Open angiechamberland opened 4 years ago
dilawar
commented
4 years ago I could reproduce this error with python3.7 on Majavae. These formulae needs updating since numpy has dropped support for python2.
Meanwhile, you can try this:
$ python3 -m pip install pymoose --user --prethis will install the wheel of nightly release. Remove the --pre if you want version 3.1.4 .
angiechamberland
commented
4 years ago Thanks for the quick response! Tried it out and still gives me the same error I've been getting using pip:
"Angies-MacBook-Pro:~ angiechamberland$ python3 -m pip install pymoose --user --pre Collecting pymoose Using cached pymoose-3.2.0.dev20200128-py3-none-any.whl (5.5 MB) Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from pymoose) (1.15.4) Installing collected packages: pymoose Successfully installed pymoose-3.2.0.dev20200128 Angies-MacBook-Pro:~ angiechamberland$ python Python 3.7.1 (default, Dec 14 2018, 13:28:58) [Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information.
import moose Traceback (most recent call last): File "
", line 1, in File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/init.py", line 10, in from moose._moose import * ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find: /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03 /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03 "
dilawar
commented
4 years ago This looks like a packaging bug. Ideally, anaconda should not install the Linux wheel on OSX. I've to dig a little to resolve this. Meanwhile, you can try the following:
Set up a virtual environment using homebrew's python.
$ /usr/local/bin/python3.7 -m venv ~/PY37 # setup isolated venv at ~/PY37 $ source ~/PY37/bin/activate # activate venv $ pip install pymoose --pre # install moose in virtualenv $ python -c 'import moose' # test importing moose
Or, use docker. There is an image on dockerhub. $ docker run -it bhallalab/moose
best, Dilawar
On Wed, Jan 29, 2020 at 5:27 PM angiechamberland notifications@github.com wrote:
Thanks for the quick response! Tried it out and still gives me the same error I've been getting using pip:
"Angies-MacBook-Pro:~ angiechamberland$ python3 -m pip install pymoose --user --pre Collecting pymoose Using cached pymoose-3.2.0.dev20200128-py3-none-any.whl (5.5 MB) Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from pymoose) (1.15.4) Installing collected packages: pymoose Successfully installed pymoose-3.2.0.dev20200128 Angies-MacBook-Pro:~ angiechamberland$ python Python 3.7.1 (default, Dec 14 2018, 13:28:58) [Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information.
import moose Traceback (most recent call last): File "", line 1, in File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/ init.py", line 10, in from moose._moose import * ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find: /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03 /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03 "
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BhallaLab/homebrew-moose/issues/1?email_source=notifications&email_token=AAG2VQLUY5E76PUA3URHR2LRAFVKNA5CNFSM4KM5T7CKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKG56XY#issuecomment-579723103, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG2VQM7TL6EUENKU3KDOJ3RAFVKNANCNFSM4KM5T7CA .
-- Dilawar NCBS Bangalore
angiechamberland
commented
4 years ago Thanks.
the virtual environment script gives me this:
-bash: /usr/local/bin/python3.7: No such file or directory
and docker script gives me:
/usr/bin/xterm: Xt error: Can't open display: /usr/bin/xterm: DISPLAY is not set
dilawar
commented
4 years ago @angiechamberland Sorry, I should have tested these commands beforehand. It seems that either our wheels for OSX are broken or pip is pulling linux wheel on OSX.
Sorry again for the docker image. The right command is the following.
$ docker run -ti --rm -e DISPLAY=:0 -v /tmp/.X11-unix:/tmp/.X11-unix bhallalab/moose:latestI'll update this issue when I fix the wheel and brew install scripts.
dilawar
commented
4 years ago UPDATE Above docker command works on Linux host. I can't figure out how to run it in a OSX host. There are some pointers here if you want to try: https://sourabhbajaj.com/blog/2017/02/07/gui-applications-docker-mac/
dilawar
commented
4 years ago I have created a test homebrew tap that should work now.
In terminal, I did the following.
$ brew untap bhallalab/moose
$ brew tap dilawar/moose
$ brew install --HEAD moose-nightly
$ python3 -c 'import moose; print(moose.version())'
3.2.0-9e0b0d1adThe official release will be after https://github.com/BhallaLab/moose-core/pull/383 and https://github.com/BhallaLab/moose-core/pull/382 are merged.
angiechamberland
commented
4 years ago Everything seemed to work right up until trying to import moose. still getting this response:
Traceback (most recent call last):
File "
angiechamberland
commented
4 years ago Also, thanks for all your help and assistance on this.
dilawar
commented
4 years ago Uninstall all instances of moose installed previously either using PIP or manually.
$ pip uninstall pymoose $ rm -rf Users/angiechamberland/.local/lib/python3.7/site-packages/moose/
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On 1 Feb 2020, 04:37, at 04:37, angiechamberland notifications@github.com wrote:
Everything seemed to work right up until trying to import moose. still getting this response:
Traceback (most recent call last): File "
", line 1, in File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/init.py", line 5, in from moose.moose import File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/moose.py", line 21, in from moose._moose import ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find: /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/BhallaLab/homebrew-moose/issues/1#issuecomment-580950056
angiechamberland
commented
4 years ago Awesome, thanks. That made some progress.
Moose seems to install, but once in moose, the commands don't seem to work:
Angies-MacBook-Pro:~ angiechamberland$ python3 -c 'import moose; print(moose.version())' 3.2.0-9e0b0d1ad
Traceback (most recent call last):
File "
import moose moose.le Traceback (most recent call last): File "
", line 1, in AttributeError: module 'moose' has no attribute 'le' moose.le() Traceback (most recent call last): File " ", line 1, in AttributeError: module 'moose' has no attribute 'le' dir(moose) ['doc', 'file', 'loader', 'name', 'package', 'path', 'spec']
any ideas?
dilawar
commented
4 years ago Yes. It's my fault :-( !
I promise next update will resolve it. It is getting embarrassing now; can't blame unfamiliarity with OSX anymore :-/. I am almost there.
angiechamberland
commented
4 years ago No problem - I keep assuming I'm doing something wrong, I appreciate how quickly you've been responding. Is there a workaround for now or do you know how long it'll take to resolve? We're using this for a class I'm taking, so just want to make whatever alternate arrangements necessary if needed. Thanks again!
dilawar
commented
4 years ago It shouldn't take more than today. Probably couple of hours. If its gonna take more than 4 hours, I'll update you.
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On 1 Feb 2020, 06:10, at 06:10, angiechamberland notifications@github.com wrote:
No problem - I keep assuming I'm doing something wrong, I appreciate how quickly you've been responding. Is there a workaround for now or do you know how long it'll take to resolve? We're using this for a class I'm taking, so just want to make whatever alternate arrangements necessary if needed. Thanks again!
-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/BhallaLab/homebrew-moose/issues/1#issuecomment-580969065
angiechamberland
commented
4 years ago Oh that's amazing then. If we can get this going and solid by Sunday I'll be ecstatic and in great shape, so take the time you need today, I'm super appreciative with how responsive you've been!
dilawar
commented
4 years ago Brew package for moose-nightly seems to be working fine.
$ brew uninstall moose # remove 3.1.5rc1
$ brew install -v --HEAD moose-nightly # -v generates logs
🍺 /usr/local/Cellar/moose-nightly/HEAD-69a3aae: 119 files, 9.5MB, built in 3 minutes 41 seconds
$ python3 -c 'import moose; print(dir(moose)); moose.test()'
['AdExIF', 'AdThreshIF', 'Adaptor', 'Annotator', 'Arith', 'BufPool', 'CaConc', 'CaConcBase', 'Cell', 'ChanBase', 'ChemCompt', 'Cinfo', 'Clock', 'Compartment', 'CompartmentBase', 'ConcChan', 'CplxEnzBase', 'CubeMesh', 'CylMesh', 'DestField', 'DiagonalMsg', 'DifBuffer', 'DifBufferBase', 'DifShell', 'DifShellBase', 'DiffAmp', 'Dsolve', 'ElementField', 'EndoMesh', 'Enz', 'EnzBase', 'ExIF', 'Finfo', 'Function', 'GapJunction', 'GraupnerBrunel2012CaPlasticitySynHandler', 'Group', 'Gsolve', 'HHChannel', 'HHChannel2D', 'HHChannelBase', 'HHGate', 'HHGate2D', 'HSolve', 'INFINITE', 'IntFire', 'IntFireBase', 'Interpol', 'Interpol2D', 'IzhIF', 'IzhikevichNrn', 'Ksolve', 'LIF', 'LOGGING_FORMAT', 'Leakage', 'LookupField', 'MMPump', 'MMenz', 'MarkovChannel', 'MarkovGslSolver', 'MarkovRateTable', 'MarkovSolver', 'MarkovSolverBase', 'MeshEntry', 'MgBlock', 'Msg', 'Mstring', 'NMDAChan', 'Nernst', 'NeuroMesh', 'Neuron', 'Neutral', 'OneToAllMsg', 'OneToOneDataIndexMsg', 'OneToOneMsg', 'OrderedDict', 'PIDController', 'Pool', 'PoolBase', 'PostMaster', 'PsdMesh', 'PulseGen', 'PyRun', 'QIF', 'RC', 'RandSpike', 'Reac', 'ReacBase', 'SBML', 'STDPSynHandler', 'STDPSynapse', 'SeqSynHandler', 'Shell', 'SimpleSynHandler', 'SingleMsg', 'SocketStreamer', 'SparseMsg', 'Species', 'SpikeGen', 'SpikeStats', 'Spine', 'SpineMesh', 'Stats', 'SteadyState', 'StimulusTable', 'Stoich', 'Streamer', 'StringIO', 'SymCompartment', 'SynChan', 'SynHandlerBase', 'Synapse', 'Table', 'Table2', 'TableBase', 'TimeTable', 'VClamp', 'VERSION', 'Variable', 'VectorTable', 'ZombieBufPool', 'ZombieCaConc', 'ZombieCompartment', 'ZombieEnz', 'ZombieFunction', 'ZombieHHChannel', 'ZombieMMenz', 'ZombiePool', 'ZombieReac', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', '_moose', 'absolute_import', 'append_finfodocs', 'ce', 'chemError_', 'chemImport_', 'chemMerge', 'chemUtil', 'closing', 'connect', 'copy', 'delete', 'division', 'doc', 'element', 'exists', 'finfotypes', 'fixXreacs', 'genesis', 'getCwe', 'getField', 'getFieldDict', 'getFieldNames', 'getfielddoc', 'getmoosedoc', 'isRunning', 'kkitImport_', 'kkitImport_error_', 'known_types', 'le', 'listmsg', 'loadModel', 'loadModelInternal', 'melement', 'mergeChemModel', 'mergechemError_', 'mergechemImport_', 'moose', 'mooseAddChemSolver', 'mooseDeleteChemSolver', 'mooseReadNML2', 'mooseReadSBML', 'mooseWriteKkit', 'mooseWriteNML2', 'mooseWriteSBML', 'moose_constants', 'moose_test', 'move', 'mu', 'neuroml2', 'nml2ImportError_', 'nml2Import_', 'os', 'pager', 'plot_utils', 'print_function', 'print_utils', 'pwe', 'pydoc', 'quit', 'rand', 'reinit', 'sbmlError_', 'sbmlImport_', 'seed', 'sequence_types', 'serve', 'server', 'setClock', 'setCwe', 'showfield', 'showfields', 'showmsg', 'start', 'stop', 'syncDataHandler', 'test', 'testSched', 'toUnicode', 'useClock', 'utils', 'vec', 'version', 'warnings', 'wildcardFind']
[INFO] Running test with timeout 60 sec
Cloning into '/var/folders/1j/s2cj3qpx0jbdbfgzcth08d980000gn/T/moose-examples'...
remote: Enumerating objects: 774, done.
remote: Counting objects: 100% (774/774), done.
remote: Compressing objects: 100% (505/505), done.
remote: Total 774 (delta 324), reused 490 (delta 255), pack-reused 0
Receiving objects: 100% (774/774), 2.23 MiB | 962.00 KiB/s, done.
Resolving deltas: 100% (324/324), done.
[TEST 0/127] convert_Genesis2Sbml.py................. 0.62 0 PASSED
[TEST 1/127] showmsg.py.............................. 0.59 0 PASSED
[TEST 2/127] scriptGssaSolver.py..................... 1.54 0 PASSED
[TEST 3/127] synapse_tutorial.py..................... 0.71 0 PASSED
[TEST 4/127] funcReacLotkaVolterra.py................ 3.16 0 PASSED
[TEST 5/127] vectors.py.............................. 0.87 0 PASSED
[TEST 6/127] vclamp.py............................... 0.59 0 PASSED
[TEST 7/127] gapjunction.py.......................... 2.56 0 PASSED
[TEST 8/127] loadCspaceModel.py...................... 3.57 0 PASSED
[TEST 9/127] funcRateHarmonicOsc.py.................. 2.61 0 PASSED
[TEST 10/127] funcInputToPools.py..................... 1.57 0 PASSED
[TEST 11/127] randomspike.py.......................... 0.90 0 PASSED
[TEST 12/127] HsolveInstability.py.................... Some tests might fail depending on installed dependencies. The version 3.1.5rc1 is broken as you reported.
angiechamberland
commented
4 years ago 🍺 /usr/local/Cellar/moose-nightly/HEAD-69a3aae: 119 files, 9.5MB, built in 1 minute 59 seconds
Angies-MacBook-Pro:~ angiechamberland$ python3 -c 'import moose; print(dir(moose)); moose.test()'
['doc', 'file', 'loader', 'name', 'package', 'path', 'spec']
Traceback (most recent call last):
File "
dilawar
commented
4 years ago Following is a bit lengthy process but It surely will install.
# remove all moose
$ brew uninstall moose moose-nightly
$ brew install git cmake # if you don't have them
$ git clone https://github.com/dilawar/moose-core --depth 10 # get the source code
$ cd moose-core
$ mkdir build
$ cd build
$ cmake .. # configure build system
$ make -j4
$ ctest --output-on-failure
$ sudo make install If ctest passes (couple of tests might fail) and because of any reason, make install does not install moose properly. then do the following:
$ export PYTHONPATH=/path/to/moose-core/build/python
$ python3 -c 'import moose; moose.test()'If something goes wrong, please upload terminal output and CMakeCache.txt from /path/to/moose-core/build directory. I sincerely hope this will work.
dilawar
commented
4 years ago It will get fixed in #2 . Brew made changes because of which though python module was getting built, it was not getting installed to the place where python usually searches.
Following should work.
$ brew update
$ brew install --HEAD moose-nightly
$ python3 -c 'import moose; moose.test()'And I am really sorry for this. It should have not been this hard. I've added tests to our pipeline which will catch this issue.
angiechamberland
commented
4 years ago [100%] Built target normal_dist Install the project... -- Install configuration: "Release" -- Up-to-date: /usr/local CMake Error at cmake_install.cmake:83 (file): file INSTALL cannot set permissions on "/usr/local"
make: *** [install] Error 1
Angies-MacBook-Pro:build angiechamberland$ export PYTHONPATH=/path/to/moose-core/build/python
Angies-MacBook-Pro:build angiechamberland$ python3 -c 'import moose; moose.test()'
Traceback (most recent call last):
File "brew reinstall moose-nightly
Angies-MacBook-Pro:build angiechamberland$ python3 -c 'import moose; moose.test()'
Traceback (most recent call last):
File "
cmakecache.txt:
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//Path to a program. P4COMMAND:FILEPATH=P4COMMAND-NOTFOUND
//High level parallelization of moose::Clock (alpha) PARALLELIZED_CLOCK:BOOL=OFF
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//Use AddressSanitizer in DEBUG mode. WITH_ASAN:BOOL=OFF
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//Use gsl-library. Alternative is WITH_BOOST WITH_GSL:BOOL=ON
//Enable Openmpi support WITH_MPI:BOOL=OFF
//Enable NSDF support. Requires hdf5 WITH_NSDF:BOOL=OFF
//Dependencies for the target _moose_LIB_DEPENDS:STATIC=general;-Wl,-all_load;general;muparser;general;moose_builtins;general;msg;general;benchmarks;general;shell;general;randnum;general;scheduling;general;moose_mpi;general;biophysics;general;utility;general;kinetics;general;synapse;general;intfire;general;hsolve;general;mesh;general;signeur;general;diffusion;general;ksolve;general;device;general;basecode;general;/usr/local/lib/libgsl.dylib;general;/usr/local/lib/libgslcblas.dylib;
//Dependencies for the target libmoose_LIB_DEPENDS:STATIC=general;-Wl,-all_load;general;muparser;general;moose_builtins;general;msg;general;benchmarks;general;shell;general;randnum;general;scheduling;general;moose_mpi;general;biophysics;general;utility;general;kinetics;general;synapse;general;intfire;general;hsolve;general;mesh;general;signeur;general;diffusion;general;ksolve;general;device;general;basecode;general;/usr/local/lib/libgsl.dylib;general;/usr/local/lib/libgslcblas.dylib;
########################
########################
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dilawar
commented
4 years ago Export your PYTHONPATH to /Users/angiechamberland/moose-core/build . I wrote /path/to/moose-core/build as a placeholder.
$ export PYTHONPATH=/Users/angiechamberland/moose-core/build
You can removed brewed moose.
Best, Dilawar
Get BlueMail for Android
On 1 Feb 2020, 10:00, at 10:00, angiechamberland notifications@github.com wrote:
[100%] Built target normal_dist Install the project... -- Install configuration: "Release" -- Up-to-date: /usr/local CMake Error at cmake_install.cmake:83 (file): file INSTALL cannot set permissions on "/usr/local"
make: *** [install] Error 1 Angies-MacBook-Pro:build angiechamberland$ export PYTHONPATH=/path/to/moose-core/build/python Angies-MacBook-Pro:build angiechamberland$ python3 -c 'import moose; moose.test()' Traceback (most recent call last): File "
", line 1, in ModuleNotFoundError: No module named 'moose' Angies-MacBook-Pro:build angiechamberland$ brew install --HEAD moose-nightly Warning: dilawar/moose/moose-nightly HEAD-69a3aae is already installed and up-to-date To reinstall HEAD, run brew reinstall moose-nightlyAngies-MacBook-Pro:build angiechamberland$ python3 -c 'import moose; moose.test()' Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'moose' Angies-MacBook-Pro:build angiechamberland$ cmakecache.txt:
This is the CMakeCache file.
For build in directory: /Users/angiechamberland/moose-core/build
It was generated by CMake:
/Users/angiechamberland/anaconda3/lib/python3.7/site-packages/cmake/data/CMake.app/Contents/bin/cmake
You can edit this file to change values found and used by cmake.
If you do not want to change any of the values, simply exit the
editor.
If you do want to change a value, simply edit, save, and exit the
editor.
The syntax for the file is as follows:
KEY:TYPE=VALUE
KEY is the name of a variable in the cache.
TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
VALUE is the current value for the KEY.
########################
EXTERNAL cache entries
########################
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//Path to the coverage program that CTest uses for performing coverage // inspection COVERAGE_COMMAND:FILEPATH=/usr/bin/gcov
//Extra command line flags to pass to the coverage tool COVERAGE_EXTRA_FLAGS:STRING=-l
//Enable to build RPM source packages CPACK_SOURCE_RPM:BOOL=OFF
//Enable to build TBZ2 source packages CPACK_SOURCE_TBZ2:BOOL=ON
//Enable to build TGZ source packages CPACK_SOURCE_TGZ:BOOL=ON
//Enable to build TXZ source packages CPACK_SOURCE_TXZ:BOOL=ON
//Enable to build TZ source packages CPACK_SOURCE_TZ:BOOL=ON
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//Build with debug support DEBUG:BOOL=OFF
//Enable unit tests (DEBUG should also be ON) ENABLE_UNIT_TESTS:BOOL=OFF
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//Path to a program. GIT_EXEC:FILEPATH=/usr/local/bin/git
//Build for profiling using gprof GPROF:BOOL=OFF
//Path to a library. GSLCBLAS_LIB:FILEPATH=/usr/local/lib/libgslcblas.dylib
//Path to a file. GSL_INCLUDE_DIRS:PATH=/usr/local/include
//Path to a library. GSL_LIB:FILEPATH=/usr/local/lib/libgsl.dylib
//Path to a program. HGCOMMAND:FILEPATH=HGCOMMAND-NOTFOUND
//Command to build the project MAKECOMMAND:STRING=/Users/angiechamberland/anaconda3/lib/python3.7/site-packages/cmake/data/CMake.app/Contents/bin/cmake --build . --config "${CTEST_CONFIGURATION_TYPE}" -- -i
//Path to the memory checking command, used for memory error detection. MEMORYCHECK_COMMAND:FILEPATH=MEMORYCHECK_COMMAND-NOTFOUND
//File that contains suppressions for the memory checker MEMORYCHECK_SUPPRESSIONS_FILE:FILEPATH=
//Value Computed by CMake MOOSE_BINARY_DIR:STATIC=/Users/angiechamberland/moose-core/build
//Value Computed by CMake MOOSE_SOURCE_DIR:STATIC=/Users/angiechamberland/moose-core
//Path to a program. P4COMMAND:FILEPATH=P4COMMAND-NOTFOUND
//High level parallelization of moose::Clock (alpha) PARALLELIZED_CLOCK:BOOL=OFF
//Path to a program. PYTHON_EXECUTABLE:FILEPATH=/Users/angiechamberland/anaconda3/bin/python3
//Name of the computer/site where compile is being run SITE:STRING=Angies-MacBook-Pro.local
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//Path to the SLURM srun executable SLURM_SRUN_COMMAND:FILEPATH=SLURM_SRUN_COMMAND-NOTFOUND
//Path to a program. SVNCOMMAND:FILEPATH=/usr/bin/svn
//Stochastic Objects use their private RNG USE_PRIVATE_RNG:BOOL=ON
//Use AddressSanitizer in DEBUG mode. WITH_ASAN:BOOL=OFF
//Enable boost. Prefer boost over stl WITH_BOOST:BOOL=OFF
//Use boost library ode2 library instead of GSL WITH_BOOST_ODE:BOOL=OFF
//Use gsl-library. Alternative is WITH_BOOST WITH_GSL:BOOL=ON
//Enable Openmpi support WITH_MPI:BOOL=OFF
//Enable NSDF support. Requires hdf5 WITH_NSDF:BOOL=OFF
//Dependencies for the target _moose_LIB_DEPENDS:STATIC=general;-Wl,-all_load;general;muparser;general;moose_builtins;general;msg;general;benchmarks;general;shell;general;randnum;general;scheduling;general;moose_mpi;general;biophysics;general;utility;general;kinetics;general;synapse;general;intfire;general;hsolve;general;mesh;general;signeur;general;diffusion;general;ksolve;general;device;general;basecode;general;/usr/local/lib/libgsl.dylib;general;/usr/local/lib/libgslcblas.dylib;
//Dependencies for the target libmoose_LIB_DEPENDS:STATIC=general;-Wl,-all_load;general;muparser;general;moose_builtins;general;msg;general;benchmarks;general;shell;general;randnum;general;scheduling;general;moose_mpi;general;biophysics;general;utility;general;kinetics;general;synapse;general;intfire;general;hsolve;general;mesh;general;signeur;general;diffusion;general;ksolve;general;device;general;basecode;general;/usr/local/lib/libgsl.dylib;general;/usr/local/lib/libgslcblas.dylib;
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-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/BhallaLab/homebrew-moose/issues/1#issuecomment-580990745
angiechamberland
commented
4 years ago Sorry for the delay. Tried it again with the correction:
[100%] Built target normal_dist Install the project... -- Install configuration: "Release" -- Up-to-date: /usr/local CMake Error at cmake_install.cmake:83 (file): file INSTALL cannot set permissions on "/usr/local"
make: *** [install] Error 1
Angies-MacBook-Pro:build angiechamberland$ export PYTHONPATH=/Users/angiechamberland/moose-core/build
Angies-MacBook-Pro:build angiechamberland$ python3 -c 'import moose; moose.test()'
Traceback (most recent call last):
File "
dilawar
commented
4 years ago I am clueless now. These instructions worked on two remote OSX machines. You can have a look at the logs below (they are not pretty to look). I can help if remote access to your machine is possible (or online chat over whatsapp or hangont.).
Another solution would be to install Ubuntu-18.04 in a virtualbox and install moose from here https://software.opensuse.org//download.html?project=home%3Amoose&package=moose or using pip.
~Another~ A drastic measure would be to remove both anaconda and homebrew. Reinstall homebrew and use brew to install moose. I am really sorry that this has been so hard to get started with moose :-( .
angiechamberland
commented
4 years ago Thanks! I was able to do it in Ubuntu via VMWare. Bummer I couldn't get it to work in OS X since VMWare slows everything down, but this will work. Thanks again for all your help and being so responsive!
I keep getting the following error when trying to install via "brew install moose":
CMake Error at cmake_modules/FindNumPy.cmake:64 (message): NumPy import failure:
Traceback (most recent call last):
ImportError: No module named numpy
Call Stack (most recent call first): pymoose/CMakeLists.txt:31 (find_package)
-- Configuring incomplete, errors occurred!
But have confirmed I already have numpy installed.