Not a problem, thanks for this information! Our users require the python stuff, so I tried the AmberTools22 workaround and it looked like it worked for the CPU build. I’m going to attempt the GPU build and have the scientists test it out.
Thanks again!
Sean
From: David A Case <david.case.rutgers.edu>
Date: Monday, January 16, 2023 at 12:50 PM
To: Tacey, Sean A <sean.tacey.abbvie.com>, AMBER Mailing List <amber.ambermd.org>
Subject: [EXTERNAL] Re: [AMBER] Amber Install Error
On Tue, Jan 10, 2023, Tacey, Sean A via AMBER wrote:
>
>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).
Sorry to be slow about replying here. I'm guessing that the python problems
arise because of setuptools/distutils problems, in turn arising from changes
in the standard python libraries. We've removed the need for distutils in
Amber22, but this (like other things) didn't get back-ported to earlier
Amber versions.
As a start, add "-DBUILD_PYTHON=FALSE" to your run_cmake script, and set
-DDOWNLOAD_PYTHON=FALSE (just in case). That should get you further, but
at the expense of not building the python-related codes.
If you *do* need the python stuff, here is an additional workaround:
download AmberTools22, which goes into a different directory hierarchy than
Amber20 does. See if that build works. You can then run the "amber.sh"
script in the amber22 folder (or whatever you chose for the installation
path), which will get all of AmberTools in your path.
You can still use the GPU programs (like pmemd.cuda) from Amber20, by
just specifying their full path. (pmemd doesn't make any use of the
AMBERHOME environment variable.)
Let us know if you still have problems or questions. I'm cc-ing this to a
couple of our python gurus, in case they have other (better) ideas.
....regards....dac
>
>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 Wed Jan 18 2023 - 11:30:03 PST
