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Error while compiling HDF5 using AOCC compilers (error while loading shared libraries: libomp.so) #1588

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Enea2301 opened this issue Apr 6, 2022 · 2 comments
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Error while compiling HDF5 using AOCC compilers (error while loading shared libraries: libomp.so) #1588

Enea2301 opened this issue Apr 6, 2022 · 2 comments
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@derobins
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Component - Build CMake, Autotools Priority - 2. Medium ⏹ It would be nice to have this in the next release Type - Bug / Bugfix Please report security issues to help@hdfgroup.org instead of creating an issue on GitHub
Milestone
1.14.3

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@Enea2301
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Enea2301 commented Apr 6, 2022

Good evening. I'm trying to compile HDF5 using latest AMD AOCC compilers (3.2), but a problem arises constantly while executing the "make" command

**./H5_buildiface: error while loading shared libraries: libomp.so: cannot open shared object file: No such file or directory
make[3]: *** [Makefile:1513: H5_gen.F90] Error 127
**

The runtime command for configure is as continues: CC="$CC" CXX="$CXX" FC="$FC" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" FCFLAGS="$FCFLAGS" LDFLAGS="$LDFLAGS" LD_LIBRARY_PATH="$LD_LIBRARY_PATH" LIBRARY_PATH="$LIBRARY_PATH" ./configure --with-zlib=$DIR/grib2 --prefix=$DIR/hdf5 --enable-hl --enable-fortran

The referenced bashrc variables:
export DIR=path/to/librariesupperfolder
export DIRAOCC=path/to/AOCCdir
export CC=$DIRAOCC/AOCC/bin/clang
export CXX=$DIRAOCC/AOCC/bin/clang++
export FC=$DIRAOCC/AOCC/bin/flang
export CFLAGS="-m64 -O3 -march=znver2 -mtune=znver2"
export CXXFLAGS="-m64 -O3 -march=znver2 -mtune=znver2"
export FCFLAGS="-m64 -O3 -march=znver2 -mtune=znver2"
export LDFLAGS="-L$DIRAOCC/AOCC/lib -L$DIRAOCC/AOCC/lib32"
export LD_LIBRARY_PATH=$DIRAOCC/AOCC/lib:$DIRAOCC/AOCC/lib32/:$DIRAOCC/AOCC/ompd:/usr/lib64:/usr/lib/x86_64-linux-gnu:/usr/lib:/usr/lib32
export LIBRARY_PATH=$DIRAOCC/AOCC/lib:$DIRAOCC/AOCC/lib32/:/usr/lib64:/usr/lib/x86_64-linux-gnu:/usr/lib:/usr/lib32

Any ideas on why it could be happening?
libomp.so does exist under both ../AOCC/lib and ../AOCC/lib32
@derobins derobins added Priority - 2. Medium ⏹ It would be nice to have this in the next release Component - Build CMake, Autotools Type - Bug / Bugfix Please report security issues to help@hdfgroup.org instead of creating an issue on GitHub labels May 4, 2023
@derobins derobins added this to the 1.14.3 milestone Oct 9, 2023
@derobins derobins assigned derobins and unassigned vchoi-hdfgroup Oct 13, 2023
@derobins
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As a part of making AOCC work better at compiling HDF5, we'll be adding -nomp to flang builds in 1.14.3. That should take care of any OpenMP library issues (we don't use it in HDF5).

derobins added a commit to derobins/hdf5 that referenced this issue Oct 14, 2023
@derobins
Add support for AOCC & Flang w/ the Autotools
2043045 
* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
  when using Flang, the MPI Fortran compiler wrappers, and building
  the shared library. This would often result in unrecognized options
  like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.

CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.

Fixes GitHub issues HDFGroup#3439, HDFGroup#1588, HDFGroup#366, HDFGroup#280
@derobins derobins mentioned this issue Oct 14, 2023
Merged
@hyoklee hyoklee mentioned this issue Oct 14, 2023
Merged
lrknox pushed a commit that referenced this issue Oct 15, 2023
@derobins
Add support for AOCC & Flang w/ the Autotools (#3674)
d5267f0 
* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
  when using Flang, the MPI Fortran compiler wrappers, and building
  the shared library. This would often result in unrecognized options
  like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.

CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.

Fixes GitHub issues #3439, #1588, #366, #280
@derobins
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Fixed w/ #3674

brtnfld pushed a commit to brtnfld/hdf5 that referenced this issue Oct 16, 2023
@derobins @brtnfld
Add support for AOCC & Flang w/ the Autotools (HDFGroup#3674)
d457b12 
* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
  when using Flang, the MPI Fortran compiler wrappers, and building
  the shared library. This would often result in unrecognized options
  like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.

CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.

Fixes GitHub issues HDFGroup#3439, HDFGroup#1588, HDFGroup#366, HDFGroup#280
jhendersonHDF pushed a commit to jhendersonHDF/hdf5 that referenced this issue Oct 18, 2023
@derobins @jhendersonHDF
Add support for AOCC & Flang w/ the Autotools (HDFGroup#3674)
71fb6ba 
* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
  when using Flang, the MPI Fortran compiler wrappers, and building
  the shared library. This would often result in unrecognized options
  like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.

CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.

Fixes GitHub issues HDFGroup#3439, HDFGroup#1588, HDFGroup#366, HDFGroup#280
derobins added a commit that referenced this issue Oct 18, 2023
@jhendersonHDF @brtnfld
@hyoklee @byrnHDF @derobins
Sync 1.14 branch with develop (#3705)
4a02890 
* Address nagfor exceptions stoppage. (#3658)

* added cmake ieee flag for nagfor

* generalized determining the nag compiler

* fixing some misc. NAG warnings

* Simplify. (#3659)


* Address @jhendersonHDF review

* Add expedited testing support to t_filters_parallel (#3665)

* Remove clang warnings (#3656)

* Fixes test failure for gfortran -O2 and -O3, -fdefault-real-16 (#3662)

* added cmake ieee flag for nagfor

* fixes gfortran -O2 and -O3, -fdefault-real-16

* fixed sync

* updated release notes

* Fix link error on clang17/gfortran13/macOS-13 (#3666) (#3671)

* Correct fortran CMake generator expressions (#3670)

* Add AOCC GitHub Action (#3504) (#3657)

* Fix uninitialized subfiling test variable (#3675)

Picked up by gcc 10 on skybridge. Probably spurious, but no harm in
initializing it to a "bad" value.

* Add support for AOCC & Flang w/ the Autotools (#3674)

* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
  when using Flang, the MPI Fortran compiler wrappers, and building
  the shared library. This would often result in unrecognized options
  like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.

CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.

Fixes GitHub issues #3439, #1588, #366, #280

* Fix a strncpy call to use dest size not src (#3677)

A strncpy call in a path construction call used the size of the src
buffer instead of the dest buffer as the limit n.

This was switched to use the dest size and properly terminate the
string if truncation occurs.

* Remove CANBE_UNUSED() from subfiling VFD (#3678)

This macro was an attempt to quiet warnings about release mode unused
variables that only appear in asserts. It resolves to a void cast, which
doesn't quiet warnings when an assignment has already taken place.

* Suppress MPI_Waitall warnings w/ MPICH (#3680)

MPICH defines MPI_STATUSES_IGNORE (a pointer) to 1, which raises warnings
w/ gcc. This is a known issue that the MPICH devs are not going to fix.

See here:
    pmodels/mpich#5687

This fix suppresses those issues w/ gcc

* Fix a possible NULL pointer dereference in tests (#3676)


The dtypes test could dereference a NULL pointer if a strdup call
failed.

* Fix printf warnings in t_mpi (#3679)

* Fix printf warnings in t_mpi

The type of MPI_Offset varies with implementation. In MPICH, it's long,
which raises warnings when we attempt to use long long format
specifiers. Casting to long long fixes the warnings.

* Fix invalid memory access in S3 comms (#3681)

In the ros3 VFD, passing an empty string parameter to an internal
API call could result in accessing the -1th element of a string.
This would cause failures on big-endian systems like s390x.

This parameter is now checked before writing to the string.

Fixes GitHub #1168

* Add Doxygen for H5Pset_fapl_sec2() (#3685)

*

* switch to using time function instead of date function (#3690)

* Initialize API context MPI types to MPI_BYTE (#3688)

* Add test info output to t_filters_parallel (#3696)

* Suppress format string warnings in subfiling test (#3699)

* Fix unused variable in tselect.c (#3701)

* Fix unused variable warning in H5F_sfile_assert_num (#3700)

* Restore floating-point suffixes in tests (#3698)

A prior commit removed too many F suffixes. This restores the suffixes
for float variables.

* Sync with changes from develop

---------

Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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@derobins derobins

Labels
Component - Build CMake, Autotools Priority - 2. Medium ⏹ It would be nice to have this in the next release Type - Bug / Bugfix Please report security issues to help@hdfgroup.org instead of creating an issue on GitHub
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Milestone
1.14.3
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@derobins @vchoi-hdfgroup @Enea2301