Closed sorenwacker closed 1 month ago
sorenwacker
commented
7 months ago I fixed the elasticsearch error by increasing vm.max_map_count.
sudo vi /etc/sysctl.conf
Add the following line at the end of the file:
vm.max_map_count=262144
Close file and run:
sudo sysctl -p
Then restart the container.
However, the tripal_web container still exits unexectedly.
sorenwacker
commented
7 months ago sudo docker-compose up
Starting docker-tripal_postgres_1 ... done
Starting docker-tripal_elasticsearch_1 ... done
Starting docker-tripal_web_1 ... done
Attaching to docker-tripal_postgres_1, docker-tripal_elasticsearch_1, docker-tripal_web_1
postgres_1 | LOG: database system was shut down at 2023-11-17 09:40:30 UTC
postgres_1 | LOG: MultiXact member wraparound protections are now enabled
postgres_1 | LOG: database system is ready to accept connections
postgres_1 | LOG: autovacuum launcher started
web_1 |
web_1 | => Trying to connect to a database using:
web_1 | Database Driver: pgsql
web_1 | Database Host: postgres
web_1 | Database Port: 5432
web_1 | Database Username: postgres
web_1 | Database Password: postgres
web_1 | Database Name: postgres
web_1 |
elasticsearch_1 | OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
web_1 | => Skipped setup - database postgres already ready.
web_1 | =>> pre-launch-scripts:
web_1 | => /scripts/pre-launch.d/00conf_php
web_1 | PHP OPcache enabled
web_1 | Memcache enabled
web_1 | => /scripts/pre-launch.d/05servername_baseurl
web_1 | => /scripts/pre-launch.d/08memcache
web_1 | Starting memcached: memcached.
web_1 | => /scripts/pre-launch.d/10cron
web_1 | => /scripts/pre-launch.d/20check_settings
web_1 | => /scripts/pre-launch.d/30apply_patches
web_1 | => /scripts/pre-launch.d/40ext_libs
web_1 | => /scripts/pre-launch.d/50modules
web_1 | Executing: PGPASSFILE=/tmp/drush_JVuKSx psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_qfQ9gW
web_1 | Executing: PGPASSFILE=/tmp/drush_5koBiL psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_0S2EA9
web_1 | Loading release_info engine. [notice]
web_1 | entity is already enabled. [ok]
web_1 | ctools is already enabled. [ok]
web_1 | views is already enabled. [ok]
web_1 | views_ui is already enabled. [ok]
web_1 | libraries is already enabled. [ok]
web_1 | services is already enabled. [ok]
web_1 | There were no extensions that could be enabled. [ok]
web_1 | Command dispatch complete [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_G2q0dS psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_uSfnof
web_1 | Executing: PGPASSFILE=/tmp/drush_E24Z67 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_0Eluav
web_1 | Loading release_info engine. [notice]
web_1 | ds is already enabled. [ok]
web_1 | field_group is already enabled. [ok]
web_1 | field_group_table is already enabled. [ok]
web_1 | field_formatter_class is already enabled. [ok]
web_1 | field_formatter_settings is already enabled. [ok]
web_1 | There were no extensions that could be enabled. [ok]
web_1 | Command dispatch complete [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_3tKdTw psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_QcYcgS
web_1 | Executing: PGPASSFILE=/tmp/drush_j4VsDQ psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_24qkLb
web_1 | Loading release_info engine. [notice]
web_1 | rest_server is already enabled. [ok]
web_1 | ultimate_cron is already enabled. [ok]
web_1 | There were no extensions that could be enabled. [ok]
web_1 | Command dispatch complete [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_9QgPvd psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_NFsxjx
web_1 | Executing: PGPASSFILE=/tmp/drush_thVk7z psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_7PdzOT
elasticsearch_1 | [2023-11-17T09:43:13,703][INFO ][o.e.n.Node ] [] initializing ...
elasticsearch_1 | [2023-11-17T09:43:13,804][INFO ][o.e.e.NodeEnvironment ] [jL6IASJ] using [1] data paths, mounts [[/ (overlay)]], net usable_space [27.6gb], net total_space [49gb], types [overlay]
elasticsearch_1 | [2023-11-17T09:43:13,809][INFO ][o.e.e.NodeEnvironment ] [jL6IASJ] heap size [1007.3mb], compressed ordinary object pointers [true]
elasticsearch_1 | [2023-11-17T09:43:13,812][INFO ][o.e.n.Node ] [jL6IASJ] node name derived from node ID [jL6IASJsRE6W6k2NIFUMZQ]; set [node.name] to override
elasticsearch_1 | [2023-11-17T09:43:13,814][INFO ][o.e.n.Node ] [jL6IASJ] version[6.4.2], pid[1], build[default/tar/04711c2/2018-09-26T13:34:09.098244Z], OS[Linux/5.15.0-88-generic/amd64], JVM["Oracle Corporation"/OpenJDK 64-Bit Server VM/10.0.2/10.0.2+13]
elasticsearch_1 | [2023-11-17T09:43:13,814][INFO ][o.e.n.Node ] [jL6IASJ] JVM arguments [-Xms1g, -Xmx1g, -XX:+UseConcMarkSweepGC, -XX:CMSInitiatingOccupancyFraction=75, -XX:+UseCMSInitiatingOccupancyOnly, -XX:+AlwaysPreTouch, -Xss1m, -Djava.awt.headless=true, -Dfile.encoding=UTF-8, -Djna.nosys=true, -XX:-OmitStackTraceInFastThrow, -Dio.netty.noUnsafe=true, -Dio.netty.noKeySetOptimization=true, -Dio.netty.recycler.maxCapacityPerThread=0, -Dlog4j.shutdownHookEnabled=false, -Dlog4j2.disable.jmx=true, -Djava.io.tmpdir=/tmp/elasticsearch.bjyHrL9i, -XX:+HeapDumpOnOutOfMemoryError, -XX:HeapDumpPath=data, -XX:ErrorFile=logs/hs_err_pid%p.log, -Xlog:gc*,gc+age=trace,safepoint:file=logs/gc.log:utctime,pid,tags:filecount=32,filesize=64m, -Djava.locale.providers=COMPAT, -XX:UseAVX=2, -Des.cgroups.hierarchy.override=/, -Des.path.home=/usr/share/elasticsearch, -Des.path.conf=/usr/share/elasticsearch/config, -Des.distribution.flavor=default, -Des.distribution.type=tar]
web_1 | Loading release_info engine. [notice]
web_1 | tripal is already enabled. [ok]
web_1 | tripal_chado is already enabled. [ok]
web_1 | tripal_ds is already enabled. [ok]
web_1 | tripal_ws is already enabled. [ok]
web_1 | There were no extensions that could be enabled. [ok]
web_1 | Command dispatch complete [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_AFDLyG psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_tma0TY
web_1 | Executing: PGPASSFILE=/tmp/drush_QVvua6 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_3ycCmo
web_1 | Loading release_info engine. [notice]
web_1 | memcache is already enabled. [ok]
web_1 | There were no extensions that could be enabled. [ok]
web_1 | Command dispatch complete [notice]
web_1 | Include /etc/tripal/ [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_A6FTBo psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_ejDoqF
web_1 | Executing: PGPASSFILE=/tmp/drush_AS1neR psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_aBU7U7
web_1 | Preparing the site by creating content types.
web_1 | /usr/local/bin/php /root/.composer/vendor/drush/drush/drush.php [notice]
web_1 | --php=/usr/local/bin/php --backend=2 --verbose --yes
web_1 | --include=/etc/tripal/ --root=/var/www/html --uri=http://default
web_1 | php-eval 'module_load_include('\''inc'\'', '\''tripal_chado'\'',
web_1 | '\''includes/setup/tripal_chado.setup'\'');
web_1 | tripal_chado_prepare_drush_submit();' 2>&1
web_1 | Include /etc/tripal/ [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_pGvBON psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_Nbzrm3
web_1 | Executing: PGPASSFILE=/tmp/drush_zSg7dj psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_D3tlwy
web_1 | Loading outputformat engine. [notice]
web_1 | Job 'Prepare Chado' submitted. [status]
web_1 | Command dispatch complete [notice]
web_1 | /usr/local/bin/php /root/.composer/vendor/drush/drush/drush.php [notice]
web_1 | --php=/usr/local/bin/php --backend=2 --verbose --yes
web_1 | --include=/etc/tripal/ --root=/var/www/html --uri=http://default
web_1 | php-eval 'module_load_include('\''inc'\'', '\''tripal'\'',
web_1 | '\''tripal.drush'\'');
web_1 | drush_tripal_trp_run_jobs_install('\''admin'\'');' 2>&1
web_1 | Include /etc/tripal/ [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_3Iyrhv psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_PIKGgJ
web_1 | Executing: PGPASSFILE=/tmp/drush_bQ0yE3 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_NqiZsh
elasticsearch_1 | [2023-11-17T09:43:16,012][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [aggs-matrix-stats]
elasticsearch_1 | [2023-11-17T09:43:16,012][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [analysis-common]
elasticsearch_1 | [2023-11-17T09:43:16,012][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [ingest-common]
elasticsearch_1 | [2023-11-17T09:43:16,012][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [lang-expression]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [lang-mustache]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [lang-painless]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [mapper-extras]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [parent-join]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [percolator]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [rank-eval]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [reindex]
elasticsearch_1 | [2023-11-17T09:43:16,013][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [repository-url]
elasticsearch_1 | [2023-11-17T09:43:16,014][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [transport-netty4]
elasticsearch_1 | [2023-11-17T09:43:16,014][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [tribe]
elasticsearch_1 | [2023-11-17T09:43:16,014][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-core]
elasticsearch_1 | [2023-11-17T09:43:16,014][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-deprecation]
elasticsearch_1 | [2023-11-17T09:43:16,014][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-graph]
elasticsearch_1 | [2023-11-17T09:43:16,014][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-logstash]
elasticsearch_1 | [2023-11-17T09:43:16,019][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-ml]
elasticsearch_1 | [2023-11-17T09:43:16,019][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-monitoring]
elasticsearch_1 | [2023-11-17T09:43:16,019][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-rollup]
elasticsearch_1 | [2023-11-17T09:43:16,019][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-security]
elasticsearch_1 | [2023-11-17T09:43:16,019][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-sql]
elasticsearch_1 | [2023-11-17T09:43:16,019][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-upgrade]
elasticsearch_1 | [2023-11-17T09:43:16,020][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded module [x-pack-watcher]
elasticsearch_1 | [2023-11-17T09:43:16,020][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded plugin [ingest-geoip]
elasticsearch_1 | [2023-11-17T09:43:16,020][INFO ][o.e.p.PluginsService ] [jL6IASJ] loaded plugin [ingest-user-agent]
web_1 | Loading outputformat engine. [notice]
web_1 |
web_1 | 2023-11-17 09:43:16
web_1 | Tripal Job Launcher
web_1 | Running as user 'admin'
web_1 | -------------------
web_1 | 2023-11-17 09:43:16: There are 1 jobs queued.
web_1 | 2023-11-17 09:43:16: Job ID 42.
web_1 | 2023-11-17 09:43:16: Calling: tripal_chado_prepare_chado()
web_1 | Creating Tripal Materialized Views and Custom Tables...
postgres_1 | ERROR: relation "tripal_obo_temp" already exists
postgres_1 | STATEMENT: CREATE TABLE tripal_obo_temp ( id character varying(255) NOT NULL, stanza text NOT NULL, type character varying(50) NOT NULL, CONSTRAINT tripal_obo_temp_uq0 UNIQUE (id) );
web_1 | PDOException: SQLSTATE[42P07]: Duplicate table: 7 ERROR: relation "tripal_obo_temp" already exists in /var/www/html/includes/database/database.inc:2284
web_1 | Stack trace:
web_1 | #0 /var/www/html/includes/database/database.inc(2284): PDOStatement->execute(Array)
web_1 | #1 /var/www/html/includes/database/pgsql/database.inc(111): DatabaseStatementBase->execute(Array, Array)
web_1 | #2 /var/www/html/includes/database/database.inc(2467): DatabaseConnection_pgsql->query(' CREATE T...', Array, Array)
web_1 | #3 /var/www/html/sites/all/modules/tripal/tripal_chado/api/tripal_chado.query.api.inc(1790): db_query(' CREATE T...', Array)
web_1 | #4 /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.chado_vx_x.inc(131): chado_query(' CREATE T...')
web_1 | #5 /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.setup.inc(834): tripal_chado_add_tripal_obo_temp_table()
web_1 | #6 /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.setup.inc(225): tripal_chado_add_vx_x_custom_tables()
web_1 | #7 /var/www/html/sites/all/modules/tripal/tripal/includes/TripalJob.inc(341): tripal_chado_prepare_chado(Object(TripalJob))
web_1 | #8 /var/www/html/sites/all/modules/tripal/tripal/api/tripal.jobs.api.inc(419): TripalJob->run()
web_1 | #9 /var/www/html/sites/all/modules/tripal/tripal/tripal.drush.inc(186): tripal_launch_job(0, '42', -1, 0)
web_1 | #10 /root/.composer/vendor/drush/drush/commands/core/core.drush.inc(1122) : eval()'d code(1): drush_tripal_trp_run_jobs_install('admin')
web_1 | #11 /root/.composer/vendor/drush/drush/commands/core/core.drush.inc(1122): eval()
web_1 | #12 /root/.composer/vendor/drush/drush/includes/command.inc(361): drush_core_php_eval('module_load_inc...')
web_1 | #13 /root/.composer/vendor/drush/drush/includes/command.inc(212): _drush_invoke_hooks(Array, Array)
web_1 | #14 /root/.composer/vendor/drush/drush/includes/command.inc(180): drush_command('module_load_inc...')
web_1 | #15 /root/.composer/vendor/drush/drush/lib/Drush/Boot/BaseBoot.php(64): drush_dispatch(Array)
web_1 | #16 /root/.composer/vendor/drush/drush/drush.php(70): Drush\Boot\BaseBoot->bootstrap_and_dispatch()
web_1 | #17 /root/.composer/vendor/drush/drush/drush.php(11): drush_main()
web_1 | #18 {main}
web_1 | Job execution failed: PDOException: SQLSTATE[42P07]: Duplicate table: [error]
web_1 | 7 ERROR: relation "tripal_obo_temp" already exists in
web_1 | /var/www/html/includes/database/database.inc:2284
web_1 | Stack trace:
web_1 | #0 /var/www/html/includes/database/database.inc(2284):
web_1 | PDOStatement->execute(Array)
web_1 | #1 /var/www/html/includes/database/pgsql/database.inc(111):
web_1 | DatabaseStatementBase->execute(Array, Array)
web_1 | #2 /var/www/html/includes/database/database.inc(2467):
web_1 | DatabaseConnection_pgsql->query(' CREATE T...', Array, Array)
web_1 | #3
web_1 | /var/www/html/sites/all/modules/tripal/tripal_chado/api/tripal_chado.query.api.inc(1790):
web_1 | db_query(' CREATE T...', Array)
web_1 | #4
web_1 | /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.chado_vx_x.inc(131):
web_1 | chado_query(' CREATE T...')
web_1 | #5
web_1 | /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.setup.inc(834):
web_1 | tripal_chado_add_tripal_obo_temp_table()
web_1 | #6
web_1 | /var/www/html/sites/all/modules/tripal/tripal_chado/includes/setup/tripal_chado.setup.inc(225):
web_1 | tripal_chado_add_vx_x_custom_tables()
web_1 | #7
web_1 | /var/www/html/sites/all/modules/tripal/tripal/includes/TripalJob.inc(341):
web_1 | tripal_chado_prepare_chado(Object(TripalJob))
web_1 | #8
web_1 | /var/www/html/sites/all/modules/tripal/tripal/api/tripal.jobs.api.inc(419):
web_1 | TripalJob->run()
web_1 | #9
web_1 | /var/www/html/sites/all/modules/tripal/tripal/tripal.drush.inc(186):
web_1 | tripal_launch_job(0, '42', -1, 0)
web_1 | #10
web_1 | /root/.composer/vendor/drush/drush/commands/core/core.drush.inc(1122)
web_1 | : eval()'d code(1): drush_tripal_trp_run_jobs_install('admin')
web_1 | #11
web_1 | /root/.composer/vendor/drush/drush/commands/core/core.drush.inc(1122):
web_1 | eval()
web_1 | #12 /root/.composer/vendor/drush/drush/includes/command.inc(361):
web_1 | drush_core_php_eval('module_load_inc...')
web_1 | #13 /root/.composer/vendor/drush/drush/includes/command.inc(212):
web_1 | _drush_invoke_hooks(Array, Array)
web_1 | #14 /root/.composer/vendor/drush/drush/includes/command.inc(180):
web_1 | drush_command('module_load_inc...')
web_1 | #15
web_1 | /root/.composer/vendor/drush/drush/lib/Drush/Boot/BaseBoot.php(64):
web_1 | drush_dispatch(Array)
web_1 | #16 /root/.composer/vendor/drush/drush/drush.php(70):
web_1 | Drush\Boot\BaseBoot->bootstrap_and_dispatch()
web_1 | #17 /root/.composer/vendor/drush/drush/drush.php(11): drush_main()
web_1 | #18 {main}
web_1 | Custom table, 'tripal_gff_temp' , already exists. Table structure not [status]
web_1 | changed, but definition array has been saved.
web_1 | Custom table, 'tripal_gffcds_temp' , already exists. Table structure [status]
web_1 | not changed, but definition array has been saved.
web_1 | Custom table, 'tripal_gffprotein_temp' , already exists. Table [status]
web_1 | structure not changed, but definition array has been saved.
web_1 | Command dispatch complete [notice]
web_1 |
web_1 | Adding permissions for the administrator to view, edit, create, and delete all the newly created content types.
web_1 | /usr/local/bin/php /root/.composer/vendor/drush/drush/drush.php [notice]
web_1 | --php=/usr/local/bin/php --backend=2 --verbose --yes
web_1 | --include=/etc/tripal/ --root=/var/www/html --uri=http://default
web_1 | role-add-perm administrator ' view bio_data_1, create bio_data_1,
web_1 | edit bio_data_1, delete bio_data_1, view bio_data_2, create
web_1 | bio_data_2, edit bio_data_2, delete bio_data_2, view bio_data_3,
web_1 | create bio_data_3, edit bio_data_3, delete bio_data_3, view
web_1 | bio_data_4, create bio_data_4, edit bio_data_4, delete bio_data_4,
web_1 | view bio_data_5, create bio_data_5, edit bio_data_5, delete
web_1 | bio_data_5, view bio_data_6, create bio_data_6, edit bio_data_6,
web_1 | delete bio_data_6, view bio_data_7, create bio_data_7, edit
web_1 | bio_data_7, delete bio_data_7, view bio_data_8, create bio_data_8,
web_1 | edit bio_data_8, delete bio_data_8, view bio_data_9, create
web_1 | bio_data_9, edit bio_data_9, delete bio_data_9, view bio_data_10,
web_1 | create bio_data_10, edit bio_data_10, delete bio_data_10, view
web_1 | bio_data_11, create bio_data_11, edit bio_data_11, delete
web_1 | bio_data_11, view bio_data_12, create bio_data_12, edit bio_data_12,
web_1 | delete bio_data_12, view bio_data_13, create bio_data_13, edit
web_1 | bio_data_13, delete bio_data_13, view bio_data_14, create
web_1 | bio_data_14, edit bio_data_14, delete bio_data_14, view bio_data_15,
web_1 | create bio_data_15, edit bio_data_15, delete bio_data_15, view
web_1 | bio_data_16, create bio_data_16, edit bio_data_16, delete
web_1 | bio_data_16, view bio_data_17, create bio_data_17, edit bio_data_17,
web_1 | delete bio_data_17, view bio_data_18, create bio_data_18, edit
web_1 | bio_data_18, delete bio_data_18, view bio_data_19, create
web_1 | bio_data_19, edit bio_data_19, delete bio_data_19, view bio_data_20,
web_1 | create bio_data_20, edit bio_data_20, delete bio_data_20, view
web_1 | bio_data_21, create bio_data_21, edit bio_data_21, delete
web_1 | bio_data_21, view bio_data_22, create bio_data_22, edit bio_data_22,
web_1 | delete bio_data_22, view bio_data_23, create bio_data_23, edit
web_1 | bio_data_23, delete bio_data_23, view bio_data_24, create
web_1 | bio_data_24, edit bio_data_24, delete bio_data_24, view bio_data_25,
web_1 | create bio_data_25, edit bio_data_25, delete bio_data_25, view
web_1 | bio_data_26, create bio_data_26, edit bio_data_26, delete
web_1 | bio_data_26, view bio_data_27, create bio_data_27, edit bio_data_27,
web_1 | delete bio_data_27, view bio_data_28, create bio_data_28, edit
web_1 | bio_data_28, delete bio_data_28, view bio_data_29, create
web_1 | bio_data_29, edit bio_data_29, delete bio_data_29' 2>&1
web_1 | Include /etc/tripal/ [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_uXuHH2 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_sS5V1e
web_1 | Executing: PGPASSFILE=/tmp/drush_G2IupE psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_eeaAyQ
web_1 | "administrator" already has the permission "view bio_data_1" [ok]
web_1 | "administrator" already has the permission "create bio_data_1" [ok]
web_1 | "administrator" already has the permission "edit bio_data_1" [ok]
web_1 | "administrator" already has the permission "delete bio_data_1" [ok]
web_1 | "administrator" already has the permission "view bio_data_2" [ok]
web_1 | "administrator" already has the permission "create bio_data_2" [ok]
web_1 | "administrator" already has the permission "edit bio_data_2" [ok]
web_1 | "administrator" already has the permission "delete bio_data_2" [ok]
web_1 | "administrator" already has the permission "view bio_data_3" [ok]
web_1 | "administrator" already has the permission "create bio_data_3" [ok]
web_1 | "administrator" already has the permission "edit bio_data_3" [ok]
web_1 | "administrator" already has the permission "delete bio_data_3" [ok]
web_1 | "administrator" already has the permission "view bio_data_4" [ok]
web_1 | "administrator" already has the permission "create bio_data_4" [ok]
web_1 | "administrator" already has the permission "edit bio_data_4" [ok]
web_1 | "administrator" already has the permission "delete bio_data_4" [ok]
web_1 | "administrator" already has the permission "view bio_data_5" [ok]
web_1 | "administrator" already has the permission "create bio_data_5" [ok]
web_1 | "administrator" already has the permission "edit bio_data_5" [ok]
web_1 | "administrator" already has the permission "delete bio_data_5" [ok]
web_1 | "administrator" already has the permission "view bio_data_6" [ok]
web_1 | "administrator" already has the permission "create bio_data_6" [ok]
web_1 | "administrator" already has the permission "edit bio_data_6" [ok]
web_1 | "administrator" already has the permission "delete bio_data_6" [ok]
web_1 | "administrator" already has the permission "view bio_data_7" [ok]
web_1 | "administrator" already has the permission "create bio_data_7" [ok]
web_1 | "administrator" already has the permission "edit bio_data_7" [ok]
web_1 | "administrator" already has the permission "delete bio_data_7" [ok]
web_1 | "administrator" already has the permission "view bio_data_8" [ok]
web_1 | "administrator" already has the permission "create bio_data_8" [ok]
web_1 | "administrator" already has the permission "edit bio_data_8" [ok]
web_1 | "administrator" already has the permission "delete bio_data_8" [ok]
web_1 | "administrator" already has the permission "view bio_data_9" [ok]
web_1 | "administrator" already has the permission "create bio_data_9" [ok]
web_1 | "administrator" already has the permission "edit bio_data_9" [ok]
web_1 | "administrator" already has the permission "delete bio_data_9" [ok]
web_1 | "administrator" already has the permission "view bio_data_10" [ok]
web_1 | "administrator" already has the permission "create bio_data_10" [ok]
web_1 | "administrator" already has the permission "edit bio_data_10" [ok]
web_1 | "administrator" already has the permission "delete bio_data_10" [ok]
web_1 | "administrator" already has the permission "view bio_data_11" [ok]
web_1 | "administrator" already has the permission "create bio_data_11" [ok]
web_1 | "administrator" already has the permission "edit bio_data_11" [ok]
web_1 | "administrator" already has the permission "delete bio_data_11" [ok]
web_1 | "administrator" already has the permission "view bio_data_12" [ok]
web_1 | "administrator" already has the permission "create bio_data_12" [ok]
web_1 | "administrator" already has the permission "edit bio_data_12" [ok]
web_1 | "administrator" already has the permission "delete bio_data_12" [ok]
web_1 | "administrator" already has the permission "view bio_data_13" [ok]
web_1 | "administrator" already has the permission "create bio_data_13" [ok]
web_1 | "administrator" already has the permission "edit bio_data_13" [ok]
web_1 | "administrator" already has the permission "delete bio_data_13" [ok]
web_1 | "administrator" already has the permission "view bio_data_14" [ok]
web_1 | "administrator" already has the permission "create bio_data_14" [ok]
web_1 | "administrator" already has the permission "edit bio_data_14" [ok]
web_1 | "administrator" already has the permission "delete bio_data_14" [ok]
web_1 | "administrator" already has the permission "view bio_data_15" [ok]
web_1 | "administrator" already has the permission "create bio_data_15" [ok]
web_1 | "administrator" already has the permission "edit bio_data_15" [ok]
web_1 | "administrator" already has the permission "delete bio_data_15" [ok]
web_1 | "administrator" already has the permission "view bio_data_16" [ok]
web_1 | "administrator" already has the permission "create bio_data_16" [ok]
web_1 | "administrator" already has the permission "edit bio_data_16" [ok]
web_1 | "administrator" already has the permission "delete bio_data_16" [ok]
web_1 | "administrator" already has the permission "view bio_data_17" [ok]
web_1 | "administrator" already has the permission "create bio_data_17" [ok]
web_1 | "administrator" already has the permission "edit bio_data_17" [ok]
web_1 | "administrator" already has the permission "delete bio_data_17" [ok]
web_1 | "administrator" already has the permission "view bio_data_18" [ok]
web_1 | "administrator" already has the permission "create bio_data_18" [ok]
web_1 | "administrator" already has the permission "edit bio_data_18" [ok]
web_1 | "administrator" already has the permission "delete bio_data_18" [ok]
web_1 | "administrator" already has the permission "view bio_data_19" [ok]
web_1 | "administrator" already has the permission "create bio_data_19" [ok]
web_1 | "administrator" already has the permission "edit bio_data_19" [ok]
web_1 | "administrator" already has the permission "delete bio_data_19" [ok]
web_1 | "administrator" already has the permission "view bio_data_20" [ok]
web_1 | "administrator" already has the permission "create bio_data_20" [ok]
web_1 | "administrator" already has the permission "edit bio_data_20" [ok]
web_1 | "administrator" already has the permission "delete bio_data_20" [ok]
web_1 | "administrator" already has the permission "view bio_data_21" [ok]
web_1 | "administrator" already has the permission "create bio_data_21" [ok]
web_1 | "administrator" already has the permission "edit bio_data_21" [ok]
web_1 | "administrator" already has the permission "delete bio_data_21" [ok]
web_1 | "administrator" already has the permission "view bio_data_22" [ok]
web_1 | "administrator" already has the permission "create bio_data_22" [ok]
web_1 | "administrator" already has the permission "edit bio_data_22" [ok]
web_1 | "administrator" already has the permission "delete bio_data_22" [ok]
web_1 | "administrator" already has the permission "view bio_data_23" [ok]
web_1 | "administrator" already has the permission "create bio_data_23" [ok]
web_1 | "administrator" already has the permission "edit bio_data_23" [ok]
web_1 | "administrator" already has the permission "delete bio_data_23" [ok]
web_1 | "administrator" already has the permission "view bio_data_24" [ok]
web_1 | "administrator" already has the permission "create bio_data_24" [ok]
web_1 | "administrator" already has the permission "edit bio_data_24" [ok]
web_1 | "administrator" already has the permission "delete bio_data_24" [ok]
web_1 | "administrator" already has the permission "view bio_data_25" [ok]
web_1 | "administrator" already has the permission "create bio_data_25" [ok]
web_1 | "administrator" already has the permission "edit bio_data_25" [ok]
web_1 | "administrator" already has the permission "delete bio_data_25" [ok]
web_1 | "administrator" already has the permission "view bio_data_26" [ok]
web_1 | "administrator" already has the permission "create bio_data_26" [ok]
web_1 | "administrator" already has the permission "edit bio_data_26" [ok]
web_1 | "administrator" already has the permission "delete bio_data_26" [ok]
web_1 | "administrator" already has the permission "view bio_data_27" [ok]
web_1 | "administrator" already has the permission "create bio_data_27" [ok]
web_1 | "administrator" already has the permission "edit bio_data_27" [ok]
web_1 | "administrator" already has the permission "delete bio_data_27" [ok]
web_1 | "administrator" already has the permission "view bio_data_28" [ok]
web_1 | "administrator" already has the permission "create bio_data_28" [ok]
web_1 | "administrator" already has the permission "edit bio_data_28" [ok]
web_1 | "administrator" already has the permission "delete bio_data_28" [ok]
web_1 | "administrator" already has the permission "view bio_data_29" [ok]
elasticsearch_1 | [2023-11-17T09:43:18,744][WARN ][o.e.d.s.ScriptModule ] Script: returning default values for missing document values is deprecated. Set system property '-Des.scripting.exception_for_missing_value=true' to make behaviour compatible with future major versions.
web_1 | "administrator" already has the permission "create bio_data_29" [ok]
web_1 | "administrator" already has the permission "edit bio_data_29" [ok]
web_1 | "administrator" already has the permission "delete bio_data_29" [ok]
web_1 | Command dispatch complete [notice]
web_1 | /usr/local/bin/php /root/.composer/vendor/drush/drush/drush.php [notice]
web_1 | --php=/usr/local/bin/php --backend=2 --verbose --yes
web_1 | --include=/etc/tripal/ --root=/var/www/html --uri=http://default
web_1 | role-add-perm 'anonymous user' ' view bio_data_1, view bio_data_2,
web_1 | view bio_data_3, view bio_data_4, view bio_data_5, view bio_data_6,
web_1 | view bio_data_7, view bio_data_8, view bio_data_9, view bio_data_10,
web_1 | view bio_data_11, view bio_data_12, view bio_data_13, view
web_1 | bio_data_14, view bio_data_15, view bio_data_16, view bio_data_17,
web_1 | view bio_data_18, view bio_data_19, view bio_data_20, view
web_1 | bio_data_21, view bio_data_22, view bio_data_23, view bio_data_24,
web_1 | view bio_data_25, view bio_data_26, view bio_data_27, view
web_1 | bio_data_28, view bio_data_29' 2>&1
web_1 |
web_1 | Adding permissions for anonymous user to view all the newly created content types.
web_1 | Include /etc/tripal/ [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_I9MlX4 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_GYXOD9
web_1 | Executing: PGPASSFILE=/tmp/drush_WNfqUV psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_SB2Rq0
web_1 | "anonymous user" already has the permission "view bio_data_1" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_2" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_3" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_4" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_5" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_6" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_7" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_8" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_9" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_10" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_11" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_12" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_13" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_14" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_15" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_16" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_17" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_18" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_19" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_20" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_21" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_22" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_23" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_24" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_25" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_26" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_27" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_28" [ok]
web_1 | "anonymous user" already has the permission "view bio_data_29" [ok]
web_1 | Command dispatch complete [notice]
web_1 |
web_1 | Adding permissions for authenticated users to view all the newly created content types.
web_1 | /usr/local/bin/php /root/.composer/vendor/drush/drush/drush.php [notice]
web_1 | --php=/usr/local/bin/php --backend=2 --verbose --yes
web_1 | --include=/etc/tripal/ --root=/var/www/html --uri=http://default
web_1 | role-add-perm 'authenticated user' ' view bio_data_1, view
web_1 | bio_data_2, view bio_data_3, view bio_data_4, view bio_data_5, view
web_1 | bio_data_6, view bio_data_7, view bio_data_8, view bio_data_9, view
web_1 | bio_data_10, view bio_data_11, view bio_data_12, view bio_data_13,
web_1 | view bio_data_14, view bio_data_15, view bio_data_16, view
web_1 | bio_data_17, view bio_data_18, view bio_data_19, view bio_data_20,
web_1 | view bio_data_21, view bio_data_22, view bio_data_23, view
web_1 | bio_data_24, view bio_data_25, view bio_data_26, view bio_data_27,
web_1 | view bio_data_28, view bio_data_29' 2>&1
web_1 | Include /etc/tripal/ [notice]
web_1 | Executing: PGPASSFILE=/tmp/drush_MUGJb8 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_OoFvR9
web_1 | Executing: PGPASSFILE=/tmp/drush_0Uyh34 psql -q --dbname=postgres --host=postgres --port=5432 --username=postgres --no-align --field-separator=' ' --pset tuples_only=on --file /tmp/drush_KFLuC6
web_1 | "authenticated user" already has the permission "view bio_data_1" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_2" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_3" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_4" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_5" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_6" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_7" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_8" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_9" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_10" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_11" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_12" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_13" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_14" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_15" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_16" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_17" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_18" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_19" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_20" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_21" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_22" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_23" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_24" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_25" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_26" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_27" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_28" [ok]
web_1 | "authenticated user" already has the permission "view bio_data_29" [ok]
web_1 | Command dispatch complete [notice]
web_1 |
web_1 | Installation is now complete. You may navigate to your new site. For more information on using Tripal please see the installation guide on tripal.info.
web_1 | Command dispatch complete [notice]
docker-tripal_web_1 exited with code 1
elasticsearch_1 | [2023-11-17T09:43:21,371][INFO ][o.e.x.s.a.s.FileRolesStore] [jL6IASJ] parsed [0] roles from file [/usr/share/elasticsearch/config/roles.yml]
elasticsearch_1 | [2023-11-17T09:43:21,778][INFO ][o.e.x.m.j.p.l.CppLogMessageHandler] [controller/79] [Main.cc@109] controller (64 bit): Version 6.4.2 (Build 660eefe6f2ea55) Copyright (c) 2018 Elasticsearch BV
elasticsearch_1 | [2023-11-17T09:43:22,431][INFO ][o.e.d.DiscoveryModule ] [jL6IASJ] using discovery type [zen]
elasticsearch_1 | [2023-11-17T09:43:23,086][INFO ][o.e.n.Node ] [jL6IASJ] initialized
elasticsearch_1 | [2023-11-17T09:43:23,087][INFO ][o.e.n.Node ] [jL6IASJ] starting ...
elasticsearch_1 | [2023-11-17T09:43:23,177][INFO ][o.e.t.TransportService ] [jL6IASJ] publish_address {172.24.0.3:9300}, bound_addresses {0.0.0.0:9300}
elasticsearch_1 | [2023-11-17T09:43:23,189][INFO ][o.e.b.BootstrapChecks ] [jL6IASJ] bound or publishing to a non-loopback address, enforcing bootstrap checks
elasticsearch_1 | [2023-11-17T09:43:26,247][INFO ][o.e.c.s.MasterService ] [jL6IASJ] zen-disco-elected-as-master ([0] nodes joined)[, ], reason: new_master {jL6IASJ}{jL6IASJsRE6W6k2NIFUMZQ}{EiTlzOQvRemGeSWcQO60Ug}{172.24.0.3}{172.24.0.3:9300}{ml.machine_memory=4064763904, xpack.installed=true, ml.max_open_jobs=20, ml.enabled=true}
elasticsearch_1 | [2023-11-17T09:43:26,251][INFO ][o.e.c.s.ClusterApplierService] [jL6IASJ] new_master {jL6IASJ}{jL6IASJsRE6W6k2NIFUMZQ}{EiTlzOQvRemGeSWcQO60Ug}{172.24.0.3}{172.24.0.3:9300}{ml.machine_memory=4064763904, xpack.installed=true, ml.max_open_jobs=20, ml.enabled=true}, reason: apply cluster state (from master [master {jL6IASJ}{jL6IASJsRE6W6k2NIFUMZQ}{EiTlzOQvRemGeSWcQO60Ug}{172.24.0.3}{172.24.0.3:9300}{ml.machine_memory=4064763904, xpack.installed=true, ml.max_open_jobs=20, ml.enabled=true} committed version [1] source [zen-disco-elected-as-master ([0] nodes joined)[, ]]])
elasticsearch_1 | [2023-11-17T09:43:26,273][INFO ][o.e.x.s.t.n.SecurityNetty4HttpServerTransport] [jL6IASJ] publish_address {172.24.0.3:9200}, bound_addresses {0.0.0.0:9200}
elasticsearch_1 | [2023-11-17T09:43:26,273][INFO ][o.e.n.Node ] [jL6IASJ] started
elasticsearch_1 | [2023-11-17T09:43:26,516][WARN ][o.e.x.s.a.s.m.NativeRoleMappingStore] [jL6IASJ] Failed to clear cache for realms [[]]
elasticsearch_1 | [2023-11-17T09:43:26,550][INFO ][o.e.l.LicenseService ] [jL6IASJ] license [1024e702-c667-4adb-bdbb-928a755aa0f2] mode [basic] - valid
elasticsearch_1 | [2023-11-17T09:43:26,563][INFO ][o.e.g.GatewayService ] [jL6IASJ] recovered [0] indices into cluster_state
I cloned the repository and ran
sudo docker-compose up, and the server started and was accessible. However, after stopping the containers, runningsudo docker-compose down, and againsudo docker-compose uplead to:You can see the docker-tripal_web_1 container stops with error code 1, not showing any error, and elasticsearch stops with error code 78. At least here seems to be an error: