Re: [Octave compilation on macOS 11.2.2 with MacPorts 2.6.4 and GCC 10.2.0]

[Maxim Abalenkov]

Dear all,

Thank you very much for your help and your replies. Please find below the contents of my configure and build bash script:

#!/opt/local/bin/bash

export V=1

CC=gcc
CXX=g++
FC=gfortran
CFLAGS=-I/opt/intel/oneapi/mkl/2021.1.1/include
CXXFLAGS=-I/opt/intel/oneapi/mkl/2021.1.1/include
FFLAGS=-I/opt/intel/oneapi/mkl/2021.1.1/include
LDFLAGS="/opt/local/lib/libiconv.a /opt/intel/oneapi/mkl/2021.1.1/lib/libmkl_blas95_lp64.a"

../configure --prefix=/opt/octave-6.2.0 --disable-readline --without-qt --without-x

make -j 4

As you may see I’m trying to point Octave to Intel’s MKL BLAS and GNU iconv library located in /opt/local/lib. However, I’m still facing the same error and compilation crashes at the same moment:

libtool: link: g++ -dynamiclib  -o liboctave/.libs/liboctave.8.dylib  liboctave/.libs/liboctave_la-liboctave-build-info.o liboctave/.libs/liboctave_la-version.o   -Wl,-force_load,liboctave/array/.libs/libarray.a -Wl,-force_load,liboctave/external/blas-xtra/.libs/libxerbla.a -Wl,-force_load,liboctave/external/ranlib/.libs/libranlib.a -Wl,-force_load,liboctave/external/.libs/libexternal.a -Wl,-force_load,liboctave/numeric/.libs/libnumeric.a -Wl,-force_load,liboctave/operators/.libs/liboperators.a -Wl,-force_load,liboctave/system/.libs/libsystem.a -Wl,-force_load,liboctave/util/.libs/libutil.a -Wl,-force_load,liboctave/wrappers/.libs/libwrappers.a -Wl,-force_load,libgnu/.libs/libgnu.a  -L/opt/local/lib -lcurl -larpack -lfftw3_threads -lfftw3 -lfftw3f_threads -lfftw3f -llapack -lblas -lncurses -lpcre -ldl -L/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0 -L/opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/../../.. -lgfortran -lquadmath -liconv -lm  -pthread -fopenmp -g -O2 -Wl,-framework -Wl,CoreFoundation   -pthread -fopenmp -install_name  /opt/octave-6.2.0/lib/octave/7.0.0/liboctave.8.dylib -compatibility_version 9 -current_version 9.0 -Wl,-single_module

Undefined symbols for architecture x86_64:

  "_cgejsv_", referenced from:

      __ZN6octave4math3svdI18FloatComplexMatrixE5gejsvERcS4_S4_S4_S4_S4_iiPSt7complexIfEiPfS7_S7_iRSt6vectorIS6_SaIS6_EERiRS9_IiSaIiEESD_ in libnumeric.a(libnumeric_la-svd.o)

  "_iconv", referenced from:

      _iconv_carefully_1 in libgnu.a(striconveh.o)

      _mem_cd_iconveh_internal in libgnu.a(striconveh.o)

     (maybe you meant: _str_iconveh, _iconveh_close , _octave_iconv_close_wrapper , _octave_iconv_open_wrapper , _mem_iconveh , _mem_cd_iconveh , _str_iconveha , _iconveh_open , _str_cd_iconveh , _mem_iconveha )

  "_iconv_close", referenced from:

      _octave_iconv_close_wrapper in libwrappers.a(libwrappers_la-iconv-wrappers.o)

      _iconveh_open in libgnu.a(striconveh.o)

      _iconveh_close in libgnu.a(striconveh.o)

     (maybe you meant: _octave_iconv_close_wrapper)

  "_iconv_open", referenced from:

      _octave_iconv_open_wrapper in libwrappers.a(libwrappers_la-iconv-wrappers.o)

      _iconveh_open in libgnu.a(striconveh.o)

     (maybe you meant: _octave_iconv_open_wrapper)

  "_zgejsv_", referenced from:

      __ZN6octave4math3svdI13ComplexMatrixE5gejsvERcS4_S4_S4_S4_S4_iiPSt7complexIdEiPdS7_S7_iRSt6vectorIS6_SaIS6_EERiRS9_IiSaIiEESD_ in libnumeric.a(libnumeric_la-svd.o)

ld: symbol(s) not found for architecture x86_64

collect2: error: ld returned 1 exit status

make[2]: *** [Makefile:14419: liboctave/liboctave.la] Error 1

make[2]: Leaving directory '/Users/mabalenk/repo/git/octave/build'

make[1]: *** [Makefile:27830: all-recursive] Error 1

make[1]: Leaving directory '/Users/mabalenk/repo/git/octave/build'

make: *** [Makefile:11298: all] Error 2

I will investigate further, but please share your thoughts and ideas. Thank you and have a good day ahead!

—

Best wishes,

Maxim

Maxim Abalenkov \\ maxim.abalenkov@gmail.com
+44 7 486 486 505 \\ http://mabalenk.gitlab.io

On 9 Mar 2021, at 15:45, Marius Schamschula <lists@schamschula.com> wrote:

Maxim,

The default MacPorts build uses +accelerate. It is the default variant. However, it is mutually exclusive with the +openblas variant. The atlas variant has long since been retired (as modern macOS kernels and atlas don’t work together). 

You should file a trac ticket or contact Marcus Calhoun-Lopez directly if you find build issue.

On Mar 9, 2021, at 4:44 AM, Maxim Abalenkov <maxim.abalenkov@gmail.com> wrote:

Hello Andrew,

Thank you very much for your help! I do need to compile Octave from source code, because in the future I will need to refactor some of the Octave source code, especially the “mxArray” variable, that conflicts with the MATLAB definition of “mxArray". You may see my yesterday’s email regarding that issue. I found this post on StackOverflow and I’m currently trying to configure and compile Octave adding the “—with-libiconv-prefix=/opt/local/“ option. Unfortunately, that failed and the /opt/local/include and /opt/local/lib directories are not picked up or picked up too late. Now I have added the /opt/local into CFLAGS=-I/opt/local/include, LDFLAGS=-L/opt/local/lib and LIBS=-liconv. I have also dubbed these flags in CXXFLAGS and FCFLAGS.

I didn’t deal with the BLAS/LAPACK errors yet. I was hoping the configure script will pick up Apple’s Accelerate framework. But it seems this is not the case. If you have any advice on how to ensure Octave uses Accelerate I would be grateful. In the worst case I will install the OpenBLAS.

I’m a regular user of MacPorts and I was fine with the version 6.1.0 until recently, when I figured out I have a conflict with MATLAB’s “mxArray” definition. That’s why I may need to refactor Octave’s codebase, renaming “mxArray” into “mtrxArray” for example. It is an intrusive change. But so far I don’t see an elegant solution.

Thank you and have a good day ahead!

—

Best wishes,

Maxim

Maxim Abalenkov \\ maxim.abalenkov@gmail.com
+44 7 486 486 505 \\ http://mabalenk.gitlab.io

On 9 Mar 2021, at 11:32, Andrew Janke <floss@apjanke.net> wrote:

On 3/9/21 3:53 AM, Maxim Abalenkov wrote:

Dear all,
I would like to compile GNU Octave from source code on a macOS BigSur 11.2.2. I obtained the source code from a GitHub repository: git@github.com <mailto:git@github.com>:gnu-octave/octave.git. To compile and install Octave I follow the steps from Octave Wiki page: https://wiki.octave.org/Building <https://wiki.octave.org/Building>. After bootstrapping and changing into the newly created “build” directory. I configure the build with the following command:
../configure --prefix=/opt/octave-6.2.0 --includedir=/opt/local/include/ --disable-readline --without-qt --without-x
Unfortunately, the compilation fails with the following error:
  CXXLD    liboctave/liboctave.la <http://liboctave.la>
Undefined symbols for architecture x86_64:
  "_cgejsv_", referenced from:
      __ZN6octave4math3svdI18FloatComplexMatrixE5gejsvERcS4_S4_S4_S4_S4_iiPSt7complexIfEiPfS7_S7_iRSt6vectorIS6_SaIS6_EERiRS9_IiSaIiEESD_ in libnumeric.a(libnumeric_la-svd.o)
  "_iconv", referenced from:
      _iconv_carefully_1 in libgnu.a(striconveh.o)
      _mem_cd_iconveh_internal in libgnu.a(striconveh.o)
     (maybe you meant: _str_iconveh, _iconveh_close , _octave_iconv_close_wrapper , _octave_iconv_open_wrapper , _mem_iconveh , _mem_cd_iconveh , _str_iconveha , _iconveh_open , _str_cd_iconveh , _mem_iconveha )
  "_iconv_close", referenced from:
      _octave_iconv_close_wrapper in libwrappers.a(libwrappers_la-iconv-wrappers.o)
      _iconveh_open in libgnu.a(striconveh.o)
      _iconveh_close in libgnu.a(striconveh.o)
     (maybe you meant: _octave_iconv_close_wrapper)
  "_iconv_open", referenced from:
      _octave_iconv_open_wrapper in libwrappers.a(libwrappers_la-iconv-wrappers.o)
      _iconveh_open in libgnu.a(striconveh.o)
     (maybe you meant: _octave_iconv_open_wrapper)
  "_zgejsv_", referenced from:
      __ZN6octave4math3svdI13ComplexMatrixE5gejsvERcS4_S4_S4_S4_S4_iiPSt7complexIdEiPdS7_S7_iRSt6vectorIS6_SaIS6_EERiRS9_IiSaIiEESD_ in libnumeric.a(libnumeric_la-svd.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:14419: liboctave/liboctave.la <http://liboctave.la>] Error 1
make[2]: Leaving directory '/Users/mabalenk/repo/git/octave/build'
make[1]: *** [Makefile:27830: all-recursive] Error 1
make[1]: Leaving directory '/Users/mabalenk/repo/git/octave/build'
make: *** [Makefile:11298: all] Error 2
To compile Octave I use the GNU toolchain from MacPorts: g++ (MacPorts gcc10 10.2.0_5) 10.2.0. I would welcome any guidance or advice on how to resolve this issue and proceed further. Thank you and have a good day ahead!
—
Best wishes,
Maxim
Maxim Abalenkov \\ maxim.abalenkov@gmail.com <mailto:maxim.abalenkov@gmail.com>
+44 7 486 486 505 \\ http://mabalenk.gitlab.io <http://mabalenk.gitlab.io>

Hi Maxim,

cgejsv and zgejsv are LAPACK functions, which should be included in your BLAS. Are you sure you have a good OpenBLAS build and it's on the path? Or are you trying to compile against Apple Accelerate as your BLAS/LAPACK implementation?

Looks like you're also missing a -liconv or similar to link GNU libiconv?

Compiling Octave on a Mac can be tricky. I think your best bet is to use a package manager definition for it instead of trying to build from source yourself, unless you have custom build requirements.

Are you a regular MacPorts user, or did you just install it to get the build environment for Octave?

If you're a MacPorts user, I'd contact their octave port maintainer and see if they can bump their port to 6.2.0 so you can just install that instead of having to build yourself. (It's currently on 6.1.0; I assume that's why you're doing your own build here.)

If you're just using MacPorts to build Octave and are in a hurry, consider switching to Homebrew: the Octave.app project has a Homebrew formula for Octave 6.2.0 that has been successful against recent macOS releases. [1] And the core Homebrew Octave formula [4] is on 6.2.0, if you don't mind some GUI hiccups.

Or just download the pre-built Octave.app. [2] There's a beta for 6.2.0 out. [3] Octave.app is primarily used for its GUI, but you can run the command-line octave from it just fine, too.

Cheers,
Andrew

[1a] https://github.com/octave-app/homebrew-octave-app/blob/master/Formula/octave%406.2.0.rb
[1b] https://github.com/octave-app/homebrew-octave-app/blob/master/Formula/octave-octave-app%406.2.0.rb
[2] https://octave-app.org/
[3] https://github.com/octave-app/octave-app/releases/tag/v6.2.0-beta1
[4] https://formulae.brew.sh/formula/octave