Installation issues related to PETSC on Apple M1 Chip

ahayden

justinquinn
Hi Justin,
Thanks for those suggestions!!

I've made a few changes to my configure.sh file (including deleting the chaco line, which was also causing problems - I removed the appropriate install in the corresponding folder in externalpackages/chaco - but I've since added the chaco line back in). As you suggested, I split up the options on three lines.

Now, different errors are coming up when I run ./configure.sh

But, I did install petsc without any issues:

I installed 3.17-mac-silicon.sh. However, it doesn't look like there's an "include" directory"

I've attached the updated configure.sh file

configure.sh

1kB

All the best,

Anna

justinquinn

ahayden Hi Anna,
Can you double check with ls $ISSM_DIR/externalpackages/petsc/install? Also, you should probably use the latest version of the PETSc install script. In case you have a copy of trunk/ and not trunk-jpl/ (the development branch), I'll attach it here. Simply download it to $ISSM_DIR/externalpackages/petsc, rename it to /install-3.21-mac.sh, modify permissions with chmod +x $ISSM_DIR/externalpackages/petsc/install-3.21-mac.sh, then run it. You will also need an updated copy of $ISSM_DIR/etc/environment.sh, which I'll also attach. (Note that these changes will be available on the public branch the next time we merge.)

install-321-mac.sh

1kB

environment.sh

20kB

ahayden

justinquinn

Hi Justin,

Ok, prior to updating the install and environment files, I double-checked the install folder, and it was empty. Then, after following your instructions, there is a /include folder. However, it doesn't have the petscblaslapack.h file.

Then, after I ran
$ cd $ISSM_DIR
$ autoreconf -ivf
$ ./configure.sh

I get the error
./configure.sh: line 14: --with-metis-dir=/Users/annahayden/Dropbox/trunk/externalpackages/petsc/install: No such file or directory

But the directory does exist... Maybe something went wrong when I ran ./configure instead of ./configure.sh?

justinquinn

ahayden There's an off-chance that the permissions were somehow messed up on this directory. To test, you could run sudo chmod -R 755 /Users/annahayden/Dropbox/trunk/externalpackages/petsc/install, then try the ISSM install again. If that still doesn't work, you might try a reinstall of PETSc.

ahayden

justinquinn
Hi Justin,
Thanks for sticking with me! Just want to clarify something, when you say

try the ISSM install again

Do you mean start from scratch i.e., re-try downloading trunk using svn?

justinquinn

ahayden No worries at all. We'll get you sorted. 🙂

No, I mean make; make install.

ahayden

justinquinn
We're getting closer! I reinstalled PETSc. then ran make, which didn't result in any errors!

However make install didn't work:

justinquinn

ahayden Ah, /usr/local generally should gave open permissions for all users, but I wouldn't recommend using /usr/local/lib as an install target for ISSM's libraries. What do you have ISSM_DIR set to? Where did you check out the repo to? I recommend setting ISSM_DIR to that location, and in your configure.sh, set the install target with --prefix=${ISSM_DIR}. Note that you'll have to start a new terminal, and may have to run autoreconf ivf again in $ISSM_DIR before make; make install.

ahayden

justinquinn
Hi Justin,

My ISSM_DIR is in my Dropbox folder, so I would have thought that the libraries would be installed there. I don't know what the repo is. My configure.sh file has the line --prefix=${ISSM_DIR}

justinquinn

Hi Anna,
The screenshot with errors indicates that ISSM's libraries have been installed to /usr/local/lib. The only way this should happen is if ISSM_DIR is defined as /usr/local. What do you get from echo $ISSM_DIR?

ahayden

justinquinn

Here's what comes up:

justinquinn

ahayden I would try a new terminal, cd $ISSM_DIR; source etc/environment.sh; ./configure.sh; make; make install

(Assuming configure.sh is located in $ISSM_DIR)

ahayden

Hi Justin,

Ok, looks like we're back to square one after opening a new terminal:

Should I try to reinstall PETSc?

justinquinn

I really don't know what's going on here, but I suspect it may have to do with the fact that you checked out the trunk to a subdirectory of Dropbox. Try checking out a new copy to, say, ~/ISSM, recompiling the external packages, copying over your configure script, then configuring and compiling ISSM. Make sure to redefine ISSM_DIR to the new location of your trunk (in this example, export ISSM_DIR=~ISSM).

ahayden

justinquinn

Hi Justin,

I did a fresh install of trunk in my home directory, and it seemed to work until I launched Matlab from the command line. Once I launched Matlab, it couldn't find the libgfortran.dylib file. I moved the contents of the gfortran folder to /usr/local/gfortran and changed the filepath in the configure.sh to match. I then re-installed the external packages and ran into errors when it came to the m1qn3 install:

patching file 'src/src/m1qn3.f'
gfortran -arch arm64 -fPIC -c m1qn3.f -o m1qn3.o
make: gfortran: No such file or directory
make: *** [m1qn3.o] Error 1

Any suggestions on what to do next?

Thanks,

Anna

ahayden

justinquinn

Hi Justin,

I removed then reinstalled gfortran from the binaries, tried to create a symbolic link in .zshrc:

sudo ln -s /usr/local/bin/gfortran /usr/local/gfortran

I reinstalled the external packages, but once I got to PETSc, the following error came up at the end of the install:

Here is what the configure.log file in PETSc looks like:

Any thoughts on what to do next?

Thanks,

Anna

justinquinn

ahayden Hi Anna,
You're very close here. I think you just need to remove the symbolic link command from ~/.zshrc, run the command manually once, then try the m1qn3 and issm compilation again.

ahayden

justinquinn

Hi Justin,

Shivani and I got it to work! In addition to moving the trunk to the home directory, here are the other fixes that we implemented:

the Fortran binaries that I downloaded had included gcc as well as gfortran, which I don't think ISSM liked since I had gcc from Command Line Tools. So I just re-downloaded the gfortran binaries
Symbolic links to the non-MATLAB gfortran files: libf70rts.dylib libgfortran.5.dylib libgfortran.dylib

Thank you so much for all your help and suggestions!

Cheers,

Anna

justinquinn

ahayden
Hi Anna,
That's great news! Glad to hear it's all worked out now. Let us know if you run into any other issues.

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