C++ Issues on Mac OS Big Sur

[Jesus Sanchez (jas220)]

Hi,
I've managed to successfully install SHARPy and perform the unittest. However, when I try to run a test case, I run into this error. I have already set the write_screen to on, and appended BeamPlot into the flow setting.
What do you recommend I do next?
Thanks in advance!

[Arturo Muñoz-Simón (ArturoMS13)]

Hi jas220,

It looks like your problem comes from the OMP library.
Can you provide us the result of the compilation of the xbeam and UVLM libraries (the output of make install)?

The case you are running here is also run in the unittest so can you also double check that the unittest were successful and report the output if they were not?

Thank you

[Norberto Goizueta (ngoiz)]

This is strange because everything seems to have installed correctly. Thanks to Arturo Muñoz-Simón (@ArturoMS13) clinical eye, he spotted that you are using zsh in your terminal. That's the only possible difference we can identify compared to our set-up. So, final try, run chsh -s /bin/bash to change your terminal to bash. You will need to open a new terminal window in order for it to take effect (you'll see that the title of the window changes to bash). More info on this: https://clay-atlas.com/us/blog/2020/12/05/mac-os-en-swith-shell-script-language-zsh-bash/

Once you have done that, go to your sharpy directory and run the tests (because your installation is done properly and I think its an issue with the script running the tests).

[Jesus Sanchez (jas220)]

I have done that, but now it cant find the sharpy_env.

[Norberto Goizueta (ngoiz)]

Ok, just try installing the environment again in the bash shell. It may have been shell dependent. conda env create -f environment_file

[Jesus Sanchez (jas220)]

Ok, now I get this.

[hemayang]

Hi jas and ngoiz. Sorry for interrupting your conversations, but I am having the same issue right now.
I really doubt if this is an issue related to the zsh/bash bcuz I was zsh before and I got the same 'segementation fault: 11' as jas's. Now I've just changed my terminal to bash but it appears the same.
Please help and many thanks!!

[Alvaro Cea (ACea15)]

Dear Jesús,

I have reinstalled SHARPy in my macOS Sierra, both in bash and in the zshell, to see if I encountered the same issues. For me it went well for both shells so a few points:

-- Changing shells is fine but make sure your Anaconda folder is ahead in the variable $PATH (by doing echo $PATH , otherwise do export PATH='anaconda_folder:$PATH' and check again).
-- Every time you try something new go to a clean directory and start from scratch with git clone... to be safe, possibilities for errors grow exponentially if trying different things.
-- In the last pic you have shown you seem to have forgotten cmake .. Please follow the instructions in the documentation carefully, otherwise we all are wasting our time here.
-- Before compilation (doing cmake .. and so on), make sure your git working directory is clean with git status. If you get modified UVLM or xbeam then do git submodule update --init --recursive as suggested, and check again with git status (however if you cloned the master branch and didn't change branches this should not be the case).
-- The OpenMP warnings you are getting should not be a problem.
-- If the problem persists you can:
- Reach out to Imperial ICT to see if they can help with your particular problem: https://www.imperial.ac.uk/admin-services/ict/contact-ict-service-desk/
- Install a virtual machine in your mac with a clean version of either Centos or Ubuntu and work with SHARPy from there. I guarantee that will work.

I hope that helps and good luck!

[Alvaro Cea (ACea15)]

Seems guys your trouble is macOS/c++ compilers. Can you do this:

1. delete your Anaconda distribution properly (google it and make sure you do it well)
2. Install Apple developer tools https://developer.apple.com/xcode/resources/
   (it comes with different c++ compilers optimised for mac)
3. Install the Anaconda distribution
4. Clone sharpy, create the environment...

It has to bloody work!! So do not hurry and make an understanding as you go.

[Jesus Sanchez (jas220)]

UPDATE: I spent the last 3 hours with the Imperial ICT help desk. He concluded it might be an issue with me running on macOS BigSurf, however, he does not recommend that I go back to an older version. They asked me if SHARPy has been tested on macOS BigSurf before. We tried installing SHARPy using Docker and it worked. The python -m unittest run successfully. They said, however, that it was an issue having to delete the container every time I wanted to start using SHARPy again. If we tried opening the container where we had left off, SHARPy would stop working again. We needed to delete the container and relaunch the image. They tried it on a macOS Sierra and it was encountering the same issue, so they told me it might not be an issue with my mac.
I will try to do what you just suggested; if that doesn't work, ill try to figure out how to use Docker because as of right now I don't know how to run the examples on the installation guide if I am using Docker.
The ICT help desk recommended I contact my department and ask if they could allocate for me a computer I could use remotely where I could install SHARPy on.
I will keep you posted though, thank you!

[Jesus Sanchez (jas220)]

Hi Alvaro,

When you say to install Apple developer tools, do you mean to install Xcode 12?

[Alvaro Cea (ACea15)]

Dear Jesús, did you click the link? The answer is yes, there is nothing else there but Xcode.
We are trying to help as Good Samaritans, but our power is, unfortunately, earthbound.
I think praying for you mac is going to be my next and final idea if a clean compilation with Xcode compilers doesn't work J.
Good luck.

[Jesus Sanchez (jas220)]

I was just trying to make sure because I had already Xcode12 downloaded on my mac.

[Norberto Goizueta (ngoiz)]

Maybe this is of use? https://stackoverflow.com/a/65485591 Looks like in general there is trouble with g++ and recent OS versions. Go through the thread and give it a go (using the cxx compilers `clang++` or `gcc-10`)

[Jesus Sanchez (jas220)]

Thank you all so much for all your help, I really appreciate it. I've tried all your recommendations but I am still getting the segmentation 11 error, but I have contacted my department to see if they could allocate a computer for me to use. For now, I will keep using a VM.
Once again, thank you very much!