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mapequation / infomap

Multi-level network clustering based on the Map Equation
https://mapequation.org/infomap
GNU General Public License v3.0
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Macos M1 OpenMP installation problem #322

Closed MatildeVaghi closed 1 year ago

MatildeVaghi commented 1 year ago

My aim is to run the following command from Matlab. [failed, message] = system([infomapfolder '/Infomap-2.6.0/Infomap --clu -2 -s' num2str(randnum) ' -N' num2str(reps) ' ' pajekfilename ' ' pathstr]);

I am working on MacOS (M1 processor...) and I have been able to successfully install infomap with pip install infomap as signalled by the messages on the terminalInstallling collected packages: infomap and Successfully installed infomap-2.6.0

However, I am unable to import the package and I get this message: 

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import infomap

File ~/opt/anaconda3/lib/python3.9/site-packages/infomap.py:38, in <module>
     36     from . import _infomap
     37 else:
---> 38     import _infomap
     40 try:
     41     import builtins as __builtin__

ImportError: dlopen(/Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
  Referenced from: /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so
  Reason: tried: '/usr/local/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

If the infomap was correctly installed, I could use pyrunfile from Matlab in order to run infomap.

I am able to import infomap when working on an old Mac. Hence, I strongly suspect the problem is related to M1 and I would welcome any advice on possible ways forward.

I tried as an alternative to compile from source with the following (always considering that I am on macOS Monterey, version 12.2.1)

git clone git@github.com:mapequation/infomap.git
cd infomap
make

However, I get an error here as well as 

c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/MetaMapEquation.cpp -o build/Infomap/core/MetaMapEquation.o
c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/MemMapEquation.cpp -o build/Infomap/core/MemMapEquation.o
c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/InfoEdge.cpp -o build/Infomap/core/InfoEdge.o
c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/BiasedMapEquation.cpp -o build/Infomap/core/BiasedMapEquation.o
c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/StateNetwork.cpp -o build/Infomap/core/StateNetwork.o
c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/iterators/InfomapIterator.cpp -o build/Infomap/core/iterators/InfomapIterator.o
c++ -Wall -Wextra -pedantic -Wnon-virtual-dtor -std=c++14 -Wshadow -O3 -Xpreprocessor -fopenmp -c src/core/InfomapBase.cpp -o build/Infomap/core/InfomapBase.o
src/core/InfomapBase.cpp:35:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^~~~~~~
1 error generated.
make: *** [build/Infomap/core/InfomapBase.o] Error 1

Thank you, Matilde

danieledler commented 1 year ago

Hi! We just had the same problem when building with macOS on Github Actions, which we fixed today in #323.

So first run pip install -U infomap to get the latest 2.6.1 version, then try brew install libomp if you haven't. Should be enough on M1.

If the problem persist, you can maybe do the same as in the fix above (brew install llvm and using that instead of Apples clang).

Please tell us how it goes!

MatildeVaghi commented 1 year ago

Thanks! Not sure how I should move forward. I did run brew install libomp fine. I get this message in the terminal:

==> Downloading https://ghcr.io/v2/homebrew/core/libomp/manifests/15.0.4
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libomp/blobs/sha256:694b2c1c0bda000cb49776222558c021cc71a57ac1a1152421131c2f9dfbf581
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:694b2c1c0bda000cb49776222558c021cc71a57ac1a1152421131c2f9dfbf581?se=2022-11-05T21%3A20%3A00Z&s
######################################################################## 100.0%
==> Pouring libomp--15.0.4.arm64_monterey.bottle.tar.gz
==> Caveats
libomp is keg-only, which means it was not symlinked into /opt/homebrew,
because it can override GCC headers and result in broken builds.

For compilers to find libomp you may need to set:
  export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
  export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"

After running brew install libomp, I am getting the same error I was having before where import infomap gives 

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import infomap

File ~/opt/anaconda3/lib/python3.9/site-packages/infomap.py:38, in <module>
     36     from . import _infomap
     37 else:
---> 38     import _infomap
     40 try:
     41     import builtins as __builtin__

ImportError: dlopen(/Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/opt/llvm/lib/libomp.dylib
  Referenced from: /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so
  Reason: tried: '/Applications/freesurfer/7.2.0/lib/gcc/lib/libomp.dylib' (no such file), '/usr/local/opt/llvm/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

libomp is installed in /opt/homebrew/opt/libomp/lib which is perhaps why it is not found by default. I created a sudo as follows by being in /usr/local/lib sudo ln -s /opt/homebrew/opt/libomp/lib/libomp.dylib libomp.dylib

The lib is now found but I get the following message:

'/usr/local/lib/libomp.dylib' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64'))

Do I need to set export LDFLAGS="-L/opt/homebrew/opt/libomp/lib" export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"

and if so, what would be the best way forward in order to set these exports?

I am not sure what you mean by : "brew install llvm and using that instead of Apples clang".

Thanks for consideration!

danieledler commented 1 year ago

As it needs the x86_64 architecture, have you somehow checked open with Rosetta on the terminal?

In any case, I would try solving the problem why homebrew doesn't link libomp to your prefix path in the first place. You can try brew link --dry-run libomp to just see first what files it would create symlinks for and check if there is any potential conflict. If not, you can try brew link libomp or brew link --force libomp if you have to. As it mentions the risk of conflict with GCC, have you installed that with homebrew too? What does g++ point to now? (Output from which g++ and g++ --version?).

MatildeVaghi commented 1 year ago

Thanks Daniel for your consideration, It would be wonderful to sort this out and have this working. It is all a bit confusing to me. Thinking about trying to solve the problem why homebrew does not link libomp to my prefix pat and answering your questions:

brew link --dry-run libomp gives the following: 

Would link:
/opt/homebrew/include/omp-tools.h
/opt/homebrew/include/omp.h
/opt/homebrew/include/ompt.h
/opt/homebrew/lib/libomp.a
/opt/homebrew/lib/libomp.dylib

which g++ gives the following: /usr/bin/g++

g++ --versiongives the following: 

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/4.2.1
Apple clang version 13.0.0 (clang-1300.0.27.3)
Target: arm64-apple-darwin21.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Shall I try: brew link libomp or brew link --force libomp? Thanks! Matilde

antoneri commented 1 year ago

Hi! Daniel is busy preparing his thesis, so I'll do my best to answer your questions from here on :)

Yes, try brew link libomp. Did you upgrade to Infomap 2.6.1 already? If not, try pip install -U infomap

To verify that the installation works, you should be able to run infomap in the terminal.

MatildeVaghi commented 1 year ago

Thanks a lot ! So appreciated. Yes, I upgraded to infomap 2.6.1 as suggested by Daniel. However, the installation does not work as when trying to run infomap from the terminal I have the following message.

traceback (most recent call last):
  File "/Users/matilde/opt/anaconda3/bin/infomap", line 5, in <module>
    from infomap import main
  File "/Users/matilde/opt/anaconda3/lib/python3.9/site-packages/infomap.py", line 38, in <module>
    import _infomap
ImportError: dlopen(/Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/opt/llvm/lib/libomp.dylib
  Referenced from: /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so
  Reason: tried: '/Applications/freesurfer/7.2.0/lib/gcc/lib/libomp.dylib' (no such file), '/usr/local/opt/llvm/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/usr/lib/libomp.dylib' (no such file)

I now tried brew link libomp --force and I got the following Linking /opt/homebrew/Cellar/libomp/15.0.4... 5 symlinks created.

However, infomap in the terminal is giving the same issue as above

antoneri commented 1 year ago

Good! Please also try pip install --upgrade --force-reinstall --no-cache -vvv infomap and paste all output (it's going to be huge!)

MatildeVaghi commented 1 year ago 
pip install --upgrade --force-reinstall --no-cache -vvv infomap
Using pip 21.2.4 from /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/pip (python 3.9)
Non-user install because site-packages writeable
Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-ephem-wheel-cache-xm5mnrl5
Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-req-tracker-_mieb17w
Initialized build tracking at /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-req-tracker-_mieb17w
Created build tracker: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-req-tracker-_mieb17w
Entered build tracker: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-req-tracker-_mieb17w
Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-install-je1jsnyn
1 location(s) to search for versions of infomap:
* https://pypi.org/simple/infomap/
Fetching project page and analyzing links: https://pypi.org/simple/infomap/
Getting page https://pypi.org/simple/infomap/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/infomap/ HTTP/1.1" 200 22168
  Found link https://files.pythonhosted.org/packages/71/aa/93a76d5fdefc23db7c5633553b00745114f9ecac273e15f1777424a974c3/infomap-1.0.0b1.tar.gz#sha256=695dd77cac6aa0c23b5a5db471e20076cfeecb7354c31fe44be3aebc40cd3760 (from https://pypi.org/simple/infomap/), version: 1.0.0b1
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  Skipping link: none of the wheel's tags (cp37-cp37m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/63/82/7a23e2174ddd628ef71f3d6fef1392f1819967742c78d422468097426849/infomap-2.4.1-cp37-cp37m-win_amd64.whl#sha256=1eb31dc988e3dbf4ddeb3d236f14b05ac78a8307f950456c8c35e303e8ff7ead (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp38-cp38-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f9/0a/412ceb9565e250a31aace99148cfbd7c927686d656bed5649f3126255ea3/infomap-2.4.1-cp38-cp38-macosx_10_15_x86_64.whl#sha256=7648d8970959a4626a36891f1076f1e3a67b892645e33c295643eaa91f933186 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp38-cp38-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ae/5e/9fbfc04ed09349d8289ab5c3a70afd41dd99823ea860a08d29ba0cebe32c/infomap-2.4.1-cp38-cp38-win_amd64.whl#sha256=170437b63559133a928fa121d6d7095433adde2adbab47122d5185350862ca56 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/9b/b2/6f4d8996ead18c071b4914eed80887b3bc06e978b34f88bc971123827514/infomap-2.4.1-cp39-cp39-macosx_10_15_x86_64.whl#sha256=84bd0310567fb1539a7ba2faf45d5d8d22c1c313b49da7c7840aabfaee73ed3a (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.4.1
  Skipping link: none of the wheel's tags (cp39-cp39-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f1/1c/6b58aa732e7b336e462e2e26e3e83f5e92f5bc8cbe11cbbb46b1a3236872/infomap-2.4.1-cp39-cp39-win_amd64.whl#sha256=9610f968cecfb8af8a07cef47cc8b695447114ad65537ba060b0eccf576c6335 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/0e/81/2d49848e371114868d642b5854bd67dd0d470c2987bdeb0a7d7e84770fee/infomap-2.4.1.tar.gz#sha256=e0b76d24635540526a74a51c39c8e06f5ebd32ea0e15ceb3266fc2c14dc583e5 (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.4.1
  Skipping link: none of the wheel's tags (cp310-cp310-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/be/a0/004887534da500c5c0756d3db584736c182db98ce2cf8c271f7adb0a54c7/infomap-2.5.0-cp310-cp310-macosx_10_15_x86_64.whl#sha256=49af7d47e1d06cfc94cc05b47f3737398ad23a662b3e21ef93b3fbf83ae99e1f (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp310-cp310-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d8/e6/082de97f5198aa2bd9880ff612997683cc3a198fbea3ff7d9b0202eca06b/infomap-2.5.0-cp310-cp310-win_amd64.whl#sha256=2a230242a26af3b9529bf7d6fb888fffae9882e3d6a3f652abd32a58695707be (from https://pypi.org/simple/infomap/) (requires-python:>=3)
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  Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/8a/1c/4cd3818f7337efbc56cec223af99e9204d8e36b4a01008e396f2076a233d/infomap-2.5.0-cp36-cp36m-win_amd64.whl#sha256=d4e402331357c5ef7eb80fa33ba01ccf1632aeef6c7c9cc2c2c48b27594a1868 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp37-cp37m-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/4d/7c/a627ab0b4042628663eebc0efdc8a99a808161022f197fff323c2337854b/infomap-2.5.0-cp37-cp37m-macosx_10_15_x86_64.whl#sha256=e6344884f94c9c310aece640f8b1779c9421763c593574e2fa0394660d1452be (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp37-cp37m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d2/74/b4ea388bd8e8fd70da39141def8fb6b63d15606d96d926610000751dac14/infomap-2.5.0-cp37-cp37m-win_amd64.whl#sha256=e05c6409752382580ffc95afbac0dd7a92976b3346cd72a393f427d881e68710 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp38-cp38-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/65/39/62f0d8910b543c54a0c36fd253e4189b60c44349827c9f6d771fe553c851/infomap-2.5.0-cp38-cp38-macosx_10_15_x86_64.whl#sha256=65cf304448a2b838748e1c65b5c0fbccfee40a18dcc73a8b8c83d3b1f1c8df36 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp38-cp38-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/b4/b9/85e58d30d25be450b3876e64da2723e8502ad7db3b3bd175677a3c7b4d90/infomap-2.5.0-cp38-cp38-win_amd64.whl#sha256=36fb9516bde0a3fd3756c5341c65dab397bd57ca2d3680e16e25e660561006f5 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/37/14/bcdf5847ca5b32771f401eed8a0ef9533cba86169c8bdb7dfcdc3a509873/infomap-2.5.0-cp39-cp39-macosx_10_15_x86_64.whl#sha256=9a76caa254061ed682b3117644b24fc5765b10cc95026a0faedcd938e6f538fa (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.5.0
  Skipping link: none of the wheel's tags (cp39-cp39-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/31/ff/bb2ae044404dc168ce4feb4f28b18951db47b2c81977a801043e3276d78c/infomap-2.5.0-cp39-cp39-win_amd64.whl#sha256=5065f45b827a25fb25f90f7d9a6cbd84db33f19b654a1712c28106ead56f255b (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/4a/15/2e203358d4c841d910ca3ee83e80a59418630bc30462b8aef959a84d3690/infomap-2.5.0.tar.gz#sha256=93734eebd7ede1a093b0b93b7a5956e0616b2d2bb3128dbe95f650ec5de342d6 (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.5.0
  Skipping link: none of the wheel's tags (cp310-cp310-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d7/3d/cb8bcaa845e4d7006d3d6de518233fdd0bf548347d7b664c0e1dcc7be92b/infomap-2.6.0-cp310-cp310-macosx_10_15_x86_64.whl#sha256=92752d54b784b22ab1bb60e82a92163f40398112c6fddbb7840db006e8fcec60 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp310-cp310-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/4a/62/9776b2defc84f2f4e53ea54b22dceefac63950fc910cf101786094a09806/infomap-2.6.0-cp310-cp310-win_amd64.whl#sha256=c2a09c07692b9d61d1c1690a0e57b40257696405e666ac8c69e1a10ed726b32e (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_14_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/9e/74/b3ddfd32ce56fa7f9c75441945eaaee3eb0aab6afa7176931f92f552d8b8/infomap-2.6.0-cp36-cp36m-macosx_10_14_x86_64.whl#sha256=1f57e5f42a590ef7233c66909c8fc977f3ff82f2590eccb35766ddef4967b066 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/e5/a7/dbbc81c6603767ec44a90b7a3ecaa8b2ee154fab5282a709b0af517abdac/infomap-2.6.0-cp36-cp36m-win_amd64.whl#sha256=bf48e11f837e3b960540b038bc4b41c6485cfbeff409b2a07ce0a5bb6553e0c3 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
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  Skipping link: none of the wheel's tags (cp37-cp37m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/18/47/e182d58f309b075da9f3c8f63a417856bef0b4337ea213e2bc54c1b9bc7e/infomap-2.6.0-cp37-cp37m-win_amd64.whl#sha256=c011a1597fb889a562790a86728380ed4be4d05cb08e52b625fc21f8bbad59bc (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp38-cp38-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1a/83/6fa8ccc9e1409bc90899b1a11a219eb2c3cdfaf99a386deff7a1d32df1de/infomap-2.6.0-cp38-cp38-macosx_10_15_x86_64.whl#sha256=5ce1c588c9b76814c9940bc10dc7268c5d21016788d0b1b7222d7cccf74d53cf (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp38-cp38-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/a5/9e/199d4e8b7e955b18cc0844d597b35a43d4b7c244547b00266e3f4617b58d/infomap-2.6.0-cp38-cp38-win_amd64.whl#sha256=9050d3b7dba667afe69229f813d2ee300210f45a3b8a30d298caa4cda9c449c8 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/d5/ff/4e6d2b541a6a9e37100d3c3d5fcd140187374a49e713f109ed0f886872e9/infomap-2.6.0-cp39-cp39-macosx_10_15_x86_64.whl#sha256=253ce73553081f5da8ec0e313115153f68cfd2580e0f86b7ddecbbef04034097 (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.6.0
  Skipping link: none of the wheel's tags (cp39-cp39-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/b7/fc/cee5f4eec7bbb0559dbd170f5567dc51d5f7714ac9f46f234013327d4eb0/infomap-2.6.0-cp39-cp39-win_amd64.whl#sha256=d031504c9d723b5753665b773f3a728d18dc45a474e113e5f6b18d06e75d64c8 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/65/bb/2d12847373a8f729cbf1544e103d6cb752b151aff40eaf6c5e80cee71497/infomap-2.6.0.tar.gz#sha256=76d2b8c77f49c7a8fb70fd4758c205150c372212b13ccbe96f05f18a72dc69a3 (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.6.0
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  Skipping link: none of the wheel's tags (cp310-cp310-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/96/44/81e11965cf734d8f4a0e3925c82da26618207404d5a1ad688781ae1dc47e/infomap-2.6.1-cp310-cp310-win_amd64.whl#sha256=e8ee9fce2a78e3c5f55485aefe6034256ef7cd7238db498e51985fa87ab0e8b3 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_14_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/bb/56/97cf3c0fa0bb6f1d066ba5715c582d1deb8252e9acc497ca5ff185044bb9/infomap-2.6.1-cp36-cp36m-macosx_10_14_x86_64.whl#sha256=e3ec18cbb196eb45bc540554be9709bb7ac354f47ea67bb012ebcd145a09a78a (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/21/27/1141a99caf779ba0e11071a82d93ba67e3db80a1c9ac53dec13286cea41f/infomap-2.6.1-cp36-cp36m-win_amd64.whl#sha256=b3e716e814586848b8ab30229370430125535f59a67b41a0150fb092e1ca2e69 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp37-cp37m-macosx_10_15_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0a/53/bd26a794fb4c791dcfcb55e4b17158af7a26a02be0ed223ce709ec036059/infomap-2.6.1-cp37-cp37m-macosx_10_15_x86_64.whl#sha256=7cb54ed5402dcc5e7358ca6a1e1c54965480cb425826124b78fade8100ab24f0 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Skipping link: none of the wheel's tags (cp37-cp37m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f5/ff/95e4697aaa1833e4d77780ed337a41fa996ef64571c7ae53f917e46b4886/infomap-2.6.1-cp37-cp37m-win_amd64.whl#sha256=6059d6bff0ca989533da84f2d4d93796da58e0f69ce739f2f6785f25a3ad7664 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
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  Skipping link: none of the wheel's tags (cp38-cp38-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/20/1d/02919826f18a5136f0d082e55c3b2f93f2a9df580362336283c2bcd9aec0/infomap-2.6.1-cp38-cp38-win_amd64.whl#sha256=5d671eee491d6e4454aa7bf433695fc660054b4e73db049c5c7eb47b7ccd7635 (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/4f/01/02cfa9f122ed09dab797d4f916d7ba26abbce65f7bd6f5abe9b4c5ce3a1d/infomap-2.6.1-cp39-cp39-macosx_10_15_x86_64.whl#sha256=66161510b5a9c352b17819824895fdc16d1250108cdf0da1a66d6ea5c5fdbfb5 (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.6.1
  Skipping link: none of the wheel's tags (cp39-cp39-win_amd64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/10/f5/57ea6e8e00c269a64f09f0d2dfde6355bd468d6c5cc90d3dcc6c779c89e7/infomap-2.6.1-cp39-cp39-win_amd64.whl#sha256=6f524476965bfa25087af037ed7813958e3d0d301641ea3c12fffc810101774d (from https://pypi.org/simple/infomap/) (requires-python:>=3)
  Found link https://files.pythonhosted.org/packages/76/72/dbe4321d6952af852a8296070d59dae11b74019b94829de066f7ec31e9ea/infomap-2.6.1.tar.gz#sha256=5fb76e8845b41c80e8a1bc522d518e5b233a1c893db11ebc6a5b3dc68ada711b (from https://pypi.org/simple/infomap/) (requires-python:>=3), version: 2.6.1
Skipping link: not a file: https://pypi.org/simple/infomap/
Given no hashes to check 55 links for project 'infomap': discarding no candidates
Collecting infomap
  Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-unpack-ja15i4l_
  Starting new HTTPS connection (1): files.pythonhosted.org:443
  https://files.pythonhosted.org:443 "GET /packages/4f/01/02cfa9f122ed09dab797d4f916d7ba26abbce65f7bd6f5abe9b4c5ce3a1d/infomap-2.6.1-cp39-cp39-macosx_10_15_x86_64.whl HTTP/1.1" 200 717767
  Downloading infomap-2.6.1-cp39-cp39-macosx_10_15_x86_64.whl (717 kB)
     |████████████████████████████████| 717 kB 2.9 MB/s 
  Added infomap from https://files.pythonhosted.org/packages/4f/01/02cfa9f122ed09dab797d4f916d7ba26abbce65f7bd6f5abe9b4c5ce3a1d/infomap-2.6.1-cp39-cp39-macosx_10_15_x86_64.whl#sha256=66161510b5a9c352b17819824895fdc16d1250108cdf0da1a66d6ea5c5fdbfb5 to build tracker '/private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-req-tracker-_mieb17w'
  Removed infomap from https://files.pythonhosted.org/packages/4f/01/02cfa9f122ed09dab797d4f916d7ba26abbce65f7bd6f5abe9b4c5ce3a1d/infomap-2.6.1-cp39-cp39-macosx_10_15_x86_64.whl#sha256=66161510b5a9c352b17819824895fdc16d1250108cdf0da1a66d6ea5c5fdbfb5 from build tracker '/private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-req-tracker-_mieb17w'
Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-unpack-akp1oz30
Installing collected packages: infomap
  Attempting uninstall: infomap
    Found existing installation: infomap 2.6.1
    Uninstalling infomap-2.6.1:
      Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-uninstall-ol6dkp0h
      Removing file or directory /Users/matilde/opt/anaconda3/bin/infomap
      Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-uninstall-bdz0_o7f
      Removing file or directory /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/__pycache__/infomap.cpython-39.pyc
      Removing file or directory /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/__pycache__/package_meta.cpython-39.pyc
      Created temporary directory: /private/var/folders/4l/qjt4zjdj6fgcmp_prmp4y2_80000gn/T/pip-uninstall-jm33hkoc
      Removing file or directory /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so
      Created temporary directory: /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/~nfomap-2.6.1.dist-info
      Removing file or directory /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/infomap-2.6.1.dist-info/
      Removing file or directory /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/infomap.py
      Removing file or directory /Users/matilde/opt/anaconda3/lib/python3.9/site-packages/package_meta.py
      Successfully uninstalled infomap-2.6.1

  changing mode of /Users/matilde/opt/anaconda3/bin/infomap to 755
Successfully installed infomap-2.6.1
1 location(s) to search for versions of pip:
* https://pypi.org/simple/pip/
Fetching project page and analyzing links: https://pypi.org/simple/pip/
Getting page https://pypi.org/simple/pip/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/pip/ HTTP/1.1" 200 20574
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antoneri commented 1 year ago

Thanks!

For now, as your goal is to run Infomap from Matlab, you can download the C++ version without OpenMP here.

If you download Infomap you need to allow it in the system settings by first running it once, then opening system settings and clicking Allow Anyway.

Screenshot 2022-11-06 at 19 15 53

You can also try building the C++ version from sources by running make or make noomp in the source directory.

There seems to be a problem in the build step on GitHub Actions. We had some indications of this a couple of days ago but we thought everything was fine. Apparently not!

MatildeVaghi commented 1 year ago

Thanks Anton! appreciated - I am getting some problems here as well (everything worked fine on the old Mac!). Here, as you suggested, I downloaded the the C++ version without OpenMP . I ran it once and proceeded to Allow Anyway as you indicated.

I double click on the Executable and I get the following in the terminal

The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
(base) Matildes-MacBook-Pro:~ matilde$ /Users/matilde/Documents/Experiments/Dense_sampling/MSCcodebase-master/Resources/infomap_v2.6.0/Infomap ; exit;
Infomap version 2.6.0
Missing required arguments.
Usage: Infomap network_file out_directory [options]. Run with option '-h' for more information.
logout

Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

Infomap is not recognized in Matlab (having the path added).

antoneri commented 1 year ago

Great!

I'm no Matlab expert, but it seems like you have to set your PATH inside Matlab: https://se.mathworks.com/matlabcentral/answers/10451-how-do-i-add-to-the-path-of-system

Hope this helps!

MatildeVaghi commented 1 year ago

Thanks! I was missing some basics.

FYI on M1 Mac I built the C++ version from sources by running make noomp in the source directory. I am able to run InfoMap from from Matlab with the following: system([infomapfolder '/Infomap-2.6.0/Infomap]

Thank you both for prompt and helpful assistance ! I will check to see when the the steps in the build step on GitHub Actions are resolved. Cheers!

antoneri commented 1 year ago

Happy to help! Cheers!