Closed dshtey2 closed 3 years ago
clinfo/pymetis do not exist as conda packages for the new Apple architecture yet, I'll ping them.
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-arm64
All mirgecom examples should work then.
@dshtey2 Can you check if #122 fixes this for you?
@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 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 theinstall.sh
file with the changes from #122, and it is returning acommand 'gcc' failed
error.
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.sh
Note that you will need to install an MPI package (such as mpich or openmpi) before installing emirge, such as:
$ brew install mpich
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:
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?
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:
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 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_64
Here is a typical output whenever I attempt anything with simple brew <command>
:
Here is a typical output whenever I attempt anything with simple
brew <command>
:
brew install mpich
brew reinstall mpich
Error: 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)?
Here is a typical output whenever I attempt anything with simple
brew <command>
:brew install mpich
brew reinstall mpich
Error: 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)?
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.
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."