Opened 2 years ago
Last modified 19 months ago
#66208 assigned defect
hdf5 @1.12.2_0+cxx+gcc12+hl: Port hdf5 is still broken (cxx_stdlib mismatch) after rebuilding it more than 3 times.
| Reported by: | massonseb | Owned by: | eborisch (Eric A. Borisch) |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | 2.8.0 |
| Keywords: | Cc: | cjones051073 (Chris Jones), Dave-Allured (Dave Allured) | |
| Port: | hdf5 |
Description
I have an issue when installing "hdf5 +gcc12". All the installation goes smoothly until the last step when it looks for broken port. Port find that hdf5 itself is broken and try to reinstall hdf5 again and agin... See bellow for all details.
Note that I don't have the problem when installing "hdf5 +gcc12 +mpich" or "hdf5 +gcc12 +openmi".
I am using macOS 12.6.1 with ARM64 (Apple M1 Pro).
Thank you for your help,
Sébastien
bash-5.1$ sudo port install hdf5 +gcc12
Password:
---> Computing dependencies for hdf5
---> Fetching archive for hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://fra.de.packages.macports.org/hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://mse.uk.packages.macports.org/hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://packages.macports.org/hdf5
---> Fetching distfiles for hdf5
---> Attempting to fetch hdf5-1.12.2.tar.bz2 from https://distfiles.macports.org/hdf5
---> Verifying checksums for hdf5
---> Extracting hdf5
---> Applying patches to hdf5
---> Configuring hdf5
---> Building hdf5
---> Staging hdf5 into destroot
---> Installing hdf5 @1.12.2_0+cxx+gcc12+hl
---> Activating hdf5 @1.12.2_0+cxx+gcc12+hl
---> Cleaning hdf5
---> Scanning binaries for linking errors
---> No broken files found.
---> Found 1 broken port, determining rebuild order
You can always run 'port rev-upgrade' again to fix errors.
The following ports will be rebuilt: hdf5 @1.12.2+cxx+gcc12+hl
Continue? [Y/n]:
---> Fetching archive for hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://fra.de.packages.macports.org/hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://mse.uk.packages.macports.org/hdf5
...
---> Cleaning hdf5
---> Scanning binaries for linking errors
---> No broken files found.
Error: Port hdf5 is still broken (cxx_stdlib mismatch) after rebuilding it more than 3 times.
Error: Please run port -d -y rev-upgrade and use the output to report a bug.
Error: rev-upgrade failed: Port hdf5 still broken after rebuilding 3 times
Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
---> Some of the ports you installed have notes:
hdf5 has the following notes:
Mac users may need to set the environment variable "HDF5_USE_FILE_LOCKING" to the five-character string "FALSE" when accessing
network mounted files. This is an application run-time setting, not a configure or build setting. Otherwise errors such as
"unable to open file" or "HDF5 error" may be encountered.
bash-5.1$ sudo port -d -y rev-upgrade Password: DEBUG: Copying /Users/smasson/Library/Preferences/com.apple.dt.Xcode.plist to /opt/local/var/macports/home/Library/Preferences ---> Scanning binaries for linking errors DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libgcc/libgfortran.5.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libgcc/libgfortran.5.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libgcc/libobjc-gnu.4.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libgcc/libstdc++.6.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/bugpoint DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/dsymutil DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llc DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/lli DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-ar DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-as DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-bcanalyzer DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-c-test DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cat DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cfi-verify DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cov DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cvtres DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cxxdump DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cxxfilt DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-cxxmap DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-debuginfod-find DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-diff DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-dis DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-dwarfdump DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-dwp DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-extract DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-gsymutil DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-ifs DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-jitlink DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-libtool-darwin DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-link DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-lipo DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-lto DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-lto2 DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-mc DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-mca DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-ml DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-modextract DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-mt DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-nm DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-objcopy DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-objdump DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-opt-report DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-pdbutil DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-profdata DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-profgen DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-rc DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-readobj DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-reduce DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-rtdyld DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-sim DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-size DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-split DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-stress DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-strings DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-symbolizer DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-tapi-diff DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-tli-checker DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-undname DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/llvm-xray DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/opt DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/sancov DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/sanstats DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/split-file DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/verify-uselistorder DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/lib/libLTO.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/lib/libRemarks.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/c-index-test DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/c-index-test DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-apply-replacements DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-apply-replacements DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-change-namespace DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-change-namespace DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-check DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-check DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-doc DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-doc DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-extdef-mapping DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-extdef-mapping DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-format DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-format DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-include-fixer DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-include-fixer DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-linker-wrapper DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-move DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-move DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-nvlink-wrapper DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-offload-bundler DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-offload-bundler DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-offload-wrapper DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-offload-wrapper DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-query DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-query DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-refactor DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-refactor DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-rename DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-rename DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-reorder-fields DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-reorder-fields DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-repl DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-repl DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-scan-deps DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-scan-deps DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-tidy DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clang-tidy DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clangd DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clangd DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clangd-xpc-test-client DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/clangd-xpc-test-client DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/diagtool DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/diagtool DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/find-all-symbols DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/find-all-symbols DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/lld DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/modularize DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/modularize DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/pp-trace DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/bin/pp-trace DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/lib/libClangdXPCLib.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/lib/libclang-cpp.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/libexec/llvm-14/lib/libclang.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/bin/emacs-28.2 DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-gcc12/libmpi_cxx.40.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-gcc12/libmpi_usempi_ignore_tkr.40.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-gcc12/libmpi_usempi_ignore_tkr.40.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-gcc12/libmpi_usempif08.40.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-gcc12/libmpi_usempif08.40.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libhdf5_cpp.200.dylib DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libhdf5_hl_cpp.200.dylib ---> No broken files found. hdf5 is using libstdc++ (this installation is configured to use libc++) ---> Found 1 broken port, determining rebuild order DEBUG: Broken: hdf5 DEBUG: Processing port hdf5 @0:1.12.2_0+cxx+gcc12+hl You can always run 'port rev-upgrade' again to fix errors. The following ports will be rebuilt: hdf5 @1.12.2+cxx+gcc12+hl Continue? [Y/n]: n DEBUG: Checking time since last reclaim run
Attachments (3)
Change History (22)
comment:1 Changed 2 years ago by ryandesign (Ryan Carsten Schmidt)
| Owner: | set to eborisch |
|---|---|
| Status: | new → assigned |
| Summary: | broken port with hdf5 → hdf5 @1.12.2_0+cxx+gcc12+hl: Port hdf5 is still broken (cxx_stdlib mismatch) after rebuilding it more than 3 times. |
comment:2 follow-up: 4 Changed 2 years ago by eborisch (Eric A. Borisch)
comment:3 Changed 2 years ago by jmroot (Joshua Root)
| Cc: | cjones051073 added |
|---|
I think this may have been caused by this commit: https://github.com/macports/macports-ports/commit/6512d33b4aacaf83c638ddaa289a98a59da4bb92
While it's correct that those gcc versions support changing the stdlib, the portgroup code is just changing the nominal stdlib without adding the necessary -stdlib option to CXXFLAGS.
comment:4 Changed 2 years ago by massonseb
Replying to eborisch:
Can you test out if this change fixes it for you?
Yes it works (after adding a missing closing bracket ;-) )
Thank you!
comment:5 Changed 2 years ago by jdenis123
I had exactly the same issue as massonseb. I tried to upgrade with the fixed version of port "hdf5" 1.12.2_1. The installation now failed at build step.
I am also using macOS 12.6.1 with ARM64.
Thank you for your help,
Julien
sudo port install hdf5 +gcc12 ---> Computing dependencies for hdf5 ---> Fetching archive for hdf5 ---> Attempting to fetch hdf5-1.12.2_1+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://packages.macports.org/hdf5 ---> Attempting to fetch hdf5-1.12.2_1+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://mse.uk.packages.macports.org/hdf5 ---> Attempting to fetch hdf5-1.12.2_1+cxx+gcc12+hl.darwin_21.arm64.tbz2 from https://fra.de.packages.macports.org/hdf5 ---> Fetching distfiles for hdf5 ---> Verifying checksums for hdf5 ---> Extracting hdf5 ---> Applying patches to hdf5 ---> Configuring hdf5 ---> Building hdf5 Error: Failed to build hdf5: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/main.log for details. Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug. Error: Processing of port hdf5 failed
comment:6 Changed 2 years ago by massonseb
I also have an issue when trying to compile hdf5 with gcc12.
sudo port install hdf5 +gcc12 or sudo port install hdf5 +gcc12 +openmpi are not working
whereas sudo port install hdf5, sudo port install hdf5 +clan15, sudo port install hdf5 +openmpi are working.
with gcc12, the error message are listed bellow. I also attach the main.log for details.
:info:build Undefined symbols for architecture arm64:
:info:build "__ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE7compareEPKc", referenced from:
:info:build __ZNK2H510AbstractDs12getTypeClassEv in H5AbstractDs.o
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_disposeEv", referenced from:
:info:build __ZN2H59ExceptionC4ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ in H5Exception.o
:info:build __ZN2H59ExceptionC4ERKS0_ in H5Exception.o
:info:build __ZNK2H59Exception14getMajorStringB5cxx11Ex in H5Exception.o
:info:build __ZNK2H59Exception14getMinorStringB5cxx11Ex in H5Exception.o
:info:build __ZN2H59Exception12setAutoPrintERPFixPvES1_ in H5Exception.o
:info:build __ZN2H59Exception9dontPrintEv in H5Exception.o
:info:build __ZN2H59Exception12getAutoPrintERPFixPvEPS1_ in H5Exception.o
:info:build ...
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_replaceEmmPKcm", referenced from:
:info:build __ZNK2H511IdComponent9inMemFuncB5cxx11EPKc in H5IdComponent.o
:info:build __ZNK2H519DSetMemXferPropList16getDataTransformB5cxx11Ev in H5DxferProp.o
:info:build __ZNK2H510H5Location10getCommentB5cxx11EPKcm in H5Location.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEaSEPKc.isra.0 in H5Attribute.o
:info:build __ZNK2H58H5Object10getObjNameB5cxx11Ev in H5Object.o
:info:build __ZNK2H58H5Object10getObjNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm in H5Object.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEaSEPKc.isra.0 in H5AtomType.o
:info:build ...
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13_S_copy_charsEPcPKcS7_", referenced from:
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5Exception.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5IdComponent.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5DataSpace.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5PropList.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5Library.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5FaccProp.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5FcreatProp.o
:info:build ...
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13_S_copy_charsEPcS5_S5_", referenced from:
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4ERKS4_ in H5Exception.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4ERKS4_ in H5Object.o
:info:build __ZNK2H55Group14throwExceptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ in H5Group.o
:info:build __ZNK2H56H5File14throwExceptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ in H5File.o
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE7_S_copyEPcPKcm", referenced from:
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEaSEOS4_.isra.0 in H5Location.o
:info:build __ZNK2H59Attribute7getNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm in H5Attribute.o
:info:build __ZNK2H58H5Object10getObjNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm in H5Object.o
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm", referenced from:
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4ERKS4_ in H5Exception.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5Exception.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5IdComponent.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5DataSpace.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5PropList.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5Library.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5FaccProp.o
:info:build ...
:info:build "__ZNSt8ios_base4InitC1Ev", referenced from:
:info:build __GLOBAL__sub_I_H5DataSpace.cpp in H5DataSpace.o
:info:build __GLOBAL__sub_I_H5PropList.cpp in H5PropList.o
:info:build __GLOBAL__sub_I_H5FaccProp.cpp in H5FaccProp.o
:info:build __GLOBAL__sub_I_H5Location.cpp in H5Location.o
:info:build __GLOBAL__sub_I_H5Attribute.cpp in H5Attribute.o
:info:build __GLOBAL__sub_I_H5DataType.cpp in H5DataType.o
:info:build __GLOBAL__sub_I_H5DataSet.cpp in H5DataSet.o
:info:build ...
:info:build "__ZNSt8ios_base4InitD1Ev", referenced from:
:info:build __GLOBAL__sub_I_H5DataSpace.cpp in H5DataSpace.o
:info:build __GLOBAL__sub_I_H5PropList.cpp in H5PropList.o
:info:build __GLOBAL__sub_I_H5FaccProp.cpp in H5FaccProp.o
:info:build __GLOBAL__sub_I_H5Location.cpp in H5Location.o
:info:build __GLOBAL__sub_I_H5Attribute.cpp in H5Attribute.o
:info:build __GLOBAL__sub_I_H5DataType.cpp in H5DataType.o
:info:build __GLOBAL__sub_I_H5DataSet.cpp in H5DataSet.o
:info:build ...
:info:build "__ZSt19__throw_logic_errorPKc", referenced from:
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5Exception.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5IdComponent.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5DataSpace.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5PropList.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5Library.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5FaccProp.o
:info:build __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0 in H5FcreatProp.o
:info:build ...
:info:build "__ZSt4cerr", referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H58DataTypeD4Ev in H5DataType.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build "__ZSt4endlIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_", referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H58DataTypeD4Ev in H5DataType.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build "__ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc", referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build "__ZStlsIcSt11char_traitsIcESaIcEERSt13basic_ostreamIT_T0_ES7_RKNSt7__cxx1112basic_stringIS4_S5_T1_EE", referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H58DataTypeD4Ev in H5DataType.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build ld: symbol(s) not found for architecture arm64
:info:build collect2: error: ld returned 1 exit status
:info:build make[2]: *** [libhdf5_cpp.la] Error 1
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2/c++/src'
:info:build make[1]: *** [all-recursive] Error 1
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2/c++'
:info:build make: *** [all-recursive] Error 1
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2'
:info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2" && /usr/bin/make -j10 -w all
:info:build Exit code: 2
:error:build Failed to build hdf5: command execution failed
:debug:build Error code: CHILDSTATUS 86150 2
:debug:build Backtrace: command execution failed
:debug:build while executing
:debug:build "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
:debug:build invoked from within
:debug:build "command_exec -callback portprogress::target_progress_callback build"
:debug:build (procedure "portbuild::build_main" line 8)
:debug:build invoked from within
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/main.log for details.
Changed 2 years ago by massonseb
main.log file for "sudo port install hdf5 +gcc12"
comment:7 follow-up: 8 Changed 2 years ago by cjones051073 (Chris Jones)
Just curious. *why* are you trying to install using gcc12 ? Using gcc to build c++ sources is problematic on macOS, due to the potential for mixing incompatible c++ runtimes (libstdc++ versus libc++). Genrially speaking its better to just stick to the defaults, which in this case work.
comment:8 Changed 2 years ago by eborisch (Eric A. Borisch)
Replying to cjones051073:
Just curious. *why* are you trying to install using gcc12 ? Using gcc to build c++ sources is problematic on macOS, due to the potential for mixing incompatible c++ runtimes (libstdc++ versus libc++). Genrially speaking its better to just stick to the defaults, which in this case work.
Chris, the CXXFLAGS are missing -stdlib=libc++, while it is set in LDFLAGS. I can reproduce this on my x86_64 system, FWIW. The hdf5 port, following the discussion in https://github.com/macports/macports-ports/pull/16629 , leaves these details to the compilers (via mpi) PortGroup. Let me know if there is something I can test to help resolve this.
That said, I echo your concerns; is there a reason you (massonseb) need to use gcc12? (Or is there some port that is trying to install this that thinks it needs it?)
comment:9 follow-up: 12 Changed 2 years ago by cjones051073 (Chris Jones)
Setting both ldflags and cxxflags should be handled via
Please make sure your builds are using the above.
But yes, using libc++ with gcc is still experimental, and in fact isn't really supported by base until
https://github.com/macports/macports-base/pull/275
is out in a public base release.
comment:10 Changed 2 years ago by massonseb
Just curious. *why* are you trying to install using gcc12 ? Using gcc to build c++ sources is problematic on macOS, due to the potential for mixing incompatible c++ runtimes (libstdc++ versus libc++). Generally speaking its better to just stick to the defaults, which in this case work.
I need to compile a fortran code with with MPI. This code also needs NetCDF that must be linked with an hdf5 library compiled with --enable-parallel (so the NetCDF command nc-config --has-parallel returns yes).
Having said that, I would like to try gcc and openmpi to compile my code.
I thought (but I may be wrong) that I should use gcc+openmpi to compile NetCDF and HDF5, as I will use gcc+openmpi to compile my fortran code. I am always afraid to mix-up libraries compiled with different compilers…
Another point that is not clear to me:
If I select openmpi-gcc12-fortran as the default version for mpi with sudo port select —set mpi openmpi-gcc12-fortran Which openmpi is used when doing sudo port install hdf5 +openmpi? is it openmpi-gcc12 that I selected?
comment:11 Changed 2 years ago by massonseb
Up to now, I was able to compile
- hdf5 @1.12.2_1+cxx+hl+openmpi which used openmpi-default
- netcdf @4.9.0_0+dap+netcdf4+openmpi which also used openmpi-default
- netcdf-fortran @4.6.0_0+gcc12+openmpi which required openmpi-gcc12 instead of openmpi-default.
I am wondering if mixing libraries compiled with openmpi-default and openmpi-gcc12 could create a problem as these 2 versions are not using the same C compiler...
I am also wondering why netcdf-fortran cannot be compiled with openmpi-default+gcc12 as it includes the same gfortran compiler than openmpi-gcc12.
comment:12 Changed 2 years ago by massonseb
Replying to cjones051073:
Setting both ldflags and cxxflags should be handled via
Please make sure your builds are using the above.
yes I have the same line L363 in my file /opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/ports/_resources/port1.0/group/compilers-1.0.tcl
comment:13 follow-up: 17 Changed 22 months ago by oliviermarti (Marti)
My 2 cents :
I use (and massonseb too) a library (https://forge.ipsl.jussieu.fr/ioserver/) that mixes C++ and Fortran code. We use it in several Fortran codes. The library needs parallel netcdf, on top of hdf5. We commonly use these code on Linux systems with Intel or GNU compilers.
Months ago (don't remember when), I've installed openmpi, hdf5, netcdf and gcc12 with MacPort. All compiled with gcc12 variants. It installed smoothly. And I succeed to use the library and my code. So this is a solution that has worked.
Mixing clang and fortran, I can compile, as massonseb, but the test cases of the library does'nt run. I've never succeed to mixed clang and GNU fortran. Is this really possible ?
That's why having back a working hdf5 and netcdf with gcc12 will be very useful for a least a few people.
Thank's !
comment:14 Changed 22 months ago by eborisch (Eric A. Borisch)
This (+cxx+gcc12+hl) is working with https://github.com/macports/macports-base/commit/ebd22613, which unfortunately is still not in any release. (Tested by cherry-picking that commit on top of 2.8.0)
comment:15 Changed 22 months ago by eborisch (Eric A. Borisch)
Both '+clang15+fortran' and '+cxx+gcc12+hl+fortran' pass tests. (With ebd22613)
comment:16 follow-up: 18 Changed 22 months ago by massonseb
ebd22613 has been added in macport 2.8.1
See https://github.com/macports/macports-base/releases/tag/v2.8.1
I installed it and I can indeed see the modifications of ebd22613 in
/opt/local/libexec/macports/lib/port1.0/portconfigure.tcl /opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/base/src/port1.0/portconfigure.tcl
which are the same files.
However hdf5 compilation with gcc12 is still not working.
1) with sudo port install hdf5 +gcc12
I have the following error (see main.2.log for the complete log file):
:info:build In file included from H5Library.cpp:13:
:info:build /opt/local/libexec/gcc12/libc++/include/c++/v1/cstdlib:135:9: error: 'at_quick_exit' has not been declared in '::'
:info:build 135 | using ::at_quick_exit _LIBCPP_USING_IF_EXISTS;
:info:build | ^~~~~~~~~~~~~
:info:build /opt/local/libexec/gcc12/libc++/include/c++/v1/cstdlib:136:9: error: 'quick_exit' has not been declared in '::'
:info:build 136 | using ::quick_exit _LIBCPP_USING_IF_EXISTS;
:info:build | ^~~~~~~~~~
...
:info:build In file included from /opt/local/libexec/gcc12/libc++/include/c++/v1/__utility/unreachable.h:13,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/__iterator/advance.h:19,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/__iterator/next.h:15,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/__algorithm/unwrap_range.h:16,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/__algorithm/copy.h:13,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/memory:841,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/__locale:18,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/ios:221,
:info:build from /opt/local/libexec/gcc12/libc++/include/c++/v1/iostream:41,
:info:build from H5FaccProp.cpp:13:
:info:build /opt/local/libexec/gcc12/libc++/include/c++/v1/cstdlib:135:9: error: 'at_quick_exit' has not been declared in '::'
:info:build 135 | using ::at_quick_exit _LIBCPP_USING_IF_EXISTS;
:info:build | ^~~~~~~~~~~~~
:info:build /opt/local/libexec/gcc12/libc++/include/c++/v1/cstdlib:136:9: error: 'quick_exit' has not been declared in '::'
:info:build 136 | using ::quick_exit _LIBCPP_USING_IF_EXISTS;
:info:build | ^~~~~~~~~~
:info:build make[2]: *** [H5Exception.lo] Error 1
:info:build make[2]: *** Waiting for unfinished jobs....
:info:build make[2]: *** [H5FcreatProp.lo] Error 1
:info:build make[2]: *** [H5Library.lo] Error 1
:info:build make[2]: *** [H5LaccProp.lo] Error 1
:info:build make[2]: *** [H5IdComponent.lo] Error 1
:info:build make[2]: *** [H5LcreatProp.lo] Error 1
:info:build make[2]: *** [H5DaccProp.lo] Error 1
:info:build make[2]: *** [H5PropList.lo] Error 1
:info:build make[2]: *** [H5DataSpace.lo] Error 1
:info:build make[2]: *** [H5FaccProp.lo] Error 1
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0/c++/src'
:info:build make[1]: *** [all-recursive] Error 1
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0/c++'
:info:build make: *** [all-recursive] Error 1
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0'
:info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0" && /usr/bin/make -j10 -w all
:info:build Exit code: 2
:error:build Failed to build hdf5: command execution failed
:debug:build Error code: CHILDSTATUS 37035 2
:debug:build Backtrace: command execution failed
:debug:build while executing
:debug:build "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
:debug:build invoked from within
:debug:build "command_exec -callback portprogress::target_progress_callback build"
:debug:build (procedure "portbuild::build_main" line 8)
:debug:build invoked from within
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/main.log for details.
2) with sudo port install hdf5 +gcc12 +openmpi
I have the same error than before (see main.3.log for the complete log file):
:info:build Undefined symbols for architecture arm64:
:info:build "__ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE7compareEPKc", referenced from:
:info:build __ZNK2H510AbstractDs12getTypeClassEv in H5AbstractDs.o
:info:build "__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_disposeEv", referenced from:
:info:build __ZN2H59ExceptionC4ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ in H5Exception.o
:info:build __ZN2H59ExceptionC4ERKS0_ in H5Exception.o
:info:build __ZN2H59ExceptionC4Ev in H5Exception.o
...
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build ld: symbol(s) not found for architecture arm64
:info:build collect2: error: ld returned 1 exit status
:info:build make[2]: *** [libhdf5_cpp.la] Error 1
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0/c++/src'
:info:build make[1]: *** [all-recursive] Error 1
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0/c++'
:info:build make: *** [all-recursive] Error 1
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0'
:info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.14.0" && /usr/bin/make -j10 -w all
:info:build Exit code: 2
:error:build Failed to build hdf5: command execution failed
:debug:build Error code: CHILDSTATUS 30715 2
:debug:build Backtrace: command execution failed
:debug:build while executing
:debug:build "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
:debug:build invoked from within
:debug:build "command_exec -callback portprogress::target_progress_callback build"
:debug:build (procedure "portbuild::build_main" line 8)
:debug:build invoked from within
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/main.log for details.
Which step did I miss?
Should I re-install gcc12 or other packages before?
Changed 21 months ago by massonseb
| Attachment: | main.3.log added |
|---|
comment:17 Changed 21 months ago by cjones051073 (Chris Jones)
Replying to oliviermarti:
My 2 cents :
I use (and massonseb too) a library (https://forge.ipsl.jussieu.fr/ioserver/) that mixes C++ and Fortran code. We use it in several Fortran codes. The library needs parallel netcdf, on top of hdf5. We commonly use these code on Linux systems with Intel or GNU compilers.
Months ago (don't remember when), I've installed openmpi, hdf5, netcdf and gcc12 with MacPort. All compiled with gcc12 variants. It installed smoothly. And I succeed to use the library and my code. So this is a solution that has worked.
Mixing clang and fortran, I can compile, as massonseb, but the test cases of the library does'nt run. I've never succeed to mixed clang and GNU fortran. Is this really possible ?
Mixing clang and gcc gfortran to build c/c++ and and fortran code indeed works just fine. Most ports in macports that need to build c/c++ and fortran infwct do this all the time. OpenBLAS is for instance one. If youmdo not believe me go check the build logs for it ;)
So, again, I see no need for you to be forcing the use of gcc12 to build c/c++ here.
That's why having back a working hdf5 and netcdf with gcc12 will be very useful for a least a few people.
Thank's !
comment:18 Changed 21 months ago by tcspestana (Tiago Pestana)
Replying to massonseb:
ebd22613 has been added in macport 2.8.1
See https://github.com/macports/macports-base/releases/tag/v2.8.1I installed it and I can indeed see the modifications of ebd22613 in
/opt/local/libexec/macports/lib/port1.0/portconfigure.tcl /opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/base/src/port1.0/portconfigure.tclwhich are the same files.
However hdf5 compilation with gcc12 is still not working.
I am also interested in this functionality. Did you make any progress in compiling hdf5 with gcc12? Did you manage to make your application work with clang/openmpi instead?
comment:19 Changed 19 months ago by Dave-Allured (Dave Allured)
| Cc: | Dave-Allured added |
|---|
Note: See
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tickets.
Can you test out if this change fixes it for you?
https://github.com/macports/macports-ports/pull/16629