Error "Segmentation fault: 11" in MacOS

[nbosc]

I am doing the tutorial. When I try to build the model I get Segmentation fault: 11

I have installed the environment you provide on a macOS 10.13.3 machine.

Also the file I use as training set is caco2.sdf.

[manuelpastor]

The message was not informative enough to diagnose the problem. Please update the code to the last version in the master branch and if it reproduces, contact me by e-mail to carry out some testing. Thanks for your feedback!

[nbosc]

Here what I can say about this error.

First, I use macOS 13.3.4 and Jupyter's version is 4.3.0. I have downloaded the latest version of the repo.

I can activate flame and use 'manage' to create a new model or to see the list of models.

The problem occurs when I use 'build' or 'predict'. In both cases, there is no additional information but 'Segmentation fault: 11'

Of course, I have the same problem if I use the GUI.

Unfortunately, this is all I can say...

[manuelpastor]

The "Segmentation fault: 11" could be related with a well documented iOS bug. Please check this thread

https://stackoverflow.com/questions/19531969/segmentation-fault-11-in-os-x

They propose some solutions. I would be gratefull if you keep me informed

[nbosc]

Thanks Manuel! Your link put me on the track and I have found the solution. Apparently there is an incompatibility between the default python and anaconda for OSX.
As mentioned in this thread deeptools/pyBigWig#58, I had to install python 3.6.4 from conda-forge. It solved the segfault issue but then I had to manually install the requests package.
Now the issue is solved and I can use flame.

[manuelpastor]

The same issue appeared again at UNIVIE in a Mac OS 10.14. The user solved it by installing Python from the conda-forge channel

The problem needs to be solved, as soon as we can get Apple hardware, reproduce it locally and test appropriate solutions

[manuelpastor]

Implemented a MacOS machine in the Travis testing system.
We were able to reproduce the problem and is now under investigation (Biel)

[BielStela]

related issue deeptools/pyBigWig#58

[BielStela]

I reproduced the error in macOS 10.13 and found some dirty fix uninstalling python and installing python from conda-forge channel:

conda install -c conda-forge python=3.6.8

But this solution blows up the environment and the dependencies must be reinstalled.
Also debugging in Travis is slow and problematic since the debug session terminates whenever Travis servers want (job timeout, or indecipherable exit codes). I will halt the investigation until I can get my hands on a mac laptop.

[BielStela]

Well I think I have a workaround for this:

• Set conda-forge as the only channel in environment.yml
• add libgfortran=3.0 to the env.yml to force conda to use this version because the conda-forge numpy dependency is libgfortran4.0.0 and this dependency is broken

[annacnev]

Having this same issue right now... I have Python 3.7 installed with home-brew running on Mojave 10.14.1. I am trying to extract data from a relatively large .json file using pandas. The function I wrote to read over the lines of select columns works for some of the columns of the dataset, but on others it stops my python completely and gives me a segmentation 11 error. Any thoughts ? I have a conda forged 3.4 installed as well and it gives the same error.

[BielStela]

sorry for late response @annacnev, it looks like you are running the local (brew) python install. If you have conda installed, try to create an env with python from conda-forge with the following commands:

conda create -n test
conda activate test
conda install python -c conda-forge

then install all the needed packages in the same environment (test)

[annacnev]

No worries, @BielStela thanks for getting back to me! I did try that recommendation at the time and had no luck. I did eventually figure out the issue though- so incase anyone stumbles upon this in the future, here might be your problem: one of the lines in my json file was an empty list that when I was running my code, I was inadvertently plugging into a pandas function and then getting the seg fault on. I noticed too when I was researching on a few forums about this problem, some were also eventually attributed to trying to perform functions on empty values in datasets. Adding a "try" and "except" to your code might fix the issue- it did for me!

[BielStela]

Great you fixed it. Anyway, looks like this is a weird old bug with python interpreter in osx that shouldn't be around...

[BielStela]

Testing on a Mac with Mojave 10.14.4 I am not able to reproduce the error.
I installed Miniconda3, cloned the master branch, created the environment, installed flame, ran the tests, created and predicted with a model and no segfault happened.

[bio-informatician]

Testing on a Mac with Mojave 10.14.4 I am not able to reproduce the error.
I installed Miniconda3, cloned the master branch, created the environment, installed flame, ran the tests, created and predicted with a model and no segfault happened.

Hi, unfortunately, I have the same problem with Mojave 10.14.3 on my MacPro. When I want to open a BigWig file by write permission this error comes up. I installed python directly from its web site https://www.python.org/downloads/release/python-372/ without conda. I will follow what you have done by Miniconda3.

[manuelpastor]

Fixed once we relaxed the rules to build the environment, thus allowing conda to select the most suitable versions for Mac Platforms