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build: cylon rivanna recipie is failing #665

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laszewsk opened this issue Aug 2, 2023 · 9 comments
Closed

build: cylon rivanna recipie is failing #665

laszewsk opened this issue Aug 2, 2023 · 9 comments
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@mstaylor @arupcsedu @vibhatha
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bug Something isn't working priority:high Tasks with high priority

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@laszewsk
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laszewsk commented Aug 2, 2023

[3%] Compiling Cython CXX source for lib...
warning: pyarrow/lib.pxd:33:60: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: pyarrow/includes/libarrow.pxd:1687:24: Rvalue-reference as function argument not supported
warning: pyarrow/includes/libarrow.pxd:1712:26: Rvalue-reference as function argument not supported
warning: pyarrow/includes/libarrow.pxd:1728:23: Rvalue-reference as function argument not supported
warning: pyarrow/includes/libarrow.pxd:1742:24: Rvalue-reference as function argument not supported
warning: pyarrow/includes/libarrow.pxd:2087:20: Rvalue-reference as function argument not supported
warning: pyarrow/error.pxi:82:60: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: pyarrow/error.pxi:143:23: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
[ 3%] Built target lib_pyx
[ 7%] Building CXX object CMakeFiles/lib.dir/lib.cpp.o
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp: In function ‘PyObject* __pyx_pf_7pyarrow_3lib_15SparseCOOTensor_9dim_names_7__get___genexpr(PyObject*, std::vector<std::__cxx11::basic_string >)’:
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:162522:58: error: passing ‘const std::vector<std::__cxx11::basic_string >’ as ‘this’ argument discards qualifiers [-fpermissive]
162522 | __pyx_cur_scope->__pyx_genexpr_arg_0 = __pyx_genexpr_arg_0;
| ^~~~~~~~~~~~~~~~~~~
In file included from /sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/vector:72,
from /gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:1132:
/sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/bits/vector.tcc:198:5: note: in call to ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator<std::__cxx11::basic_string >]’
198 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp: In function ‘PyObject* __pyx_pf_7pyarrow_3lib_15SparseCSRMatrix_9dim_names_7__get___genexpr(PyObject*, std::vector<std::__cxx11::basic_string >)’:
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:166075:58: error: passing ‘const std::vector<std::__cxx11::basic_string >’ as ‘this’ argument discards qualifiers [-fpermissive]
166075 | __pyx_cur_scope->__pyx_genexpr_arg_0 = __pyx_genexpr_arg_0;
| ^~~~~~~~~~~~~~~~~~~
In file included from /sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/vector:72,
from /gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:1132:
/sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/bits/vector.tcc:198:5: note: in call to ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator<std::__cxx11::basic_string >]’
198 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp: In function ‘PyObject* __pyx_pf_7pyarrow_3lib_15SparseCSCMatrix_9dim_names_7__get___genexpr(PyObject*, std::vector<std::__cxx11::basic_string >)’:
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:169518:58: error: passing ‘const std::vector<std::__cxx11::basic_string >’ as ‘this’ argument discards qualifiers [-fpermissive]
169518 | __pyx_cur_scope->__pyx_genexpr_arg_0 = __pyx_genexpr_arg_0;
| ^~~~~~~~~~~~~~~~~~~
In file included from /sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/vector:72,
from /gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:1132:
/sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/bits/vector.tcc:198:5: note: in call to ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator<std::__cxx11::basic_string >]’
198 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp: In function ‘PyObject* __pyx_pf_7pyarrow_3lib_15SparseCSFTensor_9dim_names_7__get___genexpr(PyObject*, std::vector<std::__cxx11::basic_string >)’:
/gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:172824:58: error: passing ‘const std::vector<std::__cxx11::basic_string >’ as ‘this’ argument discards qualifiers [-fpermissive]
172824 | __pyx_cur_scope->__pyx_genexpr_arg_0 = __pyx_genexpr_arg_0;
| ^~~~~~~~~~~~~~~~~~~
In file included from /sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/vector:72,
from /gpfs/gpfs0/project/bii_dsc_community/thf2bn/cylon/build/arrow/arrow/python/build/temp.linux-x86_64-3.7/lib.cpp:1132:
/sfs/applications/202307/software/standard/core/gcc/9.2.0/include/c++/9.2.0/bits/vector.tcc:198:5: note: in call to ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator<std::__cxx11::basic_string >]’
198 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
gmake[2]: *** [CMakeFiles/lib.dir/lib.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/lib.dir/all] Error 2
gmake: *** [all] Error 2
error: command '/apps/software/standard/core/cmake/3.23.3/bin/cmake' failed with exit code 2
(cylon_rct) thf2bn@rivanna:/project/bii_dsc_community/thf2bn/cylon$

--
Gregor von Laszewski
[email protected]
@laszewsk laszewsk added the bug Something isn't working label Aug 2, 2023
@laszewsk laszewsk added the priority:high Tasks with high priority label Aug 2, 2023
@laszewsk laszewsk changed the title cylon rivanna recipie is failing compile: cylon rivanna recipie is failing Aug 2, 2023
@laszewsk laszewsk changed the title compile: cylon rivanna recipie is failing build: cylon rivanna recipie is failing Aug 2, 2023
@laszewsk laszewsk mentioned this issue Aug 2, 2023
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@arupcsedu
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This is the new issue due to changes on cython release. Are you using conda env build or python env build?

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laszewsk commented Aug 2, 2023

This is the deployment we kicked off yesterday on rivanna.

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laszewsk commented Aug 2, 2023

I think we did this by hand. instead of using
sbatch rivanna/job_cylon_rivanna_1.slurm

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arupcsedu commented Aug 2, 2023 via email

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arupcsedu commented Aug 3, 2023 via email

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arupcsedu commented Aug 3, 2023 via email

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arupcsedu commented Aug 3, 2023 via email

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arupcsedu commented Aug 3, 2023 via email

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The issue is fixed and merged. Please pull the latest change

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