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LocalEngine 'memory leak' @ 1360023db0e1f63936941cf6917f365e657ad8c9 With crosscat repo at /opt/crosscat and mem_usage.py, script.sh, test_local_engine.py all in the current working directory, run 'bash script.sh' to generate the out and err files.
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| creating local engine | |
| done initialize | |
| done analyze | |
| done del; gc.collect() | |
| creating local engine 0.00390625 | |
| done initialize 8.71875 | |
| done analyze 376.7734375 | |
| done del; gc.collect() 0.0 |
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| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| crosscat/cython_code/ContinuousComponentModel.cpp: In function ‘void __pyx_pf_8crosscat_11cython_code_24ContinuousComponentModel_26p_ContinuousComponentModel_2__dealloc__(__pyx_obj_8crosscat_11cython_code_24ContinuousComponentModel_p_ContinuousComponentModel*)’: | |
| crosscat/cython_code/ContinuousComponentModel.cpp:881:31: warning: deleting object of polymorphic class type ‘ContinuousComponentModel’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] | |
| delete(__pyx_v_self->thisptr); | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/utils.cpp: In function ‘std::vector<std::vector<int> > draw_crp_init(std::vector<int>, double, RandomNumberGenerator&, std::string)’: | |
| cpp_code/src/utils.cpp:305:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i=0; i<global_row_indices.size(); i++) { | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/ContinuousComponentModel.cpp: In member function ‘virtual double ContinuousComponentModel::calc_element_predictive_logp_constrained(double, std::vector<double>) const’: | |
| cpp_code/src/ContinuousComponentModel.cpp:90:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cpp_code/src/ContinuousComponentModel.cpp: In member function ‘double ContinuousComponentModel::get_draw_constrained(int, std::vector<double>) const’: | |
| cpp_code/src/ContinuousComponentModel.cpp:212:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cpp_code/src/ContinuousComponentModel.cpp: In member function ‘double ContinuousComponentModel::get_predictive_cdf(double, std::vector<double>) const’: | |
| cpp_code/src/ContinuousComponentModel.cpp:240:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| crosscat/cython_code/MultinomialComponentModel.cpp: In function ‘void __pyx_pf_8crosscat_11cython_code_25MultinomialComponentModel_27p_MultinomialComponentModel_2__dealloc__(__pyx_obj_8crosscat_11cython_code_25MultinomialComponentModel_p_MultinomialComponentModel*)’: | |
| crosscat/cython_code/MultinomialComponentModel.cpp:1018:31: warning: deleting object of polymorphic class type ‘MultinomialComponentModel’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] | |
| delete(__pyx_v_self->thisptr); | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/utils.cpp: In function ‘std::vector<std::vector<int> > draw_crp_init(std::vector<int>, double, RandomNumberGenerator&, std::string)’: | |
| cpp_code/src/utils.cpp:305:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i=0; i<global_row_indices.size(); i++) { | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘virtual double MultinomialComponentModel::calc_element_predictive_logp_constrained(double, std::vector<double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:77:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘virtual std::vector<double> MultinomialComponentModel::calc_hyper_conditionals(std::string, std::vector<double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:98:10: warning: unused variable ‘dirichlet_alpha’ [-Wunused-variable] | |
| double dirichlet_alpha = hyper_dirichlet_alpha; | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘virtual void MultinomialComponentModel::init_suffstats()’: | |
| cpp_code/src/MultinomialComponentModel.cpp:151:10: warning: unused variable ‘dirichlet_alpha’ [-Wunused-variable] | |
| double dirichlet_alpha = hyper_dirichlet_alpha; | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘void MultinomialComponentModel::get_keys_counts_for_draw(std::vector<std::basic_string<char> >&, std::vector<double>&, std::map<std::basic_string<char>, double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:161:7: warning: unused variable ‘K’ [-Wunused-variable] | |
| int K = hyper_K; | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘double MultinomialComponentModel::get_draw_constrained(int, std::vector<double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:209:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); constraint_idx++) { | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| crosscat/cython_code/State.cpp: In function ‘PyObject* __pyx_pw_8crosscat_11cython_code_5State_7p_State_37transition(PyObject*, PyObject*, PyObject*)’: | |
| crosscat/cython_code/State.cpp:5434:56: warning: ‘__pyx_v_seed’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| __pyx_t_4 = PyInt_FromLong(__pyx_v_seed); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L8_error;} | |
| ^ | |
| crosscat/cython_code/State.cpp:4986:7: note: ‘__pyx_v_seed’ was declared here | |
| int __pyx_v_seed; | |
| ^ | |
| In file included from /usr/include/python2.7/numpy/ndarrayobject.h:26:0, | |
| from /usr/include/python2.7/numpy/arrayobject.h:14, | |
| from crosscat/cython_code/State.cpp:262: | |
| /usr/include/python2.7/numpy/__multiarray_api.h: At global scope: | |
| /usr/include/python2.7/numpy/__multiarray_api.h:1532:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] | |
| _import_array(void) | |
| ^ | |
| In file included from /usr/include/python2.7/numpy/ufuncobject.h:152:0, | |
| from crosscat/cython_code/State.cpp:263: | |
| /usr/include/python2.7/numpy/__ufunc_api.h:226:1: warning: ‘int _import_umath()’ defined but not used [-Wunused-function] | |
| _import_umath(void) | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/utils.cpp: In function ‘std::vector<std::vector<int> > draw_crp_init(std::vector<int>, double, RandomNumberGenerator&, std::string)’: | |
| cpp_code/src/utils.cpp:305:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int i=0; i<global_row_indices.size(); i++) { | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/View.cpp: In member function ‘void View::assert_state_consistency()’: | |
| cpp_code/src/View.cpp:688:10: warning: unused variable ‘tolerance’ [-Wunused-variable] | |
| double tolerance = 1E-10; | |
| ^ | |
| cpp_code/src/View.cpp:690:7: warning: unused variable ‘sum_via_cluster_counts’ [-Wunused-variable] | |
| int sum_via_cluster_counts = std::accumulate(cluster_counts.begin(), | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/Cluster.cpp: In member function ‘void Cluster::delete_component_models(bool)’: | |
| cpp_code/src/Cluster.cpp:40:12: warning: deleting object of polymorphic class type ‘ComponentModel’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] | |
| delete p_cm; | |
| ^ | |
| cpp_code/src/Cluster.cpp: In member function ‘double Cluster::calc_column_predictive_logp(std::vector<double>, std::string, std::vector<int>, CM_Hypers)’: | |
| cpp_code/src/Cluster.cpp:131:10: warning: deleting object of polymorphic class type ‘ComponentModel’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] | |
| delete p_cm; | |
| ^ | |
| cpp_code/src/Cluster.cpp: In member function ‘double Cluster::insert_row(std::vector<double>, int)’: | |
| cpp_code/src/Cluster.cpp:138:34: warning: variable ‘set_pair’ set but not used [-Wunused-but-set-variable] | |
| pair<set<int>::iterator, bool> set_pair = \ | |
| ^ | |
| cpp_code/src/Cluster.cpp: In member function ‘double Cluster::remove_row(std::vector<double>, int)’: | |
| cpp_code/src/Cluster.cpp:152:16: warning: unused variable ‘num_removed’ [-Wunused-variable] | |
| unsigned int num_removed = row_indices.erase(row_idx); | |
| ^ | |
| cpp_code/src/Cluster.cpp: In member function ‘double Cluster::remove_col(int)’: | |
| cpp_code/src/Cluster.cpp:169:10: warning: deleting object of polymorphic class type ‘ComponentModel’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] | |
| delete p_cm; | |
| ^ | |
| cpp_code/src/Cluster.cpp: In member function ‘double Cluster::calc_column_predictive_logp(std::vector<double>, std::string, std::vector<int>, CM_Hypers)’: | |
| cpp_code/src/Cluster.cpp:128:31: warning: ‘p_cm’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| p_cm->insert_element(value); | |
| ^ | |
| cpp_code/src/Cluster.cpp: In member function ‘double Cluster::insert_col(std::vector<double>, std::string, std::vector<int>, CM_Hypers&)’: | |
| cpp_code/src/Cluster.cpp:180:19: warning: ‘p_cm’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| ComponentModel *p_cm; | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘virtual double MultinomialComponentModel::calc_element_predictive_logp_constrained(double, std::vector<double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:77:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘virtual std::vector<double> MultinomialComponentModel::calc_hyper_conditionals(std::string, std::vector<double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:98:10: warning: unused variable ‘dirichlet_alpha’ [-Wunused-variable] | |
| double dirichlet_alpha = hyper_dirichlet_alpha; | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘virtual void MultinomialComponentModel::init_suffstats()’: | |
| cpp_code/src/MultinomialComponentModel.cpp:151:10: warning: unused variable ‘dirichlet_alpha’ [-Wunused-variable] | |
| double dirichlet_alpha = hyper_dirichlet_alpha; | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘void MultinomialComponentModel::get_keys_counts_for_draw(std::vector<std::basic_string<char> >&, std::vector<double>&, std::map<std::basic_string<char>, double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:161:7: warning: unused variable ‘K’ [-Wunused-variable] | |
| int K = hyper_K; | |
| ^ | |
| cpp_code/src/MultinomialComponentModel.cpp: In member function ‘double MultinomialComponentModel::get_draw_constrained(int, std::vector<double>) const’: | |
| cpp_code/src/MultinomialComponentModel.cpp:209:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); constraint_idx++) { | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cpp_code/src/ContinuousComponentModel.cpp: In member function ‘virtual double ContinuousComponentModel::calc_element_predictive_logp_constrained(double, std::vector<double>) const’: | |
| cpp_code/src/ContinuousComponentModel.cpp:90:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cpp_code/src/ContinuousComponentModel.cpp: In member function ‘double ContinuousComponentModel::get_draw_constrained(int, std::vector<double>) const’: | |
| cpp_code/src/ContinuousComponentModel.cpp:212:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cpp_code/src/ContinuousComponentModel.cpp: In member function ‘double ContinuousComponentModel::get_predictive_cdf(double, std::vector<double>) const’: | |
| cpp_code/src/ContinuousComponentModel.cpp:240:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for(int constraint_idx=0; constraint_idx<constraints.size(); | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] |
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| running install | |
| running build | |
| running build_py | |
| running build_ext | |
| skipping 'crosscat/cython_code/ContinuousComponentModel.cpp' Cython extension (up-to-date) | |
| building 'crosscat.cython_code.ContinuousComponentModel' extension | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c crosscat/cython_code/ContinuousComponentModel.cpp -o build/temp.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ContinuousComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o | |
| g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o -lboost_random -o build/lib.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.so | |
| skipping 'crosscat/cython_code/MultinomialComponentModel.cpp' Cython extension (up-to-date) | |
| building 'crosscat.cython_code.MultinomialComponentModel' extension | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c crosscat/cython_code/MultinomialComponentModel.cpp -o build/temp.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/MultinomialComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o | |
| g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o -lboost_random -o build/lib.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.so | |
| cythoning crosscat/cython_code/State.pyx to crosscat/cython_code/State.cpp | |
| building 'crosscat.cython_code.State' extension | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c crosscat/cython_code/State.cpp -o build/temp.linux-x86_64-2.7/crosscat/cython_code/State.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/DateTime.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/DateTime.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/View.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/View.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/Cluster.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/Cluster.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/MultinomialComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ContinuousComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/State.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/State.o | |
| g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/crosscat/cython_code/State.o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o build/temp.linux-x86_64-2.7/cpp_code/src/DateTime.o build/temp.linux-x86_64-2.7/cpp_code/src/View.o build/temp.linux-x86_64-2.7/cpp_code/src/Cluster.o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/State.o -lboost_random -o build/lib.linux-x86_64-2.7/crosscat/cython_code/State.so | |
| running install_lib | |
| copying build/lib.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.so -> /usr/local/lib/python2.7/dist-packages/crosscat/cython_code | |
| copying build/lib.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.so -> /usr/local/lib/python2.7/dist-packages/crosscat/cython_code | |
| copying build/lib.linux-x86_64-2.7/crosscat/cython_code/State.so -> /usr/local/lib/python2.7/dist-packages/crosscat/cython_code | |
| running install_egg_info | |
| Removing /usr/local/lib/python2.7/dist-packages/CrossCat-0.1.egg-info | |
| Writing /usr/local/lib/python2.7/dist-packages/CrossCat-0.1.egg-info |
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| # http://stackoverflow.com/a/938800 | |
| import os | |
| _proc_status = '/proc/%d/status' % os.getpid() | |
| _scale = {'kB': 1024.0, 'mB': 1024.0*1024.0, | |
| 'KB': 1024.0, 'MB': 1024.0*1024.0} | |
| def _VmB(VmKey): | |
| '''Private. | |
| ''' | |
| global _proc_status, _scale | |
| # get pseudo file /proc/<pid>/status | |
| try: | |
| t = open(_proc_status) | |
| v = t.read() | |
| t.close() | |
| except: | |
| return 0.0 # non-Linux? | |
| # get VmKey line e.g. 'VmRSS: 9999 kB\n ...' | |
| i = v.index(VmKey) | |
| v = v[i:].split(None, 3) # whitespace | |
| if len(v) < 3: | |
| return 0.0 # invalid format? | |
| # convert Vm value to bytes | |
| return float(v[1]) * _scale[v[2]] | |
| def memory(since=0.0): | |
| '''Return memory usage in bytes. | |
| ''' | |
| return _VmB('VmSize:') - since | |
| def resident(since=0.0): | |
| '''Return resident memory usage in bytes. | |
| ''' | |
| return _VmB('VmRSS:') - since | |
| def stacksize(since=0.0): | |
| '''Return stack size in bytes. | |
| ''' | |
| return _VmB('VmStk:') - since |
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| commits="1360023db0e1f639 SHOW_DIAGNOSTICS" | |
| git_dir=/opt/crosscat | |
| script_name=test_local_engine.py | |
| for commit in $commits; do | |
| (cd $git_dir && git checkout ${commit}) | |
| (cd $git_dir && sudo python setup.py install) >${commit}_setup.out 2>${commit}_setup.err | |
| python $script_name >${commit}_out 2>${commit}_err | |
| done |
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| creating local engine | |
| done initialize | |
| done analyze | |
| done del; gc.collect() | |
| creating local engine 0.00390625 | |
| done initialize 7.49609375 | |
| done analyze 3.7109375 | |
| done del; gc.collect() -4.1875 |
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| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| In file included from /usr/include/python2.7/numpy/ndarrayobject.h:26:0, | |
| from /usr/include/python2.7/numpy/arrayobject.h:14, | |
| from crosscat/cython_code/State.cpp:262: | |
| /usr/include/python2.7/numpy/__multiarray_api.h:1532:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] | |
| _import_array(void) | |
| ^ | |
| In file included from /usr/include/python2.7/numpy/ufuncobject.h:152:0, | |
| from crosscat/cython_code/State.cpp:263: | |
| /usr/include/python2.7/numpy/__ufunc_api.h:226:1: warning: ‘int _import_umath()’ defined but not used [-Wunused-function] | |
| _import_umath(void) | |
| ^ | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] |
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| running install | |
| running build | |
| running build_py | |
| running build_ext | |
| skipping 'crosscat/cython_code/ContinuousComponentModel.cpp' Cython extension (up-to-date) | |
| building 'crosscat.cython_code.ContinuousComponentModel' extension | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c crosscat/cython_code/ContinuousComponentModel.cpp -o build/temp.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ContinuousComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o | |
| g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o -lboost_random -o build/lib.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.so | |
| skipping 'crosscat/cython_code/MultinomialComponentModel.cpp' Cython extension (up-to-date) | |
| building 'crosscat.cython_code.MultinomialComponentModel' extension | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c crosscat/cython_code/MultinomialComponentModel.cpp -o build/temp.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/MultinomialComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o | |
| g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o -lboost_random -o build/lib.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.so | |
| cythoning crosscat/cython_code/State.pyx to crosscat/cython_code/State.cpp | |
| building 'crosscat.cython_code.State' extension | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c crosscat/cython_code/State.cpp -o build/temp.linux-x86_64-2.7/crosscat/cython_code/State.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/DateTime.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/DateTime.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/View.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/View.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/Cluster.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/Cluster.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/MultinomialComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/ContinuousComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o | |
| gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Icpp_code/include/CrossCat -I/usr/include/python2.7 -c cpp_code/src/State.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/State.o | |
| g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/crosscat/cython_code/State.o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o build/temp.linux-x86_64-2.7/cpp_code/src/DateTime.o build/temp.linux-x86_64-2.7/cpp_code/src/View.o build/temp.linux-x86_64-2.7/cpp_code/src/Cluster.o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/MultinomialComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/ContinuousComponentModel.o build/temp.linux-x86_64-2.7/cpp_code/src/State.o -lboost_random -o build/lib.linux-x86_64-2.7/crosscat/cython_code/State.so | |
| running install_lib | |
| copying build/lib.linux-x86_64-2.7/crosscat/cython_code/MultinomialComponentModel.so -> /usr/local/lib/python2.7/dist-packages/crosscat/cython_code | |
| copying build/lib.linux-x86_64-2.7/crosscat/cython_code/ContinuousComponentModel.so -> /usr/local/lib/python2.7/dist-packages/crosscat/cython_code | |
| copying build/lib.linux-x86_64-2.7/crosscat/cython_code/State.so -> /usr/local/lib/python2.7/dist-packages/crosscat/cython_code | |
| running install_egg_info | |
| Removing /usr/local/lib/python2.7/dist-packages/CrossCat-0.1.egg-info | |
| Writing /usr/local/lib/python2.7/dist-packages/CrossCat-0.1.egg-info |
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| import numpy | |
| # | |
| import crosscat.LocalEngine as LE | |
| import crosscat.utils.data_utils as du | |
| import mem_usage as mu | |
| data_filename = '/opt/crosscat/www/data/dha.csv' | |
| # | |
| gen_seed = 0 | |
| n_chains = 2 | |
| # num_transitions = 5 | |
| num_transitions = 10 | |
| T, M_r, M_c = du.read_model_data_from_csv(data_filename, gen_seed=gen_seed) | |
| # | |
| memory_usages = [] | |
| messages = [] | |
| memory_usage = mu.memory() | |
| memory_usages.append(memory_usage) | |
| engine = LE.LocalEngine() | |
| message = 'creating local engine' | |
| print message | |
| messages.append(message) | |
| memory_usage = mu.memory() | |
| memory_usages.append(memory_usage) | |
| X_L, X_D = engine.initialize(M_c, M_r, T, 'from_the_prior', n_chains=n_chains) | |
| message = 'done initialize' | |
| print message | |
| messages.append(message) | |
| memory_usage = mu.memory() | |
| memory_usages.append(memory_usage) | |
| X_L, X_D = engine.analyze(M_c, T, X_L, X_D, n_steps=num_transitions) | |
| message = 'done analyze' | |
| print message | |
| messages.append(message) | |
| memory_usage = mu.memory() | |
| memory_usages.append(memory_usage) | |
| # this seems to work! But always uses last job of memory? | |
| del X_L, X_D, M_c, M_r, T | |
| import gc; gc.collect() | |
| message = 'done del; gc.collect()' | |
| print message | |
| messages.append(message) | |
| memory_usage = mu.memory() | |
| memory_usages.append(memory_usage) | |
| def get_memory_diffs(memory_usages): | |
| memory_usages = numpy.array(memory_usages, dtype=int) / (1024. * 1024.) | |
| memory_diffs = numpy.diff(memory_usages) | |
| return memory_diffs | |
| memory_diffs = get_memory_diffs(memory_usages) | |
| for message, diff in zip(messages, memory_diffs): | |
| print message, diff |
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