> The version in configure_python is 0.25
> I'm compiling from a regular Amber18 distribution.
I see. So the pytraj used the precythonized cpp code and upgrading cython
version won't help.
AmberTools18 was released before python 3.7 so pytraj did not know how to
support it.
Please do either
- Use python 2.7 or 3.5
- Upgrade your ambertools to the latest one (v19).
- Turnoff pytraj compilation if you don't need it.
Hai
On Thu, Nov 14, 2019 at 1:40 PM Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> 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
> > >
> > >
> > >
> > > _______________________________________________
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> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
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> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
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Received on Thu Nov 14 2019 - 12:00:02 PST
