failed to build of the Nov 28 2023 distribution

[BaiMay]

I downloaded the latest distribution dated to Nov. 28, 2023. After following all the steps, the build failed with the following info,

ld: warning: directory not found for option '-L/usr/local/opt/gettext/lib' ld: warning: directory not found for option '-L/usr/local/opt/libffi/lib' ld: warning: directory not found for option '-L/usr/local/opt/readline/lib' ld: warning: directory not found for option '-L/usr/local/opt/sqlite/lib' Undefined symbols for architecture arm64: "_GOMP_barrier", referenced from: _random_mod_MOD_allocate_thread_states.part.0 in randommod.f90.o random_mod_MOD_ran_seed_put in random_mod.f90.o "_GOMP_parallel", referenced from: _opti_de_openmp_mod_MOD_opti_de_openmp in opti_de_openmp_mod.f90.o "_omp_get_maxthreads", referenced from: ___random_mod_MOD_allocate_thread_states.part.0 in randommod.f90.o random_mod_MOD_ran_seed_put in random_mod.f90.o "_omp_get_num_threads", referenced from: _opti_de_openmp_mod_MOD_opti_de_openmp._omp_fn.1 in opti_de_openmpmod.f90.o opti_de_openmp_mod_MOD_opti_de_openmp._omp_fn.0 in opti_de_openmp_mod.f90.o "_omp_get_thread_num", referenced from: _opti_de_openmp_mod_MOD_opti_de_openmp._omp_fn.1 in opti_de_openmpmod.f90.o opti_de_openmp_mod_MOD_opti_de_openmp._omp_fn.0 in opti_de_openmp_mod.f90.o "_omp_get_threadnum", referenced from: _random_mod_MOD_allocate_thread_states.part.0 in randommod.f90.o random_mod_MOD_pointer_to_ran_state in random_mod.f90.o _random_mod_MOD_super_sobseq in random_mod.f90.o ___random_mod_MOD_ran_default_state in randommod.f90.o random_mod_MOD_ran_seed_get in random_mod.f90.o _random_mod_MOD_ran_seed_put in randommod.f90.o random_mod_MOD_ran_uniform_scalar in random_mod.f90.o ... ld: symbol(s) not found for architecture arm64 collect2: error: ld returned 1 exit status gmake[2]: [CMakeFiles/sim_utils.dir/build.make:3060: /Users/mbai/Bmad/bmad_dist/production/lib/libsim_utils.dylib] Error 1 gmake[1]: [CMakeFiles/Makefile2:83: CMakeFiles/sim_utils.dir/all] Error 2 gmake: *** [Makefile:91: all] Error 2

Error in distribution build.

[DavidSagan]

@jsberg-bnl If I could trouble you for some help here it would be very much appreciated.

[jsberg-bnl]

@BaiMay, run VERBOSE=1 util/dist_build_production > build-p0.log 2>&1 and post the contents of build-p0.log. Is this a Mac? And what are you using for packages (macports/homebrew/...)? @DavidSagan, what's happening is an openmp build is being done, but for some reason the libraries are not getting found at link time. The log output should show the link command, it should be gfortran with the openmp flag, which should be sufficient to have it link against the openmp library. Looks like the error messages about directories not found are the result of very outdated HomeBrew instructions on the OffsiteDoc web page.

[BaiMay]

@jsberg-bnl and @DavidSagan Thanks. Yes it is a MAC. And, here is the content of build-p0.log,

Building directory: plplot

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: hdf5

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: fftw

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: lapack

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: lapack95

Re-run cmake no build system arguments

Build type : Production -- Mon Dec 4 06:30:13 PST 2023 Current Directory : /Users/mbai/Bmad/bmad_dist/lapack95 Linking with release : /Users/mbai/Bmad/bmad_dist/ (Off-site Distribution) C Compiler : /opt/local/bin/gcc Fortran Compiler : /opt/local/bin/gfortran Plotting Libraries : plplotfortran;plplot;csirocsa;qsastime Shared Libraries : cairo;pango-1.0;pangocairo-1.0;gobject-2.0 OpenMP gfortran Flag : -fopenmp OpenMP Linker Libs : gomp MPI Support : Not Enabled FFLAGS :
gfortran Compiler Flags : -Df2cFortran -DCESR_UNIX -DCESR_LINUX -u -traceback -cpp -fno-range-check -fdollar-ok -fbacktrace -Bstatic -ffree-line-length-none -fopenmp -DCESR_PLPLOT -fPIC -O2 gfortran Linker Flags : -lX11 -lplplotfortran -lplplot -lcsirocsa -lqsastime -lpthread;-lstdc++;-ldl gomp ACC_BMAD_LINK_LIBS Link Library list: xrlf03;xrl;forest;fgsl;gsl;gslcblas;lapack95;lapack;blas;hdf5hl_fortran;hdf5_hl;hdf5_fortran;hdf5;fftw3;fftw3_omp

SHARED DEPS : lapack;blas SHARED LINKER FLAGS : -L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/sqlite/lib

-- Configuring done -- Generating done -- Build files have been written to: /Users/mbai/Bmad/bmad_dist/lapack95/production /opt/local/bin/cmake -S/Users/mbai/Bmad/bmad_dist/lapack95 -B/Users/mbai/Bmad/bmad_dist/lapack95/production --check-build-system CMakeFiles/Makefile.cmake 0 /opt/local/bin/cmake -E cmake_progress_start /Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles /Users/mbai/Bmad/bmad_dist/lapack95/production//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/lapack95/production' gmake -f CMakeFiles/lapack95.dir/build.make CMakeFiles/lapack95.dir/depend gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/lapack95/production' cd /Users/mbai/Bmad/bmad_dist/lapack95/production && /opt/local/bin/cmake -E cmake_depends "Unix Makefiles" /Users/mbai/Bmad/bmad_dist/lapack95 /Users/mbai/Bmad/bmad_dist/lapack95 /Users/mbai/Bmad/bmad_dist/lapack95/production /Users/mbai/Bmad/bmad_dist/lapack95/production /Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles/lapack95.dir/DependInfo.cmake --color= Dependee "/Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles/lapack95.dir/DependInfo.cmake" is newer than depender "/Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles/lapack95.dir/depend.internal". Dependee "/Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles/lapack95.dir/depend.internal". Scanning dependencies of target lapack95 gmake[2]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/lapack95/production' gmake -f CMakeFiles/lapack95.dir/build.make CMakeFiles/lapack95.dir/build gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/lapack95/production' gmake[2]: Nothing to be done for 'CMakeFiles/lapack95.dir/build'. gmake[2]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/lapack95/production' [100%] Built target lapack95 gmake[1]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/lapack95/production' /opt/local/bin/cmake -E cmake_progress_start /Users/mbai/Bmad/bmad_dist/lapack95/production/CMakeFiles 0

/Users/mbai/Bmad/bmad_dist/lapack95/production Compile/Link time: 3.60sec

Building directory: gsl

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: fgsl

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: forest

Re-run cmake no build system arguments

Build type : Production -- Mon Dec 4 06:30:16 PST 2023 Current Directory : /Users/mbai/Bmad/bmad_dist/forest Linking with release : /Users/mbai/Bmad/bmad_dist/ (Off-site Distribution) C Compiler : /opt/local/bin/gcc Fortran Compiler : /opt/local/bin/gfortran Plotting Libraries : plplotfortran;plplot;csirocsa;qsastime Shared Libraries : cairo;pango-1.0;pangocairo-1.0;gobject-2.0 OpenMP gfortran Flag : -fopenmp OpenMP Linker Libs : gomp MPI Support : Not Enabled FFLAGS :
gfortran Compiler Flags : -Df2cFortran -DCESR_UNIX -DCESR_LINUX -u -traceback -cpp -fno-range-check -fdollar-ok -fbacktrace -Bstatic -ffree-line-length-none -fopenmp -DCESR_PLPLOT -fPIC -O2 gfortran Linker Flags : -lX11 -lplplotfortran -lplplot -lcsirocsa -lqsastime -lpthread;-lstdc++;-ldl gomp ACC_BMAD_LINK_LIBS Link Library list: xrlf03;xrl;forest;fgsl;gsl;gslcblas;lapack95;lapack;blas;hdf5hl_fortran;hdf5_hl;hdf5_fortran;hdf5;fftw3;fftw3_omp

SHARED DEPS : SHARED LINKER FLAGS : -L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/sqlite/lib

-- Configuring done -- Generating done -- Build files have been written to: /Users/mbai/Bmad/bmad_dist/forest/production /opt/local/bin/cmake -S/Users/mbai/Bmad/bmad_dist/forest -B/Users/mbai/Bmad/bmad_dist/forest/production --check-build-system CMakeFiles/Makefile.cmake 0 /opt/local/bin/cmake -E cmake_progress_start /Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles /Users/mbai/Bmad/bmad_dist/forest/production//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/forest/production' gmake -f CMakeFiles/forest.dir/build.make CMakeFiles/forest.dir/depend gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/forest/production' cd /Users/mbai/Bmad/bmad_dist/forest/production && /opt/local/bin/cmake -E cmake_depends "Unix Makefiles" /Users/mbai/Bmad/bmad_dist/forest /Users/mbai/Bmad/bmad_dist/forest /Users/mbai/Bmad/bmad_dist/forest/production /Users/mbai/Bmad/bmad_dist/forest/production /Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles/forest.dir/DependInfo.cmake --color= Dependee "/Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles/forest.dir/DependInfo.cmake" is newer than depender "/Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles/forest.dir/depend.internal". Dependee "/Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles/forest.dir/depend.internal". Scanning dependencies of target forest gmake[2]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/forest/production' gmake -f CMakeFiles/forest.dir/build.make CMakeFiles/forest.dir/build gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/forest/production' gmake[2]: Nothing to be done for 'CMakeFiles/forest.dir/build'. gmake[2]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/forest/production' [100%] Built target forest gmake[1]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/forest/production' /opt/local/bin/cmake -E cmake_progress_start /Users/mbai/Bmad/bmad_dist/forest/production/CMakeFiles 0

/Users/mbai/Bmad/bmad_dist/forest/production Compile/Link time: .60sec

Building directory: xraylib

The production build already exists. To force a rebuild, please type:

mk cleaner

then type:

mk

Building directory: sim_utils

Re-run cmake no build system arguments

Build type : Production -- Mon Dec 4 06:30:17 PST 2023 Current Directory : /Users/mbai/Bmad/bmad_dist/sim_utils Linking with release : /Users/mbai/Bmad/bmad_dist/ (Off-site Distribution) C Compiler : /opt/local/bin/gcc Fortran Compiler : /opt/local/bin/gfortran Plotting Libraries : plplotfortran;plplot;csirocsa;qsastime Shared Libraries : cairo;pango-1.0;pangocairo-1.0;gobject-2.0 OpenMP gfortran Flag : -fopenmp OpenMP Linker Libs : gomp MPI Support : Not Enabled FFLAGS :
gfortran Compiler Flags : -Df2cFortran -DCESR_UNIX -DCESR_LINUX -u -traceback -cpp -fno-range-check -fdollar-ok -fbacktrace -Bstatic -ffree-line-length-none -fopenmp -DCESR_PLPLOT -fPIC -O2 gfortran Linker Flags : -lX11 -lplplotfortran -lplplot -lcsirocsa -lqsastime -lpthread;-lstdc++;-ldl gomp ACC_BMAD_LINK_LIBS Link Library list: xrlf03;xrl;forest;fgsl;gsl;gslcblas;lapack95;lapack;blas;hdf5hl_fortran;hdf5_hl;hdf5_fortran;hdf5;fftw3;fftw3_omp

SHARED DEPS : plplotfortran;plplot;csirocsa;qsastime;xrlf03;xrl;forest;fgsl;gsl;gslcblas;lapack95;lapack;blas;hdf5hl_fortran;hdf5_hl;hdf5_fortran;hdf5;fftw3;fftw3_omp;X11;readline SHARED LINKER FLAGS : -L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/sqlite/lib

-- Configuring done -- Generating done -- Build files have been written to: /Users/mbai/Bmad/bmad_dist/sim_utils/production /opt/local/bin/cmake -S/Users/mbai/Bmad/bmad_dist/sim_utils -B/Users/mbai/Bmad/bmad_dist/sim_utils/production --check-build-system CMakeFiles/Makefile.cmake 0 /opt/local/bin/cmake -E cmake_progress_start /Users/mbai/Bmad/bmad_dist/sim_utils/production/CMakeFiles /Users/mbai/Bmad/bmad_dist/sim_utils/production//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/sim_utils/production' gmake -f CMakeFiles/sim_utils.dir/build.make CMakeFiles/sim_utils.dir/depend gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/sim_utils/production' cd /Users/mbai/Bmad/bmad_dist/sim_utils/production && /opt/local/bin/cmake -E cmake_depends "Unix Makefiles" /Users/mbai/Bmad/bmad_dist/sim_utils /Users/mbai/Bmad/bmad_dist/sim_utils /Users/mbai/Bmad/bmad_dist/sim_utils/production /Users/mbai/Bmad/bmad_dist/sim_utils/production /Users/mbai/Bmad/bmad_dist/sim_utils/production/CMakeFiles/sim_utils.dir/DependInfo.cmake --color= Dependee "/Users/mbai/Bmad/bmad_dist/sim_utils/production/CMakeFiles/sim_utils.dir/DependInfo.cmake" is newer than depender "/Users/mbai/Bmad/bmad_dist/sim_utils/production/CMakeFiles/sim_utils.dir/depend.internal". 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Error in distribution build.

[BaiMay]

when I tried mk cleaner, I got "This working directory is not a project supported by the ACC build system.".

[DavidSagan]

That is because mk cleaner is for when you are in a sub-directory of bmad_dist and trying to clean a single library or program build. To clean everything, goto the bmad_dist directory and use the command util/dist_clean .

[jsberg-bnl]

Problem here is that -fopenmp is not making it onto the linker line. @BaiMay, I assume you have ACC_ENABLE_OPENMP=Y in util/dist_prefs? @DavidSagan, if you look at the link line for your Mac build, does the -fopenmp flag make it there?

[BaiMay]

@jsberg-bnl Yes, I have ACC_ENABLE_OPENMP=Y in the dist_prefs.

[DavidSagan]

The answer is -fopenmp appears on compile lines but not the link line. For linking I get:

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[BaiMay]

@DavidSagan , should I try to manually execute the last two steps?

[DavidSagan]

I'm not sure that will help. Perhaps if @jsberg-bnl has some time we can zoom.

[BaiMay]

zoom will be great. How about 1:30pm or 3:30pm? Both are PDT.

[DavidSagan]

@jsberg-bnl 3:30pm PT / 6:30pm ET is possible for me.

[BaiMay]

@jsberg-bnl and @DavidSagan , it seems my homebrew is in /opt instead of /usr/local/opt. This is probably due to my .zshrc

export PATH="/opt/homebrew/bin:$PATH" export PATH="/Users/mbai/Code/miniconda3/bin:$PATH" export DIST_BASE_DIR="/Users/mbai/Bmad/bmad_dist/" export TAO_DIR="/Users/mbai/Bmad/bmad_dist/tao/" export PATH=$PATH:$DIST_BASE_DIR/production/bin

export PATH=$PATH:$DIST_BASE_DIR/tao/doc

export LD_LIBRARY_PATH=/usr/local/bin:/opt/homebrew/lib

xterm&

xterm -fa 'Monospace' -fs 1 &

export PATH=/usr/local/opt/gettext/bin:/usr/local/opt/make/libexec/gnubin:/usr/local/opt/m4/bin:/usr/local/opt/sqlite/bin:$PATH export LDFLAGS="-L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/sqlite/lib" export CPPFLAGS="-I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/sqlite/include" export PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig" export PATH=/opt/local/bin:/opt/local/sbin:$PATH

conda activate devel

source /usr/local/bin/geant4.sh source /Users/mbai/Downloads/jintonic-gears-5b2de62/gears.sh

[BaiMay]

I did try to comment out all the /opt/homebrew in my .zshrc, sourced it. Then uninstalled homebrew and reinstall homebrew. But, still ended up with /opt/homebrew...

[BaiMay]

Should I try to reinstall homebrew as /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" --prefix=/usr/local/opt?

[jsberg-bnl]

No. Let's try go get things right with a default installation of Homebrew. Homebrew shoves things into individual directories under Cellar, we need to tell it where those are. Matthew has probably done the most in this area, but in fact smoothing out a Homebrew install is something that we need to work on.

[jsberg-bnl]

@BaiMay, is your macports reasonably up to date (i.e., when was your last port selfupdate)?

[BaiMay]

@jsberg-bnl I believe so. It was set to be automatic. Just had a look and saw that I need to restart the mac for macOS Sonoma 14.1.2 to be effective. Will do after I finish what am doing at the moment.

[DavidSagan]

Macports?? Macports should not be used with Homebrew.

[DavidSagan]

@BaiMay Also with Homebrew, did you remember to set ACC_USE_MACPORTS="F" in util/dist_prefs?

[jsberg-bnl]

Sorry, I'm getting mixed up, I mean the corresponding homebrew command.

[jsberg-bnl]

brew update and brew upgrade I guess

[BaiMay]

@BaiMay Also with Homebrew, did you remember to set ACC_USE_MACPORTS="F" in util/dist_prefs?

Nope. I didn't do this step.

[BaiMay]

@jsberg-bnl @DavidSagan successfully followed up the macports package part. Then started a fresh terminal, did util/dist_clean, and then util/dist_build_production. Got the errors (see below). Seems the problem is hdf5. This makes me wonder whether I should also redo the xcode part? I remember this is quite delicate as bmad has some compatibility issues. Another thing is there is still no /usr/local/opt/

checking for config ./config/site-specific/host-PC100346... no checking for clang sanitizer checks... none checking build mode... production checking for gcc... clang checking whether the C compiler works... no configure: error: in /Users/mbai/Bmad/bmad_dist/hdf5/production': configure: error: C compiler cannot create executables Seeconfig.log' for more details gmake: *** [Makefile:31: _config] Error 77

Error in building HDF5 VERSION HDF5-1.14.3 Downloaded: 2023-11-16.

[BaiMay]

Adding to the points above, should I replace the following path with the ones for MacPorts?

export PATH=/usr/local/opt/gettext/bin:/usr/local/opt/make/libexec/gnubin:/usr/local/opt/m4/bin:/usr/local/opt/sqlite/bin:$PATH export LDFLAGS="-L/usr/local/opt/gettext/lib -L/usr/local/opt/libffi/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/sqlite/lib" export CPPFLAGS="-I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/sqlite/include" export PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig"

[jsberg-bnl]

All of those variable settings should be unnecessary with MacPorts. Could you attach hdf5/production/config.log?

[jsberg-bnl]

And what do you get for which cc and gcc --version?

[DavidSagan]

And follow the instructions at https://wiki.classe.cornell.edu/ACC/ACL/OffsiteDoc#A_42macOS_40formally_Mac_OS_X_41_42

[BaiMay]

And what do you get for which cc and gcc --version?

'which cc' gives /usr/bin/cc, 'which gcc' gives /opt/local/bin/gcc, and gcc --version: gcc (MacPorts gcc12 12.3.0_4+stdlib_flag) 12.3.0 Copyright (C) 2022 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[BaiMay]

All of those variable settings should be unnecessary with MacPorts. Could you attach hdf5/production/config.log?

config.log

I also attached the build-p0.log build-p0.log

[BaiMay]

And follow the instructions at https://wiki.classe.cornell.edu/ACC/ACL/OffsiteDoc#A_42macOS_40formally_Mac_OS_X_41_42

Just did. see below, sudo xcode-select --install Password: xcode-select: note: Command line tools are already installed. Use "Software Update" in System Settings or the softwareupdate command line interface to install updates

And my xquartz is XQuartz 2.8.5 (xorg-server 21.1.6).

I vaguely remember we had gone through the mac default xquartz to an earlier version. So, I guess I shouldn't do an update, no?

[DavidSagan]

XQuartz is separate from any compile issues but yes update.

[BaiMay]

XQuartz is separate from any compile issues but yes update.

Just tried to take a look at Xcode. It seems to be corrupted. Here is the pop-up window says "Xcode Server Builder quit unexpectedly."

[DavidSagan]

Have you updated Xcode to the latest version?

[BaiMay]

Have you updated Xcode to the latest version?

Not intentionally, at least. Also, I ran "system_profiler SPDeveloperToolsDataType" and got empty return.

[DavidSagan]

You need to update.

[BaiMay]

You need to update.

Could you please remind me the instructions on how to update the Xcode? Or, the following steps?

sudo port upgrade xcode xcodebuild -version

[DavidSagan]

Search for Xcode install.

[BaiMay]

Search for Xcode install.

Will do. One question though. This means I will get the latest version. Is it then compatible with Bmad?

[DavidSagan]

It should be.

[BaiMay]

Okay just tried to rebuild with the updated xcode. Unfortunately, I got the same error. Attach the config.log in the hdf5/production here config.log

[BaiMay]

Just realized that I still have "export LD_LIBRARY_PATH=/usr/local/bin:/opt/homebrew/lib" in my .zshrc file. Could this be the problem? Should I update it to /opt/local/lib?

[DavidSagan]

Yes fix and set ACC_USE_MACPORTS="Y"

[BaiMay]

Yes fix and set ACC_USE_MACPORTS="Y"

Oh, that too!

[jsberg-bnl]

What's going wrong is the hdf5 build is for some reason trying to build with clang rather than gcc. In looking at the detection code, my guess would be that CC was set to clang; what does echo $CC say?

[jsberg-bnl]

Never mind, it tells me what variables are set and CC is not. I'll have to delve a bit more to determine why it's trying to use clang. Proably related to the fact that /usr/bin/cc is a link to clang. Maybe try doing export CC=gcc?

[jsberg-bnl]

OK, I have a guess: what is the output of ls -l /opt/local/bin/gcc and ls -l /usr/bin/cc? And if my guess is correct, there is also a /usr/bin/gcc; what is the output of ls -l /usr/bin/gcc if that exists?

[BaiMay]

First of all, after reinstall xcode, the build went a bit further. Here is the latest error message,

gmake[1]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production' gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production' gmake[1]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production' Making install in c++ gmake[1]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production/c++' Making install in src gmake[2]: Entering directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production/c++/src' CXXLD libhdf5_cpp.la -macosx_version_min has been renamed to -macos_version_min -macosx_version_min has been renamed to -macos_version_min ld: warning: -undefined suppress is deprecated ld: warning: ignoring duplicate libraries: '-lgcc', '-lgomp' 0 0x102fdb648 __assert_rtn + 72 1 0x102f0ffac ld::AtomPlacement::findAtom(unsigned char, unsigned long long, ld::AtomPlacement::AtomLoc const&, long long&) const + 1204 2 0x102f25924 ld::InputFiles::SliceParser::parseObjectFile(mach_o::Header const) const + 15164 3 0x102f32e30 ld::InputFiles::parseAllFiles(void (ld::AtomFile const*) block_pointer)::$_7::operator()(unsigned long, ld::FileInfo const&) const + 420 4 0x181f07950 _dispatch_client_callout2 + 20 5 0x181f1c1a4 _dispatch_apply_invoke_and_wait + 176 6 0x181f1b464 _dispatch_apply_with_attr_f + 1176 7 0x181f1b650 dispatch_apply + 96 8 0x102fad3b8 ld::AtomFileConsolidator::parseFiles(bool) + 292 9 0x102f4e170 main + 9048 ld: Assertion failed: (resultIndex < sectData.atoms.size()), function findAtom, file Relocations.cpp, line 1336. collect2: error: ld returned 1 exit status gmake[2]: [Makefile:1015: libhdf5_cpp.la] Error 1 gmake[2]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production/c++/src' gmake[1]: [Makefile:892: install-recursive] Error 1 gmake[1]: Leaving directory '/Users/mbai/Bmad/bmad_dist_20231128-1/hdf5/production/c++' gmake: *** [Makefile:730: install-recursive] Error 1

Error in building HDF5 VERSION HDF5-1.14.3 Downloaded: 2023-11-16.

Error in distribution build.

[BaiMay]

echo $CC

gcc

[BaiMay]

ls -l /opt/local/bin/gcc

lrwxr-xr-x 1 root wheel 24 Dec 6 00:24 /opt/local/bin/gcc -> /opt/local/bin/gcc-mp-12