M1 Mac compile error: "Makefile:23: *** missing separator. Stop."

[rextlfung]

I'm trying to use Homebrew to install BART on an apple silicon computer but am encountering the following error when attempting to compile the code:

Makefile:23: *** missing separator. Stop.

I am unfamiliar with the Makefile syntax. Any ideas on how to fix this?

Thanks

[hcmh]

Hey,
since I added that line, I might have made a mistake there. Could you just comment out that line (prefix it with # ) and try again? For debugging your issue, that should not break anything important.

Additionally, can you post the output of make --version ?

[rextlfung]

Hi,

I commented out that line and am now running into:
clang: error: unsupported option '-fopenmp'

The output of make --version is:

GNU Make 3.81
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for i386-apple-darwin11.3.0

[hcmh]

Oh, that is a truly ancient version of GNU make. That might be the issue.

Did you follow the instructions in the README (not README.md) for Mac OS? (see here)

That should install a supported version of both gcc or clang and of make.

[rextlfung]

I see. I just followed these instructions in the README, which I guess doesn't update make:

Using HomeBrew (https://brew.sh):

$ brew install --cask gcc-arm-embedded
$ brew install libpng
$ brew install fftw
$ brew install openblas

Select gcc as the compiler when building:
$ CC=gcc make

Instead, I used brew to install gmake, which seemed to fix the issue but now I am encountering this error:

/bart/src/bart.c:50:10: fatal error: fftw3.h: No such file or directory
50 | #include <fftw3.h>
| ^~~~~~~~~
compilation terminated.

[hcmh]

Hmm, strange. Then we should probably add that to the instructions.

To your new problem: I would guess that $ brew install fftw should fix that?

[rextlfung]

I already tried that. I believe that it has something to do with fftw being installed on my machine but not being seen by the compiler. I will try to figure that out and post the solution here.

[hongzeyu0319]

I'm having the exact same issue here on my m1 mac

[hcmh]

Ok, then we probably need to adapt where bart looks for fftw.

Could you try: find /opt /usr -iname fftw3.h, to see where fftw is located? (I hope that find exists on Mac OS)

[hongzeyu0319]

Ok, then we probably need to adapt where bart looks for fftw.

Could you try: find /opt /usr -iname fftw3.h, to see where fftw is located? (I hope that find exists on Mac OS)

IIt's found here
/opt/homebrew/include/fftw3.h
/opt/homebrew/Cellar/fftw/3.3.10_1/include/fftw3.h

[hcmh]

Ok, that is not where we expect it. You could try compiling with
CC=gcc FFTW_BASE=/opt/homebrew makeand see if that fixes the problem.

And if you not, please also post the compiler command that failed

[hongzeyu0319]

I'm still having the '-fopenmp" unsupported error...

clang: error: unsupported option '-fopenmp'
make: *** [/Users/yuhongze/git/bart/src/bart.o] Error 1

[hcmh]

That error should not be possible when passing CC=clang. What are the lines directly before that message? Those should show the command line that was passed to the compiler, in addition to which compiler was used.
(some like this: gcc -Wall -Wextra -g -MMD -MF src/.bart.d -iquote /home/ch/bart/src/ -I/usr//include -DFFTWTHREADS -I/usr//include/ -Og -Wmissing-prototypes -Wno-vla-parameter -Wno-nonnull -Wno-maybe-uninitialized -g -std=gnu11 -fopenmp -c -o src/bart.o src/bart.c )

Edit: Did you do brew install --cask gcc-arm-embeddedand pass CC=gccto make?

[hongzeyu0319]

Yes I did pass CC=gcc to make. I re-followed the instructions in README for mac-os but still have this error

gcc -Wall -Wextra -DUSE_MACPORTS -MMD -MF /Users/yuhongze/git/bart/src/.bart.d -iquote /Users/yuhongze/git/bart/src/ -I/opt/local//include/ -I/opt/local//include -DFFTWTHREADS -DMAIN_LIST="avg, bench, bin, bitmask, cabs, calc, caldir, calmat, carg, casorati, cc, ccapply, cdf97, circshift, conj, conv, conway, copy, cpyphs, creal, crop, delta, ecalib, ecaltwo, epg, estdelay, estdims, estshift, estvar, extract, fakeksp, fft, fftmod, fftrot, fftshift, filter, flatten, flip, fmac, fovshift, homodyne, ictv, index, invert, itsense, join, looklocker, lrmatrix, mandelbrot, measure, mip, mnist, moba, mobafit, morphop, multicfl, nlinv, nlinvnet, nlmeans, nnet, noise, normalize, nrmse, nufft, nufftbase, onehotenc, ones, pattern, phantom, pics, pocsense, poisson, pol2mask, poly, psf, reconet, repmat, reshape, resize, rmfreq, rof, roistat, rovir, rss, rtnlinv, sake, saxpy, scale, sdot, show, signal, sim, slice, spow, sqpics, squeeze, ssa, std, svd, tensorflow, tgv, threshold, toimg, traj, transpose, twixread, upat, var, vec, version, walsh, wave, wavelet, wavepsf, whiten, window, wshfl, zeros, zexp, ()" -include src/main.h -O2 -Wmissing-prototypes -Wuseless-cast -Wno-c2x-extensions -std=gnu11 -fopenmp -c -o /Users/yuhongze/git/bart/src/bart.o /Users/yuhongze/git/bart/src/bart.c
clang: error: unsupported option '-fopenmp'
make: *** [/Users/yuhongze/git/bart/src/bart.o] Error 1

[hcmh]

Nice, on Mac OS, /usr/bin/gccis actually clang. Great, thank you Apple.

So we need to find out where the gcc that you installed with brew install --cask gcc-arm-embedded actually is.

Could you run find /usr /opt -iname gcc and find /usr /opt -iname gcc-\* for me?

[hongzeyu0319]

Sure, here is the output:

(base) yuhongze@STOP-PROCRASNATING bart % find /usr /opt -iname gcc
/usr/bin/gcc
find: /usr/sbin/authserver: Permission denied
/usr/share/file/magic/gcc
/opt/homebrew/var/homebrew/linked/gcc
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc
/opt/homebrew/Library/Homebrew/shims/super/gcc
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc
/opt/homebrew/lib/gcc
/opt/homebrew/opt/gcc
/opt/homebrew/Cellar/gcc
/opt/homebrew/Cellar/gcc/13.2.0/libexec/gcc
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13/gcc
find: /opt/cisco/anyconnect/temp/downloader: Permission denied
(base) yuhongze@STOP-PROCRASNATING bart % find /usr /opt -iname gcc-*
find: /usr/sbin/authserver: Permission denied
/opt/homebrew/bin/gcc-13
/opt/homebrew/bin/gcc-nm-13
/opt/homebrew/bin/gcc-ar-13
/opt/homebrew/bin/gcc-ranlib-13
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-4.9
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-13
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-12
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-5
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-10
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-11
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-4.2
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-8
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-6
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-7
/opt/homebrew/Library/Homebrew/shims/mac/super/gcc-9
/opt/homebrew/Library/Homebrew/shims/super/gcc-4.9
/opt/homebrew/Library/Homebrew/shims/super/gcc-13
/opt/homebrew/Library/Homebrew/shims/super/gcc-12
/opt/homebrew/Library/Homebrew/shims/super/gcc-5
/opt/homebrew/Library/Homebrew/shims/super/gcc-10
/opt/homebrew/Library/Homebrew/shims/super/gcc-11
/opt/homebrew/Library/Homebrew/shims/super/gcc-8
/opt/homebrew/Library/Homebrew/shims/super/gcc-6
/opt/homebrew/Library/Homebrew/shims/super/gcc-7
/opt/homebrew/Library/Homebrew/shims/super/gcc-9
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-4.9
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-13
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-12
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-5
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-10
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-11
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-4.2
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-8
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-6
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-7
/opt/homebrew/Library/Homebrew/shims/linux/super/gcc-9
/opt/homebrew/Caskroom/gcc-arm-embedded
/opt/homebrew/Caskroom/gcc-arm-embedded/.metadata/13.2.rel1/20231220170548.510/Casks/gcc-arm-embedded.json
/opt/homebrew/Cellar/gcc/13.2.0/bin/gcc-13
/opt/homebrew/Cellar/gcc/13.2.0/bin/gcc-nm-13
/opt/homebrew/Cellar/gcc/13.2.0/bin/gcc-ar-13
/opt/homebrew/Cellar/gcc/13.2.0/bin/gcc-ranlib-13
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/plugin/include/ada/gcc-interface
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/plugin/include/gcc-plugin.h
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/plugin/include/gcc-rich-location.h
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/plugin/include/gcc-symtab.h
/opt/homebrew/Cellar/gcc/13.2.0/share/man/man1/gcc-13.1
/opt/homebrew/Cellar/gcc/13.2.0/share/gcc-13
/opt/homebrew/share/man/man1/gcc-13.1
/opt/homebrew/share/gcc-13