The below merge includes commits made on the model_trainer branch, lo…

…gs below

Merge github.com:cyclops-community/ctf into model_training_no_log

    fully get rid of active switch

    fix a few minor memory leaks

    extract unused code from model and get mode_trainer working for non power of 2 processor counts

    address compiler warning

    disable folding for sparse * dense contraction with a Hadamard index, which corrects behavior for that case. Broaden the amount of information given by print_map()

    work on merging, including formatting fixes, separating out new code under ifdef TUNE. Normal execution seems to work, model_trainer build with -DTUNE crashes though

    Merge branch 'master' into model_training

.gitignore

@@ -1,9 +1,15 @@
 # Build directories
-*.o
+lib
+lib_shared
+lib_python
+obj
+obj_ext
+obj_shared
+bin
 
 # Autogenerated in first invocation of configure
 config.mk
+setup.py
 how-did-i-configure
-
-# Ignore the .DS_Store
-.DS_Store
+.*.swp
+.*.swo

.travis.yml

@@ -1,43 +1,57 @@
 sudo: false
-language: cpp
-os:
-  - linux
-#  - osx
-compiler:
-  - gcc
-  - clang
-#env:
-#matrix:
+os: linux
+language: python
+python:
+  - "2.7"
+  - "3.5"
+  - "3.6"
+env:
+  - CTF_CXX=clang++
+  - CTF_CXX=g++
+
 addons:
   apt:
     sources:
       - ubuntu-toolchain-r-test
-      #- llvm-toolchain-precise-3.7
     packages:
       - gcc-5
       - g++-5
       - gfortran-5
-      - libopenmpi-dev
+      - libgfortran-5-dev
       - libblas-dev
       - liblapack-dev
+      - mpich2
+      - libmpich2-dev
+      - cmake
 before_install:
-  - pwd
-  - export TRAVIS_HOME=$PWD
-  - export PATH=$TRAVIS_HOME/deps/bin:$PATH
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]] || [[ "$TRAVIS_PYTHON_VERSION" == "2.6" ]] ; then
+      export PYTHONMAJORV=2;
+    else
+      export PYTHONMAJORV=3;
+    fi
+  - wget https://repo.continuum.io/miniconda/Miniconda${PYTHONMAJORV}-latest-Linux-x86_64.sh
+  - bash Miniconda${PYTHONMAJORV}-latest-Linux-x86_64.sh -b
+  - export PATH=$HOME/miniconda${PYTHONMAJORV}/bin:$PATH
+  - conda create -y -n mypy python=$TRAVIS_PYTHON_VERSION
+  - source activate mypy
+  - conda install -y cython
+  - conda install -y numpy  
 install:
-  - mkdir -p $TRAVIS_HOME/deps
-  - sh ./travis/install-mpi.sh $TRAVIS_HOME/deps mpich
-before_script:
-  - which mpicxx ; mpicxx -v
-  - ./configure CXX=mpicxx
+  - $CTF_CXX --version
+  - FC=gfortran-5 ./configure CXX="mpicxx -cxx=$CTF_CXX" --build-hptt --build-scalapack
+  - make -j2 
+  - make python -j2
 script:
-  - make
   - make test
   - make test2
-#after_failure:
+  - make python_test
+  - make python_test2
+after_failure:
 notifications:
   email:
     recipients:
-      - jeff.science@gmail.com
+      - solomon2@illinois.edu
     on_success: change
     on_failure: always
+
+

Makefile

@@ -4,25 +4,50 @@ ifeq (,${BDIR})
 endif
 export BDIR
 export ODIR=$(BDIR)/obj
+export OEDIR=$(BDIR)/obj_ext
 include $(BDIR)/config.mk
 export FCXX
 export OFFLOAD_CXX
 export LIBS
 
-all: $(BDIR)/lib/libctf.a
+all: $(BDIR)/lib/libctf.a $(BDIR)/lib_shared/libctf.so
 
 
-EXAMPLES = algebraic_multigrid apsp bitonic_sort btwn_central ccsd checkpoint dft_3D fft force_integration force_integration_sparse jacobi matmul neural_network particle_interaction qinformatics recursive_matmul scan sparse_mp3 sparse_permuted_slice spectral_element spmv sssp strassen trace mis mis2 ao_mo_transf
-TESTS = bivar_function bivar_transform ccsdt_map_test ccsdt_t3_to_t2 dft diag_ctr diag_sym endomorphism_cust endomorphism_cust_sp endomorphism gemm_4D multi_tsr_sym permute_multiworld readall_test readwrite_test repack scalar speye sptensor_sum subworld_gemm sy_times_ns test_suite univar_function weigh_4D 
+.PHONY: install
+install: $(INSTALL_DIR)/lib/libctf.so
 
-BENCHMARKS = bench_contraction bench_nosym_transp bench_redistribution model_trainer
+$(INSTALL_DIR)/lib/libctf.so: $(BDIR)/lib/libctf.a $(BDIR)/lib_shared/libctf.so
+	if [ -d hptt ]; then  \
+		echo "WARNING: detected HPTT installation in hptt/, you might need to also install it manually separately."; \
+	fi 
+	if [ -d scalapack ]; then \
+		echo "WARNING: detected ScaLAPACK installation in scalapack/, you might need to also install it manually separately."; \
+	fi 
+	cp $(BDIR)/lib/libctf.a $(INSTALL_DIR)/lib 
+	cp $(BDIR)/lib_shared/libctf.so $(INSTALL_DIR)/lib 
+	cd src/scripts && bash ./expand_includes.sh && cd ..
+	mv include/ctf_all.hpp $(INSTALL_DIR)/include/ctf.hpp
 
-SCALAPACK_TESTS = nonsq_pgemm_test nonsq_pgemm_bench 
+.PHONY: uninstall
+uninstall: 
+	rm $(INSTALL_DIR)/lib/libctf.a 
+	rm $(INSTALL_DIR)/lib/libctf.so 
+	rm $(INSTALL_DIR)/include/ctf.hpp 
+
+
+EXAMPLES = algebraic_multigrid apsp bitonic_sort btwn_central ccsd checkpoint dft_3D fft force_integration force_integration_sparse jacobi matmul neural_network particle_interaction qinformatics recursive_matmul scan sparse_mp3 sparse_permuted_slice spectral_element spmv sssp strassen trace mis mis2 ao_mo_transf block_sparse
+TESTS = bivar_function bivar_transform ccsdt_map_test ccsdt_t3_to_t2 dft diag_ctr diag_sym endomorphism_cust endomorphism_cust_sp endomorphism gemm_4D multi_tsr_sym permute_multiworld readall_test readwrite_test repack scalar speye sptensor_sum subworld_gemm sy_times_ns test_suite univar_function weigh_4D  reduce_bcast
+
+
+BENCHMARKS = bench_contraction bench_nosym_transp bench_redistribution model_trainer 
+
+SCALAPACK_TESTS = nonsq_pgemm_test nonsq_pgemm_bench hosvd qr svd
 
 STUDIES = fast_diagram fast_3mm fast_sym fast_sym_4D \
           fast_tensor_ctr fast_sy_as_as_tensor_ctr fast_as_as_sy_tensor_ctr
 
-EXECUTABLES = $(EXAMPLES) $(TESTS) $(BENCHMARKS) $(SCALAPACK_TESTS) $(STUDIES)
+EXECUTABLES = $(EXAMPLES) $(TESTS) $(BENCHMARKS) $(SCALAPACK_TESTS) $(STUDIES) 
+
 
 export EXAMPLES
 export TESTS
@@ -32,7 +57,6 @@ export STUDIES
 
 
 
-
 .PHONY: executables
 executables: $(EXECUTABLES)
 $(EXECUTABLES): $(BDIR)/lib/libctf.a
@@ -53,8 +77,6 @@ scalapack_tests: $(SCALAPACK_TESTS)
 $(SCALAPACK_TESTS):
 	$(MAKE) $@ -C scalapack_tests
 
-
-
 .PHONY: bench
 bench: $(BENCHMARKS)
 $(BENCHMARKS):
@@ -73,55 +95,153 @@ ctf_objs:
 ctflib: ctf_objs 
 	$(AR) -crs $(BDIR)/lib/libctf.a $(ODIR)/*.o; 
 
+ctf_ext_objs:
+	$(MAKE) ctf_ext_objs -C src_python; 
+
 .PHONY: shared
 shared: ctflibso
 .PHONY: ctflibso
 ctflibso: export FCXX+=-fPIC
 ctflibso: export OFFLOAD_CXX+=-fPIC
 ctflibso: export ODIR=$(BDIR)/obj_shared
-ctflibso: ctf_objs 
-	$(FCXX) -shared -o $(BDIR)/lib_shared/libctf.so $(ODIR)/*.o; 
+ctflibso: ctf_objs ctf_ext_objs
+	$(FCXX) -shared -o $(BDIR)/lib_shared/libctf.so $(ODIR)/*.o $(OEDIR)/*.o  $(SO_LIB_PATH) $(SO_LIB_FILES) $(LDFLAGS)
+
+
+PYTHON_SRC_FILES=src_python/ctf/core.pyx src_python/ctf/random.pyx
 
 .PHONY: python
-python: pylib
-.PHONY: pylib
-pylib: lib_py/ctf.so
-lib_py/ctf.so: ctflibso src_python/ctf.pyx
-	LDFLAGS="-L./lib_shared" python setup_wrapper.py build_ext --inplace && mv ctf.so lib_py/
+python: $(BDIR)/lib_python/ctf/core.o
+
+$(BDIR)/lib_python/ctf/core.o: $(BDIR)/setup.py $(BDIR)/lib_shared/libctf.so $(PYTHON_SRC_FILES)
+	cd src_python; \
+	ln -sf $(BDIR)/setup.py setup.py; \
+	mkdir -p $(BDIR)/lib_python/ctf && cp ctf/__init__.py $(BDIR)/lib_python/ctf/; \
+	LDFLAGS="-L$(BDIR)/lib_shared" python setup.py build_ext --force -b $(BDIR)/lib_python/ -t $(BDIR)/lib_python/; \
+	rm setup.py; \
+	cd ..;
+
+
+.PHONY: python_install
+python_install: $(INSTALL_DIR)/lib/libctf.so pip
+.PHONY: pip
+pip: $(BDIR)/setup.py $(BDIR)/lib_shared/libctf.so $(PYTHON_SRC_FILES) 
+	cd src_python; \
+	ln -sf $(BDIR)/setup.py setup.py; \
+	mkdir -p $(BDIR)/lib_python/ctf && cp ctf/__init__.py $(BDIR)/lib_python/ctf/; \
+	pip install --force -b $(BDIR)/lib_python/ . --upgrade; \
+	rm setup.py; \
+	cd ..;
+
+.PHONY: python_uninstall
+python_uninstall:
+	pip uninstall ctf
+
+.PHONY: python_test
+.NOTPARALLEL: python_test
+ifneq (,$(findstring USE_SCALAPACK,$(DEFS)))
+python_test: python_base_test python_fancyindex_test python_einsum_test python_ufunc_test python_dot_test python_la_test 
+	echo "Cyclops Python tests completed."
+else
+python_test: python_base_test python_fancyindex_test python_einsum_test python_ufunc_test python_dot_test 
+	echo "Cyclops Python tests completed."
+endif
+
+.PHONY: python_test%
+.NOTPARALLEL: python_test%
+ifneq (,$(findstring USE_SCALAPACK,$(DEFS)))
+python_test%: python_base_test% python_fancyindex_test% python_einsum_test% python_ufunc_test% python_dot_test% python_la_test%
+	echo "Cyclops Python tests completed."
+else
+python_test%: python_base_test% python_fancyindex_test% python_einsum_test% python_ufunc_test% python_dot_test%
+	echo "Cyclops Python tests completed."
+endif
+
+.PHONY: python_einsum_test
+python_einsum_test: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" python ./test/python/test_einsum.py
 
-.PHONY: test_python
-test_python: lib_py/ctf.so
-	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):./lib_shared" PYTHONPATH="./lib_py" python ./test/python/test_wrapper.py
+.PHONY: python_einsum_test%
+python_einsum_test%: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" mpirun -np $* python ./test/python/test_einsum.py
 
-$(BDIR)/lib/libctf.a: src/*/*.cu src/*/*.cxx src/*/*.h Makefile src/Makefile src/*/Makefile $(BDIR)/config.mk
+.PHONY: python_ufunc_test
+python_ufunc_test: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" python ./test/python/test_ufunc.py
+
+.PHONY: python_ufunc_test%
+python_ufunc_test%: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" mpirun -np $* python ./test/python/test_ufunc.py
+
+.PHONY: python_fancyindex_test
+python_fancyindex_test: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" python ./test/python/test_fancyindex.py
+
+.PHONY: python_fancyindex_test%
+python_fancyindex_test%: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" mpirun -np $* python ./test/python/test_fancyindex.py
+
+.PHONY: python_base_test
+python_base_test: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" python ./test/python/test_base.py
+
+.PHONY: python_base_test%
+python_base_test%: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" mpirun -np $* python ./test/python/test_base.py
+
+.PHONY: python_la_test
+python_la_test: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" python ./test/python/test_la.py; 
+
+.PHONY: python_la_test%
+python_la_test%: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" mpirun -np $* python ./test/python/test_la.py;
+
+.PHONY: python_dot_test
+python_dot_test: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" python ./test/python/test_dot.py; 
+
+.PHONY: python_dot_test%
+python_dot_test%: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" mpirun -np $* python ./test/python/test_dot.py;
+
+
+.PHONY: test_live
+test_live: $(BDIR)/lib_python/ctf/core.o
+	LD_LIBRARY_PATH="$(LD_LIBRARY_PATH):$(BDIR)/lib_shared:$(BDIR)/lib_python:$(LD_LIB_PATH)" PYTHONPATH="$(PYTHONPATH):$(BDIR)/lib_python" ipython -i -c "import numpy as np; import ctf"
+
+
+$(BDIR)/lib/libctf.a: src/*/*.cu src/*/*.cxx src/*/*.h src/Makefile src/*/Makefile $(BDIR)/config.mk src_python/ctf_ext.cxx src_python/ctf_ext.h
 	$(MAKE) ctflib
 
-$(BDIR)/lib/libctf.so: src/*/*.cu src/*/*.cxx src/*/*.h Makefile src/Makefile src/*/Makefile $(BDIR)/config.mk
+$(BDIR)/lib_shared/libctf.so: src/*/*.cu src/*/*.cxx src/*/*.h src/Makefile src/*/Makefile $(BDIR)/config.mk src_python/ctf_ext.cxx src_python/ctf_ext.h
 	$(MAKE) ctflibso
 
-clean: clean_bin clean_lib clean_obj
-
-
 test: test_suite
 	$(BDIR)/bin/test_suite
 
-test2: test_suite
-	mpirun -np 2 $(BDIR)/bin/test_suite
-
-test3: test_suite
-	mpirun -np 3 $(BDIR)/bin/test_suite
+.PHONY: test%
+test%: test_suite
+	mpirun -np $* $(BDIR)/bin/test_suite
 
-test4: test_suite
-	mpirun -np 4 $(BDIR)/bin/test_suite
 
-test6: test_suite
-	mpirun -np 6 $(BDIR)/bin/test_suite
+clean: clean_bin clean_lib clean_obj clean_py
 
-test7: test_suite
-	mpirun -np 7 $(BDIR)/bin/test_suite
+clean_py:
+	rm -f $(BDIR)/src_python/ctf/core.*so
+	rm -f $(BDIR)/src_python/ctf/random.*so
+	rm -f $(BDIR)/bin/test_suite
+	rm -f $(BDIR)/src_python/ctf/core.cpp
+	rm -f $(BDIR)/src_python/ctf/random.cpp
+	rm -rf $(BDIR)/src_python/build
+	rm -rf $(BDIR)/src_python/__pycache__
+	rm -rf $(BDIR)/src_python/ctf/__pycache__
+	rm -f $(BDIR)/lib_python/ctf/core.o
+	rm -f $(BDIR)/lib_python/ctf/random.o
+	rm -f $(BDIR)/lib_python/ctf/core.*so
+	rm -f $(BDIR)/lib_python/ctf/random.*so
+	rm -rf $(BDIR)/lib_python/ctf/__pycache__
 
-test8: test_suite
-	mpirun -np 8 $(BDIR)/bin/test_suite
 
 clean_bin:
 	for comp in $(EXECUTABLES) ; do \
@@ -131,9 +251,11 @@ clean_bin:
 clean_lib:
 	rm -f $(BDIR)/lib/libctf.a
 	rm -f $(BDIR)/lib_shared/libctf.so
-	rm -f $(BDIR)/lib_py/ctf.so
+	rm -f $(BDIR)/lib_shared/libctf_ext.so
 
 clean_obj:
 	rm -f $(BDIR)/obj/*.o 
+	rm -f $(BDIR)/obj_ext/*.o 
 	rm -f $(BDIR)/obj_shared/*.o 
+	rm -rf $(BDIR)/obj_shared/ctf/ 
 	rm -f $(BDIR)/build/*/*/*.o