Install HDF5 with Intel Fortran

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Thibault Xavier

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Apr 9, 2021, 3:56:39 AM4/9/21
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Hi all,

Same issue coming back on a fresh install of HDF5 fortran with Intel compilers from Intel OneAPI suite.

I got an error when building HDF5 Fortran (even in sequential)
spack install hdf5 +fortran ~mpi %intel

- OneAPI seems to be properly installed and run test examples

My compiler.yaml is as follow

compilers:
- compiler:
    spec: in...@2021.2.0
    paths:
      cc: /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
      cxx: /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
      f77: /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
      fc: /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
    flags: {}
    operating_system: ubuntu18.04
    target: x86_64
    modules: [compiler/latest]
    environment:
      append_path:
        LD_LIBBRARY_PATH: /opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64:${LD_LIBRARY_PATH}
    extra_rpaths:
    - /opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64



The installation log is :

hdf5: Executing phase: 'autoreconf'
==> hdf5: Executing phase: 'configure'
==> [2021-04-09-09:49:57.354939] Multiple definitions of compiler in...@2021.2.0for architecture linux-ubuntu18.04-skylake_avx512:
 [intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04), intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04)]
==> [2021-04-09-09:49:57.358418] Multiple definitions of compiler in...@2021.2.0for architecture linux-ubuntu18.04-skylake_avx512:
 [intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04), intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04)]
==> [2021-04-09-09:49:57.359346] Multiple definitions of compiler in...@2021.2.0for architecture linux-ubuntu18.04-skylake_avx512:
 [intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04), intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04)]
==> [2021-04-09-09:49:57.360252] Multiple definitions of compiler in...@2021.2.0for architecture linux-ubuntu18.04-skylake_avx512:
 [intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04), intel(/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/icpc
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     /opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/ifort
     ['compiler/latest']
     ubuntu18.04)]
==> [2021-04-09-09:49:57.360839] '/tmp/xavier/spack-stage/spack-stage-hdf5-1.10.7-jlwl7kaumu5xraz4f62u6oskxgcvxexo/spack-src/configure' '--prefix=/opt/dossier_public/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/intel-2021.2.0/hdf5-1.10.7-jlwl7kaumu5xraz4f62u6oskxgcvxexo' '--enable-unsupported' '--enable-symbols=yes' '--with-zlib=/opt/dossier_public/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/intel-2021.2.0/zlib-1.2.11-pzuvcx375fxzinmyjbseodf2y3pb2mz5' '--disable-threadsafe' '--disable-cxx' '--disable-hl' '--enable-fortran' '--disable-java' '--without-szlib' '--enable-build-mode=production' '--enable-shared' 'CFLAGS=-fPIC' 'CXXFLAGS=-fPIC' 'FCFLAGS=-fPIC'
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler '/opt/dossier_public/spack/lib/spack/env/intel/icc' is Intel icc-2021.2.0
compiler '/opt/dossier_public/spack/lib/spack/env/intel/ifort' is Intel ifort-2021.2.0
compiler '/opt/dossier_public/spack/lib/spack/env/intel/icpc' is GNU g++-7.5.0
checking for config ./config/site-specific/host-comb-detoCT... no
checking for clang sanitizer checks... checking build mode... production
checking for gcc... /opt/dossier_public/spack/lib/spack/env/intel/icc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /opt/dossier_public/spack/lib/spack/env/intel/icc accepts -g... yes
checking for /opt/dossier_public/spack/lib/spack/env/intel/icc option to accept ISO C89... none needed
checking whether /opt/dossier_public/spack/lib/spack/env/intel/icc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of /opt/dossier_public/spack/lib/spack/env/intel/icc... gcc3
checking if unsupported combinations of configure options are allowed... yes
checking how to run the C preprocessor... /opt/dossier_public/spack/lib/spack/env/intel/icc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 16
checking size of _Quad... 0
checking quadmath.h usability... yes
checking quadmath.h presence... yes
checking for quadmath.h... yes
checking maximum decimal precision for C... 33
checking if Fortran interface enabled... yes
checking whether we are using the GNU Fortran compiler... no
checking whether /opt/dossier_public/spack/lib/spack/env/intel/ifort accepts -g... yes
checking for Fortran flag to compile .f90 files... none
checking whether we are using the GNU Fortran compiler... (cached) no
checking whether /opt/dossier_public/spack/lib/spack/env/intel/ifort accepts -g... (cached) yes
checking what /opt/dossier_public/spack/lib/spack/env/intel/ifort does with modules... module.mod
checking how /opt/dossier_public/spack/lib/spack/env/intel/ifort finds modules... -I
checking if Fortran compiler version compatible with Fortran 2003 HDF... yes
checking how to get verbose linking output from /opt/dossier_public/spack/lib/spack/env/intel/ifort... -v
checking for Fortran libraries of /opt/dossier_public/spack/lib/spack/env/intel/ifort...  -L/opt/intel/oneapi/compiler/2021.2.0/linux/bin/intel64/../../compiler/lib/intel64_lin -L/usr/lib/gcc/x86_64-linux-gnu/7/ -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/ -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib/ -L/lib/x86_64-linux-gnu/ -L/lib/../lib64 -L/lib/../lib/ -L/usr/lib/x86_64-linux-gnu/ -L/usr/lib/../lib/ -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../ -L/lib64 -L/lib/ -L/usr/lib -L/usr/lib/i386-linux-gnu -lifport -lifcoremt_pic -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking if Fortran compiler supports intrinsic SIZEOF... no
checking if Fortran compiler supports intrinsic C_SIZEOF... no
checking if Fortran compiler supports intrinsic STORAGE_SIZE... no
configure: error: Fortran compiler requires either intrinsic functions SIZEOF or STORAGE_SIZE


It happened to me on another computer but problem was solved by editing LD_LIBRARY_PATH as specified in compiler.yaml, but not working this time... So I suppose it's another problem, maybe external to Spack ?
Thanks for your help on a quite newbie user :D

Thibault

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