Make boost po opt-in, convert all test input files to getpot format

configure.ac

@@ -88,11 +88,11 @@ AC_ARG_ENABLE(mpi,
 # Check if the user disabled program options #
 ##############################################
 AC_ARG_ENABLE([boost-program-options],
-              AS_HELP_STRING([--disable-boost-program-options], [Disables use
+              AS_HELP_STRING([--enable-boost-program-options], [Enables use
                               of boost program options for parsing the QUESO
-                              input file.  GetPot will be used instead.]),
-              [enable_program_options="no"],
-              [enable_program_options="yes"])
+                              input file.  GetPot will not be used.]),
+              [enable_program_options="yes"],
+              [enable_program_options="no"])
 
 #-------------------
 # Compilers and MPI

test/t01_valid_cycle/tgaCycle.inp

@@ -3,9 +3,9 @@
 ###############################################
 #env_help                 = anything
 env_numSubEnvironments   = 1
-env_subDisplayFileName   = outputData/screen
+env_subDisplayFileName   = 'outputData/screen'
 env_subDisplayAllowAll   = 0
-env_subDisplayAllowedSet = 0 1
+env_subDisplayAllowedSet = '0 1'
 env_displayVerbosity     = 2
 env_syncVerbosity        = 0
 env_seed                 = 0
@@ -16,7 +16,7 @@ env_seed                 = 0
 cycle_cal_ip_help                 = anything
 cycle_cal_ip_computeSolution      = 1
 cycle_cal_ip_dataOutputFileName   = outputData/tgaCalOutput
-cycle_cal_ip_dataOutputAllowedSet = 0 1
+cycle_cal_ip_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # 'cal_ip_': information for Metropolis-Hastings algorithm
@@ -26,23 +26,23 @@ cycle_cal_ip_dataOutputAllowedSet = 0 1
 ###############################################
 cycle_cal_ip_mh_help                 = anything
 cycle_cal_ip_mh_dataOutputFileName   = outputData/tgaCalOutput
-cycle_cal_ip_mh_dataOutputAllowedSet = 0 1
+cycle_cal_ip_mh_dataOutputAllowedSet = '0 1'
 
 cycle_cal_ip_mh_rawChain_dataInputFileName    = . # outputData/file_cal_ip_raw1
 cycle_cal_ip_mh_rawChain_size                 = 16384
 cycle_cal_ip_mh_rawChain_generateExtra        = 0
 cycle_cal_ip_mh_rawChain_displayPeriod        = 20000
 cycle_cal_ip_mh_rawChain_measureRunTimes      = 1
-cycle_cal_ip_mh_rawChain_dataOutputFileName   = outputData/file_cal_ip_raw2
-cycle_cal_ip_mh_rawChain_dataOutputAllowedSet = 0 1
+cycle_cal_ip_mh_rawChain_dataOutputFileName   = 'outputData/file_cal_ip_raw2'
+cycle_cal_ip_mh_rawChain_dataOutputAllowedSet = '0 1'
 cycle_cal_ip_mh_rawChain_computeStats         = 1
 
 cycle_cal_ip_mh_displayCandidates             = 0
 cycle_cal_ip_mh_putOutOfBoundsInChain         = 1
 cycle_cal_ip_mh_tk_useLocalHessian            = 0
 cycle_cal_ip_mh_tk_useNewtonComponent         = 1
 cycle_cal_ip_mh_dr_maxNumExtraStages          = 1
-cycle_cal_ip_mh_dr_listOfScalesForExtraStages = 5. 4. 3.
+cycle_cal_ip_mh_dr_listOfScalesForExtraStages = '5. 4. 3.'
 cycle_cal_ip_mh_am_initialNonAdaptInterval    = 0
 cycle_cal_ip_mh_am_adaptInterval              = 100
 cycle_cal_ip_mh_am_eta                        = 1.92
@@ -52,13 +52,13 @@ cycle_cal_ip_mh_filteredChain_generate             = 1
 cycle_cal_ip_mh_filteredChain_discardedPortion     = 0.
 cycle_cal_ip_mh_filteredChain_lag                  = 20
 cycle_cal_ip_mh_filteredChain_dataOutputFileName   = .
-cycle_cal_ip_mh_filteredChain_dataOutputAllowedSet = 0 1
+cycle_cal_ip_mh_filteredChain_dataOutputAllowedSet = '0 1'
 cycle_cal_ip_mh_filteredChain_computeStats         = 1
 
 #cycle_cal_ip_mh_rawChain_stats_help                      = anything
-cycle_cal_ip_mh_rawChain_stats_initialDiscardedPortions  = 0. .05 .10 .15 .20 .25 .30 .35 .40
+cycle_cal_ip_mh_rawChain_stats_initialDiscardedPortions  = '0. .05 .10 .15 .20 .25 .30 .35 .40'
 cycle_cal_ip_mh_rawChain_stats_bmm_run                   = 0
-cycle_cal_ip_mh_rawChain_stats_bmm_lengths               = 50 100 200 250
+cycle_cal_ip_mh_rawChain_stats_bmm_lengths               = '50 100 200 250'
 cycle_cal_ip_mh_rawChain_stats_fft_compute               = 0
 cycle_cal_ip_mh_rawChain_stats_fft_paramId               = 0
 cycle_cal_ip_mh_rawChain_stats_fft_size                  = 2048
@@ -99,7 +99,7 @@ cycle_cal_ip_mh_rawChain_stats_corrMatrix_compute        = 1
 #cycle_cal_ip_mh_filteredChain_stats_help                      = anything
 cycle_cal_ip_mh_filteredChain_stats_initialDiscardedPortions  = 0.
 cycle_cal_ip_mh_filteredChain_stats_bmm_run                   = 0
-cycle_cal_ip_mh_filteredChain_stats_bmm_lengths               = 50 100 200 250
+cycle_cal_ip_mh_filteredChain_stats_bmm_lengths               = '50 100 200 250'
 cycle_cal_ip_mh_filteredChain_stats_fft_compute               = 0
 cycle_cal_ip_mh_filteredChain_stats_fft_paramId               = 0
 cycle_cal_ip_mh_filteredChain_stats_fft_size                  = 2048
@@ -144,8 +144,8 @@ cycle_cal_fp_help                 = anything
 cycle_cal_fp_computeSolution      = 1
 cycle_cal_fp_computeCovariances   = 1
 cycle_cal_fp_computeCorrelations  = 1
-cycle_cal_fp_dataOutputFileName   = outputData/tgaCalOutput
-cycle_cal_fp_dataOutputAllowedSet = 0 1
+cycle_cal_fp_dataOutputFileName   = 'outputData/tgaCalOutput'
+cycle_cal_fp_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # 'cal_fp_': information for Monte Carlo algorithm
@@ -154,11 +154,11 @@ cycle_cal_fp_dataOutputAllowedSet = 0 1
 #                  16384 131072 1048576 2097152 16777216
 ###############################################
 cycle_cal_fp_mc_help                 = anything
-cycle_cal_fp_mc_dataOutputFileName   = outputData/tgaCalOutput
-cycle_cal_fp_mc_dataOutputAllowedSet = 0 1
+cycle_cal_fp_mc_dataOutputFileName   = 'outputData/tgaCalOutput'
+cycle_cal_fp_mc_dataOutputAllowedSet = '0 1'
 
 cycle_cal_fp_mc_pseq_dataOutputFileName   = .
-cycle_cal_fp_mc_pseq_dataOutputAllowedSet = 0 1
+cycle_cal_fp_mc_pseq_dataOutputAllowedSet = '0 1'
 cycle_cal_fp_mc_pseq_computeStats         = 1
 
 #cycle_cal_fp_mc_pseq_stats_help                      = anything
@@ -177,14 +177,14 @@ cycle_cal_fp_mc_qseq_dataInputFileName    = . # outputData/file_cal_fp_qoi1
 cycle_cal_fp_mc_qseq_size                 = 1048576
 cycle_cal_fp_mc_qseq_displayPeriod        = 20000
 cycle_cal_fp_mc_qseq_measureRunTimes      = 1
-cycle_cal_fp_mc_qseq_dataOutputFileName   = outputData/file_cal_fp_qoi2
-cycle_cal_fp_mc_qseq_dataOutputAllowedSet = 0 1
+cycle_cal_fp_mc_qseq_dataOutputFileName   = 'outputData/file_cal_fp_qoi2'
+cycle_cal_fp_mc_qseq_dataOutputAllowedSet = '0 1'
 cycle_cal_fp_mc_qseq_computeStats         = 1
 
 #cycle_cal_fp_mc_qseq_stats_help                      = anything
 cycle_cal_fp_mc_qseq_stats_initialDiscardedPortions  = 0.
 cycle_cal_fp_mc_qseq_stats_bmm_run                   = 0
-cycle_cal_fp_mc_qseq_stats_bmm_lengths               = 50 100 200 250
+cycle_cal_fp_mc_qseq_stats_bmm_lengths               = '50 100 200 250'
 cycle_cal_fp_mc_qseq_stats_fft_compute               = 0
 cycle_cal_fp_mc_qseq_stats_fft_paramId               = 0
 cycle_cal_fp_mc_qseq_stats_fft_size                  = 2048
@@ -227,8 +227,8 @@ cycle_cal_fp_mc_qseq_stats_corrMatrix_compute        = 1
 ###############################################
 cycle_val_ip_help                 = anything
 cycle_val_ip_computeSolution      = 1
-cycle_val_ip_dataOutputFileName   = outputData/tgaValOutput
-cycle_val_ip_dataOutputAllowedSet = 0 1
+cycle_val_ip_dataOutputFileName   = 'outputData/tgaValOutput'
+cycle_val_ip_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # 'val_ip_': information for Metropolis-Hastings algorithm
@@ -237,24 +237,24 @@ cycle_val_ip_dataOutputAllowedSet = 0 1
 #                  16384 131072 1048576 2097152 16777216
 ###############################################
 cycle_val_ip_mh_help                 = anything
-cycle_val_ip_mh_dataOutputFileName   = outputData/tgaValOutput
-cycle_val_ip_mh_dataOutputAllowedSet = 0 1
+cycle_val_ip_mh_dataOutputFileName   = 'outputData/tgaValOutput'
+cycle_val_ip_mh_dataOutputAllowedSet = '0 1'
 
 cycle_val_ip_mh_rawChain_dataInputFileName    = . # outputData/file_val_ip_raw1
 cycle_val_ip_mh_rawChain_size                 = 16384
 cycle_val_ip_mh_rawChain_generateExtra        = 0
 cycle_val_ip_mh_rawChain_displayPeriod        = 20000
 cycle_val_ip_mh_rawChain_measureRunTimes      = 1
-cycle_val_ip_mh_rawChain_dataOutputFileName   = outputData/file_val_ip_raw2
-cycle_val_ip_mh_rawChain_dataOutputAllowedSet = 0 1
+cycle_val_ip_mh_rawChain_dataOutputFileName   = 'outputData/file_val_ip_raw2'
+cycle_val_ip_mh_rawChain_dataOutputAllowedSet = '0 1'
 cycle_val_ip_mh_rawChain_computeStats         = 1
 
 cycle_val_ip_mh_displayCandidates             = 0
 cycle_val_ip_mh_putOutOfBoundsInChain         = 1
 cycle_val_ip_mh_tk_useLocalHessian            = 0
 cycle_val_ip_mh_tk_useNewtonComponent         = 1
 cycle_val_ip_mh_dr_maxNumExtraStages          = 1
-cycle_val_ip_mh_dr_listOfScalesForExtraStages = 5. 4. 3.
+cycle_val_ip_mh_dr_listOfScalesForExtraStages = '5. 4. 3.'
 cycle_val_ip_mh_am_initialNonAdaptInterval    = 0
 cycle_val_ip_mh_am_adaptInterval              = 100
 cycle_val_ip_mh_am_eta                        = 1.92
@@ -264,13 +264,13 @@ cycle_val_ip_mh_filteredChain_generate             = 1
 cycle_val_ip_mh_filteredChain_discardedPortion     = 0.
 cycle_val_ip_mh_filteredChain_lag                  = 20
 cycle_val_ip_mh_filteredChain_dataOutputFileName   = .
-cycle_val_ip_mh_filteredChain_dataOutputAllowedSet = 0 1
+cycle_val_ip_mh_filteredChain_dataOutputAllowedSet = '0 1'
 cycle_val_ip_mh_filteredChain_computeStats         = 1
 
 #cycle_val_ip_mh_rawChain_stats_help                      = anything
-cycle_val_ip_mh_rawChain_stats_initialDiscardedPortions  = 0. .05 .10 .15 .20 .25 .30 .35 .40
+cycle_val_ip_mh_rawChain_stats_initialDiscardedPortions  = '0. .05 .10 .15 .20 .25 .30 .35 .40'
 cycle_val_ip_mh_rawChain_stats_bmm_run                   = 0
-cycle_val_ip_mh_rawChain_stats_bmm_lengths               = 50 100 200 250
+cycle_val_ip_mh_rawChain_stats_bmm_lengths               = '50 100 200 250'
 cycle_val_ip_mh_rawChain_stats_fft_compute               = 0
 cycle_val_ip_mh_rawChain_stats_fft_paramId               = 0
 cycle_val_ip_mh_rawChain_stats_fft_size                  = 2048
@@ -311,7 +311,7 @@ cycle_val_ip_mh_rawChain_stats_corrMatrix_compute        = 1
 #cycle_val_ip_mh_filteredChain_stats_help                      = anything
 cycle_val_ip_mh_filteredChain_stats_initialDiscardedPortions  = 0.
 cycle_val_ip_mh_filteredChain_stats_bmm_run                   = 0
-cycle_val_ip_mh_filteredChain_stats_bmm_lengths               = 50 100 200 250
+cycle_val_ip_mh_filteredChain_stats_bmm_lengths               = '50 100 200 250'
 cycle_val_ip_mh_filteredChain_stats_fft_compute               = 0
 cycle_val_ip_mh_filteredChain_stats_fft_paramId               = 0
 cycle_val_ip_mh_filteredChain_stats_fft_size                  = 2048
@@ -356,8 +356,8 @@ cycle_val_fp_help                 = anything
 cycle_val_fp_computeSolution      = 1
 cycle_val_fp_computeCovariances   = 1
 cycle_val_fp_computeCorrelations  = 1
-cycle_val_fp_dataOutputFileName   = outputData/tgaValOutput
-cycle_val_fp_dataOutputAllowedSet = 0 1
+cycle_val_fp_dataOutputFileName   = 'outputData/tgaValOutput'
+cycle_val_fp_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # 'val_fp_': information for Monte Carlo algorithm
@@ -366,11 +366,11 @@ cycle_val_fp_dataOutputAllowedSet = 0 1
 #                  16384 131072 1048576 2097152 16777216
 ###############################################
 cycle_val_fp_mc_help                 = anything
-cycle_val_fp_mc_dataOutputFileName   = outputData/tgaValOutput
-cycle_val_fp_mc_dataOutputAllowedSet = 0 1
+cycle_val_fp_mc_dataOutputFileName   = 'outputData/tgaValOutput'
+cycle_val_fp_mc_dataOutputAllowedSet = '0 1'
 
 cycle_val_fp_mc_pseq_dataOutputFileName   = .
-cycle_val_fp_mc_pseq_dataOutputAllowedSet = 0 1
+cycle_val_fp_mc_pseq_dataOutputAllowedSet = '0 1'
 cycle_val_fp_mc_pseq_computeStats         = 1
 
 #cycle_val_fp_mc_pseq_stats_help                      = anything
@@ -389,14 +389,14 @@ cycle_val_fp_mc_qseq_dataInputFileName    = . # outputData/file_val_fp_qoi1
 cycle_val_fp_mc_qseq_size                 = 1048576
 cycle_val_fp_mc_qseq_displayPeriod        = 20000
 cycle_val_fp_mc_qseq_measureRunTimes      = 1
-cycle_val_fp_mc_qseq_dataOutputFileName   = outputData/file_val_fp_qoi2
-cycle_val_fp_mc_qseq_dataOutputAllowedSet = 0 1
+cycle_val_fp_mc_qseq_dataOutputFileName   = 'outputData/file_val_fp_qoi2'
+cycle_val_fp_mc_qseq_dataOutputAllowedSet = '0 1'
 cycle_val_fp_mc_qseq_computeStats         = 1
 
 #cycle_val_fp_mc_qseq_stats_help                      = anything
 cycle_val_fp_mc_qseq_stats_initialDiscardedPortions  = 0.
 cycle_val_fp_mc_qseq_stats_bmm_run                   = 0
-cycle_val_fp_mc_qseq_stats_bmm_lengths               = 50 100 200 250
+cycle_val_fp_mc_qseq_stats_bmm_lengths               = '50 100 200 250'
 cycle_val_fp_mc_qseq_stats_fft_compute               = 0
 cycle_val_fp_mc_qseq_stats_fft_paramId               = 0
 cycle_val_fp_mc_qseq_stats_fft_size                  = 2048

test/t02_sip_sfp/example.inp

@@ -3,7 +3,7 @@
 ###############################################
 #env_help                = anything
 env_numSubEnvironments   = 1
-env_subDisplayFileName   = outputData/display
+env_subDisplayFileName   = 'outputData/display'
 env_subDisplayAllowAll   = 0
 env_subDisplayAllowedSet = 0
 env_displayVerbosity     = 2
@@ -15,23 +15,23 @@ env_seed                 = 0
 ###############################################
 #ip_help                 = anything
 ip_computeSolution      = 1
-ip_dataOutputFileName   = outputData/sipOutput
+ip_dataOutputFileName   = 'outputData/sipOutput'
 ip_dataOutputAllowedSet = 0
 
 ###############################################
 # 'ip_': information for Metropolis-Hastings algorithm
 ###############################################
 #ip_mh_help                 = anything
-ip_mh_dataOutputFileName   = outputData/sipOutput
-ip_mh_dataOutputAllowedSet = 0 1
+ip_mh_dataOutputFileName   = 'outputData/sipOutput'
+ip_mh_dataOutputAllowedSet = '0 1'
 
 ip_mh_rawChain_dataInputFileName    = .
 ip_mh_rawChain_size                 = 32768
 ip_mh_rawChain_generateExtra        = 0
 ip_mh_rawChain_displayPeriod        = 50000
 ip_mh_rawChain_measureRunTimes      = 1
-ip_mh_rawChain_dataOutputFileName   = outputData/ip_raw_chain
-ip_mh_rawChain_dataOutputAllowedSet = 0 1
+ip_mh_rawChain_dataOutputFileName   = 'outputData/ip_raw_chain'
+ip_mh_rawChain_dataOutputAllowedSet = '0 1'
 ip_mh_rawChain_computeStats         = 1
 
 ip_mh_displayCandidates             = 0
@@ -48,8 +48,8 @@ ip_mh_am_epsilon                    = 1.e-5
 ip_mh_filteredChain_generate             = 1
 ip_mh_filteredChain_discardedPortion     = 0.
 ip_mh_filteredChain_lag                  = 16
-ip_mh_filteredChain_dataOutputFileName   = outputData/ip_filt_chain
-ip_mh_filteredChain_dataOutputAllowedSet = 0 1
+ip_mh_filteredChain_dataOutputFileName   = 'outputData/ip_filt_chain'
+ip_mh_filteredChain_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # Statistical forward problem (fp)
@@ -58,22 +58,22 @@ ip_mh_filteredChain_dataOutputAllowedSet = 0 1
 fp_computeSolution      = 1
 fp_computeCovariances   = 1
 fp_computeCorrelations  = 1
-fp_dataOutputFileName   = outputData/sfpOutput
-fp_dataOutputAllowedSet = 0 1
+fp_dataOutputFileName   = 'outputData/sfpOutput'
+fp_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # 'fp_': information for Monte Carlo algorithm
 ###############################################
 #fp_mc_help                 = anything
-fp_mc_dataOutputFileName   = outputData/sfpOutput
-fp_mc_dataOutputAllowedSet = 0 1
+fp_mc_dataOutputFileName   = 'outputData/sfpOutput'
+fp_mc_dataOutputAllowedSet = '0 1'
 
-fp_mc_pseq_dataOutputFileName   = outputData/fp_p_seq
-fp_mc_pseq_dataOutputAllowedSet = 0 1
+fp_mc_pseq_dataOutputFileName   = 'outputData/fp_p_seq'
+fp_mc_pseq_dataOutputAllowedSet = '0 1'
 
 fp_mc_qseq_size                 = 1048576
 fp_mc_qseq_displayPeriod        = 20000
 fp_mc_qseq_measureRunTimes      = 1
-fp_mc_qseq_dataOutputFileName   = outputData/fp_q_seq
-fp_mc_qseq_dataOutputAllowedSet = 0 1
+fp_mc_qseq_dataOutputFileName   = 'outputData/fp_q_seq'
+fp_mc_qseq_dataOutputAllowedSet = '0 1'
 

test/t03_sequence/example.inp

@@ -3,7 +3,7 @@
 ###############################################
 #env_help                = anything
 env_numSubEnvironments   = 1
-env_subDisplayFileName   = outputData/display
+env_subDisplayFileName   = 'outputData/display'
 env_subDisplayAllowAll   = 0
 env_subDisplayAllowedSet = 0
 env_displayVerbosity     = 2

test/t04_bimodal/example_1chain.inp

@@ -3,9 +3,9 @@
 ###############################################
 #env_help                 = anything
 env_numSubEnvironments   = 1
-env_subDisplayFileName   = outputData/display
+env_subDisplayFileName   = 'outputData/display'
 env_subDisplayAllowAll   = 0
-env_subDisplayAllowedSet = 0 1
+env_subDisplayAllowedSet = '0 1'
 env_displayVerbosity     = 2
 env_syncVerbosity        = 0
 env_seed                 = -1
@@ -15,7 +15,7 @@ env_seed                 = -1
 ###############################################
 #ip_help                 = anything
 ip_computeSolution      = 1
-ip_dataOutputFileName   = outputData/sipOutput
+ip_dataOutputFileName   = 'outputData/sipOutput'
 ip_dataOutputAllowedSet = 0
 
 ###############################################
@@ -24,8 +24,8 @@ ip_dataOutputAllowedSet = 0
 #ip_ml_help                 = anything
 #ip_ml_restartInputFileName = outputData/rawChain_ml_input
 #ip_ml_restartChainSize     = 10000
-ip_ml_dataOutputFileName   = outputData/sipOutput_ml
-ip_ml_dataOutputAllowedSet = 0 1
+ip_ml_dataOutputFileName   = 'outputData/sipOutput_ml'
+ip_ml_dataOutputAllowedSet = '0 1'
 
 ###############################################
 # All levels, unless otherwise specified
@@ -53,12 +53,12 @@ ip_ml_6_putOutOfBoundsInChain = 0
 ###############################################
 # Last level (level 4 for 'example_gsl' executable)
 ###############################################
-ip_ml_last_dataOutputFileName                  = outputData/sipOutput_ml
-ip_ml_last_dataOutputAllowedSet                = 0 1
+ip_ml_last_dataOutputFileName                  = 'outputData/sipOutput_ml'
+ip_ml_last_dataOutputAllowedSet                = '0 1'
 
 #ip_ml_last_loadBalance                         = 0
 ip_ml_last_rawChain_size                       = 10000
-ip_ml_last_rawChain_dataOutputFileName         = outputData/rawChain_ml
+ip_ml_last_rawChain_dataOutputFileName         = 'outputData/rawChain_ml'
 ip_ml_last_rawChain_dataOutputAllowedSet       = 0
 ip_ml_last_rawChain_computeStats               = 1
 ip_ml_last_rawChain_stats_kde_compute          = 1
@@ -68,7 +68,7 @@ ip_ml_last_rawChain_stats_corrMatrix_compute   = 1
 
 ip_ml_last_filteredChain_generate                   = 1
 ip_ml_last_filteredChain_lag                        = 2
-ip_ml_last_filteredChain_dataOutputFileName         = outputData/filtChain_ml
+ip_ml_last_filteredChain_dataOutputFileName         = 'outputData/filtChain_ml'
 ip_ml_last_filteredChain_dataOutputAllowedSet       = 0
 ip_ml_last_filteredChain_computeStats               = 1
 ip_ml_last_filteredChain_stats_kde_compute          = 1