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Problem with installing banditPAM #167
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Hi @retzerjj , thanks for filing an issue. Could you try The error message you surfaced ( |
I also just took a closer look at your full error output and it looks like your LLVM installation is having trouble finding the C++ standard library headers. Did you try to install LLVM from source? If so, could you install it instead via More helpful details are here: https://github.com/ThrunGroup/BanditPAM/blob/main/docs/install_mac.md |
Thanks very much for your response. I did install llvm using brew. When executing the command again (brew install llvm) I get the following message: Warning: llvm 13.0.0_2 is already installed and up-to-date. I next downloaded and extracted banditPAM and ran pip install --no-cache-dir -e . in the downloaded directory. It does indeed look like there is a problem finding the stdio.h header file (new error message text attached) but since the llvm installation looks ok, I'm not sure what to do next. Thanks again very much Note: not sure if this plays a role however armadillo appears to have been installed correctly too:
To reinstall 10.7.5, run: |
Thanks @retzerjj ! Just to confirm, did you also install the xcode command line tools via the Mac installation guide? This post suggests that might be the issue |
Hi @motiwari, yes I did. When I try
I get xcode-select: error: command line tools are already installed, use "Software Update" to install updates Thanks again. |
Interesting -- could you update the Xcode tools by opening the "App Store" app and Choosing "Updates" on the left-hand sidebar? Also, does your |
Hello @motiwari I checked and I do have a /usr/local directory. I also checked and there was no update for xcode in the app store app. I tried to update xcode command line tools (which were installed). I deleted them and re-installed from the command I then re-booted the computer and after trying to install banditPAM (this time version 3) and it did in fact work!! Many thanks for all your help! However, I next went to install banditPAM on my macbook (apple silicon). I made sure I had armadillo/llvm installed and echo $PATH I've attached the error message to this note. Again, any suggestions would be greatly appreciated, your help is P.S. Two additional notes (not sure if they are material) Thanks again very much! |
Hey @retzerjj , that's great to hear! Thanks for reporting back with the fix -- I've added this to the install guide to help future generations. Regarding the new error on the Macbook Air, could you confirm you've run Also, is there a file called
By the way, the |
Oh, it also looks like M1 Macs have changed some important directories. Thanks for surfacing this bug, I'll work on a fix! In the meantime, you can likely get it to work by creating a symlink in a (new) |
@retzerjj could you try the following command and let me know if it works? You may need a
|
Hello @motiwari ,
Thanks again for all your help, Happy New Year! |
Happy New Year, @retzerjj ! Could you try running the command below again? I just updated something.
If that still doesn't work, could you try running the following command
and then running If neither of those work, could you provide the output of the following command?
A few tips that might help:
|
Hello @motiwari #include "armadillo_bits/config.hpp" I also ran the tree command, output is in the attached txt file. |
@retzerjj We are making progress! Can you try one more time:
|
@motiwari |
Oops sorry, can you try this command instead?
|
Looks like a similar error |
Sorry for the churn here, @retzerjj . Let me get my hands on an M1 Mac so I can debug locally and save you the time. I'll get back to you shortly |
Thanks very much @motiwari, I very much appreciate it. |
Hey @retzerjj , just letting you know I haven't forgotten about this. It turns out building for M1 Macs is much harder than I initially thought, but I'm making progress and should have an update soon |
Fantastic! Thanks so much for doing this, I’ll look forward to your update,
Take care,
Joe
… On Jan 10, 2022, at 11:12 PM, Mo Tiwari ***@***.***> wrote:
Hey @retzerjj <https://github.com/retzerjj> , just letting you know I haven't forgotten about this. It turns out building for M1 Macs is much harder than I initially thought, but I'm making progress and should have an update soon
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Hi @retzerjj ; I think I was able to build the Python wheel for M1 Macs; could you install banditpam via The code in Example 1 should run. A caveat: you'll have to use In case you get an error like |
Hello @motiwari
It appears to install correctly:
However I’m getting errors when I try running the code:
>> from banditpam import KMedoids
TypeError: object of type 'module' has no len()
>> import numpy as np
>> import matplotlib.pyplot as plt
>>
>> # Generate data from a Gaussian Mixture Model with the given means:
>> np.random.seed(0)
>> n_per_cluster = 40
>> means = np.array([[0,0], [-5,5], [5,5]])
>> X = np.vstack([np.random.randn(n_per_cluster, 2) + mu for mu in means])
>>
>> # Fit the data with BanditPAM:
>> kmed = KMedoids(n_medoids=3, algorithm="BanditPAM")
NameError: name 'KMedoids' is not defined
>> kmed.fit(X, 'L2')
NameError: name 'kmed' is not defined
I suspect this is because I’m not installing using CPython however I can’t seem to find instructions for downloading / installing CPython on a Mac. Is there a GitHub site that would have the instructions/code?
Thanks
Joe
… On Jan 25, 2022, at 3:45 PM, Mo Tiwari ***@***.***> wrote:
Hi @retzerjj <https://github.com/retzerjj> ; I think I was able to build the Python wheel for M1 Macs; could you install the appropriate wheel (attached) for your python version and let me know if it works?
E.g., download the wheel from the attached zip and run
pip install pip install banditpam-3.0.3a1-cp39-cp39-macosx_10_14_universal2.whl
Then run the code in Example 1 <https://github.com/ThrunGroup/BanditPAM#example-1-synthetic-data-from-a-gaussian-mixture-model>?
A caveat: you'll have to use CPython 3.8+
banditpam-3.0.3a1-cp38-cp38-macosx_10_14_universal2.whl.zip <https://github.com/ThrunGroup/BanditPAM/files/7937399/banditpam-3.0.3a1-cp38-cp38-macosx_10_14_universal2.whl.zip>
banditpam-3.0.3a1-cp39-cp39-macosx_10_14_universal2.whl.zip <https://github.com/ThrunGroup/BanditPAM/files/7937404/banditpam-3.0.3a1-cp39-cp39-macosx_10_14_universal2.whl.zip>
banditpam-3.0.3a1-cp310-cp310-macosx_10_14_universal2.whl.zip <https://github.com/ThrunGroup/BanditPAM/files/7937409/banditpam-3.0.3a1-cp310-cp310-macosx_10_14_universal2.whl.zip>
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Thanks @retzerjj ! It's strange; CPython should be the default Python implementation when using Anaconda, which I highly recommend! If you're running CPython, the version is a) the output when you open a python shell:
b) the output of |
Hello @motiwari
The results of pip -V and python are below. Also the message I get when trying to install banditPAM from the terminal is shown.
Note that when the install did appear to work I was installing from the “terminal” tab inside of RStudio.
Thanks
Joe
Hello
It appears to install correctly:
However I’m getting errors when I try running the code:
>> from banditpam import KMedoids
TypeError: object of type 'module' has no len()
>> import numpy as np
>> import matplotlib.pyplot as plt
>>
>> # Generate data from a Gaussian Mixture Model with the given means:
>> np.random.seed(0)
>> n_per_cluster = 40
>> means = np.array([[0,0], [-5,5], [5,5]])
>> X = np.vstack([np.random.randn(n_per_cluster, 2) + mu for mu in means])
>>
>> # Fit the data with BanditPAM:
>> kmed = KMedoids(n_medoids=3, algorithm="BanditPAM")
NameError: name 'KMedoids' is not defined
>> kmed.fit(X, 'L2')
NameError: name 'kmed' is not defined
I suspect this is because I’m not installing using CPython however I can’t seem to find instructions for downloading / installing CPython on a Mac. Is there a GitHub site that would have the instructions/code?
Thanks
Joe
… On Jan 26, 2022, at 9:35 AM, Joseph Retzer ***@***.***> wrote:
> Begin forwarded message:
>
> From: Mo Tiwari ***@***.*** ***@***.***>>
> Subject: Re: [ThrunGroup/BanditPAM] Problem with installing banditPAM (Issue #167)
> Date: January 25, 2022 at 3:45:14 PM CST
> To: ThrunGroup/BanditPAM ***@***.*** ***@***.***>>
> Cc: Joseph Retzer ***@***.*** ***@***.***>>, Mention ***@***.*** ***@***.***>>
> Reply-To: ThrunGroup/BanditPAM ***@***.*** ***@***.***>>
>
>
> Hi @retzerjj <https://github.com/retzerjj> ; I think I was able to build the Python wheel for M1 Macs; could you install the appropriate wheel (attached) for your python version and let me know if it works?
>
> E.g., download the wheel from the attached zip and run
> pip install pip install banditpam-3.0.3a1-cp39-cp39-macosx_10_14_universal2.whl
>
> Then run the code in Example 1 <https://github.com/ThrunGroup/BanditPAM#example-1-synthetic-data-from-a-gaussian-mixture-model>?
>
> A caveat: you'll have to use CPython 3.8+
>
> banditpam-3.0.3a1-cp38-cp38-macosx_10_14_universal2.whl.zip <https://github.com/ThrunGroup/BanditPAM/files/7937399/banditpam-3.0.3a1-cp38-cp38-macosx_10_14_universal2.whl.zip>
> banditpam-3.0.3a1-cp39-cp39-macosx_10_14_universal2.whl.zip <https://github.com/ThrunGroup/BanditPAM/files/7937404/banditpam-3.0.3a1-cp39-cp39-macosx_10_14_universal2.whl.zip>
> banditpam-3.0.3a1-cp310-cp310-macosx_10_14_universal2.whl.zip <https://github.com/ThrunGroup/BanditPAM/files/7937409/banditpam-3.0.3a1-cp310-cp310-macosx_10_14_universal2.whl.zip>
> —
> Reply to this email directly, view it on GitHub <#167 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAP5KCW3I2ONRMFWRADDRK3UX4KWVANCNFSM5K4PG5MA>.
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> You are receiving this because you were mentioned.
On Jan 26, 2022, at 12:28 PM, Mo Tiwari ***@***.***> wrote:
Thanks @retzerjj <https://github.com/retzerjj> ! It's strange; pip install -i https://test.pypi.org/simple/ banditpam==3.0.3a1 should not have succeeded unless you're using CPython. In the pip output, did it somehow fall back to a previous version? What's the output if you run python -c "import platform; print(platform.python_implementation())"?
CPython should be the default Python implementation when using Anaconda <https://www.anaconda.com/>, which I highly recommend!
If you're running CPython, the version is >=3.8, and you're still getting this error, could you provide the output of the following commands?
a) the output when you open a python shell:
>>> python
Python 3.8.12 | packaged by conda-forge | (default, Oct 12 2021, 21:50:38)
[Clang 11.1.0 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
b) the output of pip -V
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Hello Sudhir,
Thats great. Could you let me know how you installed it through Anaconda? I tried adding the plpi channel but it does not show up. I also tried to install the .whl file downloaded from GitHub but I’m not able to do that (not sure how to access the file).
Thanks & take care,
Joe
… On Feb 1, 2022, at 7:18 AM, Sudhir Kumar Suman ***@***.***> wrote:
@retzerjj <https://github.com/retzerjj> I'm having the same problem when trying to install banditpam on my Mac M1[unresolved]. For the time being, I've tried Anaconda and installed banditpam there, and it's working.
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Hmmm it seems Sudhir deleted his comment, but we owe a thank you to him! @retzerjj you can install Python from Anaconda here; it should provide instructions on how to activate the appropriate Anaconda environment after you've installed it. By the way, did you copy-paste the wrong information in this comment? Probably it works on Anaconda because I did at least something right when creating the M1 Mac wheels; but I've also heard from others that the wheels don't work with Miniconda or other Python installations. I'll leave this issue open until the package is working everywhere |
Yes, Banditpam was successfully installed, but I was unable to use it because it displayed an error while importing it.
|
It appears my .png attachments of my error messages are not visible in my email, is there another way I could send them?
I have Anaconda installed with multiple versions of Python (3.9 and 3.10 included). I also added pypi as a channel. However, bandiPAM does not appear in the “Not Installed” file list and I’m not sure how to install the .whl file I downloaded using Anaconda.
… On Feb 1, 2022, at 3:57 PM, Mo Tiwari ***@***.***> wrote:
Hmmm it seems Sudhir deleted his comment, but we owe a thank you to him!
@retzerjj <https://github.com/retzerjj> you can install Python from Anaconda here <https://www.anaconda.com/>; it should provide instructions on how to activate the appropriate Anaconda environment after you've installed it. By the way, did you copy-paste the wrong information in this comment <#167 (comment)>?
Probably it works on Anaconda because I did at least something right when creating the M1 Mac wheels; but I've also heard from others that the wheels don't work with Miniconda or other Python installations. I'll leave this issue open until the package is working everywhere
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Sorry for the late response @retzerjj . I'm not sure how to attach pictures by email-replying to Github email notifications, but if you sign into Github and view this link, you can attach an image in the comment box. At the moment, I'm not sure what to do for this because I can't reproduce your or Sudhir's error locally without an M1 Mac. Two of my friends with M1 Mac where able to use the M1 wheel successfully, but another one surfaced an error like this:
This looks like this is different from Sudhir's error message, which seems to be complaining about an I ordered an M1 Mac on 12/29/21, but it still won't be delivered until 3/10/22 (presumably due to existing supply chain issues). If you provide your error message then I can investigate it when I receive the M1 Mac |
When I install banditPAM from the console in my RStudio session, it appears to install w/o error. However when I try to import the KMedoids function I get:
>> from banditpam import KMedoids
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/banditpam.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace ‘_omp_get_max_threads'
Thanks
Joe
… On Feb 7, 2022, at 5:39 PM, Mo Tiwari ***@***.***> wrote:
Sorry for the late response @retzerjj <https://github.com/retzerjj> . I'm not sure how to attach pictures by email-replying to Github email notifications, but if you sign into Github and view this link <#167>, you can attach an image in the comment box.
At the moment, I'm not sure what to do for this because I can't reproduce your or Sudhir's error locally without an M1 Mac. Two of my friends with M1 Mac where able to use the M1 wheel successfully, but another one surfaced an error like this:
ImportError: dlopen(/Users/frieda/miniconda3/envs/behavior/lib/python3.8/site-packages/banditpam.cpython-38-darwin.so, 0x0002): symbol not found in flat namespace '_omp_get_max_threads'
This looks like this is different from Sudhir's error message, which seems to be complaining about an armadillo symbol.
I ordered an M1 Mac on 12/29/21, but it still won't be delivered until 3/10/22 (presumably due to existing supply chain issues). If you provide your error message then I can investigate it when I receive the M1 Mac
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Hi @retzerjj , my apologies for the late response. I've still been unable to acquire an M1 Mac to test this locally, so to unblock you I've deleted the offending functions and shipped a new version to PyPI. When the new builds for If the issue persists, please let me know and I'll take a look. |
Hi,
Thanks for doing this. Quick update, when I try loading KMedoids from banditPAM I get the following error:
>> from banditpam import KMedoids
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/banditpam.cpython-310-darwin.so,
0x0002): symbol not found in flat namespace ‘__ZTWN4arma19mt19937_64_instanceE'
Best
Joe
… On Apr 21, 2022, at 8:57 PM, Mo Tiwari ***@***.***> wrote:
Hi @retzerjj <https://github.com/retzerjj> , my apologies for the late response. I've still been unable to acquire an M1 Mac to test this locally, so to unblock you I've deleted the offending functions and shipped a new version to PyPI.
When the new builds for v3.0.4 hit PyPI in about an hour, you should be able to run pip install --upgrade banditpam and upgrade to a version runnable on M1 Macs.
If the issue persists, please let me know and I'll take a look.
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@retzerjj sorry for the very long delay here. I've revisited this issue with the release of If so, could you try installing BanditPAM inside an Anaconda environment and let me know if you still have the same error? |
@mo ***@***.***> So I tried to find the package in Anaconda but I am unable to locate it (even though pypi is available).
I then tried installing from the command line using pip and conda install. I also tried installing the whl package downloaded for ARM64 (which I assumed was the correct file). Results are below
Best
Joe
(base) Josephs-MacBook-Pro-5:/ retzerjj$ pip install banditpam
Requirement already satisfied: banditpam in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (3.0.4)
(base) Josephs-MacBook-Pro-5:/ retzerjj$ conda install banditpam
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- banditpam
Current channels:
- https://conda.anaconda.org/pypI/osx-64
- https://conda.anaconda.org/pypI/noarch
- https://conda.anaconda.org/anaconda-fusion/osx-64
- https://conda.anaconda.org/anaconda-fusion/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
(base) Josephs-MacBook-Pro-5:/ retzerjj$ python3.10 -m pip install ~/desktop/banditpam-4.0.0-cp311-cp311-macosx_11_0_arm64.whl
ERROR: banditpam-4.0.0-cp311-cp311-macosx_11_0_arm64.whl is not a supported wheel on this platform.
(base) Josephs-MacBook-Pro-5:/ retzerjj$
From: Mo Tiwari ***@***.***>
Date: Monday, February 20, 2023 at 8:02 PM
To: motiwari/BanditPAM ***@***.***>
Cc: Joseph Retzer ***@***.***>, Mention ***@***.***>
Subject: Re: [motiwari/BanditPAM] Problem with installing banditPAM (Issue #167)
@retzerjj<https://github.com/retzerjj> sorry for the very long delay here. I've revisited this issue with the release of BanditPAM v4.0.0. Does this issue still persist?
If so, could you try installing BanditPAM inside an Anaconda environment and let me know if you still have the same error?
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Hey Joe, the output of your first command ( |
I managed to update the package using
python3.10 -m pip install --upgrade banditpam
however when I try to load Kmedoids I get:
>> from banditpam import KMedoids
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/banditpam.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace '_omp_get_max_threads'
From: Mo Tiwari ***@***.***>
Date: Friday, March 3, 2023 at 4:33 PM
To: motiwari/BanditPAM ***@***.***>
Cc: Joseph Retzer ***@***.***>, Mention ***@***.***>
Subject: Re: [motiwari/BanditPAM] Problem with installing banditPAM (Issue #167)
Hey Joe, the output of your first command (pip install banditpam) shows that you currently have BanditPAM v3.0.4 installed. If you run pip install --upgrade banditpam and try to run a python script that runs import banditpam, what output do you get?
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Thanks @retzerjj . Unfortunately I spent several days trying to debug this issue and wasn't able to fix it. I'm not sure how this could possibly be happening, as the necessary libraries like OpenMP are statically linked within the Python wheel. It seems that other users are experiencing the same issue (#230 ); if they are able to find a solution, I'll update this thread. |
Note to self: ContinuumIO/anaconda-issues#12933 looks relevant |
Thanks @thucnc, I'll let you know if I find a solution. @Adarsh321123 could you try installing |
Sorry for the late response, @motiwari. I am able to reproduce the result. Specifically, after installing the |
Hi @retzerjj @SumanSudhir @thucnc I believe we have finally diagnosed the source of the problem. TL;DR: Could you please install Anaconda from https://github.com/conda-forge/miniforge#miniforge3 specifically for More context: We realized that the default installer for Anaconda, even on M1 Macs, runs in |
Hi, I'm running into a similar issue. I'm not using anaconda, I'm just using pyenv/python.
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Hi @li-dennis, could you provide the output of the following two commands?
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Sorry, just seeing this :) sure
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Something is weird about that output -- it looks like you're downloading In any case, I think we know the root cause of the problem and are trying to fix. |
Ah, yeah, my bad -- was messing around with pipenv and v3.0.4 as well to see if the fault lied there so there was some version mismatching
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I've been following some discussions about install issues however I still can't seem to successfully install banditPAM. I'm getting a long error message that seems to indicate that building the wheel for banditPAM failed (full error attached).
I'm working with a MAC intel using Monterrey. I successfully install llvm and armadillo. To answer some questions asked previously:
When I try pip install ., I get:
ERROR: Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.
When I execute gcc --version I get:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-
dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 13.0.0 (clang-1300.0.29.30)
Target: x86_64-apple-darwin21.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
When I try pip3 -V I get:
pip 21.3.1 from /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip (python 3.10)
I've tried multiple install commands (e.g. pip, pip3 etc.) but with no luck. Any suggestions would be greatly appreciated,
Thanks!
banditPAMError.txt
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