Open Deathn0t opened 1 year ago
iamyixuan
commented
1 year ago With the new spack.yaml specified in the repository.
+mpi gave the following error:
Error: Cannot find valid provider for virtual java. Consider setting `concretizer:unify` to `when_possible` or `false` to relax the concretizer strictness.Installing other packages gave the same error. Any suggestions how to solve this?
iamyixuan
commented
1 year ago Installed with Spack.
A working workflow (at least for these two) on Swing is
spack env using the default configuration.clang using spack add llvm and spack install.clang to the compiler list by spack compiler find.spack.yaml contains proper compiler information, including the spec version and path, automatically (also system info auto-fiiled as well).spack.yaml file by adding -repo: path_to/deephyper-spack-packages.spack add py-deephyper@develop +........spack installError occurred during +nas as the following
==> py-numpy: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
'/gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/bin/python3.10' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso' '.'
23 errors found in build log:
11 Created temporary directory: /tmp/pip-install-bit5iu7p
12 Processing /tmp/yixuan.sun/spack-stage/spack-stage-py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkz
b4uwso/spack-src
13 Added file:///tmp/yixuan.sun/spack-stage/spack-stage-py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hk
kpkzb4uwso/spack-src to build tracker '/tmp/pip-build-tracker-aojkbqdm'
14 Created temporary directory: /tmp/pip-modern-metadata-47zyisa8
15 Preparing metadata (pyproject.toml): started
16 Running command Preparing metadata (pyproject.toml)
>> 17 setup.py:67: RuntimeWarning: NumPy 1.19.5 may not yet support Python 3.10.
18 warnings.warn(
19 Running from numpy source directory.
>> 20 setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cyth
on sources and expanding templates
21 run_build = parse_setuppy_commands()
>> 22 /tmp/yixuan.sun/spack-stage/spack-stage-py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso/sp
ack-src/tools/cythonize.py:67: DeprecationWarning: The distutils package is deprecated and sl
ated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
23 from distutils.version import LooseVersion
24 Processing numpy/random/_bounded_integers.pxd.in
25 Processing numpy/random/mtrand.pyx
26 Processing numpy/random/_pcg64.pyx
27 Processing numpy/random/bit_generator.pyx
28 Processing numpy/random/_sfc64.pyx
...
76 libraries = ['openblas', 'openblas']
77 library_dirs = ['/gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9
.4.0/openblas-0.3.21-bg3k6yaipchlpgq44v3egqk6h3rimu56/lib']
78 language = c
79 define_macros = [('HAVE_CBLAS', None)]
80 runtime_library_dirs = ['/gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-ze
n2/gcc-9.4.0/openblas-0.3.21-bg3k6yaipchlpgq44v3egqk6h3rimu56/lib']
81
>> 82 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aqqa
eaaaqhfw6asutruozartdq6dqpni/lib/python3.10/distutils/dist.py:274: UserWarning: Unknown distr
ibution option: 'define_macros'
83 warnings.warn(msg)
84 running dist_info
85 running build_src
86 build_src
87 building py_modules sources
88 creating build
...
160 building extension "numpy.random.bit_generator" sources
161 building extension "numpy.random._generator" sources
162 building extension "numpy.random._bounded_integers" sources
163 building extension "numpy.random.mtrand" sources
164 building data_files sources
165 build_src: building npy-pkg config files
>> 166 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-setuptools-59.4
.0-zvvrzhv4n6h77qvdaaj5d542e5vhevvq/lib/python3.10/site-packages/setuptools/command/install.p
y:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and oth
er standards-based tools.
167 warnings.warn(
168 creating /tmp/pip-modern-metadata-47zyisa8/numpy.egg-info
169 writing /tmp/pip-modern-metadata-47zyisa8/numpy.egg-info/PKG-INFO
170 writing dependency_links to /tmp/pip-modern-metadata-47zyisa8/numpy.egg-info/dependency_lin
ks.txt
171 writing entry points to /tmp/pip-modern-metadata-47zyisa8/numpy.egg-info/entry_points.txt
172 writing top-level names to /tmp/pip-modern-metadata-47zyisa8/numpy.egg-info/top_level.txt
173 writing manifest file '/tmp/pip-modern-metadata-47zyisa8/numpy.egg-info/SOURCES.txt'
>> 174 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-setuptools-59.4
.0-zvvrzhv4n6h77qvdaaj5d542e5vhevvq/lib/python3.10/site-packages/setuptools/command/egg_info.
py:624: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_wi
thout_manifest'.
175 Please extend command classes from setuptools instead of distutils.
176 warnings.warn(
177 reading manifest file '/tmp/pip-modern-metadata-47zyisa8/numpy.egg-info/SOURCES.txt'
178 reading manifest template 'MANIFEST.in'
179 no previously-included directories found matching 'doc/build'
180 no previously-included directories found matching 'doc/source/generated'
...
198 Created temporary directory: /tmp/pip-unpack-d7xsxgm3
199 Building wheels for collected packages: numpy
200 Created temporary directory: /tmp/pip-wheel-6z4tdh_d
201 Destination directory: /tmp/pip-wheel-6z4tdh_d
202 Building wheel for numpy (pyproject.toml): started
203 Running command Building wheel for numpy (pyproject.toml)
>> 204 setup.py:67: RuntimeWarning: NumPy 1.19.5 may not yet support Python 3.10.
205 warnings.warn(
206 Running from numpy source directory.
>> 207 /tmp/yixuan.sun/spack-stage/spack-stage-py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso/sp
ack-src/tools/cythonize.py:67: DeprecationWarning: The distutils package is deprecated and sl
ated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
208 from distutils.version import LooseVersion
209 numpy/random/_bounded_integers.pxd.in has not changed
210 Processing numpy/random/_bounded_integers.pyx
211 numpy/random/mtrand.pyx has not changed
212 numpy/random/_pcg64.pyx has not changed
213 numpy/random/bit_generator.pyx has not changed
...
262 libraries = ['openblas', 'openblas']
263 library_dirs = ['/gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9
.4.0/openblas-0.3.21-bg3k6yaipchlpgq44v3egqk6h3rimu56/lib']
264 language = c
265 define_macros = [('HAVE_CBLAS', None)]
266 runtime_library_dirs = ['/gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-ze
n2/gcc-9.4.0/openblas-0.3.21-bg3k6yaipchlpgq44v3egqk6h3rimu56/lib']
267
>> 268 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aqqa
eaaaqhfw6asutruozartdq6dqpni/lib/python3.10/distutils/dist.py:274: UserWarning: Unknown distr
ibution option: 'define_macros'
269 warnings.warn(msg)
270 running bdist_wheel
271 running build
272 running config_cc
273 unifing config_cc, config, build_clib, build_ext, build commands --compiler options
274 running config_fc
...
821 gcc: numpy/core/src/multiarray/typeinfo.c
822 gcc: numpy/core/src/multiarray/sequence.c
823 gcc: build/src.linux-x86_64-3.10/numpy/core/src/multiarray/scalartypes.c
824 gcc: numpy/core/src/multiarray/usertypes.c
825 gcc: numpy/core/src/multiarray/shape.c
826 numpy/core/src/multiarray/scalartypes.c.src: In function 'float_arrtype_hash':
>> 827 numpy/core/src/multiarray/scalartypes.c.src:2968:27: error: incompatible type for argument 1
of '_Py_HashDouble'
828 2968 | return _Py_HashDouble((double) PyArrayScalar_VAL(obj, @name@));
829 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
830 from numpy/core/src/multiarray/scalartypes.c.src:3:
831 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
832 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
833 | ^~~~~~~~~~
>> 834 numpy/core/src/multiarray/scalartypes.c.src:2968:12: error: too few arguments to function '_P
y_HashDouble'
835 2968 | return _Py_HashDouble((double) PyArrayScalar_VAL(obj, @name@));
836 | ^~~~~~~~~~~~~~
837 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
838 from numpy/core/src/multiarray/scalartypes.c.src:3:
839 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
840 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
841 | ^~~~~~~~~~~~~~
842 numpy/core/src/multiarray/scalartypes.c.src: In function 'cfloat_arrtype_hash':
>> 843 numpy/core/src/multiarray/scalartypes.c.src:2976:31: error: incompatible type for argument 1
of '_Py_HashDouble'
844 2976 | hashreal = _Py_HashDouble((double)
845 | ^~~~~~~~
846 | |
847 | double
848 2977 | PyArrayScalar_VAL(obj, C@name@).real);
849 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
851 from numpy/core/src/multiarray/scalartypes.c.src:3:
852 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
853 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
854 | ^~~~~~~~~~
>> 855 numpy/core/src/multiarray/scalartypes.c.src:2976:16: error: too few arguments to function '_P
y_HashDouble'
856 2976 | hashreal = _Py_HashDouble((double)
857 | ^~~~~~~~~~~~~~
858 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
859 from numpy/core/src/multiarray/scalartypes.c.src:3:
860 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
861 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
862 | ^~~~~~~~~~~~~~
>> 863 numpy/core/src/multiarray/scalartypes.c.src:2982:31: error: incompatible type for argument 1
of '_Py_HashDouble'
864 2982 | hashimag = _Py_HashDouble((double)
865 | ^~~~~~~~
866 | |
867 | double
868 2983 | PyArrayScalar_VAL(obj, C@name@).imag);
869 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
870 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
871 from numpy/core/src/multiarray/scalartypes.c.src:3:
872 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
873 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
874 | ^~~~~~~~~~
>> 875 numpy/core/src/multiarray/scalartypes.c.src:2982:16: error: too few arguments to function '_P
y_HashDouble'
876 2982 | hashimag = _Py_HashDouble((double)
877 | ^~~~~~~~~~~~~~
878 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
879 from numpy/core/src/multiarray/scalartypes.c.src:3:
880 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
881 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
882 | ^~~~~~~~~~~~~~
883 numpy/core/src/multiarray/scalartypes.c.src: In function 'longdouble_arrtype_hash':
>> 884 numpy/core/src/multiarray/scalartypes.c.src:2968:27: error: incompatible type for argument 1
of '_Py_HashDouble'
885 2968 | return _Py_HashDouble((double) PyArrayScalar_VAL(obj, @name@));
886 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
887 from numpy/core/src/multiarray/scalartypes.c.src:3:
888 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
889 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
890 | ^~~~~~~~~~
>> 891 numpy/core/src/multiarray/scalartypes.c.src:2968:12: error: too few arguments to function '_P
y_HashDouble'
892 2968 | return _Py_HashDouble((double) PyArrayScalar_VAL(obj, @name@));
893 | ^~~~~~~~~~~~~~
894 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
895 from numpy/core/src/multiarray/scalartypes.c.src:3:
896 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
897 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
898 | ^~~~~~~~~~~~~~
899 numpy/core/src/multiarray/scalartypes.c.src: In function 'clongdouble_arrtype_hash':
>> 900 numpy/core/src/multiarray/scalartypes.c.src:2976:31: error: incompatible type for argument 1
of '_Py_HashDouble'
901 2976 | hashreal = _Py_HashDouble((double)
902 | ^~~~~~~~
903 | |
904 | double
905 2977 | PyArrayScalar_VAL(obj, C@name@).real);
906 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
907 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
908 from numpy/core/src/multiarray/scalartypes.c.src:3:
909 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
910 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
911 | ^~~~~~~~~~
>> 912 numpy/core/src/multiarray/scalartypes.c.src:2976:16: error: too few arguments to function '_P
y_HashDouble'
913 2976 | hashreal = _Py_HashDouble((double)
914 | ^~~~~~~~~~~~~~
915 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
916 from numpy/core/src/multiarray/scalartypes.c.src:3:
917 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
918 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
919 | ^~~~~~~~~~~~~~
>> 920 numpy/core/src/multiarray/scalartypes.c.src:2982:31: error: incompatible type for argument 1
of '_Py_HashDouble'
921 2982 | hashimag = _Py_HashDouble((double)
922 | ^~~~~~~~
923 | |
924 | double
925 2983 | PyArrayScalar_VAL(obj, C@name@).imag);
926 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
927 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
928 from numpy/core/src/multiarray/scalartypes.c.src:3:
929 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
930 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
931 | ^~~~~~~~~~
>> 932 numpy/core/src/multiarray/scalartypes.c.src:2982:16: error: too few arguments to function '_P
y_HashDouble'
933 2982 | hashimag = _Py_HashDouble((double)
934 | ^~~~~~~~~~~~~~
935 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
936 from numpy/core/src/multiarray/scalartypes.c.src:3:
937 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
938 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
939 | ^~~~~~~~~~~~~~
940 numpy/core/src/multiarray/scalartypes.c.src: In function 'half_arrtype_hash':
>> 941 numpy/core/src/multiarray/scalartypes.c.src:2998:27: error: incompatible type for argument 1
of '_Py_HashDouble'
942 2998 | return _Py_HashDouble(npy_half_to_double(PyArrayScalar_VAL(obj, Half)));
943 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
944 | |
945 | double
946 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
947 from numpy/core/src/multiarray/scalartypes.c.src:3:
948 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:38: note: expected 'PyObject *'
{aka 'struct _object *'} but argument is of type 'double'
949 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
950 | ^~~~~~~~~~
>> 951 numpy/core/src/multiarray/scalartypes.c.src:2998:12: error: too few arguments to function '_P
y_HashDouble'
952 2998 | return _Py_HashDouble(npy_half_to_double(PyArrayScalar_VAL(obj, Half)));
953 | ^~~~~~~~~~~~~~
954 In file included from /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-
9.4.0/python-3.10.0-aqqaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/Python.h:90,
955 from numpy/core/src/multiarray/scalartypes.c.src:3:
956 /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/python-3.10.0-aq
qaeaaaqhfw6asutruozartdq6dqpni/include/python3.10/pyhash.h:10:23: note: declared here
957 10 | PyAPI_FUNC(Py_hash_t) _Py_HashDouble(PyObject *, double);
See build log for details:
/tmp/yixuan.sun/spack-stage/spack-stage-py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso/spack-build-out.txt
==> Warning: Skipping build of py-pandas-1.4.4-64yrjn2tpihfcqgehwz7pulmjqjikt5o since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-deephyper-develop-uopudtaxfiilkjiwvuzjhpyuydmw4dkk since py-pandas-1.4.4-64yrjn2tpihfcqgehwz7pulmjqjikt5o failed
==> Warning: Skipping build of py-scipy-1.5.4-h67jqi3l3vsi7p2cznnh2rkcn5vpprbu since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-scikit-learn-1.2.1-frejvoacexxnmc6r6k5yaiixs44hdypg since py-scipy-1.5.4-h67jqi3l3vsi7p2cznnh2rkcn5vpprbu failed
==> Warning: Skipping build of py-tensorboard-2.6.0-2yxdbfmpe2fk7fvzrifa6xf3wmcauffg since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-tensorflow-2.6.5-lk3od7aar5qe5fhcshxxhrnmnmiwkkjg since py-tensorboard-2.6.0-2yxdbfmpe2fk7fvzrifa6xf3wmcauffg failed
==> Warning: Skipping build of py-numexpr-2.8.3-ckbsr4v63475o7qemiwsj632uvmbzu64 since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-keras-preprocessing-1.1.2-xgairqpwyw6ewthjnzz7dsficsxiwemn since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-bottleneck-1.3.5-pdtzfqhrvs6huj3slk4foqqwugrtim4p since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-opt-einsum-3.3.0-5zwhy33tvncjjuqpi47kfr3m5puv5t6r since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-configspace-0.4.20-524fopzdtdpwqx4ibqm3yg5typk5dr64 since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Warning: Skipping build of py-h5py-3.1.0-hxupgeeehk5cdipfvpwkxijpyrd76bjm since py-numpy-1.19.5-rjrji3zdqfbbitn25rz6hkkpkzb4uwso failed
==> Installing py-requests-2.28.1-skbkb5mxiellt5yxk2ov4ackfnyj5hpa
==> No binary for py-requests-2.28.1-skbkb5mxiellt5yxk2ov4ackfnyj5hpa found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/7c/7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983.tar.gz
==> No patches needed for py-requests
==> py-requests: Executing phase: 'install'
==> py-requests: Successfully installed py-requests-2.28.1-skbkb5mxiellt5yxk2ov4ackfnyj5hpa
Stage: 0.10s. Install: 2.34s. Total: 2.77s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-requests-2.28.1-skbkb5mxiellt5yxk2ov4ackfnyj5hpa
==> Installing py-packaging-21.3-t6ef73qis2ajapla4bmnrg2mmx5fiz7b
==> No binary for py-packaging-21.3-t6ef73qis2ajapla4bmnrg2mmx5fiz7b found: installing from source
==> Using cached archive: /gpfs/fs1/home/yixuan.sun/spack/var/spack/cache/_source-cache/archive/dd/dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb.tar.gz
==> No patches needed for py-packaging
==> py-packaging: Executing phase: 'install'
==> py-packaging: Successfully installed py-packaging-21.3-t6ef73qis2ajapla4bmnrg2mmx5fiz7b
Stage: 0.03s. Install: 2.05s. Total: 2.31s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-packaging-21.3-t6ef73qis2ajapla4bmnrg2mmx5fiz7b
==> Installing py-pydot-1.4.2-z6lpggc4zrubzxomled73dgt7xfro2ea
==> No binary for py-pydot-1.4.2-z6lpggc4zrubzxomled73dgt7xfro2ea found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/24/248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d.tar.gz
==> No patches needed for py-pydot
==> py-pydot: Executing phase: 'install'
==> py-pydot: Successfully installed py-pydot-1.4.2-z6lpggc4zrubzxomled73dgt7xfro2ea
Stage: 0.53s. Install: 1.89s. Total: 2.85s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-pydot-1.4.2-z6lpggc4zrubzxomled73dgt7xfro2ea
==> Installing py-google-auth-1.6.3-rywpeq4efenxvtrwag6bv2rukmbmmyub
==> No binary for py-google-auth-1.6.3-rywpeq4efenxvtrwag6bv2rukmbmmyub found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0f/0f7c6a64927d34c1a474da92cfc59e552a5d3b940d3266606c6a28b72888b9e4.tar.gz
==> No patches needed for py-google-auth
==> py-google-auth: Executing phase: 'install'
==> py-google-auth: Successfully installed py-google-auth-1.6.3-rywpeq4efenxvtrwag6bv2rukmbmmyub
Stage: 0.76s. Install: 2.11s. Total: 3.13s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-google-auth-1.6.3-rywpeq4efenxvtrwag6bv2rukmbmmyub
==> Installing py-requests-oauthlib-1.3.1-zkkjvmdqarzzyjybgputv65qifempca3
==> No binary for py-requests-oauthlib-1.3.1-zkkjvmdqarzzyjybgputv65qifempca3 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/75/75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a.tar.gz
==> No patches needed for py-requests-oauthlib
==> py-requests-oauthlib: Executing phase: 'install'
==> py-requests-oauthlib: Successfully installed py-requests-oauthlib-1.3.1-zkkjvmdqarzzyjybgputv65qifempca3
Stage: 0.46s. Install: 2.07s. Total: 2.78s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-requests-oauthlib-1.3.1-zkkjvmdqarzzyjybgputv65qifempca3
==> Installing py-setuptools-scm-7.0.5-uwbgonsb3gslkg4dhrsjyhhe2vkezf5o
==> No binary for py-setuptools-scm-7.0.5-uwbgonsb3gslkg4dhrsjyhhe2vkezf5o found: installing from source
==> Using cached archive: /gpfs/fs1/home/yixuan.sun/spack/var/spack/cache/_source-cache/archive/03/031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844.tar.gz
==> No patches needed for py-setuptools-scm
==> py-setuptools-scm: Executing phase: 'install'
==> py-setuptools-scm: Successfully installed py-setuptools-scm-7.0.5-uwbgonsb3gslkg4dhrsjyhhe2vkezf5o
Stage: 0.03s. Install: 2.20s. Total: 2.46s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-setuptools-scm-7.0.5-uwbgonsb3gslkg4dhrsjyhhe2vkezf5o
==> Installing py-google-auth-oauthlib-0.4.6-wn32446tlrk5hmfxhn7ci3weevh555uf
==> No binary for py-google-auth-oauthlib-0.4.6-wn32446tlrk5hmfxhn7ci3weevh555uf found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/a9/a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a.tar.gz
==> No patches needed for py-google-auth-oauthlib
==> py-google-auth-oauthlib: Executing phase: 'install'
==> py-google-auth-oauthlib: Successfully installed py-google-auth-oauthlib-0.4.6-wn32446tlrk5hmfxhn7ci3weevh555uf
Stage: 0.08s. Install: 2.15s. Total: 2.51s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-google-auth-oauthlib-0.4.6-wn32446tlrk5hmfxhn7ci3weevh555uf
==> Installing py-tqdm-4.64.1-ow5k6rzklr54utcdg3iy25dx5cxtufcy
==> No binary for py-tqdm-4.64.1-ow5k6rzklr54utcdg3iy25dx5cxtufcy found: installing from source
==> Using cached archive: /gpfs/fs1/home/yixuan.sun/spack/var/spack/cache/_source-cache/archive/5f/5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4.tar.gz
==> No patches needed for py-tqdm
==> py-tqdm: Executing phase: 'install'
==> py-tqdm: Successfully installed py-tqdm-4.64.1-ow5k6rzklr54utcdg3iy25dx5cxtufcy
Stage: 0.03s. Install: 2.40s. Total: 2.65s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-tqdm-4.64.1-ow5k6rzklr54utcdg3iy25dx5cxtufcy
==> Installing py-python-dateutil-2.8.2-ngi2pdvgqvmhzw66t46ejdochnj4foxh
==> No binary for py-python-dateutil-2.8.2-ngi2pdvgqvmhzw66t46ejdochnj4foxh found: installing from source
==> Using cached archive: /gpfs/fs1/home/yixuan.sun/spack/var/spack/cache/_source-cache/archive/01/0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86.tar.gz
==> No patches needed for py-python-dateutil
==> py-python-dateutil: Executing phase: 'install'
==> py-python-dateutil: Successfully installed py-python-dateutil-2.8.2-ngi2pdvgqvmhzw66t46ejdochnj4foxh
Stage: 0.03s. Install: 2.32s. Total: 2.56s
[+] /gpfs/fs1/home/yixuan.sun/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.4.0/py-python-dateutil-2.8.2-ngi2pdvgqvmhzw66t46ejdochnj4foxh
==> Error: py-deephyper-develop-uopudtaxfiilkjiwvuzjhpyuydmw4dkk: Package was not installed
==> Error: py-deephyper-develop-uopudtaxfiilkjiwvuzjhpyuydmw4dkk: Package was not installed
==> Error: py-deephyper-develop-uopudtaxfiilkjiwvuzjhpyuydmw4dkk: Package was not installed
==> Updating view at /gpfs/fs1/home/yixuan.sun/spack/var/spack/environments/deephyper/.spack-env/view
==> Error: Installation request failed. Refer to reported errors for failing package(s).
Deathn0t
commented
1 year ago Nice to have +mpi and +redis working! Also it is strange to this py-numpy failing in this build when using +nas because it is also installed with the deephyper@develop .
Can you check spack find after installing deephyper@develop +mpi +redis to check the py-numpy version which was installed?
iamyixuan
commented
1 year ago py-numpy is somehow not in the list. The complete list is the following.
==> Installed packages
-- linux-ubuntu20.04-zen2 / gcc@9.4.0 ---------------------------
autoconf@2.69 libiconv@1.17 protobuf@3.17.3 py-pkgconfig@1.5.5 py-urllib3@1.26.12
automake@1.16.5 libmd@1.0.4 py-absl-py@0.13.0 py-poetry-core@1.2.0 py-versioneer@0.26
bazel@3.7.2 libpciaccess@0.16 py-astunparse@1.6.3 py-protobuf@3.17.3 py-werkzeug@2.2.2
berkeley-db@18.1.40 libsigsegv@2.13 py-cachetools@5.2.0 py-pyasn1@0.4.8 py-wheel@0.37.1
binutils@2.40 libssh2@1.10.0 py-certifi@2022.9.14 py-pyasn1-modules@0.2.8 py-wrapt@1.12.1
bison@3.8.2 libtool@2.4.7 py-charset-normalizer@2.0.12 py-pybind11@2.10.1 python@3.10.0
bzip2@1.0.8 libxcrypt@4.4.33 py-cython@0.29.32 py-pydot@1.4.2 python@3.10.8
c-ares@1.15.0 libxml2@2.10.3 py-dm-tree@0.1.6 py-pyparsing@3.0.9 re2@2021-06-01
ca-certificates-mozilla@2023-01-10 libyaml@0.2.5 py-flatbuffers@1.12 py-python-dateutil@2.8.2 re2c@2.2
cmake@3.25.1 llvm@15.0.7 py-flit-core@3.7.1 py-pytz@2022.2.1 readline@8.2
diffutils@3.8 m4@1.4.19 py-gast@0.4.0 py-pyyaml@6.0 redis@7.0.5
expat@2.5.0 ncurses@6.4 py-google-auth@1.6.3 py-redis@3.5.3 redisjson@2.4.3
findutils@4.9.0 ninja@1.11.1 py-google-auth-oauthlib@0.4.6 py-requests@2.28.1 rust@1.65.0
flex@2.6.3 numactl@2.0.14 py-google-pasta@0.2.0 py-requests-oauthlib@1.3.1 sed@4.8
gdbm@1.23 openblas@0.3.21 py-grpcio@1.48.1 py-rsa@4.9 sqlite@3.40.1
gettext@0.21.1 openjdk@11.0.17_8 py-idna@3.4 py-setuptools@59.4.0 swig@4.1.1
gmake@4.4 openmpi@4.1.4 py-jinja2@3.0.3 py-setuptools-scm@7.0.5 tar@1.34
graphviz@2.49.0 openssh@9.1p1 py-joblib@1.2.0 py-six@1.15.0 texinfo@7.0
hdf5@1.12.2 openssl@1.1.1s py-markdown@3.4.1 py-tensorboard-data-server@0.6.1 util-linux-uuid@2.38.1
hwloc@2.9.0 pcre@8.45 py-markupsafe@2.1.1 py-tensorboard-plugin-wit@1.8.1 util-macros@1.19.3
krb5@1.20.1 pcre2@10.42 py-mpi4py@3.1.4 py-termcolor@1.1.0 xz@5.4.1
libbsd@0.11.7 perl@5.36.0 py-networkx@2.7.1 py-threadpoolctl@3.1.0 zip@3.0
libedit@3.1-20210216 perl-data-dumper@2.173 py-oauthlib@3.2.1 py-tinydb@4.7.1 zlib@1.2.13
libevent@2.1.12 pigz@2.7 py-packaging@21.3 py-tomli@2.0.1 zstd@1.5.2
libffi@3.4.4 pkgconf@1.8.0 py-parse@1.18.0 py-tqdm@4.64.1
libgit2@1.5.0 pmix@4.1.2 py-pip@22.2.2 py-typing-extensions@3.7.4.3
==> 128 installed packagesI don't see py-scikit-learn, py-pandas either so the default installation must have said something about skipping these packages when installing +mpi and +redis or maybe this is happening when adding +nas (therefore tensorflow).
From
py-deephyper@developthe following spec must be installed:+mpi+redis+nas(GPU support?)+sdv+ray+jax(GPU support?)