External Package Installation on Apple M1 Chip

lawrence-bird

Thanks Justin - that was an easy fix! Libtool is now taken care of.

I'm still having issues with petsc - which version of the install script would you recommend using, and which version of gfortran? I have gfortran version 11.2.0 which appears to be the latest release, but is intended for intel processors. I wonder if this might be my issue. When I try the install-3.14-mac.sh script, it fails with the following error:

*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Unknown Fortran name mangling: Are you sure the C and Fortran compilers are compatible?
  Perhaps one is 64 bit and one is 32 bit?
  See https://www.mcs.anl.gov/petsc/documentation/faq.html#gfortran
*******************************************************************************

I checked the type of compilers I have:

/usr/local/bin/gfortran: Mach-O 64-bit executable x86_64
/usr/bin/gcc: Mach-O universal binary with 2 architectures: [x86_64:Mach-O 64-bit executable x86_64] [arm64e:Mach-O 64-bit executable arm64e]
/usr/bin/gcc (for architecture x86_64): Mach-O 64-bit executable x86_64
/usr/bin/gcc (for architecture arm64e): Mach-O 64-bit executable arm64e

Based on this, I tried to force the script to run using the x86_64 architecture, since I don't have an arm64 version of gfortran. I used "arch -x86_64e ./install-3.14-mac.sh" and the install progressed further, but gets hung up on HDF5 (see my first post for that error). When trying the install-3.15-mac-arm.sh script, I get the following error:

*******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
-------------------------------------------------------------------------------
Could not locate a functional C compiler
*******************************************************************************

I'm missing something here, but struggling to figure out exactly what it is!

Thanks for your advice.

Lawrence

justinquinn

lawrence-bird
Glad to hear that worked.

To reiterate, once you have the external packages built, you will have to use the Python API for ISSM until MathWorks have updated MATLAB. If that is okay with you, I can help you with a configuration that works for me under Monterey (I do not have a machine with the M1 chipset, so hopefully we do not hit any snags in that respect).

mathieumorlighem

Hi @lawrence-bird

we have a new script for installing PETSc on M1 chips. Can you try install-3.15-mac-arm.sh ?
Mathieu

lawrence-bird

mathieumorlighem
Hi Mathieu:

I'd tried that install script too, but it was failing with an error around being unable to find a functional C compiler (see second error included on my post above).

Thanks.

Lawrence

justinquinn

lawrence-bird
Could you attach src/configure.log?

lawrence-bird

justinquinn
Hi Justin:

The Forum doesn't appear to let me upload a *.log or a *.txt file - is there perhaps an email I can send the configure.log to you at?

As for using Python, I am okay with that for now - hopefully an update to MATLAB is released in the not too distant future.

@mathieumorlighem - thanks for the note on gfortran. I'll see if Justin spots anything obvious in the configure.log, otherwise I'll definitely try a different gfortran version.

Thank you both for your help - I appreciate it!

Lawrence

mathieumorlighem

We installed gfortran from https://github.com/fxcoudert/gfortran-for-macOS/releases (I think it was gfortran 11-experimental-2 for ARM Big Sur (macOS 11))

justinquinn

lawrence-bird

That is odd indeed. I'll have to look further into this restriction.

That said, I suspect Mathieu is correct: it is likely due to having a copy of gfortran that is not designed to compile for the M1 target.

lawrence-bird

justinquinn

Thanks Justin - I'll give that a whirl and let you know how it works out.

lawrence-bird

@justinquinn @mathieumorlighem

Hi Justin/Mathieu:

Updating gfortran to an experimental ARM version for MacOS Monterey (gfortran 12-experimental for ARM, macOS 12 (Monterey)) did indeed allow me to successfully install PETSc. That said, I was able to install all external packages.

Moving on to the next step, ISSM appears to configure successfully, but is failing during make. I am receiving the following error:

ld: file not found: @rpath/libgcc_s.1.1.dylib for architecture arm64 clang: error: linker command failed with exit code 1 (use -v to see invocation)

It seems to be something to do with gcc; however, when I interrogate the gcc version on my system (below), it looks like there is a gcc version suitable for arm64:

$ which gcc /usr/bin/gcc

$ file /usr/bin/gcc /usr/bin/gcc: Mach-O universal binary with 2 architectures: [x86_64:Mach-O 64-bit executable x86_64] [arm64e:Mach-O 64-bit executable arm64e] /usr/bin/gcc (for architecture x86_64): Mach-O 64-bit executable x86_64 /usr/bin/gcc (for architecture arm64e): Mach-O 64-bit executable arm64e

$ gcc --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 Apple clang version 13.0.0 (clang-1300.0.29.30) Target: arm64-apple-darwin21.2.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

If you have any ideas on this, I'm all ears!

Thanks.

Lawrence

justinquinn

lawrence-bird
What do you get from find /usr -name libgcc_s*?

lawrence-bird

justinquinn

Hi Justin:

That command returns the following location: /usr/local/gfortran/lib/libgcc_s.1.1.dylib

Thanks.

Lawrence

justinquinn

lawrence-bird Okay, you may have to,

export LD_LIBRARY_PATH=/usr/local/gfortran/lib:${LD_LIBRARY_PATH}
export DYLD_LIBRARY_PATH=/usr/local/gfortran/lib:${DYLD_LIBRARY_PATH}

in your shell profile (the above assumes bash). You may be able to test this ahead of time by exporting (or otherwise setting these environment variables) directly in the terminal instance and recompiling.

lawrence-bird

justinquinn

Hi Justin - I implemented this, but the same error persists, unfortunately. I assume this would not affect the external package installations and I don't need to recompile those?

lawrence-bird

justinquinn

I am not sure if it's relevant where this error is occurring during the make process, but this is the full error:

ld: file not found: @rpath/libgcc_s.1.1.dylib for architecture arm64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: *** [libISSMCore.la] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2

This is preceded by a number of warnings similar to this:

*** Warning: Linking the shared library libISSMCore.la against the *** static library /Users/lbir0005/ISSM/trunk/externalpackages/m1qn3/install/libddot.a is not portable! ld: warning: object file (./modules/FourierLoveCorex/.libs/lnb_param.o) was built for newer macOS version (12.1) than being linked (12.0)

justinquinn

lawrence-bird
I wouldn't think that this would affect any of the external packages, no.

justinquinn

lawrence-bird
Could you post the 10 lines or so before ld: file not found: @rpath/libgcc_s.1.1.dylib for architecture arm64?

lawrence-bird

justinquinn

Here's the full output once things start going awry:

*** Warning: Linking the shared library libISSMCore.la against the *** static library /Users/lbir0005/ISSM/trunk/externalpackages/m1qn3/install/libm1qn3.a is not portable! *** Warning: Linking the shared library libISSMCore.la against the *** static library /Users/lbir0005/ISSM/trunk/externalpackages/m1qn3/install/libddot.a is not portable! ld: warning: object file (./modules/FourierLoveCorex/.libs/lnb_param.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: object file (./modules/FourierLoveCorex/.libs/model.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: object file (./modules/FourierLoveCorex/.libs/util.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: could not create compact unwind for ___model_MOD_earth_nlayers: register 28 saved somewhere other than in frame ld: warning: could not create compact unwind for ___model_MOD_earth_nlayers_viscoelas: register 75 saved somewhere other than in frame ld: warning: could not create compact unwind for ___model_MOD_model_init2: register 73 saved somewhere other than in frame ld: warning: object file (./modules/FourierLoveCorex/.libs/lovenb_sub.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: could not create compact unwind for ___lovenb_sub_MOD_solution_nbloutput: registers 78 and 79 not saved contiguously in frame ld: warning: could not create compact unwind for ___util_MOD_ludcmp: register 24 saved somewhere other than in frame ld: warning: ld: warning: could not create compact unwind for ___util_MOD_derivs: registers 78 and 79 not saved contiguously in frameld: warning: could not create compact unwind for ___lovenb_sub_MOD_solution: registers 78 and 79 not saved contiguously in frameld: warning: object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-ojrule.o) was built for newer macOS version (12.1) than being linked (12.0)ld: warning: object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-freed.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: ld: warning: object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-distme.o) was built for newer macOS version (12.1) than being linked (12.0) object file (./modules/FourierLoveCorex/.libs/love_numbers.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-pwise.o) was built for newer macOS version (12.1) than being linked (12.0) object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-qwise.o) was built for newer macOS version (12.1) than being linked (12.0)ld: warning: ld: warning: object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-what0.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: could not create compact unwind for _what0_: registers 78 and 79 not saved contiguously in frame ld: warning: could not create compact unwind for ___lovenb_sub_MOD_boundary_conditions_matrix: register 77 saved somewhere other than in frame ld: warning: object file (./modules/GiaDeflectionCorex/.libs/libISSMCore_la-stot.o) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: could not create compact unwind for _stot_: registers 72 and 73 not saved contiguously in frame could not create compact unwind for _love_numbers_: registers 27 and 28 not saved contiguously in frame ld: warning: could not create compact unwind for _lnb_setup_: registers 27 and 28 not saved contiguously in frame ld: warning: could not create compact unwind for _distme_: register 75 saved somewhere other than in frame ld: warning: dylib (/Users/lbir0005/ISSM/trunk/externalpackages/petsc/install/lib/libmpifort.dylib) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: dylib (/usr/local/gfortran/lib/gcc/aarch64-apple-darwin21/12.0.0/../../..//libgfortran.5.dylib) was built for newer macOS version (12.1) than being linked (12.0) ld: warning: dylib (/usr/local/gfortran/lib/gcc/aarch64-apple-darwin21/12.0.0/../../..//libquadmath.0.dylib) was built for newer macOS version (12.1) than being linked (12.0) ld: file not found: @rpath/libgcc_s.1.1.dylib for architecture arm64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: *** [libISSMCore.la] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2

justinquinn

lawrence-bird
Hi Lawrence,
The warnings may look alarming but do not indicate an actual failure. I think what might be going on is that the binaries of the this copy of gfortran are functional but the /usr/local/gfortran/lib/libgcc_s.1.1.dylib may not be compiled with ARM as the target. To be perfectly honest, I don't know what is trying to linke against libgcc_s. What do you get from ldd /usr/local/bin/gfortran? Also, what does your configuration look like?

lawrence-bird

justinquinn

Hi Justin:

ldd doesn't appear to work (I'm not sure if it's all Mac's or just these new systems), but apparently otool -L is the equivalent. Output from this:

$ otool -L /usr/local/bin/gfortran /usr/local/bin/gfortran: /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1311.0.0)

Perhaps I will try rolling back my gfortran version to the one listed by Mathieu and see if that works on Monterey (as well as it's intended MacOS 11).

justinquinn

lawrence-bird
Right, ldd aliases to otool-classic in my case.

Okay, the output looks the same as mine. You might try running down the dependency trail by running otool -L on each of the libraries that are listed to see if they, in turn, load libgcc_s.1.1.dylib. That said, I suspect it is something else that is linking to this library. It may, after all, be one of the external package libraries, so you may have to check those too with otool.

Try rolling back your gfortran version though first and let's see if that resolves it.