Hi,
What's the cython version in AmberTools/src/configure_python?
If it's different, can you try to install that version?
Did you compile from amber master branch or from AmberTools19 release?
(I don't have access to source code right now)
Hai
On Thu, Nov 14, 2019 at 1:16 PM Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Hi guys,
>
> I'm trying to compile amber with my local (conda) python install, but I'm
> getting this error from pytraj. Apparently it is related to some recent
> change in the Cython behavior (see below). Does anyone here has any
> experience with that?
>
> My configuration:
> - RedHat 8
> - Python 3.7.5
> - Cython 0.29.13
> - Gcc 8.3.1
>
> Thanks,
> Gustavo.
> -------
>
> (base) [seabra.proline amber18]$ ./configure --with-python
> /opt/anaconda3/bin/python gnu
>
> [...]
> (all works as expected)
>
> (base) [seabra.proline amber18]$ make install
>
> [...]
>
> creating build/lib.linux-x86_64-3.7/pytraj/utils/css
> copying pytraj/utils/css/oceans16.css ->
> build/lib.linux-x86_64-3.7/pytraj/utils/css
> running build_ext
> building 'pytraj.core.c_core' extension
> creating build/temp.linux-x86_64-3.7
> creating build/temp.linux-x86_64-3.7/pytraj
> creating build/temp.linux-x86_64-3.7/pytraj/core
> gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
> -I/opt/amber/amber18/AmberTools/src/cpptraj/src
> -I/opt/amber/amber18/AmberTools/src/pytraj/pytraj
> -I/opt/anaconda3/include/python3.7m -c pytraj/core/c_core.cpp -o
> build/temp.linux-x86_64-3.7/pytraj/core/c_core.o -O0 -ggdb
> -Wl,-rpath=/opt/amber/amber18/lib
> cc1plus: warning: command line option '-Wstrict-prototypes' is valid for
> C/ObjC but not for C++
> pytraj/core/c_core.cpp: In function 'void __Pyx_ExceptionSave(PyObject**,
> PyObject**, PyObject**)':
> pytraj/core/c_core.cpp:26256:21: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> *type = tstate->exc_type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26257:22: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> *value = tstate->exc_value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26258:19: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> *tb = tstate->exc_traceback;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp: In function 'void __Pyx_ExceptionReset(PyObject*,
> PyObject*, PyObject*)':
> pytraj/core/c_core.cpp:26270:24: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> tmp_type = tstate->exc_type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26271:25: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> tmp_value = tstate->exc_value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26272:22: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> tmp_tb = tstate->exc_traceback;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp:26273:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> tstate->exc_type = type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26274:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> tstate->exc_value = value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26275:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> tstate->exc_traceback = tb;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp: In function 'int __Pyx_GetException(PyObject**,
> PyObject**, PyObject**)':
> pytraj/core/c_core.cpp:26318:24: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> tmp_type = tstate->exc_type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26319:25: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> tmp_value = tstate->exc_value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26320:22: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> tmp_tb = tstate->exc_traceback;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp:26321:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> tstate->exc_type = local_type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26322:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> tstate->exc_value = local_value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26323:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> tstate->exc_traceback = local_tb;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp: In function 'void __Pyx_ExceptionSwap(PyObject**,
> PyObject**, PyObject**)':
> pytraj/core/c_core.cpp:26345:24: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> tmp_type = tstate->exc_type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26346:25: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> tmp_value = tstate->exc_value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26347:22: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> tmp_tb = tstate->exc_traceback;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp:26348:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_type'; did you mean 'curexc_type'?
> tstate->exc_type = *type;
> ^~~~~~~~
> curexc_type
> pytraj/core/c_core.cpp:26349:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_value'; did you mean 'curexc_value'?
> tstate->exc_value = *value;
> ^~~~~~~~~
> curexc_value
> pytraj/core/c_core.cpp:26350:13: error: 'PyThreadState' {aka 'struct _ts'}
> has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
> tstate->exc_traceback = *tb;
> ^~~~~~~~~~~~~
> curexc_traceback
> pytraj/core/c_core.cpp: At global scope:
> pytraj/core/c_core.cpp:6030:18: warning: 'PyObject*
> __pyx_pw_6pytraj_4core_6c_core_8NameType_7__str__(PyObject*)' defined but
> not used [-Wunused-function]
> static PyObject
> *__pyx_pw_6pytraj_4core_6c_core_8NameType_7__str__(PyObject
> *__pyx_v_self) {
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> error: command 'gcc' failed with exit status 1
> make[2]: *** [Makefile:508: pytraj] Error 1
> make[2]: Leaving directory '/opt/amber/amber18/AmberTools/src'
> make[1]: *** [Makefile:56: serial] Error 2
> make[1]: Leaving directory '/opt/amber/amber18/AmberTools/src'
> make: *** [Makefile:7: install] Error 2
>
>
>
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>
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Received on Thu Nov 14 2019 - 10:30:03 PST
