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Installing error messages in MacOS with conda/pip #593
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I tried to update pip, but it seemed to already be up to date: $ python3 -m pip install -U pip
Requirement already up-to-date: pip in /anaconda3/lib/python3.7/site-packages (19.3.1) |
Dear Dr. Amorim, please excuse the inconveniences that this installation might have caused, let me explain what happened. I forgot that conda-forge does not yet ship MPI-enabled binaries for Just as a note: In the meantime, and as you already did, going to install The Thanks for updating Finally, the export DYLD_LIBRARY_PATH=/anaconda3/lib/python3.7/site-packages/:${DYLD_LIBRARY_PATH} |
Dear Dr Hübl, Thank you very much for your super quick reply! I understood the Following your detailed instructions, I tried to re-do the installation of OpenPMD-api first running The long error message I get from [ 62%] Linking CXX shared library ../lib.macosx-10.7-x86_64-3.7/libopenPMD.dylib
ld: file not found: @rpath/libblosc.1.dylib for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [../lib.macosx-10.7-x86_64-3.7/libopenPMD.dylib] Error 1
make[1]: *** [CMakeFiles/openPMD.dir/all] Error 2
make: *** [all] Error 2
Traceback (most recent call last):
File "/anaconda3/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line 257, in <module>
main()
File "/anaconda3/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/anaconda3/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line 182, in build_wheel
metadata_directory)
File "/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-build-env-34btri2a/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 209, in build_wheel
wheel_directory, config_settings)
File "/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-build-env-34btri2a/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 194, in _build_with_temp_dir
self.run_setup()
File "/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-build-env-34btri2a/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 237, in run_setup
self).run_setup(setup_script=setup_script)
File "/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-build-env-34btri2a/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 142, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 177, in <module>
('License :: OSI Approved :: '
File "/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-build-env-34btri2a/overlay/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
return distutils.core.setup(**attrs)
File "//anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "//anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "//anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-build-env-34btri2a/overlay/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 192, in run
self.run_command('build')
File "//anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "//anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "//anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "//anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "//anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "setup.py", line 36, in run
self.build_extension(ext)
File "setup.py", line 97, in build_extension
cwd=self.build_temp
File "//anaconda3/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
Building wheel for openpmd-api (PEP 517) ... error
ERROR: Failed building wheel for openpmd-api
Running setup.py clean for openpmd-api
Running command //anaconda3/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-install-og_bxsvz/openpmd-api/setup.py'"'"'; __file__='"'"'/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-install-og_bxsvz/openpmd-api/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
running clean
removing 'build/temp.macosx-10.7-x86_64-3.7' (and everything under it)
removing 'build/lib.macosx-10.7-x86_64-3.7' (and everything under it)
'build/bdist.macosx-10.7-x86_64' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
removing 'build'
Failed to build openpmd-api
Cleaning up...
Removing source in /private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-install-og_bxsvz/openpmd-api
Removed build tracker '/private/var/folders/5_/fw95mbwj7bl5mym1th0zmfw40000gr/T/pip-req-tracker-yrxbwcnh'
ERROR: Could not build wheels for openpmd-api which use PEP 517 and cannot be installed directly
Exception information:
Traceback (most recent call last):
File "/anaconda3/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 153, in _main
status = self.run(options, args)
File "/anaconda3/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 426, in run
", ".join(r.name for r in build_failures)))
pip._internal.exceptions.InstallationError: Could not build wheels for openpmd-api which use PEP 517 and cannot be installed directly The very end of it, The initial error message Thanks, |
The problem does not appear on the latest development openPMD_USE_MPI=ON python3 -m pip install -v git+git://github.com/openPMD/openPMD-api.git We still have to set export DYLD_FALLBACK_LIBRARY_PATH=/anaconda3/lib/python3.7/site-packages:$DYLD_FALLBACK_LIBRARY_PATH (or to the respective path on your machine) on OSX since relative RPATHS via
|
The |
Furthermore, we now have MPI-enabled OSX packages for conda-forge! :) Only limitation: have to figure out a problem with the combination OSX+MPICH+ADIOS1, which is why I had to disable the ADIOS1 backend on OSX for now if we build with MPICH (but OpenMPI works already; also parallel HDF5 works with both MPICH as well as OpenMPI). |
I think we pushed through and have all issues addressed! :) |
I am trying to follow up on the answer to issue #591 and install OpenPMD-api with MPI support through
conda install -c conda-forge openpmd-api=*=mpi_mpich*
.But found an error that I don't know how to fix. I then tried the pip installation commands, but still encountered errors.
I will try spack next, but decided to leave this issue here in case I am doing something wrong that you can spot and correct me on.
(Sorry if this is related to issues already here or on
conda
's GitHub repo, but I couldn't find something that seemed similar to me.)Initially I tried the command and when I found the error reported below, I decided to try its dependencies so I did:
From the latter command, I got the following (and the same as the one I saw initially) error messages:
So then I tried to use
openPMD_USE_MPI=ON python3 -m pip install openpmd-api --no-binary :all:
instead. This led to the error messages below:I thought that that error was due to missing
skbuild
so I didconda install -c conda-forge scikit-build
, but after came an error that seemed related to make (which I had installed from cmake). I uninstalledcmake
and ranconda install -c anaconda cmake
.When I tried again to install OpenPMD, I got the error messages below:
Just for curiosity I tried to run the command without
--no-binary :all:
, i.e. as:And the installation finished with the
Successfully built openpmd-api
message. But I was not able to load the library:The location of that library is
/anaconda3/lib/python3.7/site-packages/libopenPMD.dylib
, which is in thePYTHONPATH
that points to/anaconda3/lib/python3.7/site-packages
as I think can be seen in:$ env | grep PATH PATH=//anaconda3/bin://anaconda3/condabin:/Users/diana/Documents/opt/spack/bin:/Users/diana/Documents/opt/spack/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin MODULEPATH=/Users/diana/Documents/opt/spack/share/spack/modules/darwin-highsierra-x86_64 PYTHONPATH=/Users/diana/Documents/opt/WarpX/Tools:/anaconda3/lib/python3.7/site-packages:
Do you know what I am doing wrong?
Or do you have any suggestions on how to fix this installation?
Do you think I need to update my software and re-try this?
Or that I should use
gcc
instead ofclang
?Thanks and sorry for the trouble!
Environment used:
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