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openmm / openmm-plumed

OpenMM plugin to interface with PLUMED
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Getting problems with make PythonInstall #1

Closed msultan closed 7 years ago

msultan commented 7 years ago

Hey Peter, I am getting the following error with installing the python wrapper even though it seems to have installed the plugin. 

make install
[ 30%] Built target OpenMMPlumed
[ 38%] Built target TestSerializePlumedForce
[ 53%] Built target OpenMMPlumedReference
[ 61%] Built target TestReferencePlumedForce
[ 92%] Built target OpenMMPlumedCUDA
[100%] Built target TestCudaPlumedForce
Install the project...
-- Install configuration: ""
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/include/PlumedForce.h
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/include/PlumedKernels.h
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/include/internal/PlumedForceImpl.h
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/include/internal/windowsExportPlumed.h
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/lib/libOpenMMPlumed.so
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/lib/plugins/libOpenMMPlumedReference.so
-- Up-to-date: /home/stanford/pande/users/msultan/software/installation/lib/plugins/libOpenMMPlumedCUDA.so

 make PythonInstall 
running build
running build_py
running build_ext
building '_openmmplumed' extension
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/stanford/pande/users/msultan/software/installation/include -I/home/stanford/pande/users/msultan/software/openmm-plumed/openmmapi/include -I/home/stanford/pande/users/msultan/software/anaconda/include/python3.5m -c PlumedPluginWrapper.cpp -o build/temp.linux-x86_64-3.5/PlumedPluginWrapper.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
PlumedPluginWrapper.cpp: In function ‘swig_module_info* SWIG_Python_GetModule()’:
PlumedPluginWrapper.cpp:2452:51: error: ‘PyCObject_Import’ was not declared in this scope
         (char*)"type_pointer" SWIG_TYPE_TABLE_NAME);
                                                   ^
PlumedPluginWrapper.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
PlumedPluginWrapper.cpp:2521:92: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope
   PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
                                                                                            ^
PlumedPluginWrapper.cpp:2512:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
   static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                      ^
PlumedPluginWrapper.cpp: In function ‘swig_type_info* SWIG_Python_TypeQuery(const char*)’:
PlumedPluginWrapper.cpp:2544:60: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope
     descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
                                                            ^
PlumedPluginWrapper.cpp:2549:51: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope
       obj = PyCObject_FromVoidPtr(descriptor, NULL);
                                                   ^
error: command 'gcc' failed with exit status 1
make[3]: *** [PythonInstall] Error 1
make[2]: *** [python/CMakeFiles/PythonInstall.dir/all] Error 2
make[1]: *** [python/CMakeFiles/PythonInstall.dir/rule] Error 2
make: *** [PythonInstall] Error 2

The swig version is 1.3

swig -version

SWIG Version 1.3.40

Compiled with g++ [x86_64-redhat-linux-gnu]
Please see http://www.swig.org for reporting bugs and further information

Any recommendations on what to try?

msultan commented 7 years ago

tagging @peastman

peastman commented 7 years ago

SWIG 1.3 is a totally ancient version. OpenMM requires 3.0.5 or later.

msultan commented 7 years ago

With 

swig -version

SWIG Version 3.0.7

Compiled with icpc [x86_64-unknown-linux-gnu]

Configured options: +pcre

I am now getting 


make PythonInstall
[100%] Generating PlumedPluginWrapper.cpp
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:717: Warning(401): Nothing known about base class 'std::exception'. Ignored.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:334: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:408: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:438: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:450: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:512: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:558: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:575: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:576: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:586: Warning(453): Can't apply (std::set< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:587: Warning(453): Can't apply (std::set< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:592: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:610: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:658: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:671: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:703: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:711: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:732: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:763: Warning(453): Can't apply (OpenMM::SerializationNode &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:775: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:806: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:929: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:954: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:959: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:973: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:999: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1032: Warning(453): Can't apply (std::vector< Vec3 > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1035: Warning(453): Can't apply (std::vector< Vec3 > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1050: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1051: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1091: Warning(453): Can't apply (std::vector< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1092: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1102: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1103: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1112: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1146: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1231: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1291: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1305: Warning(453): Can't apply (std::set< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1313: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1411: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1422: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1441: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1442: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1451: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1477: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1483: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1510: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1517: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1546: Warning(453): Can't apply (std::vector< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1547: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1553: Warning(453): Can't apply (std::vector< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1554: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1563: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1636: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1646: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1705: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1733: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1784: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1833: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1892: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1897: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1898: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1906: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1924: Warning(453): Can't apply (std::string &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1925: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1934: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1968: Warning(453): Can't apply (std::vector< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:1975: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2072: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2143: Warning(453): Can't apply (std::vector< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2158: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2159: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2180: Warning(453): Can't apply (std::vector< int > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2183: Warning(453): Can't apply (std::vector< std::vector< int > > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2194: Warning(453): Can't apply (std::vector< Vec3 > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2197: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2200: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2201: Warning(453): Can't apply (std::vector< double > &OUTPUT). No typemaps are defined.
/home/stanford/pande/users/msultan/software/installation/include/swig/OpenMMSwigHeaders.i:2205: Warning(453): Can't apply (OpenMM::Context &OUTPUT). No typemaps are defined.
running build
running build_py
copying openmmplumed.py -> build/lib.linux-x86_64-3.5
running build_ext
building '_openmmplumed' extension
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/stanford/pande/users/msultan/software/installation/include -I/home/stanford/pande/users/msultan/software/openmm-plumed/openmmapi/include -I/home/stanford/pande/users/msultan/software/anaconda/include/python3.5m -c PlumedPluginWrapper.cpp -o build/temp.linux-x86_64-3.5/PlumedPluginWrapper.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
PlumedPluginWrapper.cpp: In function 'swig_module_info* SWIG_Python_GetModule()':
PlumedPluginWrapper.cpp:2452:51: error: 'PyCObject_Import' was not declared in this scope
         (char*)"type_pointer" SWIG_TYPE_TABLE_NAME);
                                                   ^
PlumedPluginWrapper.cpp: In function 'void SWIG_Python_SetModule(swig_module_info*)':
PlumedPluginWrapper.cpp:2521:92: error: 'PyCObject_FromVoidPtr' was not declared in this scope
   PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
                                                                                            ^
PlumedPluginWrapper.cpp:2512:22: warning: unused variable 'swig_empty_runtime_method_table' [-Wunused-variable]
   static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                      ^
PlumedPluginWrapper.cpp: In function 'swig_type_info* SWIG_Python_TypeQuery(const char*)':
PlumedPluginWrapper.cpp:2544:60: error: 'PyCObject_AsVoidPtr' was not declared in this scope
     descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
                                                            ^
PlumedPluginWrapper.cpp:2549:51: error: 'PyCObject_FromVoidPtr' was not declared in this scope
       obj = PyCObject_FromVoidPtr(descriptor, NULL);
                                                   ^
error: command 'gcc' failed with exit status 1
make[3]: *** [PythonInstall] Error 1
make[2]: *** [python/CMakeFiles/PythonInstall.dir/all] Error 2
make[1]: *** [python/CMakeFiles/PythonInstall.dir/rule] Error 2
make: *** [PythonInstall] Error 2
msultan commented 7 years ago

should i reinstall openmm?

msultan commented 7 years ago

This is on python 3.5 btw.

msultan commented 7 years ago

@peastman any ideas about what to try next?

msultan commented 7 years ago

Talked with @peastman offline. Basically it needed a new fresh install and is working now. Thanks @peastman

peastman commented 7 years ago

In case anyone else with the same problem finds this thread, the problem was that the build directory still had some files in it created by the old version of SWIG. Recreating the build directory from scratch fixed it.