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Merge remote-tracking branch 'upstream/v0.51.0-release'
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‎.gitignore

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@@ -5,6 +5,11 @@
55
*.gcda
66
*.gcno
77
*~
8+
*.log
9+
*.trs
10+
*.dirstamp
11+
*.aux
12+
queso-*tar.gz
813

914
Makefile.in
1015
Makefile
@@ -17,6 +22,13 @@ aminclude.am
1722
autom4te.cache
1823
build-aux
1924
.license.stamp
25+
queso.pc
26+
queso-deps.pc
27+
m4/libtool.m4
28+
m4/ltoptions.m4
29+
m4/ltsugar.m4
30+
m4/ltversion.m4
31+
m4/lt~obsolete.m4
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2133
_configs.sed
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config.log
@@ -27,9 +39,22 @@ config_queso.h.tmp.in
2739
config_queso.h.tmp.in~
2840
configure
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42+
m4/libtool.m4
43+
m4/ltoptions.m4
44+
m4/ltsugar.m4
45+
m4/ltversion.m4
46+
m4/lt~obsolete.m4
47+
3048
doxygen/txt_common/about_vpath.page
3149
doxygen/queso.dox
3250
docs
51+
manual/users/figs
52+
manual/users/make_all_failed
53+
manual/users/users.bbl
54+
manual/users/users.blg
55+
manual/users/users.out
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manual/users/users.toc
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manual/users/QUESO_users_manual.pdf
3358

3459
examples/exInfoTheory_gsl
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examples/exSimpleStatisticalInverseProblem_gsl
@@ -45,6 +70,17 @@ examples/infinite_dim/parallel_inverse_options
4570
examples/inverse_problem
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examples/operator
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examples/parallel_inverse_problem
73+
examples/gpmsa_scalar
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examples/bimodal_gsl
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examples/exSimpleStatisticalForwardProblem_gsl
76+
examples/gp/scalar/outputData
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examples/gpscalar
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examples/gpscalar2
79+
examples/hysteretic_gsl
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examples/outputData
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examples/template_eg
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examples/template_example/outputData
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examples/template_example/template_example
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4985
src/core/inc/queso.h
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src/libqueso.la
@@ -94,3 +130,34 @@ test/test_infinite/inf_options
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test/test_operator
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test/test_uqexception
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test/test_SequenceOfVectorsErase
133+
test/test_gpmsa_cobra
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test/test_LlhdTargetOutput
135+
test/test_StatisticalInverseProblem/both_input.txt
136+
test/test_StatisticalInverseProblem/llhdout_input.txt
137+
test/test_StatisticalInverseProblem/neither_input.txt
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test/test_StatisticalInverseProblem/targetout_input.txt
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test/test_StatisticalInverseProblem/test_LlhdTargetOutput.sh
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test/test_outputBoth/
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test/test_outputLlhd/
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test/test_outputNeither/
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test/test_outputTarget/
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test/test_Regression/jeffreys_input.txt
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test/test_Regression/test_jeffreys_samples.m
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test/test_Regression/test_jeffreys_samples.diff.sh
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test/test_jeffreys
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test/test_gsloptimizer
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test/test_seedwithmap
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test/test_seedwithmap_fd
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test/test_GammaVectorRVDomain
152+
test/test_GaussianMean1DRegression
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test/test_Regression/GaussianMean1DRegression_options
154+
test/test_Regression/ctf_dat.txt
155+
test/test_Regression/dakota_pstudy.dat
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test/test_Regression/gpmsa_cobra_input.txt
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test/test_Regression/test_cobra_samples_diff.sh
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test/test_Regression/test_gpmsa_cobra_samples.m
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test/test_Regression/adaptedcov_input.txt
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test/test_Regression/test_jeffreys_samples_diff.sh
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test/test_adaptedcov_output/
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test/test_gpmsa_cobra_output/
163+
test/test_logitadaptedcov

‎AUTHORS

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@@ -1,12 +1,12 @@
1-
21
Contributors to QUESO Development:
32

43
Paul T. Bauman
54
Sai Hung Cheung
65
Nicholas Malaya
76
Damon McDougall
8-
Todd Oliver
7+
Todd A. Oliver
98
Ernesto E. Prudencio
109
Karl W. Schulz
1110
Rhys Ulerich
12-
11+
Eric Wright
12+
Rebecca E. Morrison

‎CHANGES

+18-11
Original file line numberDiff line numberDiff line change
@@ -2,22 +2,29 @@
22
QUESO: Quantification of Uncertainty for Estimation,
33
Simulation, and Optimization.
44
-----------------------------------------------------
5+
6+
Version 0.51.0
7+
* Add canned likelihood for scalar GPMSA use-case a la Higdon et al
8+
* Add a logit-transformed transition kernel for more efficient proposals
9+
* Adding jeffreys distribution as an available prior distribution
10+
* Adding likelihood value caching to ML sampler
11+
* Adding Eric Wright to contributors list
12+
13+
Version 0.50.0
14+
* Implemented MCMC sampling on function spaces
15+
* Added function space MCMC unit tests
16+
* Added serial and parallel function space MCMC examples
17+
* Replace exit() calls with a macro exception handler
18+
519
Version 0.47.1
620
* created two simple statistical examples, simpleStatisticalForwardProblem and simpleStatisticalInverseProblem
721
* included description of the new examples on QUESO user's manual, including how to run and to process the generated data
822
* updated QUESO user's manual to include description of validationCycle example
923
* updated links for how to obtain QUESO and contact information (github/git)
10-
24+
1125
Version 0.47.0
1226
* removed example statisticalInverseProblem as it has a bug - it fails to recreate the problem described in the Normal test from Laine's MCMC tool: http://helios.fmi.fi/~lainema/mcmc/ex/normalex.html.
1327

14-
Version 0.50.0 (In progress)
15-
16-
* Implemented MCMC sampling on function spaces
17-
* Added function space MCMC unit tests
18-
* Added serial and parallel function space MCMC examples
19-
* Replace exit() calls with a macro exception handler
20-
2128
Version 0.47.1 (23 Sep 2013)
2229

2330
* Update manual and fix broken Makefile
@@ -97,7 +104,7 @@ https://svn.ices.utexas.edu/repos/pecos/uq/queso/releases/0.44.0
97104
* added uqMpiCommClass
98105
* added uqMapClass
99106
* added uqDistArrayClass
100-
* configure options modified to allow for optional use of Trilinos, HDF5 and GLPK;
107+
* configure options modified to allow for optional use of Trilinos, HDF5 and GLPK;
101108
with the change, the minimum dependencies for QUESO are Boost, GSL, and GRVY
102109
* improved uqScalarSequenceClass and uqSequenceOfVectorsClass
103110

@@ -118,7 +125,7 @@ https://svn.ices.utexas.edu/repos/pecos/uq/queso/releases/0.42
118125
* fixed output runtime failure when running multiple chains in parallel
119126
* fixed race condition in output directory creation
120127
* inclusion of automatic licensing header support
121-
* added minimum version requirement for autoconf
128+
* added minimum version requirement for autoconf
122129
* added configuration support for the GNU Linear Programming Toolkit (GLPK)
123130
* added interface to HDF5 for some I/O
124131
* added quadrature classes
@@ -140,7 +147,7 @@ https://svn.ices.utexas.edu/repos/pecos/uq/queso/releases/0.41
140147

141148
* user likelihood routines should now return ln(value), instead of -2*ln(value)
142149
* inclusion of inverse Gamma random variable (in addition to standard uniform and Gaussian options)
143-
* uniform pdf now returns (1/volume of domain), instead of just 1. If volume is infinite or zero,
150+
* uniform pdf now returns (1/volume of domain), instead of just 1. If volume is infinite or zero,
144151
then the uniform pdf returns 1.
145152
* random variables can be now be formed by concatenation of existing random variable
146153
definitions (uniform, Gaussian, inverse Gamma)

‎Makefile.am

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@@ -14,6 +14,9 @@ include $(top_srcdir)/doxygen/aminclude.am
1414
AUX_DIST = build-aux/install-sh \
1515
build-aux/missing
1616

17+
pkgconfigdir = $(libdir)/pkgconfig
18+
pkgconfig_DATA = queso.pc queso-deps.pc
19+
1720
if CODE_COVERAGE_ENABLED
1821

1922
lcov_dir=$(top_builddir)/docs/html/lcov
@@ -124,6 +127,14 @@ DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_fp_qoi2.m
124127
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2.m
125128
DISTCLEANFILES += test/t01_valid_cycle/outputData/tgaValOutput_sub0.m
126129
DISTCLEANFILES += test/t01_valid_cycle/outputData/tgaCalOutput_sub0.m
130+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_ip_raw2_loglikelihood.m
131+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_ip_raw2_loglikelihood_sub0.m
132+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_ip_raw2_logtarget.m
133+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_ip_raw2_logtarget_sub0.m
134+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2_loglikelihood.m
135+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2_loglikelihood_sub0.m
136+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2_logtarget.m
137+
DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2_logtarget_sub0.m
127138
DISTCLEANFILES += test/t04_bimodal/outputData/display_sub0.txt
128139
DISTCLEANFILES += test/t04_bimodal/outputData/sipOutput_ml_sub0.m
129140
DISTCLEANFILES += test/t04_bimodal/outputData/filtChain_ml.m
@@ -143,6 +154,14 @@ DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain_sub0.m
143154
DISTCLEANFILES += test/t02_sip_sfp/outputData/fp_q_seq_sub0.m
144155
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain.m
145156
DISTCLEANFILES += test/t02_sip_sfp/outputData/fp_p_seq_sub0.m
157+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain_loglikelihood.m
158+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain_loglikelihood_sub0.m
159+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain_logtarget.m
160+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain_logtarget_sub0.m
161+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_raw_chain_loglikelihood.m
162+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_raw_chain_loglikelihood_sub0.m
163+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_raw_chain_logtarget.m
164+
DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_raw_chain_logtarget_sub0.m
146165
DISTCLEANFILES += test/outputData/*
147166
DISTCLEANFILES += aminclude.am
148167
DISTCLEANFILES += config_queso.h

‎README.md

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@@ -83,3 +83,21 @@ feel free to ask questions on one of the mailing lists:
8383
list for questions regarding usage and reporting bugs
8484
- [queso-dev](https://groups.google.com/forum/#!forum/queso-dev) mailing list
8585
for discussion regarding development of `QUESO`
86+
87+
Citing QUESO
88+
-------
89+
Please add the following citation to any paper, technical report or
90+
article describing the use of the `QUESO` library:
91+
92+
```bibtex
93+
@inproceedings{Prudencio2012,
94+
author = {Prudencio, Ernesto E and Schulz, Karl W},
95+
booktitle = {Euro-Par 2011: Parallel Processing Workshops},
96+
pages = {398--407},
97+
publisher = {Springer},
98+
title = {{The parallel C++ statistical library ‘QUESO’: Quantification of
99+
Uncertainty for Estimation, Simulation and Optimization}},
100+
url = {http://dx.doi.org/10.1007/978-3-642-29737-3\_44},
101+
year = {2012}
102+
}
103+
```

‎configure.ac

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22
# Process this file with autoconf to produce a configure script.
33

44
AC_PREREQ(2.65)
5-
AC_INIT([queso], [0.50.1], [[email protected]])
5+
AC_INIT([queso], [0.51.0], [[email protected]])
6+
PACKAGE_DESCRIPTION="The parallel C++ statistical library QUESO: Quantification of uncertainty for estimation, simulation and optimization"
7+
AC_SUBST([PACKAGE_DESCRIPTION])
8+
PACKAGE_URL="https://github.com/libqueso/queso"
9+
AC_SUBST([PACKAGE_URL])
10+
611
AC_CONFIG_MACRO_DIR([m4])
712

813
AC_CONFIG_HEADERS(config_queso.h.tmp)
@@ -11,7 +16,7 @@ AX_PREFIX_CONFIG_H(config_queso.h,QUESO,config_queso.h.tmp)
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1217
AC_CONFIG_AUX_DIR([build-aux])
1318
AC_CANONICAL_TARGET()
14-
AM_INIT_AUTOMAKE
19+
AM_INIT_AUTOMAKE([color-tests subdir-objects])
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# Release versioning
1722

@@ -171,11 +176,12 @@ AX_SUMMARIZE_ENV
171176
# Generate makefiles
172177

173178
AC_CONFIG_FILES([
179+
queso.pc
180+
queso-deps.pc
174181
Makefile
175182
inc/queso/Makefile
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src/Makefile
177184
src/contrib/ANN/Makefile
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src/contrib/ANN/lib/Makefile
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src/contrib/ANN/test/Makefile
180186
src/core/inc/queso.h
181187
examples/Makefile
@@ -190,11 +196,41 @@ AC_CONFIG_FILES([
190196
test/gsl_tests/input
191197
test/test_Environment/copy_env
192198
test/test_infinite/inf_options
199+
test/test_Regression/GaussianMean1DRegression_options
200+
test/test_Regression/gpmsa_cobra_input.txt
201+
test/test_Regression/test_cobra_samples_diff.sh
202+
test/test_Regression/test_gpmsa_cobra_samples.m
203+
test/test_Regression/ctf_dat.txt
204+
test/test_Regression/dakota_pstudy.dat
205+
test/test_StatisticalInverseProblem/test_LlhdTargetOutput.sh
206+
test/test_StatisticalInverseProblem/both_input.txt
207+
test/test_StatisticalInverseProblem/llhdout_input.txt
208+
test/test_StatisticalInverseProblem/neither_input.txt
209+
test/test_StatisticalInverseProblem/targetout_input.txt
210+
test/test_Regression/jeffreys_input.txt
211+
test/test_Regression/test_jeffreys_samples_diff.sh
212+
test/test_Regression/test_jeffreys_samples.m
213+
test/test_Regression/adaptedcov_input.txt
193214
doxygen/Makefile
194215
doxygen/queso.dox
195216
doxygen/txt_common/about_vpath.page
217+
],
218+
[
219+
chmod +x test/test_Regression/test_cobra_samples_diff.sh
220+
chmod +x test/test_StatisticalInverseProblem/test_LlhdTargetOutput.sh
221+
chmod +x test/test_Regression/test_jeffreys_samples_diff.sh
196222
])
197223

224+
dnl ----------------------------------------------
225+
dnl Collect files for licence header stamping here
226+
dnl ----------------------------------------------
227+
_AC_SRCDIRS(.)
228+
229+
# We have to do this by subdirectory because otherwise distcheck breaks as we
230+
# start picking up files in the directories that it uses
231+
QUESO_STAMPED_FILES=$(find $ac_abs_top_srcdir/{src,examples,test} -name "*.h" -or -name "*.C" | tr "\n" " ")
232+
AC_SUBST(QUESO_STAMPED_FILES)
233+
198234
AC_OUTPUT()
199235

200236
#---------------

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