Hi,
Just to give a feedback: it seems that installation with AmberTools19 works
fine... Here's what I did:
1. Untar Amber18.tgz (creates Amber18 folder)
2. Rename "Amber18" folder to "amber18"
3. Untar AmberTools19.tar.bz2 (overwriting files in amber18 folder)
4. cd amber18
5. $ ./configure --with-python /opt/anaconda3/bin/python gnu
6. make install
Works just fine.
Gustavo.
> -----Original Message-----
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Thursday, November 14, 2019 2:54 PM
> To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> Subject: Re: [AMBER-Developers] Pytraj not compiling with Python 3.7
>
> > 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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> >
> >
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Received on Sat Nov 16 2019 - 12:00:02 PST
