I am trying to compile 4.2.1 using GCC 12.2.0. cmake seems to go OK;
. the notice about doxygen missing components: dot I read is related
to graphviz, and is only needed to produce the documents.
$ CMAKE ..
-- CMAKE VERSION: 3.24.3
-- THE CXX COMPILER IDENTIFICATION IS GNU 12.2.0
-- DETECTING CXX COMPILER ABI INFO
-- DETECTING CXX COMPILER ABI INFO - DONE
-- CHECK FOR WORKING CXX COMPILER:
/HOME/APPS/EASYBUILD/SOFTWARE/GCCCORE/12.2.0/BIN/C++ - SKIPPED
-- DETECTING CXX COMPILE FEATURES
-- DETECTING CXX COMPILE FEATURES - DONE
-- THE C COMPILER IDENTIFICATION IS GNU 12.2.0
-- DETECTING C COMPILER ABI INFO
-- DETECTING C COMPILER ABI INFO - DONE
-- CHECK FOR WORKING C COMPILER:
/HOME/APPS/EASYBUILD/SOFTWARE/GCCCORE/12.2.0/BIN/CC - SKIPPED
-- DETECTING C COMPILE FEATURES
-- DETECTING C COMPILE FEATURES - DONE
-- CONFIG FILE:
/HOME/APPS/CUSTOM/SOFTWARE/ESPRESSO/4.2.1/ESPRESSO/SRC/CONFIG/MYCONFIG-DEFAULT.HPP
-- PERFORMING TEST RESULT__PRETTY_FUNCTION__
-- PERFORMING TEST RESULT__PRETTY_FUNCTION__ - SUCCESS
-- FOUND PYTHONINTERP:
/HOME/APPS/EASYBUILD/SOFTWARE/PYTHON/3.10.8-GCCCORE-12.2.0/BIN/PYTHON3
(FOUND SUITABLE VERSION "3.10.8", MINIMUM REQUIRED IS "3.8")
-- FOUND CYTHON:
/HOME/APPS/EASYBUILD/SOFTWARE/PYTHON/3.10.8-GCCCORE-12.2.0/BIN/PYTHON3;-M;CYTHON
(FOUND SUITABLE VERSION "0.29.36", MINIMUM REQUIRED IS "0.29.14")
-- FOUND PYTHONHEADERS:
/HOME/APPS/EASYBUILD/SOFTWARE/PYTHON/3.10.8-GCCCORE-12.2.0/INCLUDE/PYTHON3.10
-- FOUND NUMPY:
/HOME/APPS/EASYBUILD/SOFTWARE/SCIPY-BUNDLE/2023.02-GFBF-2022B/LIB/PYTHON3.10/SITE-PACKAGES/NUMPY/CORE/INCLUDE
(FOUND VERSION "1.24.2")
-- FOUND FFTW3:
/HOME/APPS/EASYBUILD/SOFTWARE/FFTW.MPI/3.3.10-GOMPI-2022B/LIB/LIBFFTW3.SO
-- FOUND HDF5:
/HOME/APPS/EASYBUILD/SOFTWARE/HDF5/1.14.0-GOMPI-2022B/LIB/LIBHDF5.SO;/USR/LIB64/LIBPTHREAD.SO;/HOME/APPS/EASYBUILD/SOFTWARE/SZIP/2.1.1-GCCCORE-12.2.0/LIB/LIBSZ.SO;/HOME/APPS/EASYBUILD/SOFTWARE/ZLIB/1.2.12-GCCCORE-12.2.0/LIB/LIBZ.SO;/USR/LIB64/LIBDL.SO;/USR/LIB64/LIBM.SO;/USR/LIB64/LIBM.SO;/USR/LIB64/LIBPTHREAD.SO
(FOUND SUITABLE VERSION "1.14.0", MINIMUM REQUIRED IS "1.8") FOUND
COMPONENTS: C
-- FOUND GSL: /HOME/APPS/EASYBUILD/SOFTWARE/GSL/2.7-GCC-12.2.0/INCLUDE
(FOUND VERSION "2.7")
-- FOUND MPI_C:
/HOME/APPS/EASYBUILD/SOFTWARE/OPENMPI/4.1.4-GCC-12.2.0/LIB/LIBMPI.SO
(FOUND SUITABLE VERSION "3.1", MINIMUM REQUIRED IS "3.0")
-- FOUND MPI_CXX:
/HOME/APPS/EASYBUILD/SOFTWARE/OPENMPI/4.1.4-GCC-12.2.0/LIB/LIBMPI.SO
(FOUND SUITABLE VERSION "3.1", MINIMUM REQUIRED IS "3.0")
-- FOUND MPI: TRUE (FOUND SUITABLE VERSION "3.1", MINIMUM REQUIRED IS
"3.0")
-- FOUND MPIEXECBACKEND:
/HOME/APPS/EASYBUILD/SOFTWARE/OPENMPI/4.1.4-GCC-12.2.0/BIN/MPIEXEC
-- FOUND BOOST:
/HOME/APPS/EASYBUILD/SOFTWARE/BOOST.MPI/1.81.0-GOMPI-2022B/LIB64/CMAKE/BOOST-1.81.0/BOOSTCONFIG.CMAKE
(FOUND SUITABLE VERSION "1.81.0", MINIMUM REQUIRED IS "1.69.0") FOUND
COMPONENTS: MPI SERIALIZATION FILESYSTEM SYSTEM UNIT_TEST_FRAMEWORK
-- FOUND DOXYGEN: /USR/BIN/DOXYGEN (FOUND VERSION "1.8.5") FOUND
COMPONENTS: DOXYGEN MISSING COMPONENTS: DOT
-- FOUND SPHINX:
/HOME/APPS/EASYBUILD/SOFTWARE/PYTHON/3.10.8-GCCCORE-12.2.0/BIN/PYTHON3;-M;SPHINX
(FOUND SUITABLE VERSION "5.3.0", MINIMUM REQUIRED IS "2.3.0")
-- FOUND GIT: /USR/BIN/GIT (FOUND VERSION "1.8.3.1")
-- THE FOLLOWING FEATURES HAVE BEEN ENABLED:
* HDF5 (REQUIRED VERSION >= 1.8), PARALLEL
-- THE FOLLOWING OPTIONAL PACKAGES HAVE BEEN FOUND:
* FFTW3
* MPIEXECBACKEND
* DOXYGEN
* SPHINX (REQUIRED VERSION >= 2.3.0)
* GIT
-- THE FOLLOWING REQUIRED PACKAGES HAVE BEEN FOUND:
* PYTHONINTERP (REQUIRED VERSION >= 3.8)
* CYTHON (REQUIRED VERSION >= 0.29.14)
* PYTHONHEADERS
* NUMPY
* HDF5 (REQUIRED VERSION >= 1.8), PARALLEL
* GSL
* MPI
* BOOST_MPI (REQUIRED VERSION == 1.81.0)
* BOOST_SERIALIZATION (REQUIRED VERSION == 1.81.0)
* BOOST_ATOMIC (REQUIRED VERSION == 1.81.0)
* BOOST_FILESYSTEM (REQUIRED VERSION == 1.81.0)
* BOOST_SYSTEM (REQUIRED VERSION == 1.81.0)
* BOOST_HEADERS (REQUIRED VERSION == 1.81.0)
* BOOST_UNIT_TEST_FRAMEWORK (REQUIRED VERSION == 1.81.0)
* BOOST (REQUIRED VERSION >= 1.69.0)
-- CONFIGURING DONE
-- GENERATING DONE
-- BUILD FILES HAVE BEEN WRITTEN TO:
/HOME/APPS/CUSTOM/SOFTWARE/ESPRESSO/4.2.1/ESPRESSO/BUILD
However the compilation fails:
.
.
[ 44%] Building CXX object
src/core/CMakeFiles/Espresso_core.dir/magnetostatics/dds_gpu.cpp.o
[ 44%] Building CXX object
src/core/CMakeFiles/Espresso_core.dir/magnetostatics/dds_replica.cpp.o
[ 44%] Building CXX object
src/core/CMakeFiles/Espresso_core.dir/magnetostatics/dlc.cpp.o
In file included from
/home/apps/custom/software/espresso/4.2.1/espresso/libs/h5xx/h5xx/dataspace.hpp:16,
from
/home/apps/custom/software/espresso/4.2.1/espresso/libs/h5xx/h5xx/attribute/attribute.hpp:17,
from
/home/apps/custom/software/espresso/4.2.1/espresso/libs/h5xx/h5xx/attribute.hpp:17,
from
/home/apps/custom/software/espresso/4.2.1/espresso/libs/h5xx/h5xx/h5xx.hpp:23,
from
/home/apps/custom/software/espresso/4.2.1/espresso/src/core/io/writer/h5md_specification.hpp:24,
from
/home/apps/custom/software/espresso/4.2.1/espresso/src/core/io/writer/h5md_core.hpp:27,
from
/home/apps/custom/software/espresso/4.2.1/espresso/src/core/io/writer/h5md_core.cpp:22:
/home/apps/custom/software/espresso/4.2.1/espresso/libs/h5xx/h5xx/dataspace/dataspace.hpp:52:5:
error: 'template<long unsigned int N> h5xx::dataspace::dataspace(const
boost::array<long unsigned int, NumDims>&)' cannot be overloaded with
'template<long unsigned int N> h5xx::dataspace::dataspace(const
boost::array<long unsigned int, NumDims>&)'
52 | dataspace(boost::array<hsize_t, N> const& dims);
| ^~~~~~~~~
/home/apps/custom/software/espresso/4.2.1/espresso/libs/h5xx/h5xx/dataspace/dataspace.hpp:50:5:
note: previous declaration 'template<long unsigned int N>
h5xx::dataspace::dataspace(const boost::array<long unsigned int,
NumDims>&)'
50 | dataspace(boost::array<std::size_t, N> const& dims);
| ^~~~~~~~~
.
.
These are the lines from
espresso/libs/h5xx/h5xx/dataspace/dataspace.hpp relating to the first
two error messages:
/** construct simple dataspace of given extents, boost::array
version */
template <std::size_t N>
dataspace(boost::array<std::size_t, N> const& dims);
template <std::size_t N>
dataspace(boost::array<hsize_t, N> const& dims);
There are more errors in a similar vein about overloading that follow.
I see that h5xx ships with Espresso, so I am wondering if there is a
compatibility issue with the versions of HDF5 or Boost, or GCC 12. I
did not have this problem building Espresso 4.1.4 with Boost/1.74 and
HDF5/1.10.7 and GCC 10. I see that h5xx is identical in 4.1.4 and
4.2.1 and dates to 2018 and is # 89d8d43 [1] - and I see that h5xx has
more recently had a version 0.9.2 which specifically mentions C++ 11
changes: https://github.com/fhoefling/h5xx/issues. I have tried
building with h5xx 0.9.2 but I get the same errors.
I am using Easybuild and Lmod and these are the loaded versions of the
required software:
Currently Loaded Modules:
1) GCCcore/12.2.0 25)
FFTW.MPI/3.3.10-gompi-2022b (H)
2) zlib/1.2.12-GCCcore-12.2.0 (H) 26)
OpenBLAS/0.3.21-GCC-12.2.0 (H)
3) binutils/2.39-GCCcore-12.2.0 (H) 27)
FlexiBLAS/3.2.1-GCC-12.2.0 (H)
4) GCC/12.2.0 28)
ScaLAPACK/2.2.0-gompi-2022b-fb (H)
5) numactl/2.0.16-GCCcore-12.2.0 (H) 29) foss/2022b
6) XZ/5.2.7-GCCcore-12.2.0 (H) 30)
ncurses/6.3-GCCcore-12.2.0 (H)
7) libxml2/2.10.3-GCCcore-12.2.0 (H) 31)
libreadline/8.2-GCCcore-12.2.0 (H)
8) libpciaccess/0.17-GCCcore-12.2.0 (H) 32)
Tcl/8.6.12-GCCcore-12.2.0 (H)
9) hwloc/2.8.0-GCCcore-12.2.0 (H) 33)
SQLite/3.39.4-GCCcore-12.2.0 (H)
10) OpenSSL/1.1 (H) 34) GMP/6.2.1-GCCcore-12.2.0
11) libevent/2.1.12-GCCcore-12.2.0 (H) 35)
libffi/3.4.4-GCCcore-12.2.0 (H)
12) UCX/1.13.1-GCCcore-12.2.0 (H) 36)
Python/3.10.8-GCCcore-12.2.0
13) libfabric/1.16.1-GCCcore-12.2.0 (H) 37) gfbf/2022b
(H)
14) PMIx/4.2.2-GCCcore-12.2.0 (H) 38)
pybind11/2.10.3-GCCcore-12.2.0 (H)
15) UCC/1.1.0-GCCcore-12.2.0 (H) 39)
SciPy-bundle/2023.02-gfbf-2022b (H)
16) OpenMPI/4.1.4-GCC-12.2.0 (H) 40)
Biopython/1.81-foss-2022b
17) gompi/2022b (H) 41)
Cython/0.29.36-GCCcore-12.2.0
18) bzip2/1.0.8-GCCcore-12.2.0 (H) 42) GSL/2.7-GCC-12.2.0
19) gzip/1.12-GCCcore-12.2.0 43)
Szip/2.1.1-GCCcore-12.2.0
20) lz4/1.9.4-GCCcore-12.2.0 44) HDF5/1.14.0-gompi-2022b
21) zstd/1.5.2-GCCcore-12.2.0 45)
cURL/7.86.0-GCCcore-12.2.0
22) ICU/72.1-GCCcore-12.2.0 46)
libarchive/3.6.1-GCCcore-12.2.0 (H)
23) Boost.MPI/1.81.0-gompi-2022b 47)
CMake/3.24.3-GCCcore-12.2.0 (H)
24) FFTW/3.3.10-GCC-12.2.0 (H)
Where:
H: Hidden Module
I have looked around but I have not find any report of a similar
issue. I need to use GCC 12 as the user needs to use this with
Biopython/1.81, which has been built to use GCC 12 under Easybuild.
I would be grateful for any suggestions as to what to try next.
William
William Brown
Senior System Administrator (Research IT)
Information Technology
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[1]
https://github.com/h5md/h5xx/commit/89d8d435872ec77dd931e709df98eefac8cbc925
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