tjhei commented 2 years ago

I need to investigate why the arm build on MacOS currently fails when installing Trilinos. This might be due to #297 ... The error message is ld: symbol(s) not found for architecture arm64 collect2: error: ld returned 1 exit status

Francyrad commented 2 years ago

Thank you, I'll follow the resolution problem

tjhei commented 2 years ago

Going back to v9.4.0-r2 fixes the issue:

git checkout v9.4.0-r2

It is not because of the update to 13.2, but related to explicit instantiations, I think.

Francyrad commented 2 years ago

Dear tkhei

This solution doesn't work. I installed trilinos positively. However, i cannot install dealii now! This is not the only problem, i cannot install many packages that i need to run the program that i want to install (Aspect). The aspect's developers recommend:

deal.II 9.3 or newer configured with: MPI, Trilinos, p4est (required) BLAS/LAPACK, zlib (strongly recommended) HDF5 (optional) optional: PerpleX, LIBDAP, NETCDF

I could not install blas, lapack and dealii with 9.4

Do you have any solution for this? For example, installing trilinos with 9.4 and other packages with newer versions, i don't even know if this is possible...

Thank you for your work, I’m waiting for new news

tjhei commented 2 years ago

This solution doesn't work. I installed trilinos positively. However, i cannot install dealii now!

I can confirm that deal.II and ASPECT work for me with my suggestion. Please try removing everything from the output directory and run again. If it still fails, send the precise error message.

i cannot install many packages that i need to run the program that i want to install

You just need "p4est trilinos deal.II" from candi as described here: https://github.com/geodynamics/aspect/wiki/Installation-on-ARM-OSX

Francyrad commented 2 years ago

It cannot build dealii now, i attach you the error...

dealii_9.4_error.txt

I apologize for the inconvenience. I deleted everything the installer tried to install previously... I hope you can solve

tjhei commented 2 years ago

The error you are seeing is due to hdf5. Try installing without hdf5 for now.

tjhei commented 2 years ago

Trilinos 12.4 and 13.2 are broken with explicit instantiations enabled on ARM.

hdf5 causes a problem when compiling deal.II.

NikkiGwh commented 1 year ago

hi @tjhei I am facing exactly the same problem with my new M1 Pro mac (I starting to regret my choice..) After following your instructions to switch to branch "v9.4.0-r2" and invoking the installation script with: sudo ./candi.sh -j 8 --packages="p4est trilinos dealii" (without hdf5) I still get following errors: It seems like there are some issues with "boost"..

Anyway, if you have a solution for this problem let us know.

kind regards Niklas

Francyrad commented 1 year ago

@nikkighw I solved in this way months ago (with 9.4):

git clone https://github.com/dealii/candi cd candi ./candi.sh -j 8 --packages="p4est trilinos dealii"

I installed hdf5 in other ways.

tjhei commented 1 year ago

@NikkiGwh : Can you set BUILD_EXAMPLES=OFF in candi.cfg?

NikkiGwh commented 1 year ago

@tjhei thank you for your quick response !

the build finished successfully with turning BUILD_EXAMPLES=OFF. I used branch [v9.4.0-r2] (to avoid the trilions 13.2 error) and I didn't install hdf5. Since the example were not able to build.. do you know which features I can't use with my current installation?

@Francyrad So you were able to build it from the normal main branch without switching to [v9.4.0-r2] ? How did you fix the trillions 13.2 error then?

And could you tell me how you installed hdf5 separately (using brew or build manually etc.) and what kind of configuration you had to do so that candi was able to find this installation (cmake configuration or adding stuff to path variable etc.)

Francyrad commented 1 year ago

Maybe I explained it wrong. I installed version 9.4, which is enough to use the program of my interest. As for hdf5, I installed it with "brew install hdf5". I don’t remember doing other things in particular, since I solved the problem as Thjei suggested.

KiralyAgi commented 1 year ago

Hi Timo (@tjhei)!

As I mentioned in issue #316, I am now facing problems with the trilinos installation too. I looked over the suggestions here, but none of the problems seems the same as mine (see below) and none of the solution helps.

Here is the error: ld: warning: ignoring file /opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/12/libgcc.a, building for macOS-x86_64 but attempting to link with file built for macOS-arm64 Undefined symbols for architecture x86_64: "_VerifyFortran", referenced from: _main in main.c.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: [VerifyFortranC] Error 1 make[2]: [CMakeFiles/VerifyFortranC.dir/all] Error 2 make[1]: [CMakeFiles/VerifyFortranC.dir/rule] Error 2 make: [VerifyFortranC] Error 2

Is there a way to get around this? I use the mpicc, mpicxx and mpifort from my /usr/local/bin folder (i.e. not the homebrew installations), because that was working for the hdf5 and p4est installation. Update: I get the same error also with the homebrew link to mpi.

Francyrad commented 1 year ago

What version of MacOS do you have? If you upgraded to MacOS Ventura you may face problems, because it doesn't full support Fortran

KiralyAgi commented 1 year ago

Indeed, I updated to Ventura 13.1. Is there a way to get around this problem?

Francyrad commented 1 year ago

The problem may be MacOS Ventura, but I'm not sure. Can you please do a make clean, make again any then post there the full error with a .txt?

If the problem is Ventura, you should downgrade in a non easy process. The best would be to use Time Machine if you did a backup

KiralyAgi commented 1 year ago

CMakeError.log Here is the error file. I wasn't sure how(&where) to do make clean, but after clearing the tmp folder, I tried again to install trilinos via candi, with the same error.

tjhei commented 1 year ago

Agi: Are you running in a native terminal? What does machine return when you run it in the terminal?

Also, what does git show -q and git diff show?

KiralyAgi commented 1 year ago

I think so: (base) kiraly@Agness-MacBook-Pro ~ % machine arm64e (base) kiraly@Agness-MacBook-Pro ~ % git show -q fatal: not a git repository (or any of the parent directories): .git (base) kiraly@Agness-MacBook-Pro ~ % cd /Applications/candi (base) kiraly@Agness-MacBook-Pro candi % machine arm64e (base) kiraly@Agness-MacBook-Pro candi % git show -q commit 438b4a17de34a66776f69765f84dacb0e6913764 (HEAD, tag: v9.4.0-r2) Author: Timo Heister timo.heister@gmail.com Date: Sat Jul 2 13:08:58 2022 -0400

version 9.4.0-r2

(base) kiraly@Agness-MacBook-Pro candi % git diff diff --git a/candi.cfg b/candi.cfg index 2638bcd..487ad5b 100644 --- a/candi.cfg +++ b/candi.cfg @@ -37,7 +37,7 @@ NATIVE_OPTIMIZATIONS=OFF USE_64_BIT_INDICES=OFF

Option {ON|OFF}: Enable building of dealii examples?

-BUILD_EXAMPLES=ON +BUILD_EXAMPLES=OFF

Option {ON|OFF}: Unset CXX and set the compiler as MPI_CXX_COMPILER when configuring deal.II

# //NOTE: I also tried the installation on the dealii-9.4 branch with the same results.

bobmyhill commented 1 year ago

Hi @KiralyAgi,

I've just successfully installed deal.II and ASPECT on the Apple M1 Pro, Ventura 13.1 (22C65)

Use this version of candi: https://github.com/dealii/candi/releases/tag/v9.4.0-r2 (this exact commit)
Use these instructions: https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX (including update of software with homebrew)
No need to change BUILD_EXAMPLES=ON
Follow the instructions at the end of the output from candi
ASPECT then compiled from source

Result:

-- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion. -- . version 2.5.0-pre (field_types_for_elasticity_2, 9234dde4e) -- . using deal.II 9.4.0 -- . with 32 bit indices and vectorization level 0 (64 bits) -- . using Trilinos 12.18.1 -- . using p4est 2.3.2 -- . running in DEBUG mode -- . running with 8 MPI processes

KiralyAgi commented 1 year ago

Hi Bob!

I tried many times and the hdf5 and p4est installation goes through if I export mpicc, mpicxx, FC and FF from my usr/local/bin. But whatever I do I always get problem with trilinos, which seems to try building for architecture x86_64 instead of arm64e.

bobmyhill commented 1 year ago

Hi @KiralyAgi

Ok, a few ideas:

Did you delete the trilinos-x and tmp directories inside the dealii-candi directory before retrying your installation?
For me, mpicc, mpicxx and mpifort are linked from /opt/homebrew/bin/. I think your files in usr/local/bin are probably symlinks though (maybe worth checking).
For what it's worth, my bashrc exports are:

export CC=mpicc export CXX=mpicxx export FC=mpifort export FF=mpifort export OMPI_CC=gcc export OMPI_CXX=g++ export OMPI_FC=gfortran
Maybe worth also checking which compilers you're using (see below for mine).
If you haven't updated Command Line Tools recently, it might be worth doing that (tedious though it is): https://stackoverflow.com/a/47725718/6272561

$ mpicc -v Apple clang version 14.0.0 (clang-1400.0.29.202) Target: arm64-apple-darwin22.2.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

$ mpicxx -v Apple clang version 14.0.0 (clang-1400.0.29.202) Target: arm64-apple-darwin22.2.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

$ mpifort -v Using built-in specs. COLLECT_GCC=/opt/homebrew/bin/gfortran COLLECT_LTO_WRAPPER=/opt/homebrew/Cellar/gcc/12.2.0/bin/../libexec/gcc/aarch64-apple-darwin21/12/lto-wrapper Target: aarch64-apple-darwin21 Configured with: ../configure --prefix=/opt/homebrew/opt/gcc --libdir=/opt/homebrew/opt/gcc/lib/gcc/current --disable-nls --enable-checking=release --with-gcc-major-version-only --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-12 --with-gmp=/opt/homebrew/opt/gmp --with-mpfr=/opt/homebrew/opt/mpfr --with-mpc=/opt/homebrew/opt/libmpc --with-isl=/opt/homebrew/opt/isl --with-zstd=/opt/homebrew/opt/zstd --with-pkgversion='Homebrew GCC 12.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --with-system-zlib --build=aarch64-apple-darwin21 --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Homebrew GCC 12.2.0)

emcgowen commented 1 year ago

Hi @bobmyhill

This method with branch "v9.4.0-r2" works for me to build deal.II but not ASPECT. I used the compiler exports requested by the messages when you start candi.sh.

I've just successfully installed deal.II and ASPECT on the Apple M1 Pro, Ventura 13.1 (22C65)

Use this version of candi: https://github.com/dealii/candi/releases/tag/v9.4.0-r2 (this exact commit)

Use these instructions: https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX (including update of software with homebrew)

No need to change BUILD_EXAMPLES=ON

Follow the instructions at the end of the output from candi

ASPECT then compiled from source

Using this method I have been able to build Deal.II on an M1 Mac running Ventura 13.2, but step-32 does not run successfully (it aborts with a timeout).

Also Aspect fails to build with the same compiler exports as I used to run candi.sh: CC=mpicc CXX=mpicxx FC=mpifort FF=mpifort OMPI_CXX=g++-11 OMPI_FC=gfortran-11

mpicc -v Apple clang version 14.0.0 (clang-1400.0.29.202) Target: arm64-apple-darwin22.3.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

mpicxx -v Using built-in specs. COLLECT_GCC=/opt/homebrew/bin/g++-11 COLLECT_LTO_WRAPPER=/opt/homebrew/Cellar/gcc@11/11.3.0/bin/../libexec/gcc/aarch64-apple-darwin22/11/lto-wrapper Target: aarch64-apple-darwin22 Configured with: ../configure --prefix=/opt/homebrew/opt/gcc@11 --libdir=/opt/homebrew/opt/gcc@11/lib/gcc/11 --disable-nls --enable-checking=release --with-gcc-major-version-only --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-11 --with-gmp=/opt/homebrew/opt/gmp --with-mpfr=/opt/homebrew/opt/mpfr --with-mpc=/opt/homebrew/opt/libmpc --with-isl=/opt/homebrew/opt/isl --with-zstd=/opt/homebrew/opt/zstd --with-pkgversion='Homebrew GCC 11.3.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --build=aarch64-apple-darwin22 --with-system-zlib --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.3.0 (Homebrew GCC 11.3.0)

After compiling the WorldBuilder files, the Unity files give compiler errors that gcc-11 does not recognize the flag -Xarch-arm64:

[58%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/wrapper_c.cc.o [ 64%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/wrapper_cpp.cc.o [ 64%] Building CXX object CMakeFiles/aspect.dir/contrib/world_builder/source/parameters.cc.o [ 64%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_39_cxx.cxx.o [ 64%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_38_cxx.cxx.o [ 64%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_36_cxx.cxx.o [ 64%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_42_cxx.cxx.o [ 64%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_35_cxx.cxx.o [ 70%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_37_cxx.cxx.o [ 70%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_41_cxx.cxx.o [ 70%] Building CXX object CMakeFiles/aspect.dir/Unity/unity_40_cxx.cxx.o g++-11: error: unrecognized command-line option '-Xarch_arm64' g++-11: error: unrecognized command-line option '-Xarch_arm64' g++-11: error: unrecognized command-line option '-Xarch_arm64' g++-11: error: unrecognized command-line option '-Xarch_arm64' g++-11: error: unrecognized command-line option '-Xarch_arm64' make[2]: [CMakeFiles/aspect.dir/Unity/unity_40_cxx.cxx.o] Error 1 make[2]: Waiting for unfinished jobs.... make[2]: *** [CMakeFiles/aspect.dir/Unity/unity_41_cxx.cxx.o] Error 1

Perhaps the wrong compiler is being invoked for these files? The mpicxx compiler is g++-11, and I've tried passing the Apple Clang compiler for mpicxx, but then I get syntax errors from the worldbuilder files.

Also, the ASPECT source was checked out with: git clone https://github.com/geodynamics/aspect.git Is this a stable version or a development version?

In case this was a problem only with top-of-trunk, I tried building ASPECT with the aspect-2.4.0.tar release and got the exact same compiler errors as before.

Thanks

bobmyhill commented 1 year ago

Hi @emcgowen

Just to check my instructions still work, I updated my M1 Macbook to Ventura 13.2, deleted and reinstalled xcode CLT (https://stackoverflow.com/a/47804075/6272561) and then deleted and reinstalled deal.II and ASPECT as per the instructions in my original post. Everything still works fine.

Some output before I reinstalled deal.II:

$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables package-id: com.apple.pkg.CLTools_Executables version: 14.2.0.0.1.1668646533

$mpicxx -v Apple clang version 14.0.0 (clang-1400.0.29.202)

From what you've written, the mpicxx alias does not point to clang, as recommended in the instructions linked to in my original post (https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX). You should make sure that mpicxx points to the right compiler, then delete your deal.II installation (probably ~/dealii-candi/ if you didn't change the destination in candi.cfg), and try again.

emcgowen commented 1 year ago

This solved it for me, and now I have a working Deal II and an ASPECT which prints out:

-- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion. -- . version 2.5.0-pre (main, 2b14e1b8e) -- . using deal.II 9.4.0 -- . with 32 bit indices and vectorization level 0 (64 bits) -- . using Trilinos 12.18.1 -- . using p4est 2.3.2 -- . running in DEBUG mode -- . running with 1 MPI process ——————————————————————————————————————

For future reference, the instructions about how to use homebrew need to be corrected. By default

brew install openmpi

installs mpicc = gcc and mpicxx = gcc. To keep the native clang compiler you must do

brew CC=clang install openmpi

This causes brew to recompile openmpi using the clang compiler.

Also, candi.sh prints out misleading instructions about exporting compiler environment variables:

export CC=mpicc; export CXX=mpicxx, FC=mpifort, FF=mpifort \ export OMPI_CC=gcc-11, export OMPI_CXX=g++-11, export OMPI_FC=gfortran+11

DO NOT export the OMPI_ environment variables unless you intend to build with the GNU C compiler!

And finally, a nit. When testing Deal II with the step-32 test, I had to do

export LC_ALL=C

to get the test to run.

Thanks!

Ellen McGowen

On Feb 5, 2023, at 4:35 AM, Bob Myhill @.***> wrote:

Hi @emcgowen https://github.com/emcgowen Just to check my instructions still work, I updated my M1 Macbook to Ventura 13.2, deleted and reinstalled xcode CLT (https://stackoverflow.com/a/47804075/6272561) and then deleted and reinstalled deal.II and ASPECT as per the instructions in my original post. Everything still works fine.

Some output before I reinstalled deal.II:

$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables package-id: com.apple.pkg.CLTools_Executables version: 14.2.0.0.1.1668646533

$mpicxx -v Apple clang version 14.0.0 (clang-1400.0.29.202)

From what you've written, the mpicxx alias does not point to clang, as recommended in the instructions linked to in my original post (https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX). You should make sure that mpicxx points to the right compiler, then delete your deal.II installation (probably ~/dealii-candi/ if you didn't change the destination in candi.cfg), and try again.

— Reply to this email directly, view it on GitHub https://github.com/dealii/candi/issues/309#issuecomment-1417712964, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABTDMVLULMJYZMHQSLEXQC3WV6NAZANCNFSM6AAAAAARPBZ2ZA. You are receiving this because you were mentioned.

tjhei commented 1 year ago

brew --cc=clang install openmpi

Thank you, I updated the instructions at https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX

bobmyhill commented 1 year ago

Glad it worked! Thank you for the additional information, that's very useful. And thanks again @tjhei for all your work on this problem.

Francyrad commented 1 year ago

Hello. I needed to reinstall Dealii to make aspect workwith Ventura 13.1. So i downloaded the version you said above. Then ./candi.sh -j 8 --packages="p4est trilinos dealii" It install p4est and trillnos, but not dealii. This is the error. How can i solve? Thank you for your support

tjhei commented 1 year ago

You are not showing the error message, can you post errors higher up?

Francyrad commented 1 year ago

candierror2.txt Sure!

tjhei commented 1 year ago

/Users/francyrad/dealii-candi/tmp/unpack/deal.II-v9.4.0/source/lac/sparse_direct.cc:104:14: error: non-const lvalue reference to type 'vector<long, allocator<long>>' cannot bind to a value of unrelated type 'vector<types::suitesparse_index, allocator<long long>>'

This error is fixed in https://github.com/dealii/dealii/pull/14721 but is not in the latest deal.II version 9.4.1 yet. You could set DEAL_II_VERSION=dealii-9.4 in your candi.cfg to get the fix (or switch to master or wait for 9.4.2)

Francyrad commented 1 year ago

I was already using the 9.4 error. i tried to install the master of the version 9.4. i cannot install trilinos now. What can i do? trilinos.error.txt

tjhei commented 1 year ago

I was already using the 9.4 error. i tried to install the master of the version 9.4.

I don't understand what you are saying.

We just released 9.4.2, so you should be able to do DEAL_II_VERSION=v9.4.2 now.

Francyrad commented 1 year ago

I downloaded the new version 9.4.2 and i still get errors :( errorrr.txt

bobmyhill commented 1 year ago

If you have a Mac with an M1 chip (maybe also M2, I haven't tested this) running Ventura 13.1, our instructions should work. It is possible that you have some independently installed dependencies that are interfering with the installation, or that you're using some incompatible version of clang / command line tools.

If you are happy using deal.ii 9.4.0, I recommend that you use candi v9.4.0-r2 unmodified, and with our instructions, just because it's then easier for us to troubleshoot your problems. (@tjhei's suggestion was good, but it didn't fix your problem, so I'd rather you go back to something we know works on our machines).

I also recommend that you remove your brew-installed version of hdf5, as it doesn't have MPI support. candi v9.4.0-r2 installs hdf5 just fine on my machine. If it still doesn't install correctly on yours following these instructions - https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX - let us know, along with the verbose information on your compilers and version of command line tools. I'd rather get your machine to a state close to ours rather than find an independent set of workarounds and hacks.

KiralyAgi commented 1 year ago

Finally I made it! Thanks for all the suggestions. Afterall a slightly different method has worked for me.

1) Remove and re-install X-code 2) Remove and re-install brew (might not be important) Now here before I went to brew install openmpi and others I checked, that I already have all of these. $ mpicxx -v Apple clang version 14.0.0 (clang-1400.0.29.202) Target: x86_64-apple-darwin22.3.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin

So, I tried to install the released 9.4.0 package without the brew install and it worked like a charm.

_Here is what I think happens: If I install openmpi and gcc11 with brew (even with cc=clang, that brew developers obviously don't like) then I have everything in 2 places $ where mpicxx /usr/local/bin/mpicxx /opt/homebrew/bin/brew/mpicxx

And this somehow creates problems even if I export all the locations._

Anyway, after this I managed to install ASPECT and run all the tests succesfully.

bobmyhill commented 1 year ago

Hallelujah :) Thanks for the info @KiralyAgi. Your hunch sounds plausible to me.

Removing brew sounds a bit excessive, presumably removing the offending package would be enough. Any ideas where /opt/homebrew/bin/brew/mpicxx came from? Did you maybe have mpich on your system and not unlink it before installing open-mpi? (Blind guess; I don't really want to test this). /opt/homebrew/bin/brew is a bash script on my machine, not a directory.

tjhei commented 1 year ago

So, I tried to install the released 9.4.0 package without the brew install

You must have gotten an MPI installation at /usr/local/bin/mpicxx from somewhere, though. I wonder how you installed it if not through homebrew?

bobmyhill commented 1 year ago

I also have/usr/local/bin/mpicxx, which (on my machine) is a symlink to /opt/homebrew/bin/opal_wrapper, which then calls /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/mpicxx.

tjhei commented 1 year ago

Fascinating, they are shipping MPI? I don't have access to my M1 for another week or two and I will look into all of these problems then.

bobmyhill commented 1 year ago

I don't think Macs are shipping with MPI - the creation date for the symlink is around when I first installed deal.II. But as for where it came from ... . It hasn't been touched since.

KiralyAgi commented 1 year ago

Hallelujah :) Thanks for the info @KiralyAgi. Your hunch sounds plausible to me.

Removing brew sounds a bit excessive, presumably removing the offending package would be enough. Any ideas where /opt/homebrew/bin/brew/mpicxx came from? Did you maybe have mpich on your system and not unlink it before installing open-mpi? (Blind guess; I don't really want to test this). /opt/homebrew/bin/brew is a bash script on my machine, not a directory.

After removing and reinstalling brew I didn't have mpi in homebrew just in my usr/local/bin. And having it only in one location was (I think) the key for me to get everything installed.

Francyrad commented 1 year ago

Hello, i still have the problem. I'm using a macbookPro with M1PRO. I did everything that you said. I followed the guide (that is the same as always) I used the version 6.4 r2. I installed Ventura 13.2, I removed and reinstalled the latest command line. Then:

./candi.sh -j 8 --packages="p4est trilinos dealii"

I didn't install hdf5 because i already it in other ways. With Big Sur that worked. and i installed candi and aspect successfully.

I still cannot install DEALII. With the 9.4.2 I cannot install Trillinos.

This is the error message, i have no idea how to solve the problem. t.t

error_dealii.txt

bobmyhill commented 1 year ago

@Francyrad you didn't follow the instructions in my message:

(1) As @emcgowen suggests,

DO NOT export the OMPI_ environment variables unless you intend to build with the GNU C compiler!

Instead: export CC=mpicc; export CXX=mpicxx, FC=mpifort, FF=mpifort export OMPI_CC=gcc, export OMPI_CXX=g++, export OMPI_FC=gfortran where gcc, g++ should also point to clang, as you can confirm via the following command: gcc -v; g++ -v

(2)

If you are happy using deal.ii 9.4.0, I recommend that you use candi v9.4.0-r2 unmodified

So, not 9.4.2. Let's try to fix one problem at a time.

(3)

I also recommend that you remove your brew-installed version of hdf5, as it doesn't have MPI support.

You can see this in the first error message you posted; the other dependencies don't actually use the brew version of hdf5. So, remove the brew version and try ./candi.sh -j 8 --packages="hdf5 p4est trilinos dealii"

(4)

If it still doesn't install correctly on your [machine] following these instructions ... let us know, along with the verbose information on your compilers and version of command line tools.

So that means report to us the command line output from the following commands: mpicxx -v, mpicc -v mpifort -v pkgutil --pkg-info=com.apple.pkg.CLTools_Executables

bobmyhill commented 1 year ago

Another thought. When you tried to install 9.4.2 you changed your candi branch (according to errorrr.txt). Instead of doing this, use v9.4.0-r2 but just change line 97 in candi.cfg from DEAL_II_VERSION=v9.4.0 to DEAL_II_VERSION=v9.4.2 and see whether that fixes your deal.II issue.

Francyrad commented 1 year ago

I finally installed it, so thank you for your help!. Now i'll try to install aspect, the point is that i have a lot of doubts:

The only thing that i did is to remove the hdf5 homebrew installation and i used the 9.4.0 -r2 with changing the config to 9.4.2.

Then i did ./candi.sh -j 8 --packages="p4est trilinos dealii" As i wrote i didn't reinstall HDF5 for a mistake, but i think it did something with hdf5. I release there the installation:

installation.txt

My point is. i can try to reinstall everything with HDF5. But is there another solution? i use the homebrew HDF5 for many programs and i need it. Aspect doesn't need hdf5 to run simulations. May i encounter problems if i reinstall hdf5 with homebrew? I didn’t really understand the involvement of hdf5 when installing dealii if I didn’t require the installation of the same hdf5. With the old operating system I was able to run the various aspect tests and to have hdf5 installed with homebrew. Thank you for your support

bobmyhill commented 1 year ago

Great, glad to hear that editing the line in candi.cfg fixed your problem.

i use the homebrew HDF5 for many programs and i need it

Ah, sorry. I assumed you had installed HDF5 because you wanted it for ASPECT.

Aspect doesn't need hdf5 to run simulations.

True. If you don't want ASPECT to output hdf5 files, there's no problem.

May i encounter problems if i reinstall hdf5 with homebrew?

No, that should be fine. The brew installation wasn't interfering with the compilation, but it also wasn't being used. (You could also use the version of hdf5 installed by candi, or install hdf5-mpi with homebrew, to use in your other projects and with deal.II / ASPECT).

Francyrad commented 1 year ago

oK. i have been able to install aspect and pass all the tests. I also installed hdf5 via homebrew and i could run my programs. So thank you!

For the future:

Downlaod dealii 9.4.0 -r2 change the config to 9.4.2 run: ./candi.sh -j 8 --packages="p4est trilinos dealii"

Francyrad commented 1 year ago

Dear developers

I'm not able to install candii in MacOS Sonoma 14.1.1

It was the same for MacOS Ventura, the latest version.

First of all, to compile "far" i'm using the following environmental variables:

export CC="/opt/homebrew/bin/mpicc"
export CXX="/opt/homebrew/bin/mpicxx"
export FC="/opt/homebrew/bin/mpifort"
export FF="/opt/homebrew/bin/mpifort"
export OMPI_CC="/opt/homebrew/bin/gcc-12"
export OMPI_CXX="/opt/homebrew/bin/g++-12"
export OMPI_FC="/opt/homebrew/bin/gfortran-12"

I also TRIED to use gcc11, 13 and clang: the installation won't even start. So i can't use this setup anymore because clang libraries have been updated (the old successfull configuration):

#  deal.II configuration:
#        CMAKE_BUILD_TYPE:       DebugRelease
#        BUILD_SHARED_LIBS:      ON
#        CMAKE_INSTALL_PREFIX:   /Users/francyrad/dealii-candi/deal.II-v9.4.2
#        CMAKE_SOURCE_DIR:       /Users/francyrad/dealii-candi/tmp/unpack/deal.II-v9.4.2
#                                (version 9.4.2, shortrev 53a7623c7c)
#        CMAKE_BINARY_DIR:       /Users/francyrad/dealii-candi/tmp/build/deal.II-v9.4.2
#        CMAKE_CXX_COMPILER:     Clang 11.1.0 on platform Darwin arm64
#                                /opt/homebrew/bin/mpicxx
#        C++ language standard:  C++14
#

The version is 9.4.0-r2

in the .cfg i settled native configuration = ON and my path for OpenBlas and Lapack. I also changed the version to 9.4.2 as suggested above. I also tried to install other versions of candii (9.5.1 etc.) Without any success.

I attach here the error. I need a reinstallation of ASPECT because i wanted to install some new additional libraries and I have also to write a cookbook

error_candi.txt

I also take the opportunity to ask what does this configuration will do to my ASPECT simulations if it's ON:

USE_64_BIT_INDICES=OFF

Thank you in advance for the help.

bobmyhill commented 1 year ago

You should be able to update to the newest version of candi.

That probably won't fix your problem, which seems to be that you are missing some linker flags to boost (the missing symbols error). I had a similar problem in #367, but with different missing symbols. I'm afraid I don't know which flags will fix your problem, you might have to hunt around for the right directories.

Alternatively you could not use optional packages causing problems.

dealii / candi

MacOS ARM build is broken #309

Option {ON|OFF}: Enable building of dealii examples?

Option {ON|OFF}: Unset CXX and set the compiler as MPI_CXX_COMPILER when configuring deal.II