Hi,
The version in configure_python is 0.25, but that version isn't even
available in conda any longer. I tried to downgrade cython to 0.26, but it
gives a bunch of conflicts with python versions.
I'm compiling from a regular Amber18 distribution.
Thanks!
Gustavo.
> -----Original Message-----
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Thursday, November 14, 2019 1:24 PM
> To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> Subject: Re: [AMBER-Developers] Pytraj not compiling with Python 3.7
>
> 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
> >
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
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Received on Thu Nov 14 2019 - 11:00:02 PST
