OS upgrade to Catalina: "gcc", "gfortran", "libstdc++.6.dylib"

parizek

I just updated my OS on my MacBook Pro to Catalina and while "ISSM development path correctly loaded" still appears in Matlab, the freely available compilers are not being recognized as "macOS cannot verify that this app is free from malware", "cannot be opened because the developer cannot be verified". Can anyone let me know what changes I need to make to use ISSM with the Catalina OS? Will this require a complete reinstallation of ISSM or just adjusting the links or grabbing new XCode apps? Many thanks!

mathieumorlighem

Hi Byron! if you installed from source, you will need to reinstall everything because the libraries changed 🙁 if you are using the binaries we should be able to help
Mathieu

parizek

That's what I was afraid of... 🙁. Is there a thread or help page detailing which source files and settings I should select when reinstalling with Catalina as the OS? Thank you Mathieu. I hope this finds you and yours doing well.

mathieumorlighem

it is exactly the same process as before, there is nothing special you need to do: https://issm.jpl.nasa.gov/download/unix/ you can remove your installation of mpich (rm -rf $ISSM_DIR/externalpackages/mpich) and install the latest PETSc version (3.12) which comes with mpich. The rest is unchanged. Let us know if you need any help!
Mathieu

parizek

Will do. One quick starting question: Do you recommend following Apple's suggestion to update the interactive shell from bash to zsh and transition all of the .bash_profile and .bashrc info over to the .zprofile and .zshrc equivalents?

mathieumorlighem

I just switched everything to zsh and I do like it 🙂 It is very very similar to bash, you can copy everything you have in your ~/.bash_profile to ~/.zshrc and it should work out of the box. I only had to convert the prompt: this is what I am using in zsh:
PROMPT='%(?.%F{green}√%f.%F{red}?%?%f)%F{203}%m%f:%F{76}%1~%f%F{226}$%f '