Hello,
When trying to install a GPU-enabled Amber20, we are running into an issue during run_cmake, followed by an error during make install. Before running run_cmake, we do run “./update_amber –upgrade” to ensure we have all the latest updates before installing (ran into other, different issues when installing the base CPU Amber20 before the holidays that these updates resolved).
For run_cmake, we receive the following error message that repeats numerous times throughout the process for different python files:
%%%%%%%%%
Error processing line 1 of /tmp/amber/gpu_install/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.10/site-packages/distutils-precedence.pth:
Traceback (most recent call last):
File "/tmp/amber/gpu_install/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.10/site.py", line 186, in addpackage
exec(line)
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named '_distutils_hack'
%%%%%%%%%
Looking into this issue, it seems to be an issue with setuptools, however run_cmake installs this before this error occurs. Although, it is replacing the installed version (setuptools-65.5.0) with an older version (setuptools-47.3.1). Not sure if this older version is causing problems?
Run_cmake still finishes with these errors, so we figured we’d give “make install” a go. When we do this, it gets to about 93% complete before printing the following error messages and crashing (install incomplete). It seems to be an issue with the
%%%%%%%%%
In file included from /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/Python.h:74:0,
from pytraj/utils/cyutils.cpp:18:
pytraj/utils/cyutils.cpp: In function ‘void __pyx_tp_dealloc_array(PyObject*)’:
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58: error: lvalue required as increment operand
#define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
^
pytraj/utils/cyutils.cpp:19992:7: note: in expansion of macro ‘Py_REFCNT’
++Py_REFCNT(o);
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58: error: lvalue required as decrement operand
#define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
^
pytraj/utils/cyutils.cpp:19994:7: note: in expansion of macro ‘Py_REFCNT’
--Py_REFCNT(o);
^
pytraj/utils/cyutils.cpp: In function ‘void __pyx_tp_dealloc_memoryview(PyObject*)’:
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58: error: lvalue required as increment operand
#define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
^
pytraj/utils/cyutils.cpp:20303:7: note: in expansion of macro ‘Py_REFCNT’
++Py_REFCNT(o);
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58: error: lvalue required as decrement operand
#define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
^
pytraj/utils/cyutils.cpp:20305:7: note: in expansion of macro ‘Py_REFCNT’
--Py_REFCNT(o);
^
pytraj/utils/cyutils.cpp: In function ‘void __pyx_tp_dealloc__memoryviewslice(PyObject*)’:
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58: error: lvalue required as increment operand
#define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
^
pytraj/utils/cyutils.cpp:20553:7: note: in expansion of macro ‘Py_REFCNT’
++Py_REFCNT(o);
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/object.h:133:58: error: lvalue required as decrement operand
#define Py_REFCNT(ob) _Py_REFCNT(_PyObject_CAST_CONST(ob))
^
pytraj/utils/cyutils.cpp:20555:7: note: in expansion of macro ‘Py_REFCNT’
--Py_REFCNT(o);
^
In file included from /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/unicodeobject.h:1046:0,
from /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/Python.h:83,
from pytraj/utils/cyutils.cpp:18:
pytraj/utils/cyutils.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’:
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22200:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22200:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22200:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22200:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22200:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22200:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22200:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22200:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22200:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22200:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22200:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22200:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22216:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22216:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22216:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22216:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22216:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22216:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22216:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op) : \
^
pytraj/utils/cyutils.cpp:22216:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22216:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580) [-Wdeprecated-declarations]
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
pytraj/utils/cyutils.cpp:22216:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22216:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:446) [-Wdeprecated-declarations]
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’
PyUnicode_WSTR_LENGTH(op)))
^
pytraj/utils/cyutils.cpp:22216:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
pytraj/utils/cyutils.cpp: In function ‘PyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’:
pytraj/utils/cyutils.cpp:23832:16: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:551) [-Wdeprecated-declarations]
return PyUnicode_FromUnicode(NULL, 0);
^
pytraj/utils/cyutils.cpp:23832:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated (declared at /homes/taceysa/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:551) [-Wdeprecated-declarations]
return PyUnicode_FromUnicode(NULL, 0);
^
pytraj/utils/cyutils.cpp: In function ‘PyObject* __Pyx_Coroutine_Send(PyObject*, PyObject*)’:
pytraj/utils/cyutils.cpp:27782:80: error: ‘_PyGen_Send’ was not declared in this scope
ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
^
pytraj/utils/cyutils.cpp:27787:80: error: ‘_PyGen_Send’ was not declared in this scope
ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
^
pytraj/utils/cyutils.cpp: In function ‘PyObject* __Pyx_Generator_Next(PyObject*)’:
pytraj/utils/cyutils.cpp:27871:53: error: ‘_PyGen_Send’ was not declared in this scope
ret = _PyGen_Send((PyGenObject*)yf, NULL);
^
error: command '/usr/bin/gcc' failed with exit code 1
make[2]: *** [AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Error 1
make[1]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Error 2
make: *** [all] Error 2
%%%%%%%%%
Any thoughts on how to resolve these issues?
Thanks!
Sean
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Received on Tue Jan 10 2023 - 11:30:03 PST
