Error running make; make install on MPICH

elizadawson

Hi @justinquinn just wanted to follow up about the petsc installation problems to see if you have any suggestions. Also I forgot to mention before that I am installing on a mac with apple silicon chip (sonoma 14.7.2). Thanks for your help!

justinquinn

elizadawson
Hi Eliza,
Sorry, I haven't forgotten about you, just tied up on another task. I'm hoping to get to this today!

mathieumorlighem

Hello @elizadawson it seems from your configure file that you have Anaconda installed. Could you deactivate it while you install PETSC? see https://issm.jpl.nasa.gov/download/unix/
Cheers
Mathieu

justinquinn

mathieumorlighem Good catch, Mathieu!

elizadawson

justinquinn

mathieumorlighem Thanks for the catch. I deactivated my conda environment however I still have an error with MPICH when I try to install petsc (install-3.22-mac). Here is the new configure.log: https://drive.google.com/file/d/1NKcOg-gRgk0t8Bw-bXRqliC589LxJ-Ct/view?usp=sharing

justinquinn

elizadawson Do you have the Command Line Tools installed? If not, you can install them with xcode-select --install. If they are already installed, you can switch from using Xcode to the Command Line tools with sudo xcode-select -switch /Library/Developer/CommandLineTools. Then try building again.

justinquinn

elizadawson
Hi Eliza,
Just checking in. Were you able to get things working?

elizadawson

justinquinn Hi, I've made some progress but petsc is still not successfully installing.
I ran the sudo command to switch from xcode to command line tools and now when I run the petsc installation, mpich configure, make and install is successful. However after that, as part of building and installing zlib, I get a message:

       TESTING: consistencyChecks from config.packages.fblaslapack(config/BuildSystem/config/package.py:1112)

       UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):

Cannot use fblaslapack without Fortran, make sure you do NOT have --with-fc=0

So it appears the error is now potentially something related to fortran however I also see other errors in the configure.log. I have attached the newest configure.log here: https://drive.google.com/file/d/1cLXRp5BiaD-VhvnLH6ov64WFQfn_9g-8/view?usp=sharing
If you have more suggestions, let me know. Thanks for the help!

justinquinn

elizadawson
Hi Eliza,
Looks like conda is active again. Can you try deactivating with conda deactivate and run the PETSc install script again in that same terminal session?

elizadawson

justinquinn Hmm that's interesting that it looks like its still active. I deactivated it before the PETSc install and it is not showing as active in my terminal session...

justinquinn

elizadawson Yeah, _CONDA_EXE=/Users/edawson31/miniconda3/bin/conda and the existence of /Users/edawson31/miniconda3/condabin on PATH imply it's still active, but if you've deactivated it then it's a non issue. Actually, looking at it closer, there' something funny going on with all of the ISSM related additions to PATH, for example {{{/Users/edawson31/issm/trunk}/externalpackages}/cmake/install}. There shouldn't be any curly braces in the expansion there. Where is ISSM_DIR defined and what it is set to? Is it enclosed in single quotes (if anything, it should be double quotes)?

Also, can you update with git pull. There are some important changes I committed for $ISSM_DIR/etc/environment.sh just last night.

elizadawson

justinquinn I figured out the problems with installing PETSc and now I think I have successfully installed all the external packages. However, running make I get the following error (I also included a few lines above the error message):

ld: warning: could not create compact unwind for zunmbr: does not use standard frame
ld: warning: could not create compact unwind for zunmhr: does not use standard frame
ld: warning: could not create compact unwind for zunml2: does not use standard frame
ld: warning: could not create compact unwind for zunmlq: does not use standard frame
ld: warning: could not create compact unwind for zunmql: does not use standard frame
ld: warning: could not create compact unwind for zunmqr: does not use standard frame
ld: warning: could not create compact unwind for zunmr2: does not use standard frame
ld: warning: could not create compact unwind for zunmr3: does not use standard frame
ld: warning: could not create compact unwind for zunmrq: does not use standard frame
ld: warning: could not create compact unwind for zunmtr: does not use standard frame
ld: warning: could not create compact unwind for zupgtr: does not use standard frame
ld: warning: could not create compact unwind for zupmtr: does not use standard frame
ld: file not found: @rpath/libquadmath.0.dylib for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [libISSMApi_matlab.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

I am pretty sure this is related to gcc/gfortran but not sure how to fix it. When I ran my configure.sh (before make) I see:

checking for Fortran compilation... yes

so it looks like the directory is found. I attached my configure.sh file incase that helps. I also tried setting:

export DYLD_LIBRARY_PATH="/Users/edawson31/issm/trunk/externalpackages/triangle/install/lib:/opt/homebrew/Cellar/gcc/14.2.0_1/lib/gcc/14:$DYLD_LIBRARY_PATH"

since that is where I see libquadmath, but that also didn't fix the problem. Let me know if you have suggestions. Thanks!

configure.sh

909B

justinquinn

elizadawson Hi Eliza, that's great progress. Yes, the rpath issue on macOS Silicon especially is very annoying and we don't have a great fix for it despite our best efforts. The best thing to do it seems is something like,

sudo ln -s /opt/homebrew/Cellar/gcc/14.2.0_1/lib/gcc/14/libgfortran.5.dylib /usr/local/lib/libgfortran.5.dylib
sudo ln -s /opt/homebrew/Cellar/gcc/14.2.0_1/lib/gcc/14/libquadmath.0.dylib /usr/local/lib/libquadmath.0.dylib

correction the version of libgfortran as needed. Not ideal, but should work. Note that you will need to manually rm this link and recreate it if you upgrade gfortran under Homebrew and the version (i.e. 14.2.0_1) and corresponding path changes.

elizadawson

justinquinn Thank you for all the help. That did it!

justinquinn

elizadawson No problem at all! Glad to hear you’re up and running. Do let us know if you run into further issues.

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