matthiasdiener
commented
3 years ago clinfo/pymetis do not exist as conda packages for the new Apple architecture yet, I'll ping them.
Closed dshtey2 closed 3 years ago
matthiasdiener
commented
3 years ago clinfo/pymetis do not exist as conda packages for the new Apple architecture yet, I'll ping them.
matthiasdiener
commented
3 years ago As a workaround, you can comment out the clinfo and pymetis lines in mirgecom/conda-env.yml, and then run
$ pip install pymetis
$ conda install clang_osx-arm64All mirgecom examples should work then.
matthiasdiener
commented
3 years ago @dshtey2 Can you check if #122 fixes this for you?
dshtey2
commented
3 years ago @matthiasdiener I attempted to install pymetis with pip, but pip is not installed on my machine and whichever way I tried to install it (brew, apt-get, easy_install) threw an error at me. I then ran only the conda install clang_osx-arm64 line, and after a long time trying to resolve the environment it threw a wall of output with all the package conflicts. At this point I have uninstalled everything and am restarting the install process from scratch to confirm that this is indeed an issue and not simply the wrong order of operations on my end. I have also replaced the install.sh file with the changes from #122, and it is returning a command 'gcc' failed error.
matthiasdiener
commented
3 years ago @matthiasdiener I attempted to install pymetis with pip, but pip is not installed on my machine and whichever way I tried to install it (brew, apt-get, easy_install) threw an error at me. I then ran only the
conda install clang_osx-arm64line, and after a long time trying to resolve the environment it threw a wall of output with all the package conflicts. At this point I have uninstalled everything and am restarting the install process from scratch to confirm that this is indeed an issue and not simply the wrong order of operations on my end. I have also replaced theinstall.shfile with the changes from #122, and it is returning acommand 'gcc' failederror.
Ok, could you please run a fresh install with the branch from #122? I've pushed a small change this morning and it works out of the box on my M1 laptop:
$ git clone --branch m1 https://github.com/illinois-ceesd/emirge
$ cd emirge
$ ./install.shNote that you will need to install an MPI package (such as mpich or openmpi) before installing emirge, such as:
$ brew install mpichIt seems that I am having trouble with the MPI packages. I installed mpi4py, mpich, and open-mpi, but even with all of them installed I get the following error:
undef: _MPI_Init
undef: _MPI_Finalize
Undefined symbols for architecture arm64:
"_MPI_Init", referenced from:
_main in lto.o
"_MPI_Finalize", referenced from:
_main in lto.o
ld: symbol(s) not found for architecture arm64
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!It seems that I am having trouble with the MPI packages. I installed mpi4py, mpich, and open-mpi, but even with all of them installed I get the following error:
Please don't install both mpich and openmpi at the same time, they might interfere with each other. How did you install these packages? Also, you should not need to install mpi4py manually at all, it should be built when installing emirge. Can you post the full output here?
dshtey2
commented
3 years ago There is apparently an issue where ARM makes using the standard brew install impossible, so I first installed Rosetta2 emulator and reinstalled homebrew on the M1 chip (the new command is arch -x86_64 brew <command>). Afterward, I brew installed mpich, open-mpi, and mpi4py individually, unlinking mpich when the latter two were installed, and in between each installation I tried to run the ./install.sh emirge script. Regardless of which mpi package I used, I kept getting the following 3 error outputs:
matthiasdiener
commented
3 years ago There is apparently an issue where ARM makes using the standard
brew installimpossible, so I first installed Rosetta2 emulator and reinstalled homebrew on the M1 chip (the new command isarch -x86_64 brew <command>).
This is weird. I did not have to do this on my M1, and is likely the source of the main error:
ld: warning: ignoring file /usr/local/Cellar/open-mpi/4.1.0/lib/libmpi.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64Here is a typical output whenever I attempt anything with simple brew <command>:
matthiasdiener
commented
3 years ago Here is a typical output whenever I attempt anything with simple
brew <command>:
brew install mpichbrew reinstall mpichError: Cannot install in Homebrew on ARM processor in Intel default prefix (/usr/local)! Please create a new installation in /opt/homebrew using one of the "Alternative Installs" from: https://docs.brew.sh/Installation You can migrate your previously installed formula list with: brew bundle dump
Yeah, you can not have homebrew installed in /usr/local on the M1. I installed mine in my home folder. Can you try removing your homebrew installation and start from scratch in a different folder (e.g. /opt/homebrew or ~/homebrew)?
dshtey2
commented
3 years ago Here is a typical output whenever I attempt anything with simple
brew <command>:brew install mpichbrew reinstall mpichError: Cannot install in Homebrew on ARM processor in Intel default prefix (/usr/local)! Please create a new installation in /opt/homebrew using one of the "Alternative Installs" from: https://docs.brew.sh/Installation You can migrate your previously installed formula list with: brew bundle dumpYeah, you can not have homebrew installed in /usr/local on the M1. I installed mine in my home folder. Can you try removing your homebrew installation and start from scratch in a different folder (e.g. /opt/homebrew or ~/homebrew)?
This fixed the issue, and everything is running as expected now. Thanks! I suppose the /usr/local installation was an artifact of migrating over from a pre-M1 Macbook device.
matthiasdiener
commented
3 years ago Yeah, you can not have homebrew installed in /usr/local on the M1. I installed mine in my home folder. Can you try removing your homebrew installation and start from scratch in a different folder (e.g. /opt/homebrew or ~/homebrew)?
This fixed the issue, and everything is running as expected now. Thanks! I suppose the /usr/local installation was an artifact of migrating over from a pre-M1 Macbook device.
Great, thanks for testing this!
I am trying to install emirge on the new M1 MacBook Pro, OS Big Sur 11.2.3. When attempting to run the installation, I get the following terminal output (posting full install output to cover all bases):
To try to install these packages I had to install my own local copy of anaconda, but even then the packages were "not available from current channels."