java.lang.RuntimeException: GLM[dest=glm-d216d362-8687-4a88-a897-26192ef32bde, iteration=1, lambda = 0.0]: got NaNs and/or Infs in beta

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  • for -" ~/h2o-dev/bigdata/laptop/citibike-nyc/2013-07.csv" on a two node cluster, when run - {code:java} buildModel 'glm', {"model_id":"glm-d216d362-8687-4a88-a897-26192ef32bde","training_frame":"X2013_07.hex","nfolds":0,"response_column":"tripduration","ignored_columns":["starttime","stoptime","start station id","start station longitude","end station id","end station name","end station latitude","end station longitude","bikeid","usertype","birth year","gender"],"ignore_const_cols":true,"family":"gaussian","tweedie_variance_power":0,"tweedie_link_power":1,"solver":"IRLSM","alpha":[],"lambda":[0],"lambda_search":false,"nlambdas":100,"standardize":true,"non_negative":false,"fold_assignment":"AUTO","score_each_iteration":false,"compute_p_values":true,"remove_colinear_columns":false,"max_iterations":-1,"link":"family_default","balance_classes":false,"max_confusion_matrix_size":20,"max_hit_ratio_k":10,"keep_cross_validation_predictions":false,"intercept":true,"objective_epsilon":0.000001,"beta_epsilon":0.0001,"gradient_epsilon":0.0001,"prior":-1,"lambda_min_ratio":-1,"max_active_predictors":-1,"class_sampling_factors":[],"max_after_balance_size":5} {code} {code:java} Got exception 'class java.lang.RuntimeException', with msg 'GLM[dest=glm-d216d362-8687-4a88-a897-26192ef32bde, iteration=1, lambda = 0.0]: got NaNs and/or Infs in beta' java.lang.RuntimeException: GLM[dest=glm-d216d362-8687-4a88-a897-26192ef32bde, iteration=1, lambda = 0.0]: got NaNs and/or Infs in beta at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:2038) at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1921) at water.H2O$H2OCallback.onCompletion(H2O.java:1116) at jsr166y.CountedCompleter.__tryComplete(CountedCompleter.java:425) at water.RPC$2.compute2(RPC.java:621) at water.H2O$H2OCountedCompleter.compute(H2O.java:1057) at jsr166y.CountedCompleter.exec(CountedCompleter.java:468) at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263) at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974) at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477) at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104) {code} but when run on 1 node runs fine, but get a bad model (p-values all one) {code:java} hdata = h2o.importFile("/Users/nidhimehta/h2o-dev/bigdata/laptop/citibike-nyc/2013-07.csv") hh =h2o.glm(x =c("start station name","start station latitude"),y = "tripduration",training_frame = hdata, lambda = 0,compute_p_values = T,remove_colinear_columns = F) --- names coefficients std_error z_value 325 start station name.Willoughby Ave & Hall St -60.672039 93997415.051949 -0.000001 326 start station name.Willoughby Ave & Walworth St 1287.155073 90829446.884767 0.000014 327 start station name.Willoughby St & Fleet St -117.654894 93985016.918904 -0.000001 328 start station name.Wythe Ave & Metropolitan Ave 659.314909 35797052.643935 0.000018 329 start station name.York St & Jay St 207.768930 71758409.736402 0.000003 330 start station latitude -1408.199133 2334864990.210110 -0.000001 p_value standardized_coefficients 325 1.000000 -60.672039 326 0.999989 1287.155073 327 1.000000 -117.654894 328 0.999985 659.314909 329 1.000000 207.768930 330 1.000000 -28.986619 {code} while R-glm na's out the last predictor and returns a decent model {code:java} x = read.csv("/Users/nidhimehta/h2o-dev/bigdata/laptop/citibike-nyc/2013-07.csv") gg = glm(formula = tripduration~start.station.name+start.station.latitude,data = x) summary(gg) ......... start.station.nameWilloughby Ave & Walworth St 1341.93595 311.89845 4.302 1.69e-05 *** start.station.nameWilloughby St & Fleet St -60.97084 276.97337 -0.220 0.825768 start.station.nameWythe Ave & Metropolitan Ave 680.90476 200.01770 3.404 0.000664 *** start.station.nameYork St & Jay St 251.04772 209.87106 1.196 0.231619 start.station.latitude NA NA NA NA --- {code} Would be good if H2O - tells the user - #got NaNs and/or Infs in beta : try running with regularization (and returns the NAed out last predictor model?)
    via by Nidhi Mehta,
  • in Build project version: 3.7.0.3283 see attached log, data availalble upon request {code} 12-04 11:27:27.400 10.22.80.122:54321 18732 FJ-0-7 INFO: Building cross-validation model 1 / 5. 12-04 11:27:27.404 10.22.80.122:54321 18732 FJ-1-5 INFO: Building H2O GLM model with these parameters: 12-04 11:27:27.405 10.22.80.122:54321 18732 FJ-1-5 INFO: {"_model_id":{"name":"glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab","type":"Key"},"_train":{"name":"glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1_Key_Frame__cdw_modeldata_sample.hex_train","type":"Key"},"_valid":{"name":"glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1_Key_Frame__cdw_modeldata_sample.hex_valid","type":"Key"},"_nfolds":0,"_keep_cross_validation_predictions":false,"_fold_assignment":"AUTO","_distribution":"AUTO","_tweedie_power":1.5,"_ignored_columns":["cmc_chn_nbr","dsum","end_date","eqvolchange","pctdol","pid_key","pl_cat_dollars","pl_cat_n","pl_cat_pctdollars","pl_cat_pctn","pl_cat_pctunits","pl_cat_pctxtrans","pl_cat_units","pl_cat_xtrans","pl_first_date","pl_last_date","ppoint","pre_end_dt","preweeks","pt_factor","sharechange","volgroup"],"_ignore_const_cols":true,"_weights_column":"weights","_offset_column":null,"_fold_column":null,"_score_each_iteration":false,"_stopping_rounds":0,"_stopping_metric":"AUTO","_stopping_tolerance":0.001,"_response_column":"sharegroup","_balance_classes":false,"_max_after_balance_size":5.0,"_class_sampling_factors":null,"_max_hit_ratio_k":10,"_max_confusion_matrix_size":20,"_checkpoint":null,"_standardize":true,"_family":"multinomial","_link":"family_default","_solver":"AUTO","_tweedie_variance_power":0.0,"_tweedie_link_power":1.0,"_alpha":null,"_lambda":null,"_prior":-1.0,"_lambda_search":false,"_nlambdas":100,"_non_negative":false,"_exactLambdas":false,"_lambda_min_ratio":-1.0,"_use_all_factor_levels":false,"_max_iterations":-1,"_intercept":true,"_beta_epsilon":1.0E-4,"_objective_epsilon":1.0E-5,"_gradient_epsilon":1.0E-5,"_obj_reg":-1.0,"_beta_constraints":null,"_max_active_predictors":-1} 12-04 11:27:27.407 10.22.80.122:54321 18732 FJ-1-5 INFO: Dropping ignored columns: [cmc_chn_nbr, dsum, end_date, eqvolchange, pctdol, pid_key, pl_cat_dollars, pl_cat_n, pl_cat_pctdollars, pl_cat_pctn, pl_cat_pctunits, pl_cat_pctxtrans, pl_cat_units, pl_cat_xtrans, pl_first_date, pl_last_date, ppoint, pre_end_dt, preweeks, pt_factor, sharechange, volgroup] 12-04 11:27:29.641 10.22.80.122:54321 18732 FJ-1-5 WARN: _training_frame: Dataset has less than 1/2 of the data after filtering out rows with NAs 12-04 11:27:29.705 10.22.80.122:54321 18732 FJ-0-5 INFO: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=0, lambda = 0.332]: All 432 coefficients are active 12-04 11:27:31.741 10.22.80.122:54321 18732 FJ-0-5 INFO: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: iteration computed in 1971 + 59 ms 12-04 11:27:31.741 10.22.80.122:54321 18732 FJ-0-5 INFO: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: got NaNs and/or Infs in beta 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: FLOW: Job failure.; Got exception 'class java.lang.RuntimeException', with msg 'GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: got NaNs and/or Infs in beta' 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: java.lang.RuntimeException: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: got NaNs and/or Infs in beta 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1976) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1901) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at water.H2O$H2OCallback.onCompletion(H2O.java:1126) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.CountedCompleter.__tryComplete(CountedCompleter.java:425) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.CountedCompleter.tryComplete(CountedCompleter.java:383) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at water.MRTask.compute2(MRTask.java:683) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at water.H2O$H2OCountedCompleter.compute(H2O.java:1069) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.CountedCompleter.exec(CountedCompleter.java:468) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104) 12-04 11:28:10.573 10.22.80.122:54321 18732 #13503-14 INFO: {code}
    via by Hank Roark,
  • in Build project version: 3.7.0.3283 see attached log, data availalble upon request {code} 12-04 11:27:27.400 10.22.80.122:54321 18732 FJ-0-7 INFO: Building cross-validation model 1 / 5. 12-04 11:27:27.404 10.22.80.122:54321 18732 FJ-1-5 INFO: Building H2O GLM model with these parameters: 12-04 11:27:27.405 10.22.80.122:54321 18732 FJ-1-5 INFO: {"_model_id":{"name":"glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab","type":"Key"},"_train":{"name":"glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1_Key_Frame__cdw_modeldata_sample.hex_train","type":"Key"},"_valid":{"name":"glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1_Key_Frame__cdw_modeldata_sample.hex_valid","type":"Key"},"_nfolds":0,"_keep_cross_validation_predictions":false,"_fold_assignment":"AUTO","_distribution":"AUTO","_tweedie_power":1.5,"_ignored_columns":["cmc_chn_nbr","dsum","end_date","eqvolchange","pctdol","pid_key","pl_cat_dollars","pl_cat_n","pl_cat_pctdollars","pl_cat_pctn","pl_cat_pctunits","pl_cat_pctxtrans","pl_cat_units","pl_cat_xtrans","pl_first_date","pl_last_date","ppoint","pre_end_dt","preweeks","pt_factor","sharechange","volgroup"],"_ignore_const_cols":true,"_weights_column":"weights","_offset_column":null,"_fold_column":null,"_score_each_iteration":false,"_stopping_rounds":0,"_stopping_metric":"AUTO","_stopping_tolerance":0.001,"_response_column":"sharegroup","_balance_classes":false,"_max_after_balance_size":5.0,"_class_sampling_factors":null,"_max_hit_ratio_k":10,"_max_confusion_matrix_size":20,"_checkpoint":null,"_standardize":true,"_family":"multinomial","_link":"family_default","_solver":"AUTO","_tweedie_variance_power":0.0,"_tweedie_link_power":1.0,"_alpha":null,"_lambda":null,"_prior":-1.0,"_lambda_search":false,"_nlambdas":100,"_non_negative":false,"_exactLambdas":false,"_lambda_min_ratio":-1.0,"_use_all_factor_levels":false,"_max_iterations":-1,"_intercept":true,"_beta_epsilon":1.0E-4,"_objective_epsilon":1.0E-5,"_gradient_epsilon":1.0E-5,"_obj_reg":-1.0,"_beta_constraints":null,"_max_active_predictors":-1} 12-04 11:27:27.407 10.22.80.122:54321 18732 FJ-1-5 INFO: Dropping ignored columns: [cmc_chn_nbr, dsum, end_date, eqvolchange, pctdol, pid_key, pl_cat_dollars, pl_cat_n, pl_cat_pctdollars, pl_cat_pctn, pl_cat_pctunits, pl_cat_pctxtrans, pl_cat_units, pl_cat_xtrans, pl_first_date, pl_last_date, ppoint, pre_end_dt, preweeks, pt_factor, sharechange, volgroup] 12-04 11:27:29.641 10.22.80.122:54321 18732 FJ-1-5 WARN: _training_frame: Dataset has less than 1/2 of the data after filtering out rows with NAs 12-04 11:27:29.705 10.22.80.122:54321 18732 FJ-0-5 INFO: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=0, lambda = 0.332]: All 432 coefficients are active 12-04 11:27:31.741 10.22.80.122:54321 18732 FJ-0-5 INFO: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: iteration computed in 1971 + 59 ms 12-04 11:27:31.741 10.22.80.122:54321 18732 FJ-0-5 INFO: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: got NaNs and/or Infs in beta 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: FLOW: Job failure.; Got exception 'class java.lang.RuntimeException', with msg 'GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: got NaNs and/or Infs in beta' 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: java.lang.RuntimeException: GLM[dest=glm-843b15fb-ad4e-4d8b-9172-d4193b4d9aab_cv_1, iteration=1, lambda = 0.332]: got NaNs and/or Infs in beta 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1976) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1901) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at water.H2O$H2OCallback.onCompletion(H2O.java:1126) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.CountedCompleter.__tryComplete(CountedCompleter.java:425) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.CountedCompleter.tryComplete(CountedCompleter.java:383) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at water.MRTask.compute2(MRTask.java:683) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at water.H2O$H2OCountedCompleter.compute(H2O.java:1069) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.CountedCompleter.exec(CountedCompleter.java:468) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477) 12-04 11:27:31.836 10.22.80.122:54321 18732 #13503-14 INFO: at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104) 12-04 11:28:10.573 10.22.80.122:54321 18732 #13503-14 INFO: {code}
    via by Hank Roark,
  • parse attached file to flow and run glm with x1(last column) as weight and y as response when run with -ea option get - Got exception 'class java.lang.AssertionError', with msg 'invalid weight -0.9905744277979471' java.lang.AssertionError: invalid weight -0.9905744277979471 at hex.glm.GLMTask$GLMIterationTask.processRow(GLMTask.java:771) at hex.glm.GLMTask$GLMIterationTask.map(GLMTask.java:738) at water.MRTask.compute2(MRTask.java:443) at water.H2O$H2OCountedCompleter.compute(H2O.java:666) at jsr166y.CountedCompleter.exec(CountedCompleter.java:429) at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263) at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974) at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477) at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104) when run without -ea option get - Got exception 'class java.lang.RuntimeException', with msg 'GLM[dest=glm-a31066ea-2808-4849-8b31-0a05477d4f57, iteration=1, lambda = 0.1041]: got NaNs and/or Infs in beta' java.lang.RuntimeException: GLM[dest=glm-a31066ea-2808-4849-8b31-0a05477d4f57, iteration=1, lambda = 0.1041]: got NaNs and/or Infs in beta at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1142) at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1078) at water.H2O$H2OCallback.onCompletion(H2O.java:724) at jsr166y.CountedCompleter.tryComplete(CountedCompleter.java:386) at water.MRTask.compute2(MRTask.java:469) at water.H2O$H2OCountedCompleter.compute(H2O.java:666) at jsr166y.CountedCompleter.exec(CountedCompleter.java:429) at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263) at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974) at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477) at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104) would be good to tell the user like in R- glm(y~.,data = df,weights = x1) Error in glm(y ~ ., data = df, weights = x1) : negative weights not allowed
    via by Nidhi Mehta,
    • java.lang.RuntimeException: GLM[dest=glm-d216d362-8687-4a88-a897-26192ef32bde, iteration=1, lambda = 0.0]: got NaNs and/or Infs in beta at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:2038) at hex.glm.GLM$GLMSingleLambdaTsk$Iteration.callback(GLM.java:1921) at water.H2O$H2OCallback.onCompletion(H2O.java:1116) at jsr166y.CountedCompleter.__tryComplete(CountedCompleter.java:425) at water.RPC$2.compute2(RPC.java:621) at water.H2O$H2OCountedCompleter.compute(H2O.java:1057) at jsr166y.CountedCompleter.exec(CountedCompleter.java:468) at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263) at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974) at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477) at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104)
    No Bugmate found.