ^libmd@1.0.4%gcc@10.2.1 arch=linux-debian11-nehalem
- ^libffi@3.4.2%gcc@10.2.1 arch=linux-debian11-nehalem
- ^sqlite@3.38.5%gcc@10.2.1+column_metadata+dynamic_extensions+fts~functions+rtree arch=linux-debian11-nehalem
- ^util-linux-uuid@2.37.4%gcc@10.2.1 arch=linux-debian11-nehalem
- ^superlu-dist@7.2.0%gcc@10.2.1~cuda~int64~ipo~openmp~rocm+shared build_type=RelWithDebInfo patches=8da9e21 arch=linux-debian11-nehalem
$ TMPDIR=/var/tmp spack install petsc
...
==> petsc: Successfully installed petsc-3.17.2-3xpx3b2sqop33vq3dubotpaewzxoq3zg
Fetch: 2.73s. Build: 6m 42.01s. Total: 6m 44.74s.
[+] /home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-10.2.1/petsc-3.17.2-3xpx3b2sqop33vq3dubotpaewzxoq3zg
$ spack compiler find $(spack location -i gcc@12.1.0)
==> Added 1 new compiler to /home/omsai/.spack/linux/compilers.yaml
gcc@12.1.0
==> Compilers are defined in the following files:
/home/omsai/.spack/linux/compilers.yaml
$ spack spec --install-status petsc %gcc@12.1.0 # Using gcc@12.1.0 compiler.
Input spec
--------------------------------
- petsc%gcc@12.1.0
Concretized
--------------------------------
- petsc@3.17.2%gcc@12.1.0~X~batch~cgns~complex~cuda~debug+double~exodusii~fftw+fortran~giflib+hdf5~hpddm~hwloc+hypre~int64~jpeg~knl~kokkos~libpng~libyaml~memkind+metis~mkl-pardiso~mmg~moab~mpfr+mpi~mumps~openmp~p4est~parmmg~ptscotch~random123~rocm~saws~scalapack+shared~strumpack~suite-sparse+superlu-dist~tetgen~trilinos~valgrind clanguage=C arch=linux-debian11-nehalem
- ^diffutils@3.8%gcc@12.1.0 arch=linux-debian11-nehalem
- ^libiconv@1.16%gcc@12.1.0 libs=shared,static arch=linux-debian11-nehalem
- ^hdf5@1.12.2%gcc@12.1.0~cxx~fortran~hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-debian11-nehalem
- ^cmake@3.23.2%gcc@12.1.0~doc+ncurses+ownlibs~qt build_type=Release arch=linux-debian11-nehalem
- ^ncurses@6.2%gcc@12.1.0~symlinks+termlib abi=none arch=linux-debian11-nehalem
- ^pkgconf@1.8.0%gcc@12.1.0 arch=linux-debian11-nehalem
- ^openssl@1.1.1o%gcc@12.1.0~docs~shared certs=mozilla arch=linux-debian11-nehalem
- ^ca-certificates-mozilla@2022-03-29%gcc@12.1.0 arch=linux-debian11-nehalem
- ^perl@5.34.1%gcc@12.1.0+cpanm+shared+threads arch=linux-debian11-nehalem
- ^berkeley-db@18.1.40%gcc@12.1.0+cxx~docs+stl patches=b231fcc arch=linux-debian11-nehalem
- ^bzip2@1.0.8%gcc@12.1.0~debug~pic+shared arch=linux-debian11-nehalem
- ^gdbm@1.19%gcc@12.1.0 arch=linux-debian11-nehalem
- ^readline@8.1%gcc@12.1.0 arch=linux-debian11-nehalem
- ^zlib@1.2.12%gcc@12.1.0+optimize+pic+shared patches=0d38234 arch=linux-debian11-nehalem
- ^openmpi@4.1.4%gcc@12.1.0~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker~pmi+romio+rsh~singularity+static+vt+wrapper-rpath fabrics=none schedulers=none arch=linux-debian11-nehalem
- ^hwloc@2.7.1%gcc@12.1.0~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm+shared arch=linux-debian11-nehalem
- ^libpciaccess@0.16%gcc@12.1.0 arch=linux-debian11-nehalem
- ^libtool@2.4.7%gcc@12.1.0 arch=linux-debian11-nehalem
- ^m4@1.4.19%gcc@12.1.0+sigsegv patches=9dc5fbd,bfdffa7 arch=linux-debian11-nehalem
- ^libsigsegv@2.13%gcc@12.1.0 arch=linux-debian11-nehalem
- ^util-macros@1.19.3%gcc@12.1.0 arch=linux-debian11-nehalem
- ^libxml2@2.9.13%gcc@12.1.0~python arch=linux-debian11-nehalem
- ^xz@5.2.5%gcc@12.1.0~pic libs=shared,static arch=linux-debian11-nehalem
- ^numactl@2.0.14%gcc@12.1.0 patches=4e1d78c,62fc8a8,ff37630 arch=linux-debian11-nehalem
- ^autoconf@2.69%gcc@12.1.0 patches=35c4492,7793209,a49dd5b arch=linux-debian11-nehalem
- ^automake@1.16.5%gcc@12.1.0 arch=linux-debian11-nehalem
- ^openssh@9.0p1%gcc@12.1.0+gssapi arch=linux-debian11-nehalem
- ^krb5@1.19.3%gcc@12.1.0+shared arch=linux-debian11-nehalem
- ^bison@3.8.2%gcc@12.1.0 arch=linux-debian11-nehalem
- ^gettext@0.21%gcc@12.1.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-debian11-nehalem
- ^tar@1.34%gcc@12.1.0 zip=pigz arch=linux-debian11-nehalem
- ^pigz@2.7%gcc@12.1.0 arch=linux-debian11-nehalem
- ^zstd@1.5.2%gcc@12.1.0+programs compression=none libs=shared,static arch=linux-debian11-nehalem
- ^libedit@3.1-20210216%gcc@12.1.0 arch=linux-debian11-nehalem
- ^pmix@4.1.2%gcc@12.1.0~docs+pmi_backwards_compatibility~restful arch=linux-debian11-nehalem
- ^libevent@2.1.12%gcc@12.1.0+openssl arch=linux-debian11-nehalem
- ^hypre@2.25.0%gcc@12.1.0~complex~cuda~debug+fortran~gptune~int64~internal-superlu~mixedint+mpi~openmp~rocm+shared~superlu-dist~unified-memory arch=linux-debian11-nehalem
- ^openblas@0.3.20%gcc@12.1.0~bignuma~consistent_fpcsr~ilp64+locking+pic+shared symbol_suffix=none threads=none arch=linux-debian11-nehalem
- ^metis@5.1.0%gcc@12.1.0~gdb~int64~real64+shared build_type=Release patches=4991da9,b1225da arch=linux-debian11-nehalem
- ^parmetis@4.0.3%gcc@12.1.0~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f89253,50ed208,704b84f arch=linux-debian11-nehalem
- ^python@3.9.13%gcc@12.1.0+bz2+ctypes+dbm~debug+ensurepip+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93,4c24573,f2fd060 arch=linux-debian11-nehalem
- ^expat@2.4.8%gcc@12.1.0+libbsd arch=linux-debian11-nehalem
- ^libbsd@0.11.5%gcc@12.1.0 arch=linux-debian11-nehalem
- ^libmd@1.0.4%gcc@12.1.0 arch=linux-debian11-nehalem
- ^libffi@3.4.2%gcc@12.1.0 arch=linux-debian11-nehalem
- ^sqlite@3.38.5%gcc@12.1.0+column_metadata+dynamic_extensions+fts~functions+rtree arch=linux-debian11-nehalem
- ^util-linux-uuid@2.37.4%gcc@12.1.0 arch=linux-debian11-nehalem
- ^superlu-dist@7.2.0%gcc@12.1.0~cuda~int64~ipo~openmp~rocm+shared build_type=RelWithDebInfo patches=8da9e21 arch=linux-debian11-nehalem
$ spack install petsc %gcc@12.1.0
...
==> petsc: Successfully installed petsc-3.17.2-gz6otnvfknujk2pdy2kxm7ennanrttwc
Fetch: 1.03s. Build: 8m 41.09s. Total: 8m 42.12s.
[+] /home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/petsc-3.17.2-gz6otnvfknujk2pdy2kxm7ennanrttwc
Here are my spack files in the installation directory for superlu-dist %gcc@12.1.0
:
$ spack cd -i superlu-dist %gcc@12.1.0
$ tr ' ' '\n' < .spack/spack-configure-args.txt ; echo
-DCMAKE_C_COMPILER:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/openmpi-4.1.4-bpvu2g74elizi2ntx7rsb3opxg7cgbjv/bin/mpicc
-DCMAKE_CXX_COMPILER:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/openmpi-4.1.4-bpvu2g74elizi2ntx7rsb3opxg7cgbjv/bin/mpic++
-DCMAKE_INSTALL_LIBDIR:STRING:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/superlu-dist-7.2.0-imxfk7uxopeot7jpbv44mmniu45fg7w3/lib
-DCMAKE_INSTALL_BINDIR:STRING:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/superlu-dist-7.2.0-imxfk7uxopeot7jpbv44mmniu45fg7w3/bin
-DTPL_BLAS_LIBRARIES:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/openblas-0.3.20-u4vqt2cg2e2yx6pnjevweho6imxerfva/lib/libopenblas.so
-DTPL_LAPACK_LIBRARIES:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/openblas-0.3.20-u4vqt2cg2e2yx6pnjevweho6imxerfva/lib/libopenblas.so
-DTPL_ENABLE_LAPACKLIB:BOOL=ON
-DUSE_XSDK_DEFAULTS:BOOL=ON
-DTPL_PARMETIS_LIBRARIES:STRING=-L/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/parmetis-4.0.3-rc5ldkl7h7obgos6gohii6q2svtbti7w/lib
-lparmetis;-L/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/metis-5.1.0-2tp733mcdokiacjyapltjfebuubuwfnt/lib
-lmetis
-DTPL_PARMETIS_INCLUDE_DIRS:STRING=/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/parmetis-4.0.3-rc5ldkl7h7obgos6gohii6q2svtbti7w/include;/home/omsai/src/spack/opt/spack/linux-debian11-nehalem/gcc-12.1.0/metis-5.1.0-2tp733mcdokiacjyapltjfebuubuwfnt/include
-DXSDK_INDEX_SIZE:STRING=32
-Denable_openmp:BOOL=OFF
-DCMAKE_DISABLE_FIND_PACKAGE_OpenMP:BOOL=ON
-DBUILD_SHARED_LIBS:BOOL=ON
# Below are the uploaded .spack/spack-build-{out,env}.txt files:
Thank you @omsai ! So the computer I produced the error on is borked, and I tried it on two other systems and couldn't reproduce it again either! :laughing: :sob: <- laughing and crying!
So I think it's safe to close for now - and maybe someone will reproduce it (or I'll get my computer when it's sent back and fixed to test). Thank you for you help!
@vsoch no worries! I'm glad you were able to make progress. I actually don't mind running tests that don't reproduce a bug because I much prefer that to fixable errors that might otherwise go unreported.
Using gcc 12.1, I get: