search

HazyResearch / deepdive

DeepDive
deepdive.stanford.edu
1.95k stars 539 forks source link

master 0.9.0rc2 goes wrong when execute deepdive do sentences #631

Open yejunjin opened 7 years ago

yejunjin commented 7 years ago

Hi!

When I followed the tutorial (exmaple-spouse)[https://github.com/HazyResearch/deepdive/blob/master/doc/example-spouse.md] in master 0.9.0rc2 version, when i execute step1.2 ‘deepdive do sentences’， something goes wrong with me. Here is the log info:

2017-03-12 12:29:28.372237 ################################################################################
2017-03-12 12:29:28.372352 # Host: ga89
2017-03-12 12:29:28.372383 # DeepDive: deepdive v0.9.0rc2-1063-g7b82f5a (Linux x86_64)
2017-03-12 12:29:28.372407 export PATH='/home/jyj/local/bin':"$PATH"
2017-03-12 12:29:28.372432 export DEEPDIVE_PWD='/home/jyj/spouse_example'
2017-03-12 12:29:28.372456 export DEEPDIVE_APP='/home/jyj/spouse_example'
2017-03-12 12:29:28.372480 cd "$DEEPDIVE_APP"/run
2017-03-12 12:29:28.372504 export DEEPDIVE_RUN_ID='20170312/122928.147677579'
2017-03-12 12:29:28.372526 # Plan: 20170312/122928.147677579/plan.sh
2017-03-12 12:29:28.372559 # Targets: sentences
2017-03-12 12:29:28.372583 ################################################################################
2017-03-12 12:29:28.372605 
2017-03-12 12:29:28.372629     # process/init/app/run.sh ####################################### last done: 2017-03-12T09:44:29+0800 (2h 44m 59s ago
2017-03-12 12:29:28.372654     # process/init/relation/articles/run.sh ######################### last done: 2017-03-12T09:45:55+0800 (2h 43m 33s ago
2017-03-12 12:29:28.372677     # deepdive mark 'done' data/articles ############################ last done: 2017-03-12T09:45:55+0800 (2h 43m 33s ago
2017-03-12 12:29:28.372699 process/ext_sentences_by_nlp_markup/run.sh ########################## last done: N/A
2017-03-12 12:29:28.372722 ++ dirname process/ext_sentences_by_nlp_markup/run.sh
2017-03-12 12:29:28.372746 + cd process/ext_sentences_by_nlp_markup
2017-03-12 12:29:28.372770 + : dd_tmp_ dd_old_
2017-03-12 12:29:28.372793 + export DEEPDIVE_CURRENT_PROCESS_NAME=process/ext_sentences_by_nlp_markup
2017-03-12 12:29:28.372817 + DEEPDIVE_CURRENT_PROCESS_NAME=process/ext_sentences_by_nlp_markup
2017-03-12 12:29:28.372840 + export DEEPDIVE_LOAD_FORMAT=tsv
2017-03-12 12:29:28.372864 + DEEPDIVE_LOAD_FORMAT=tsv
2017-03-12 12:29:28.372887 + output_relation=sentences
2017-03-12 12:29:28.372911 + output_relation_tmp=dd_tmp_sentences
2017-03-12 12:29:28.372934 + output_relation_old=dd_old_sentences
2017-03-12 12:29:28.372957 + deepdive create table-if-not-exists sentences
2017-03-12 12:29:28.510974 + deepdive create table dd_tmp_sentences like sentences
2017-03-12 12:29:28.766148 CREATE TABLE
2017-03-12 12:29:28.767107 + deepdive compute execute 'input_sql=
2017-03-12 12:29:28.767176 
2017-03-12 12:29:28.767202 SELECT R0.id AS column_0
2017-03-12 12:29:28.767225      , R0.content AS column_1
2017-03-12 12:29:28.767249 FROM articles R0
2017-03-12 12:29:28.767271 
2017-03-12 12:29:28.767295 ' 'command=cd "$DEEPDIVE_APP" && udf/nlp_markup.sh' output_relation=dd_tmp_sentences
2017-03-12 12:29:28.918606 Executing with the following configuration:
2017-03-12 12:29:28.918673  DEEPDIVE_NUM_PROCESSES=31
2017-03-12 12:29:28.918700  DEEPDIVE_NUM_PARALLEL_UNLOADS=1
2017-03-12 12:29:28.918730  DEEPDIVE_NUM_PARALLEL_LOADS=1
2017-03-12 12:29:28.918754  DEEPDIVE_NAMED_PIPES_DIR=/home/jyj/spouse_example/run/process/ext_sentences_by_nlp_markup
2017-03-12 12:29:29.016113 unloading to /home/jyj/spouse_example/run/process/ext_sentences_by_nlp_markup/deepdive-compute-execute.96hSQAD/feed_processes-1: '
2017-03-12 12:29:29.016211 
2017-03-12 12:29:29.016274 SELECT R0.id AS column_0
2017-03-12 12:29:29.016315      , R0.content AS column_1
2017-03-12 12:29:29.016346 FROM articles R0
2017-03-12 12:29:29.016368 
2017-03-12 12:29:29.016390 '
2017-03-12 12:29:29.171637 Loading dd_tmp_sentences from /home/jyj/spouse_example/run/process/ext_sentences_by_nlp_markup/deepdive-compute-execute.96hSQAD/output_computed-1 (tsv format)
2017-03-12 12:29:29.437548 Parsing db60062c-cd21-40a5-ab3b-648d5a320bf2
2017-03-12 12:29:29.437652 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "A Beverley businessm...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.437702 Parsing fc6ad33a-ae70-41ff-9f0e-7283f85878f6
2017-03-12 12:29:29.437748 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "Today I have a speci...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.450501 Parsing 9d486048-bcc2-488c-be8a-32d7913c3b3b
2017-03-12 12:29:29.450610 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "You can learn a lot ...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.456443 Parsing 9662058b-fca5-4771-8058-c7fd7bd548a3
2017-03-12 12:29:29.456519 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "Rick Perry is gone. ...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.475290 Parsing 82c0c1d4-45b1-4861-b880-c414de299948
2017-03-12 12:29:29.475392 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "I took the Man to hi...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.476808 Parsing dbc798be-9a6e-48b7-8721-31f84e89c10b
2017-03-12 12:29:29.476885 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "Is Reformed Theology...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.479385 Parsing d8ec5d11-bf4d-4464-8dc7-c0984563181b
2017-03-12 12:29:29.479440 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "FOX LAKE, Ill. \x{2014}...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.486478 Parsing c27a162d-f2d1-4bdb-84ba-0915a082775b
2017-03-12 12:29:29.486542 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "NBC's new drama The ...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.491662 Parsing e7ea7dd7-0266-431a-bfb4-c8e88532c0d4
2017-03-12 12:29:29.491717 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "After four days of i...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.501727 Parsing 2dea8451-cbcd-42b9-a263-ffc3397bde43
2017-03-12 12:29:29.501797 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "The veteran captain ...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.503267 Parsing 340bb625-bb7e-49af-aa8d-781e5762f7a3
2017-03-12 12:29:29.503321 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "Peter Edelstein M.D....") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.507124 Parsing 70ecb3ad-cbbe-4097-8608-e3373a34a728
2017-03-12 12:29:29.507175 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "The President of the...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.509941 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3961) - No such process
2017-03-12 12:29:29.510023 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3971) - No such process
2017-03-12 12:29:29.510064 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3973) - No such process
2017-03-12 12:29:29.510109 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3974) - No such process
2017-03-12 12:29:29.510149 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3977) - No such process
2017-03-12 12:29:29.510186 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3978) - No such process
2017-03-12 12:29:29.510222 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3980) - No such process
2017-03-12 12:29:29.510256 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3982) - No such process
2017-03-12 12:29:29.510290 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3983) - No such process
2017-03-12 12:29:29.510329 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3984) - No such process
2017-03-12 12:29:29.510356 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3985) - No such process
2017-03-12 12:29:29.510378 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3986) - No such process
2017-03-12 12:29:29.510404 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3998) - No such process
2017-03-12 12:29:29.510426 /home/jyj/local/util/compute-driver/local/compute-execute: line 129: kill: (3999) - No such process
2017-03-12 12:29:29.511309 Parsing f6e047d0-e409-42a6-ab0e-13ab926719a6
2017-03-12 12:29:29.511391 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "Valley Journal/Times...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.514226 [ERROR] deepdive-unload: PID 3999: finished with non-zero exit status (141)
2017-03-12 12:29:29.514454 Parsing ba44d0cd-bff2-4875-8036-86f37419b5e7
2017-03-12 12:29:29.514523 malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "Words kill or give l...") at /home/jyj/local/util/nlp/tsj2corenlp-http-reqs line 38, <STDIN> line 1.
2017-03-12 12:29:29.522593 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3962 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522650 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3963 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522678 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3964 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522703 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3965 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522727 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3966 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522750 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3967 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522774 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3968 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522798 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3969 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522824 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3970 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522848 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3972 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522872 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3975 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522896 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3976 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522920 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3979 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522943 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3981 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522967 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3987 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.522991 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3988 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.523015 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3989 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.523038 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3990 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.523062 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3991 Terminated              DEEPDIVE_CURRENT_PROCESS_INDEX=$i bash -c "$command" < "$pipes"/process-$i.input > "$pipes"/process-$i.output
2017-03-12 12:29:29.523086 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3994 Terminated              mkmimo "$pipes"/process-*.output \> "$pipes"/output_computed-*
2017-03-12 12:29:29.523109 /home/jyj/local/util/compute-driver/local/compute-execute: line 126:  3995 Terminated              deepdive-load "$output_relation" "$pipes"/output_computed-*
dqqcasia commented 7 years ago

Have you solved it? That also goes wrong with me

yejunjin commented 7 years ago 
        Sorry but not solved with me.
        On 04/23/2017 16:01, dqqian wrote: Have you solved it? That also goes wrong with me

—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or mute the thread.

{"api_version":"1.0","publisher":{"api_key":"05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity":{"external_key":"github/HazyResearch/deepdive","title":"HazyResearch/deepdive","subtitle":"GitHub repository","main_image_url":"https://cloud.githubusercontent.com/assets/143418/17495839/a5054eac-5d88-11e6-95fc-7290892c7bb5.png","avatar_image_url":"https://cloud.githubusercontent.com/assets/143418/15842166/7c72db34-2c0b-11e6-9aed-b52498112777.png","action":{"name":"Open in GitHub","url":"https://github.com/HazyResearch/deepdive"}},"updates":{"snippets":[{"icon":"PERSON","message":"@dqqian in #631: Have you solved it? That also goes wrong with me"}],"action":{"name":"View Issue","url":"https://github.com/HazyResearch/deepdive/issues/631#issuecomment-296426548"}}}