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amusecode / amuse

Astrophysical Multipurpose Software Environment. This is the main repository for AMUSE
http://www.amusecode.org
Apache License 2.0
151 stars 99 forks source link

Community Packages not installing properly #911

Closed dnrgodilano7 closed 1 year ago

dnrgodilano7 commented 1 year ago

The installation kept terminating because some of the packages have installation errors. I'm using MacOS Ventura, M1 Pro chip

I used: export AMUSE_ALLOW_BUILD_FAILURES=all to bypass them and was able to install most of the packages.

I used the amuse.test.suite to know which packages didn't go through:

errors.txt

I tried installing the community packages separately.

This is the common problem with the installation:

It seems that you are using distutils.command.build to add new subcommands. Using distutils directly is considered deprecated, please use setuptools.command.build.

then it returns termination error saying that it cannot find or create file/directory.

Error reports below:

Thank You!

EXAMPLE 1: [11:28:40] building brutus error in call, tail output:

amusifier --type=c interface.py BrutusInterface -o worker_code.cc amusifier --type=H -i amuse.community.interface.stopping_conditions.StoppingConditionInterface interface.py BrutusInterface -o worker_code.h make -C src all CXXFLAGS="-g -O2 -fno-common -I./mpfrc++ -std=c++0x -I../mpfrc++" g++ -O1 -g -O2 -fno-common -I./mpfrc++ -std=c++0x -I../mpfrc++ -c Star.cpp In file included from Star.h:6, from Star.cpp:1: ../mpfrc++/mpreal.h:125:10: fatal error: mpfr.h: No such file or directory 125 | #include | ^~~~ compilation terminated. make[1]: [Star.o] Error 1 make: [src/libbrutus.a] Error 2

EXAMPLE 2:

Running command Building wheel for amuse-simplex (pyproject.toml) running bdist_wheel running build /private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-4x1_1gyr/overlay/lib/python3.9/site-packages/setuptools/command/build.py:31: SetuptoolsDeprecationWarning: It seems that you are using distutils.command.build to add new subcommands. Using distutils directly is considered deprecated, please use setuptools.command.build.

warnings.warn(msg, SetuptoolsDeprecationWarning)

running build_py creating build creating build/lib creating build/lib/amuse creating build/lib/amuse/community creating build/lib/amuse/community/simplex copying src/amuse/community/simplex/version.py -> build/lib/amuse/community/simplex copying src/amuse/community/simplex/interface.py -> build/lib/amuse/community/simplex copying src/amuse/community/simplex/init.py -> build/lib/amuse/community/simplex running build_codes building libraries and community codes . . . copying src/amuse/community/simplex/src/src/Main.cpp -> build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/src/src [18:43:23] building simplex error in call, tail output:

    ...
"_H5Sselect_hyperslab", referenced from:
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w9read_dataIdEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIiEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIjEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIlEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    ...
"_H5T_C_S1_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
"_H5T_NATIVE_DOUBLE_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_FLOAT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_INT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_LDOUBLE_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
"_H5T_NATIVE_LLONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_LONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_SCHAR_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_SHORT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_UCHAR_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_UINT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_ULLONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_ULONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_USHORT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5Tclose", referenced from:
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w12make_datasetEPKcS1_iPy in h5w_serial.o
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
    __ZN3h5w9read_dataIdEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIiEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    ...
"_H5Tcopy", referenced from:
    __ZN3h5w9read_attrIjEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIdEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIsEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_attrIjEEvPKcS2_T_ in SimpleX.o
    __ZN3h5w10write_attrIdEEvPKcS2_T_ in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    ...
"_H5Tequal", referenced from:
    __ZN3h5w9read_attrIjEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIdEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIsEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
    ...
"_H5Tget_size", referenced from:
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
"_H5Tset_order", referenced from:
    __ZN3h5w12make_datasetEPKcS1_iPy in h5w_serial.o
"_H5Tset_size", referenced from:
    __ZN3h5w10write_attrEPKcS1_Pc in h5w_serial.o
    __ZN3h5w10write_attrEPKcS1_S1_ in h5w_serial.o
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
"_H5check_version", referenced from:
    __ZN3h5wC1EPc in h5w_serial.o
    __ZN3h5wC1EPcc in h5w_serial.o
    __ZN3h5w4openEPc in h5w_serial.o
    __ZN3h5w4openEPcc in h5w_serial.o
"_H5open", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5wC1EPc in h5w_serial.o
    __ZN3h5wC1EPcc in h5w_serial.o
    __ZN3h5w4openEPc in h5w_serial.o
    __ZN3h5w4openEPcc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o

ld: symbol(s) not found for architecture arm64 collect2: error: ld returned 1 exit status make: *** [simplex_worker] Error 1

will copy worker: src/amuse/community/simplex simplex creating build/lib/amuse/community/simplex/data creating build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/N.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/vertices_10.txt -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/H.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/vertices_test.txt -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/O.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Fe.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/vertices_test2.txt -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/vertices_test3.txt -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/H2.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Ne.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Fe.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/He.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Si.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/H.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/He.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/C.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/C.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/O.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/N.cool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Ne.Hcool -> build/lib/amuse/community/simplex/data/input copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Si.Hcool -> build/lib/amuse/community/simplex/data/input Community codes not built (because of errors):

Thank You!

rieder commented 1 year ago

It looks like you’re missing some prerequisites, specifically mpfr and hdf5. Apart from that, the codes that fail to build are mostly codes requiring special libraries, e.g. CUDA. Your installation seems to be mostly in order.

dnrgodilano7 commented 1 year ago

I checked if they're installed, they seem to be installed:

h5ls -V h5ls: Version 1.13.1

python -c 'import h5py; print(h5py.version.version)' 3.7.0

port search mpfr

gawk-mpfr @1.1.0 (lang, textproc) mpfr extension for gawk

mpfi @1.5.4 (math) A multiple precision interval arithmetic library based on MPFR

mpfr @4.1.0 (devel, math) C library for multiple-precision floating-point computations

p5-math-mpfr @4.240.0 (perl, math) Perl interface to the MPFR library

p5.28-math-mpfr @4.240.0 (perl, math) Perl interface to the MPFR library

p5.30-math-mpfr @4.240.0 (perl, math) Perl interface to the MPFR library

p5.32-math-mpfr @4.240.0 (perl, math) Perl interface to the MPFR library

p5.34-math-mpfr @4.240.0 (perl, math) Perl interface to the MPFR library

pure-mpfr @0.5_1 (pure, devel, math) an interface to GNU MPFR from Pure

py-bigfloat @0.4.0 (python, math) Arbitrary-precision correctly-rounded floating-point arithmetic, via MPFR.

py37-bigfloat @0.4.0 (python, math) Arbitrary-precision correctly-rounded floating-point arithmetic, via MPFR.

py38-bigfloat @0.4.0 (python, math) Arbitrary-precision correctly-rounded floating-point arithmetic, via MPFR.

py39-bigfloat @0.4.0 (python, math) Arbitrary-precision correctly-rounded floating-point arithmetic, via MPFR.

py310-bigfloat @0.4.0 (python, math) Arbitrary-precision correctly-rounded floating-point arithmetic, via MPFR.

Found 14 ports.

I still can't install the amuse-simplex

rieder commented 1 year ago

port search will only list available ports, not installed ones. Could you check with port install mpfr hdf5? Also, please make sure pkgconfig is installed (port install pkgconfig). You may need to re-install amuse-framework after this: pip install --force-reinstall --no-cache-dir amuse-framework

dnrgodilano7 commented 1 year ago

(Amuse-env) (base) dnrgodilano7@dnrG mesa-r22.11.1 % sudo port install pkgconfig Password: ---> Computing dependencies for pkgconfig ---> Cleaning pkgconfig ---> Scanning binaries for linking errors ---> No broken files found. ---> No broken ports found.

(Amuse-env) (base) dnrgodilano7@dnrG mesa-r22.11.1 % sudo port install mpfr hdf5 ---> Computing dependencies for mpfr ---> Cleaning mpfr ---> Computing dependencies for hdf5 ---> Cleaning hdf5 ---> Scanning binaries for linking errors ---> No broken files found. ---> No broken ports found.

Successfully installed amuse-framework-2022.11.0 attrs-22.1.0 docutils-0.19 exceptiongroup-1.0.4 h5py-3.7.0 iniconfig-1.1.1 numpy-1.23.5 packaging-21.3 pip-22.3.1 pluggy-1.0.0 pyparsing-3.0.9 pytest-7.2.0 setuptools-65.6.3 setuptools-scm-7.0.5 tomli-2.0.1 typing-extensions-4.4.0 wheel-0.38.4

I will try to install again amuse-simplex. Thank you!

dnrgodilano7 commented 1 year ago

pip install amuse -v Using pip 22.3.1 from /Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/lib/python3.9/site-packages/pip (python 3.9) Collecting amuse . . . Building wheels for collected packages: amuse-simplex Building wheel for amuse-simplex (pyproject.toml): started Building wheel for amuse-simplex (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error

× Building wheel for amuse-simplex (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [610 lines of output]
    running bdist_wheel
    running build
    /private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/command/build.py:31: SetuptoolsDeprecationWarning:
                It seems that you are using `distutils.command.build` to add
                new subcommands. Using `distutils` directly is considered deprecated,
                please use `setuptools.command.build`.

      warnings.warn(msg, SetuptoolsDeprecationWarning)
    running build_py

. . . [19:58:10] building simplex error in call, tail output:

          ...
      "_H5Sselect_hyperslab", referenced from:
          __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w9read_dataIdEEvPKcPyP6arr_1DIT_E in h5w_serial.o
          __ZN3h5w9read_dataIiEEvPKcPyP6arr_1DIT_E in h5w_serial.o
          __ZN3h5w9read_dataIjEEvPKcPyP6arr_1DIT_E in h5w_serial.o
          __ZN3h5w9read_dataIlEEvPKcPyP6arr_1DIT_E in h5w_serial.o
          ...
      "_H5T_C_S1_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
      "_H5T_NATIVE_DOUBLE_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_FLOAT_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_INT_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_LDOUBLE_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
      "_H5T_NATIVE_LLONG_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_LONG_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_SCHAR_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_SHORT_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_UCHAR_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_UINT_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_ULLONG_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_ULONG_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5T_NATIVE_USHORT_g", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
      "_H5Tclose", referenced from:
          __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w12make_datasetEPKcS1_iPy in h5w_serial.o
          __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
          __ZN3h5w9read_dataIdEEvPKcPyP6arr_1DIT_E in h5w_serial.o
          __ZN3h5w9read_dataIiEEvPKcPyP6arr_1DIT_E in h5w_serial.o
          ...
      "_H5Tcopy", referenced from:
          __ZN3h5w9read_attrIjEEvPKcS2_PT_ in SimpleX.o
          __ZN3h5w9read_attrIdEEvPKcS2_PT_ in SimpleX.o
          __ZN3h5w9read_attrIsEEvPKcS2_PT_ in SimpleX.o
          __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_attrIjEEvPKcS2_T_ in SimpleX.o
          __ZN3h5w10write_attrIdEEvPKcS2_T_ in SimpleX.o
          __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
          ...
      "_H5Tequal", referenced from:
          __ZN3h5w9read_attrIjEEvPKcS2_PT_ in SimpleX.o
          __ZN3h5w9read_attrIdEEvPKcS2_PT_ in SimpleX.o
          __ZN3h5w9read_attrIsEEvPKcS2_PT_ in SimpleX.o
          __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
          __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
          ...
      "_H5Tget_size", referenced from:
          __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
      "_H5Tset_order", referenced from:
          __ZN3h5w12make_datasetEPKcS1_iPy in h5w_serial.o
      "_H5Tset_size", referenced from:
          __ZN3h5w10write_attrEPKcS1_Pc in h5w_serial.o
          __ZN3h5w10write_attrEPKcS1_S1_ in h5w_serial.o
          __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
      "_H5check_version", referenced from:
          __ZN3h5wC1EPc in h5w_serial.o
          __ZN3h5wC1EPcc in h5w_serial.o
          __ZN3h5w4openEPc in h5w_serial.o
          __ZN3h5w4openEPcc in h5w_serial.o
      "_H5open", referenced from:
          __Z15get_h5_datatypePKc in h5w_serial.o
          __ZN3h5wC1EPc in h5w_serial.o
          __ZN3h5wC1EPcc in h5w_serial.o
          __ZN3h5w4openEPc in h5w_serial.o
          __ZN3h5w4openEPcc in h5w_serial.o
          __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
    ld: symbol(s) not found for architecture arm64
    collect2: error: ld returned 1 exit status
    make: *** [simplex_worker] Error 1

will copy worker: src/amuse/community/simplex simplex creating build/lib/amuse/community/simplex/data creating build/lib/amuse/community/simplex/data/input . . .

copying build/temp.macosx-10.9-x86_64-cpython-39/codes/simplex/data/input/Si.Hcool -> build/lib/amuse/community/simplex/data/input Community codes not built (because of errors):

     * simplex
    ================================================================================
    0 out of 1 codes built, 0 out of 0 libraries built
    Traceback (most recent call last):
      File "/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
        main()
      File "/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
        json_out['return_val'] = hook(**hook_input['kwargs'])
      File "/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 249, in build_wheel
        return _build_backend().build_wheel(wheel_directory, config_settings,
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 413, in build_wheel
        return self._build_with_temp_dir(['bdist_wheel'], '.whl',
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 398, in _build_with_temp_dir
        self.run_setup()
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 484, in run_setup
        super(_BuildMetaLegacyBackend,
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 335, in run_setup
        exec(code, locals())
      File "<string>", line 50, in <module>
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 87, in setup
        return distutils.core.setup(**attrs)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
        return run_commands(dist)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
        dist.run_commands()
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
        self.run_command(cmd)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1208, in run_command
        super().run_command(command)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
        cmd_obj.run()
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 325, in run
        self.run_command("build")
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
        self.distribution.run_command(command)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1208, in run_command
        super().run_command(command)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
        cmd_obj.run()
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 132, in run
        self.run_command(cmd_name)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
        self.distribution.run_command(command)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1208, in run_command
        super().run_command(command)
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-3vdlk52l/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
        cmd_obj.run()
      File "/private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-install-_5ui3v_m/amuse-simplex_251cfcddd3194e03adaf0f1114af8990/support/setup_codes.py", line 1100, in run
        raise Exception("No succesful builds detected. Aborting.")
    Exception: No succesful builds detected. Aborting.
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for amuse-simplex

Failed to build amuse-simplex ERROR: Could not build wheels for amuse-simplex, which is required to install pyproject.toml-based projects error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. full command: /Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/bin/python3 /Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/lib/python3.9/site-packages/pip/pip-runner.py install --ignore-installed --no-user --prefix /private/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/pip-build-env-91c5_x90/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'amuse-framework[MPI]>=2021.7.0' 'amuse-athena>=2021.7.0' 'amuse-bhtree>=2021.7.0' 'amuse-bse>=2021.7.0' 'amuse-capreole>=2021.7.0' 'amuse-evtwin>=2021.7.0' 'amuse-fastkick>=2021.7.0' 'amuse-fi>=2021.7.0' 'amuse-fractalcluster>=2021.7.0' 'amuse-gadget2>=2021.7.0' 'amuse-galactics>=2021.7.0' 'amuse-galaxia>=2021.7.0' 'amuse-halogen>=2021.7.0' 'amuse-hermite>=2021.7.0' 'amuse-hop>=2021.7.0' 'amuse-huayno>=2021.7.0' 'amuse-kepler>=2021.7.0' 'amuse-kepler-orbiters>=2021.7.0' 'amuse-mameclot>=2021.7.0' 'amuse-mercury>=2021.7.0' 'amuse-mmams>=2021.7.0' 'amuse-ph4>=2021.7.0' 'amuse-seba>=2021.7.0' 'amuse-secularmultiple>=2021.7.0' 'amuse-simplex>=2021.7.0' 'amuse-smalln>=2021.7.0' 'amuse-sphray>=2021.7.0' 'amuse-sse>=2021.7.0' 'amuse-twobody>=2021.7.0' cwd: [inherit] Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

I still get the same error.

rieder commented 1 year ago

It looks like there may be a conflicting HDF5 library somewhere. Could you post the output of export?

dnrgodilano7 commented 1 year ago

export CONDA_DEFAULT_ENV=base CONDA_EXE=/Users/dnrgodilano7/opt/anaconda3/bin/conda CONDA_PREFIX=/Users/dnrgodilano7/opt/anaconda3 CONDA_PROMPT_MODIFIER='(base) ' CONDA_PYTHON_EXE=/Users/dnrgodilano7/opt/anaconda3/bin/python CONDA_SHLVL=1 HOME=/Users/dnrgodilano7 LC_CTYPE=UTF-8 LOGNAME=dnrgodilano7 MANPATH=/Applications/mesasdk/share/man: MESASDK_ROOT=/Applications/mesasdk MESASDK_VERSION=aarch64-macos-22.10.1 MESA_DIR=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1python3 OLDPWD=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1 OMP_NUM_THREADS=10 PATH=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/bin:/Applications/mesasdk/bin:/Users/dnrgodilano7/opt/anaconda3/bin:/Users/dnrgodilano7/opt/anaconda3/condabin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin PGPLOT_DIR=/Applications/mesasdk/lib/pgplot PS1='(Amuse-env) (base) %n@%m %1~ %# ' PWD=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1 SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk SHELL=/bin/zsh SHLVL=1 SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.CIamqDgZ6W/Listeners TERM=xterm-256color TERM_PROGRAM=Apple_Terminal TERM_PROGRAM_VERSION=447 TERM_SESSION_ID=62BD139F-0C93-4ABB-AF3A-F53DFB4BB7EA TMPDIR=/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/ USER=dnrgodilano7 VIRTUAL_ENV=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 _CE_CONDA='' _CE_M='' __CFBundleIdentifier=com.apple.Terminal venv=''

rieder commented 1 year ago

Having both Anaconda and Mesa variables defined unfortunately makes errors like you're experiencing very likely - these cause conflicting, incompatible versions of the required libraries to be found (see numerous other issues here, e.g. #910). Please could you try deactivating Conda, and making sure no mesa or anaconda paths are found in your PATH?

dnrgodilano7 commented 1 year ago

So I removed them

export CONDA_EXE=/Users/dnrgodilano7/opt/anaconda3/bin/conda CONDA_PYTHON_EXE=/Users/dnrgodilano7/opt/anaconda3/bin/python CONDA_SHLVL=0 HOME=/Users/dnrgodilano7 LC_CTYPE=UTF-8 LOGNAME=dnrgodilano7 OLDPWD=/Users/dnrgodilano7 PATH=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin PS1='(Amuse-env) %n@%m %1~ %# ' PWD=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1 SHELL=/bin/zsh SHLVL=1 SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.CIamqDgZ6W/Listeners TERM=xterm-256color TERM_PROGRAM=Apple_Terminal TERM_PROGRAM_VERSION=447 TERM_SESSION_ID=28066F6C-3234-47F0-851F-34D031F677F7 TMPDIR=/var/folders/q3/6wt9wt6s1wn9lv1y8w_lm3xc0000gn/T/ USER=dnrgodilano7 VIRTUAL_ENV=/Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 _CE_CONDA='' _CE_M='' __CFBundleIdentifier=com.apple.Terminal

and I still get the same errors:

Using pip 22.3.1 from /Users/dnrgodilano7/Documents/AMUSE/mesa-r22.11.1/Amuse-env/lib/python3.9/site-packages/pip (python 3.9) Collecting amuse-simplex . . . [20:49:59] building simplex error in call, tail output:

    ...
"_H5Sselect_hyperslab", referenced from:
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w9read_dataIdEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIiEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIjEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIlEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    ...
"_H5T_C_S1_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
"_H5T_NATIVE_DOUBLE_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_FLOAT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_INT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_LDOUBLE_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
"_H5T_NATIVE_LLONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_LONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_SCHAR_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_SHORT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_UCHAR_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_UINT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_ULLONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_ULONG_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5T_NATIVE_USHORT_g", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o
"_H5Tclose", referenced from:
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w12make_datasetEPKcS1_iPy in h5w_serial.o
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
    __ZN3h5w9read_dataIdEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    __ZN3h5w9read_dataIiEEvPKcPyP6arr_1DIT_E in h5w_serial.o
    ...
"_H5Tcopy", referenced from:
    __ZN3h5w9read_attrIjEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIdEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIsEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_attrIjEEvPKcS2_T_ in SimpleX.o
    __ZN3h5w10write_attrIdEEvPKcS2_T_ in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    ...
"_H5Tequal", referenced from:
    __ZN3h5w9read_attrIjEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIdEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_attrIsEEvPKcS2_PT_ in SimpleX.o
    __ZN3h5w9read_dataIfEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIdEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w10write_dataIjEEvPKcPyP6arr_1DIT_E in SimpleX.o
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
    ...
"_H5Tget_size", referenced from:
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
"_H5Tset_order", referenced from:
    __ZN3h5w12make_datasetEPKcS1_iPy in h5w_serial.o
"_H5Tset_size", referenced from:
    __ZN3h5w10write_attrEPKcS1_Pc in h5w_serial.o
    __ZN3h5w10write_attrEPKcS1_S1_ in h5w_serial.o
    __ZN3h5w9read_attrEPKcS1_Pc in h5w_serial.o
"_H5check_version", referenced from:
    __ZN3h5wC1EPc in h5w_serial.o
    __ZN3h5wC1EPcc in h5w_serial.o
    __ZN3h5w4openEPc in h5w_serial.o
    __ZN3h5w4openEPcc in h5w_serial.o
"_H5open", referenced from:
    __Z15get_h5_datatypePKc in h5w_serial.o
    __ZN3h5wC1EPc in h5w_serial.o
    __ZN3h5wC1EPcc in h5w_serial.o
    __ZN3h5w4openEPc in h5w_serial.o
    __ZN3h5w4openEPcc in h5w_serial.o
    __ZN3h5w13get_data_typeB5cxx11EPc in h5w_serial.o

ld: symbol(s) not found for architecture arm64 collect2: error: ld returned 1 exit status make: *** [simplex_worker] Error 1

Community codes not built (because of errors):

rieder commented 1 year ago

You will also have to remove your pip cache files, and re-install amuse-framework. At installation time, this package finds the location of required libraries - if this is set incorrectly, you have to redo this step.

stale[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed in 28 days if no further activity occurs. Thank you for your contributions.