On Thu, Nov 14, 2019 at 1:29 PM Cruzeiro, Vinicius <vcruzeiro.ucsd.edu>
wrote:
> Hello Gustavo,
>
> I was having some issues a few months ago to compile the python related
> Amber functionalities with my anaconda3 installation.
Technically --with-python should work nicely. Please do not hesitate to
report the issues to the mail-list so we can resolve the issue.
cheers
Hai
> I was never able to figure this out. I was only able to solve the problem
> when I completely deactivated anaconda3 from my environment and I installed
> miniconda through Amber. Now, every time I need to recompile anything
> python related I deactivate anaconda3 first to avoid conflicts/errors.
>
> I hope this helps,
> Best,
>
> VinÃcius Wilian D. Cruzeiro, PhD
> Postdoctoral Researcher
> San Diego Supercomputer Center
> Department of Chemistry and Biochemistry
> University of California, San Diego
> Voice: +1(858)246-5584
> ________________________________
> From: Gustavo Seabra <gustavo.seabra.gmail.com>
> Sent: Thursday, November 14, 2019 10:15 AM
> To: amber-developers.ambermd.org <amber-developers.ambermd.org>
> Subject: [AMBER-Developers] Pytraj not compiling with Python 3.7
>
> 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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Received on Thu Nov 14 2019 - 12:00:02 PST
