Hi,
It looks like your compiler is too far in the future relative to Amber 20.
Quoting from my post minutes ago:
Zeroth: if you've been following this list then you know what's first
(quoting from the master himself ;-):
First: is there a reason to use Amber20? It is not unlikely that
problem you see would not exist in the current codes.
First plus a half:
On behalf of the Amber development team, announcing the release of AmberTools23.
This is also a good time to remind people that Amber22 (basically, the pmemd
program) is now also free for non-commercial use. We encourage people using
older versions of Amber to update:
https://ambermd.org/GetAmber.php
scott
On Tue, May 02, 2023 at 07:05:35PM +0000, Markus Metz via AMBER wrote:
> Hello:
> I tried to follow the instructions posted here:
> https://ambermd.org/InstMacOS.php
> and in the Amber 2021 Amber Manual.
>
> I am trying to install Amber2022 and AmberTools2021.
>
> Here is the info on the installation tools I am using:
> Xcode-select version 2397
> gcc installed via brew:
> Gcc 13.1.0
> cmake version 3.26.3
>
> Next, I am running:
>
> ./run_cmake works fine
>
> The only thing noteworthy is that there is no module _distutils_hack
>
>
>
> Then I am running:
>
> make install
>
> Here are the last lines (up to this point no errors occurred):
>
> In file included from /Applications/amber/amber20_src/AmberTools/src/pytraj/../cpptraj/src/ParameterSet.h:4:
>
> /Applications/amber/amber20_src/AmberTools/src/pytraj/../cpptraj/src/ParameterHolders.h:200:13: warning: 'typename' occurs outside of a template [-Wc++11-extensions]
>
> typedef typename Bmap::const_iterator const_iterator;
>
> ^~~~~~~~~
>
> pytraj/topology/topology.cpp:34820:5: error: expression is not assignable
>
> ++Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:34822:5: error: expression is not assignable
>
> --Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:35176:5: error: expression is not assignable
>
> ++Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:35178:5: error: expression is not assignable
>
> --Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:36327:5: error: expression is not assignable
>
> ++Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:36329:5: error: expression is not assignable
>
> --Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:36638:5: error: expression is not assignable
>
> ++Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:36640:5: error: expression is not assignable
>
> --Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:36888:5: error: expression is not assignable
>
> ++Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:36890:5: error: expression is not assignable
>
> --Py_REFCNT(o);
>
> ^ ~~~~~~~~~~~~
>
> pytraj/topology/topology.cpp:39677:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op) : \
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39677:22: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39677:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op)))
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39677:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op) : \
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39677:52: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39677:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op)))
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39693:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op) : \
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39693:26: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39693:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op)))
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39693:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op) : \
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39693:59: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:39693:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
>
> (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
>
> PyUnicode_WSTR_LENGTH(op)))
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
>
> #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3)
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:41876:16: warning: 'PyUnicode_FromUnicode' is deprecated [-Wdeprecated-declarations]
>
> return PyUnicode_FromUnicode(NULL, 0);
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:551:1: note: 'PyUnicode_FromUnicode' has been explicitly marked deprecated here
>
> Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
>
> ^
>
> /Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
>
> #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
>
> ^
>
> pytraj/topology/topology.cpp:46265:19: error: use of undeclared identifier '_PyGen_Send'
>
> ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
>
> ^
>
> pytraj/topology/topology.cpp:46270:19: error: use of undeclared identifier '_PyGen_Send'
>
> ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
>
> ^
>
> pytraj/topology/topology.cpp:46354:19: error: use of undeclared identifier '_PyGen_Send'
>
> ret = _PyGen_Send((PyGenObject*)yf, NULL);
>
> ^
>
> 14 warnings and 13 errors generated.
>
> error: command '/usr/bin/clang' 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
>
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Received on Tue May 02 2023 - 14:30:02 PDT
