Installation failure on Mac.

[Nicholas Webster]

Hi everyone, I am trying to install Majiq 2.5 on a Mac.  I have python 3.13, pip and Xcode are up to date. I have previously used older versions of Majiq with no problem but the new release is giving me problems.  The installation fails while compiling scipy.  I have gcc installed as clang cannot handle it, and installed HTSLib, openblas, scipy, numpy etc. Building numpy2.0.0 works okay but the next step with scipy1.14.0 fails.  Here is the last section of the output.

Found ninja-1.11.1.git.kitware.jobserver-1 at /private/var/folders/9q/jtb1y2zn6dg5gw99h4x46vpc0000gn/T/pip-build-env-t80a96vi/normal/bin/ninja

      + /private/var/folders/9q/jtb1y2zn6dg5gw99h4x46vpc0000gn/T/pip-build-env-t80a96vi/normal/bin/ninja

      [1/1383] Compiling C object scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o

      FAILED: scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o

      cc -Iscipy/libdummy_g77_abi_wrappers.a.p -Iscipy -I../scipy -I../../../pip-build-env-t80a96vi/overlay/lib/python3.13/site-packages/numpy/_core/include -I/opt/homebrew/opt/pyt...@3.13/Frameworks/Python.framework/Versions/3.13/include/python3.13 -I/opt/homebrew/Cellar/openblas/0.3.29/include -fvisibility=hidden -fdiagnostics-color=always -DNDEBUG -Wall -Winvalid-pch -std=c17 -O3 -Wno-unused-but-set-variable -Wno-unused-function -Wno-conversion -Wno-misleading-indentation -DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -fopenmp -MD -MQ scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o -MF scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o.d -o scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o -c ../scipy/_build_utils/src/wrap_dummy_g77_abi.c

      clang: error: unsupported option '-fopenmp'

      [2/1383] Generating scipy/generate-version with a custom command

      [3/1383] Copying file scipy/__init__.py

      [4/1383] Copying file scipy/_lib/ccallback.pxd

      [5/1383] Copying file scipy/_lib/messagestream.pxd

      [6/1383] Copying file scipy/_lib/__init__.py

      [7/1383] Copying file scipy/special.pxd

      [8/1383] Copying file scipy/linalg.pxd

      [9/1383] Copying file scipy/_lib/_ccallback_c.pxd

      [10/1383] Copying file scipy/special/__init__.py

      [11/1383] Copying file scipy/optimize.pxd

      [12/1383] Compiling C object scipy/_lib/_fpumode.cpython-313-darwin.so.p/_fpumode.c.o

      [13/1383] Compiling C object scipy/_lib/_test_ccallback.cpython-313-darwin.so.p/src__test_ccallback.c.o

      [14/1383] Compiling C++ object scipy/_lib/_uarray/_uarray.cpython-313-darwin.so.p/vectorcall.cxx.o

      [15/1383] Compiling C object scipy/lib_fortranobject.a.p/e607009551dd8d49b2d72d873d79e3067b0c0ccc_site-packages_numpy_f2py_src_fortranobject.c.o

      [16/1383] Compiling C++ object scipy/_lib/_uarray/_uarray.cpython-313-darwin.so.p/_uarray_dispatch.cxx.o

      ninja: build stopped: subcommand failed.

      [end of output]

The C++ installer is g++ that is installed with gcc.  The directory is in PATH ahead of /usr/bin/ which has clang, so gcc g++ and gfortan should be called correctly. 

Does anyone have any suggestions?  Thanks, Nick

[San Jewell]

Hello,

In general majiq uses openMP for it's multithreading, which is not supported on clang historically. You'll need to use gcc instead of clang. The process is documented here: https://groups.google.com/g/majiq_voila/c/Nal5OBGWj7g/m/H8jaFHHiAAAJ among other places on the board.

Also, in general I would recommend using the officially supported python version which is currently 3.10.

Let me know if either of these suggestions resolve the installation issue.

Thanks,

-San

[Nicholas Webster]

Hi San,  

got it to install ok by forcing the use of gcc and g++ (pip was still going to clang) and following Matt Gazzara's instructions (https://groups.google.com/g/majiq_voila/c/ecjrfZzWOKs/m/ZNx-ZaaRCAAJ) to install in conda environment with python 3.10. 

Thanks, Nick