Initialize doc_topic_counts to zero before counting

apps/medlda_release/README.txt

@@ -0,0 +1,17 @@
+Input data file format:
+
+Each line represents 1 document, and consists of the following in order:
+
+     0 or more integer labels [0 to num_label) in a one-hot encoding.
+
+     num_xtra real values as constant extra predictors in the classifier matrix.
+
+     num_target real values as regression targets (each regression target is a separate "task" to predict a scalar).
+
+     any number of word:count pairs where word is an arbitrary string containing no spaces or ':'s and count is a positive integer.
+
+
+
+
+
+

apps/medlda_release/dSFMT/CHANGE-LOG.txt

@@ -0,0 +1,93 @@
+ver 2.2.3
+-------
+change Makefile for nmake
+
+ver 2.2.2
+-------
+fix MSC 2012 compile error.
+
+ver 2.2.1
+-------
+The code for ALTIVEC is changed, to fit to the ISA manual.
+This was reported by Tao Yao, thanks.
+
+ver 2.2.0
+-------
+move do_recursion to dSFMT-common.h
+
+ver 2.1.1
+-------
+The initialization of the constants for sse2 is changed.
+Old version may cause trouble in parallel environment like OpenMP.
+
+ver 2.1
+-------
+This version supports the periods from 2^521-1 to 2^216091-1.
+We added new function dsfmt_genrand_uint32, which returns 32-bit
+unsigned integer. If you need many floating point pseudo random
+numbers and a few integers, you don't need to use another
+integer generator.
+
+ver 2.0
+-------
+The recursion formula of dSFMT is changed.
+The supported periods are changed.
+The output sequences are completely changed.
+The generation speed is improved.
+The variable for initialization check is removed, because it causes
+an execution error in cygwin.
+
+ver 1.3.1
+-------
+change dSFMT.h not to include dSFMT-params.h
+change Makefile to clean test files.
+
+ver 1.3
+-------
+add `dsfmt_' prefix to functions.
+changed to structure base code.
+put Intel Compiler into silence.
+bug fix checking BIG_ENDIAN and BYTE_ORDER
+change test.c not to include dSFMT.c
+dSFMT-alti.h and dSFMT-sse2.h are marged into dSFMT.c
+
+ver 1.2.1
+-------
+add #include <altivec.h> to dSFMT.c
+
+ver 1.2
+-------
+The precision specifier of printf was too large in test.c
+CAUTION! *.out.txt is changed.
+add dSFMT-params216091.h
+gcc compile option changed form -O9 to -O3.
+add AltiVec parameter format for systems which are not OSX.
+change Makefile for systems which are not OSX and support AltiVec.
+change sample2 of howto-compile for Free BSD.
+change period certification code more smart.
+change source files for BORLANDC and Visual Studio.
+
+ver 1.1.1
+-------
+BUG in dSFMT-sse2.h is fixed.
+This bug didn't change the result.
+Change test.c
+
+ver 1.1
+-------
+add dSFMT-params132049.h
+fix bug in period_certification. It's a bug but result is the same for
+all parameter files.
+change macro definition names and global variables. Thank you, Adam Piatyszek.
+remove L suffix from floating point constants. It's Saito's misunderstanding.
+fix bug of sfmt_idxof definition for BIG ENDIAN machine.
+
+ver 1.0.1
+-------
+change name dSFMT-alti.c to SFMT-alti.h
+change name dSFMT-sse2.c to SFMT-sse2.h
+This version is not released.
+
+ver 1.0
+-------
+The first version.

apps/medlda_release/dSFMT/FILES.txt

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+This archive contails following directories and files.
+
+TOP DIRECTORY
+FILES.txt:		This file.
+CHANGE-LOG.txt		change log.
+LICENSE.txt:		License file.
+Makefile:		Makefile for test programs.
+dSFMT.h:		Header file.
+dSFMT-common.h:		Header file.
+dSFMT-params.h:		parameter file control for various Mersenne expornent
+dSFMT-params521.h:	parameters for period of 2^{521}-1
+dSFMT-params1279.h:	parameters for period of 2^{1279}-1
+dSFMT-params2203.h:	parameters for period of 2^{2203}-1
+dSFMT-params4253.h:	parameters for period of 2^{4253}-1
+dSFMT-params11213.h:	parameters for period of 2^{11213}-1
+dSFMT-params19937.h:	parameters for period of 2^{19937}-1
+dSFMT.c:		C code for standard C (c99) and unix like systems.
+test.c:			Test driver for standard C.
+check.sh:		Test shell script.
+dSFMT.521.out.txt:	correct output of dSFMT MEXP=521
+dSFMT.1279.out.txt:	correct output of dSFMT MEXP=1279
+dSFMT.2203.out.txt:	correct output of dSFMT MEXP=2203
+dSFMT.4253.out.txt:	correct output of dSFMT MEXP=4253
+dSFMT.11213.out.txt:	correct output of dSFMT MEXP=11213
+dSFMT.19937.out.txt:	correct output of dSFMT MEXP=19937
+
+html DIRECTORY:		The documents generated by doxygen.

apps/medlda_release/dSFMT/LICENSE.txt

@@ -0,0 +1,32 @@
+Copyright (c) 2007, 2008, 2009 Mutsuo Saito, Makoto Matsumoto
+and Hiroshima University.
+Copyright (c) 2011, 2002 Mutsuo Saito, Makoto Matsumoto, Hiroshima
+University and The University of Tokyo.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above
+      copyright notice, this list of conditions and the following
+      disclaimer in the documentation and/or other materials provided
+      with the distribution.
+    * Neither the name of the Hiroshima University nor the names of
+      its contributors may be used to endorse or promote products
+      derived from this software without specific prior written
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

apps/medlda_release/dSFMT/Makefile

@@ -0,0 +1,198 @@
+# @file  Makefile
+# @brief Makefile
+#
+# @author Mutsuo Saito (Hiroshima University)
+# @author Makoto Matsumoto (Hiroshima University)
+#
+# Copyright (C) 2007, 2008, 2013 Mutsuo Saito, Makoto Matsumoto and
+# Hiroshima University. All rights reserved.
+#
+# The new BSD License is applied to this software.
+# see LICENSE.txt
+#
+# @note
+# We could comple test-sse2-Mxxx using gcc 3.4.4 of cygwin.
+# We could comple test-sse2-Mxxx using gcc 4.0.1 of Linux.
+# We coundn't comple test-sse2-Mxxx using gcc 3.3.2 of Linux.
+# We could comple test-alti-Mxxx using gcc 3.3 of osx.
+# We could comple test-alti-Mxxx using gcc 4.0 of osx.
+
+WARN = -Wmissing-prototypes -Wall #-Winline
+#WARN = -Wmissing-prototypes -Wall -W
+#WARN = /Wall
+OPTI = -O3 -finline-functions -fomit-frame-pointer -DNDEBUG \
+-fno-strict-aliasing --param max-inline-insns-single=1800
+#--param inline-unit-growth=500 --param large-function-growth=900 #for gcc 4
+#OPTI = /Ot /Ob2 /Oy /Ox /Oi /GL /G6
+#STD =
+#STD = -std=c89 -pedantic
+#STD = -std=c99 -pedantic
+STD = -std=c99
+CC = gcc
+CCFLAGS = $(OPTI) $(WARN) $(STD)
+ALTIFLAGS = -mabi=altivec -maltivec -DHAVE_ALTIVEC
+OSXALTIFLAGS = -faltivec -maltivec -DHAVE_ALTIVEC
+SSE2FLAGS = -msse2 -DHAVE_SSE2
+#SSE2FLAGS = /arch:SSE2 /DHAVE_SSE2
+STD_TARGET = test-std-M19937
+ALL_STD_TARGET = test-std-M521 test-std-M1279 test-std-M2203 test-std-M4253 \
+test-std-M11213 test-std-M19937 test-std-M44497 test-std-M86243 \
+test-std-M132049 test-std-M216091
+ALTI_TARGET = $(STD_TARGET) test-alti-M19937
+ALL_ALTI_TARGET = test-alti-M521 test-alti-M1279 test-alti-M2203 \
+test-alti-M4253 test-alti-M11213 test-alti-M19937 test-alti-M44497 \
+test-alti-M86243 test-alti-M132049 test-alti-M216091
+SSE2_TARGET = $(STD_TARGET) test-sse2-M19937
+ALL_SSE2_TARGET = test-sse2-M521 test-sse2-M1279 test-sse2-M2203 \
+test-sse2-M4253 test-sse2-M11213 test-sse2-M19937 test-sse2-M44497 \
+test-sse2-M86243 test-sse2-M132049 test-sse2-M216091
+# ==========================================================
+# comment out or EDIT following lines to get max performance
+# ==========================================================
+# --------------------
+# for gcc 4
+# --------------------
+CCFLAGS += --param inline-unit-growth=500 \
+ --param large-function-growth=900
+# --------------------
+# for icl
+# --------------------
+#CC = icl /Wcheck /O3 /QxB /Qprefetch
+# --------------------
+# for icc
+# --------------------
+#CC = icc
+#OPTI = -O3 -finline-functions -fomit-frame-pointer -DNDEBUG \
+#-fno-strict-aliasing
+#CCFLAGS = $(OPTI) $(WARN) $(STD)
+# -----------------
+# for PowerPC
+# -----------------
+#CCFLAGS += -arch ppc
+# -----------------
+# for Pentium M
+# -----------------
+#CCFLAGS += -march=prescott
+# -----------------
+# for Athlon 64
+# -----------------
+#CCFLAGS += -march=athlon64
+
+.PHONY: std-check sse2-check alti-check
+
+std: $(STD_TARGET)
+
+sse2: $(SSE2_TARGET)
+
+alti: $(ALTI_TARGET)
+
+osx-alti:
+	$(MAKE) "ALTIFLAGS=$(OSXALTIFLAGS)" alti
+
+std-check: $(ALL_STD_TARGET)
+	./check.sh test-std
+
+sse2-check: $(ALL_SSE2_TARGET)
+	./check.sh test-sse2
+
+alti-check: $(ALL_ALTI_TARGET)
+	./check.sh test-alti
+
+osx-alti-check:
+	make "ALTIFLAGS=$(OSXALTIFLAGS)" alti-check
+
+test-std-M521: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=521 -o $@ dSFMT.c test.c
+
+test-alti-M521: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=521 -o $@ dSFMT.c test.c
+
+test-sse2-M521: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=521 -o $@ dSFMT.c test.c
+
+test-std-M1279: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=1279 -o $@ dSFMT.c test.c
+
+test-alti-M1279: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=1279 -o $@ dSFMT.c test.c
+
+test-sse2-M1279: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=1279 -o $@ dSFMT.c test.c
+
+test-std-M2203: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=2203 -o $@ dSFMT.c test.c
+
+test-alti-M2203: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=2203 -o $@ dSFMT.c test.c
+
+test-sse2-M2203: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=2203 -o $@ dSFMT.c test.c
+
+test-std-M4253: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=4253 -o $@ dSFMT.c test.c
+
+test-alti-M4253: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=4253 -o $@ dSFMT.c test.c
+
+test-sse2-M4253: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=4253 -o $@ dSFMT.c test.c
+
+test-std-M11213: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=11213 -o $@ dSFMT.c test.c
+
+test-alti-M11213: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=11213 -o $@ dSFMT.c test.c
+
+test-sse2-M11213: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=11213 -o $@ dSFMT.c test.c
+
+test-std-M19937: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=19937 -o $@ dSFMT.c test.c
+
+test-alti-M19937: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=19937 -o $@ dSFMT.c test.c
+
+test-sse2-M19937: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=19937 -o $@ dSFMT.c test.c
+
+test-std-M44497: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=44497 -o $@ dSFMT.c test.c
+
+test-alti-M44497: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=44497 -o $@ dSFMT.c test.c
+
+test-sse2-M44497: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=44497 -o $@ dSFMT.c test.c
+
+test-std-M86243: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=86243 -o $@ dSFMT.c test.c
+
+test-alti-M86243: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=86243 -o $@ dSFMT.c test.c
+
+test-sse2-M86243: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=86243 -o $@ dSFMT.c test.c
+
+test-std-M132049: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=132049 -o $@ dSFMT.c test.c
+
+test-alti-M132049: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=132049 -o $@ dSFMT.c test.c
+
+test-sse2-M132049: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=132049 -o $@ dSFMT.c test.c
+
+test-std-M216091: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) -DDSFMT_MEXP=216091 -o $@ dSFMT.c test.c
+
+test-alti-M216091: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(ALTIFLAGS) -DDSFMT_MEXP=216091 -o $@ dSFMT.c test.c
+
+test-sse2-M216091: test.c dSFMT.c dSFMT.h
+	$(CC) $(CCFLAGS) $(SSE2FLAGS) -DDSFMT_MEXP=216091 -o $@ dSFMT.c test.c
+
+.c.o:
+	$(CC) $(CCFLAGS) -c $<
+
+clean:
+	rm -f *.o *~ test-*-M*