Installation issue: [email protected]+hdf5 #35546
Description
Steps to reproduce the issue
$ spack spec -I [email protected]%[email protected]+hdf5
Input spec
--------------------------------
[email protected]%[email protected]+hdf5
Concretized
--------------------------------
ccifr6k [email protected]%[email protected]~amrdata~cuda~eb~fortran+hdf5~hypre~ipo+linear_solvers+mpi~openmp~particles~petsc~pic~plotfile_tools~rocm~shared~sundials~sycl~tiny_profile build_system=cmake build_type=RelWithDebInfo dimensions=3 precision=double arch=linu
x-rhel7-skylake_avx512
nbe2xqn ^[email protected]%[email protected]~doc+ncurses+ownlibs~qt build_system=generic build_type=Release arch=linux-rhel7-skylake_avx512
ex5yyfs ^[email protected]%[email protected]~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake_avx512
3g6w4fu ^[email protected]%[email protected]~docs~shared build_system=generic certs=mozilla arch=linux-rhel7-skylake_avx512
au3vaca ^ca-certificates-mozilla@2023-01-10%[email protected] build_system=generic arch=linux-rhel7-skylake_avx512
vzu47cs ^[email protected]%[email protected]+cpanm+open+shared+threads build_system=generic arch=linux-rhel7-skylake_avx512
fsrsn6r ^[email protected]%[email protected]+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rhel7-skylake_avx512
4cm2qmx ^[email protected]%[email protected]~debug~pic+shared build_system=generic arch=linux-rhel7-skylake_avx512
fok6ki4 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
rcybyat ^[email protected]%[email protected] build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake_avx512
lhy5jq7 ^[email protected]%[email protected]~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=RelWithDebInfo patches=0b5dd6f arch=linux-rhel7-skylake_avx512
xp45tof ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
pv3fue4 ^[email protected]%[email protected]+optimize+pic+shared build_system=makefile arch=linux-rhel7-skylake_avx512
v6i343e ^[email protected]%[email protected]~alloca~cuda~debug+regcache+wrapperrpath build_system=autotools ch3_rank_bits=32 file_systems=auto netmod=ofi process_managers=auto threads=multiple arch=linux-rhel7-skylake_avx512
bi4bnqn ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
oud47uw ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
a2xcvvp ^[email protected]%[email protected]+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rhel7-skylake_avx512
rpgflvg ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
ymspxqm ^[email protected]%[email protected] build_system=autotools patches=440b954 arch=linux-rhel7-skylake_avx512
uzxnsoe ^[email protected]%[email protected]~debug~kdreg build_system=autotools fabrics=sockets,tcp,udp arch=linux-rhel7-skylake_avx512
jks3j5x ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
qxy2bgr ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
uisde6u ^[email protected]%[email protected] build_system=autotools arch=linux-rhel7-skylake_avx512
u5yxcrw ^[email protected]%[email protected]~python build_system=autotools arch=linux-rhel7-skylake_avx512
boo6zb3 ^[email protected]%[email protected] build_system=autotools libs=shared,static arch=linux-rhel7-skylake_avx512
dc4igz5 ^[email protected]%[email protected]~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake_avx512Error message
Error message
==> Installing amrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5
==> No binary for amrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5 found: installing from source
==> Using cached archive: /dev/shm/bsmits_spack/var/spack/cache/_source-cache/archive/f4/f443c5eb4b89f4a74bf0e1b8a5943da18ab81cdc76aff12e8282ca43ffd06412.tar.gz
==> No patches needed for amrex
==> amrex: Executing phase: 'cmake'
==> Error: ProcessError: Command exited with status 1:
'/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/cmake-3.25.2-nbe2xqn25boaqufnsaeqtdnil4pfwpgy/bin/cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/a
mrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DBUILD_TESTING:BOOL=OFF' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON' '-DCMAKE_I
NSTALL_RPATH:STRING=/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/amrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5/lib;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/amrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5/li
b64;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/hdf5-1.14.0-lhy5jq7rjm6psfjbs7vde5ny57yhour5/lib;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/mvapich-3.0a-v6i343egxor3ggvm5ifk53vhlzvtcunx/lib;/dev/shm/bsmi
ts_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libfabric-1.16.1-uzxnsoe27thisgcp3yo3py3ffgewsxju/lib;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libpciaccess-0.16-jks3j5xtmwd4jof5nbotydlyvabd55xc/lib;/dev/shm/bsmits_spac
k/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libxml2-2.10.3-u5yxcrw5qcck3o5u2dtlqkwrjmezeorg/lib;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libiconv-1.17-boo6zb3seinlrqpvirr44waxik4atl3b/lib;/dev/shm/bsmits_spack/opt/spack/l
inux-rhel7-skylake_avx512/gcc-9.3.0/xz-5.4.1-dc4igz55iuvtzjuckgqr2eedllfrkjxe/lib;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/zlib-1.2.13-pv3fue4yfrg2wwftonn6mhox6oworevh/lib' '-DCMAKE_PREFIX_PATH:STRING=/dev/shm/bsmits_spack/opt
/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/hdf5-1.14.0-lhy5jq7rjm6psfjbs7vde5ny57yhour5;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/mvapich-3.0a-v6i343egxor3ggvm5ifk53vhlzvtcunx;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylak
e_avx512/gcc-9.3.0/libxml2-2.10.3-u5yxcrw5qcck3o5u2dtlqkwrjmezeorg;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/xz-5.4.1-dc4igz55iuvtzjuckgqr2eedllfrkjxe;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libpcia
ccess-0.16-jks3j5xtmwd4jof5nbotydlyvabd55xc;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libfabric-1.16.1-uzxnsoe27thisgcp3yo3py3ffgewsxju;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/cmake-3.25.2-nbe2xqn25
boaqufnsaeqtdnil4pfwpgy;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/zlib-1.2.13-pv3fue4yfrg2wwftonn6mhox6oworevh;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/libiconv-1.17-boo6zb3seinlrqpvirr44waxik4atl3b'
'-DUSE_XSDK_DEFAULTS=ON' '-DAMReX_SPACEDIM:STRING=3' '-DBUILD_SHARED_LIBS:BOOL=OFF' '-DAMReX_MPI:BOOL=ON' '-DAMReX_OMP:BOOL=OFF' '-DXSDK_PRECISION:STRING=DOUBLE' '-DXSDK_ENABLE_Fortran:BOOL=OFF' '-DAMReX_FORTRAN_INTERFACES:BOOL=OFF' '-DAMReX_EB:BOOL=OFF
' '-DAMReX_LINEAR_SOLVERS:BOOL=ON' '-DAMReX_AMRDATA:BOOL=OFF' '-DAMReX_PARTICLES:BOOL=OFF' '-DAMReX_PLOTFILE_TOOLS:BOOL=OFF' '-DAMReX_TINY_PROFILE:BOOL=OFF' '-DAMReX_HDF5:BOOL=ON' '-DAMReX_HYPRE:BOOL=OFF' '-DAMReX_PETSC:BOOL=OFF' '-DAMReX_SUNDIALS:BOOL=O
FF' '-DAMReX_PIC:BOOL=OFF' '/dev/shm/spack/stage/bsmits/spack-stage-amrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5/spack-src'
1 error found in build log:
31 -- Check if compiler accepts -pthread - yes
32 -- Found Threads: TRUE
33 -- Found MPI_C: /dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/mvapich-3.0a-v6i343egxor3ggvm5ifk53vhlzvtcunx/lib/libmpi.so (found version "3.1")
34 -- Found MPI_CXX: /dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/mvapich-3.0a-v6i343egxor3ggvm5ifk53vhlzvtcunx/lib/libmpicxx.so (found version "3.1")
35 -- Found MPI: TRUE (found version "3.1") found components: C CXX
36 -- Found HDF5: /dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/hdf5-1.14.0-lhy5jq7rjm6psfjbs7vde5ny57yhour5/lib/libhdf5.so;/dev/shm/bsmits_spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/mvapich-3.0a-v6i343egxor3ggvm
5ifk53vhlzvtcunx/lib/libmpi.so (found suitable version "1.14.0", minimum required is "1.10.4")
37 CMake Error at Tools/CMake/AMReXThirdPartyLibraries.cmake:10 (message):
38
39
40 HDF5 library does not support parallel I/O
41 Call Stack (most recent call first):
42 Src/CMakeLists.txt:28 (include)
43
See build log for details:
/dev/shm/spack/stage/bsmits/spack-stage-amrex-23.02-ccifr6kx7zxeqv3k7mif25o6gf7xkcw5/spack-build-out.txt
Information on your system
$ spack debug report
* **Spack:** 0.20.0.dev0
* **Python:** 3.6.8
* **Platform:** linux-rhel7-skylake_avx512
* **Concretizer:** clingo
Additional information
@WeiqunZhang
@asalmgren
@etpalmer63
General information
- I have run
spack debug reportand 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