AtoM on Fedora CoreOS

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jesus san miguel

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May 27, 2021, 11:21:50 AM5/27/21
to AtoM Users
Hi all,

I am testing AtoM on Fedora CoreOS, but I am getting some errors when starting the elasticsearch container and when connecting to the atom_worker process. Please see below:

[core@atom containers]$ docker-compose up 

Starting docker_elasticsearch_1 ... done

Recreating docker_percona_1     ... done

Recreating docker_atom_1        ... done

Starting docker_gearmand_1      ... done

Starting docker_memcached_1     ... done

Recreating docker_nginx_1       ... done

Recreating docker_atom_worker_1 ... done

Attaching to docker_elasticsearch_1, docker_memcached_1, docker_gearmand_1, docker_atom_1, docker_nginx_1, docker_percona_1, docker_atom_worker_1

atom_1           | [27-May-2021 15:00:43] NOTICE: fpm is running, pid 1

atom_1           | [27-May-2021 15:00:43] NOTICE: ready to handle connections

gearmand_1       |    INFO 2021-05-27 15:00:42.803675 [  main ] Initializing Gear on port 4730 with SSL: false

gearmand_1       |    INFO 2021-05-27 15:00:42.000000 [  main ] Starting up with pid 1, verbose is set to INFO

gearmand_1       |    INFO 2021-05-27 15:00:42.000000 [  main ] Listening on 0.0.0.0:4730 (9)

gearmand_1       |    INFO 2021-05-27 15:00:42.000000 [  main ] Adding event for listening socket (9)

nginx_1          | /docker-entrypoint.sh: /docker-entrypoint.d/ is not empty, will attempt to perform configuration

nginx_1          | /docker-entrypoint.sh: Looking for shell scripts in /docker-entrypoint.d/

percona_1        | 2021-05-27T15:00:43.253692Z 0 [Warning] [MY-010139] [Server] Changed limits: max_open_files: 1024 (requested 8161)

percona_1        | 2021-05-27T15:00:43.253711Z 0 [Warning] [MY-010142] [Server] Changed limits: table_open_cache: 431 (requested 4000)

percona_1        | 2021-05-27T15:00:43.503256Z 0 [Warning] [MY-010915] [Server] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.

percona_1        | 2021-05-27T15:00:43.505242Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.23-14) starting as process 1

percona_1        | 2021-05-27T15:00:43.516734Z 1 [System] [MY-013576] [InnoDB] InnoDB initialization has started.

nginx_1          | /docker-entrypoint.sh: Launching /docker-entrypoint.d/10-listen-on-ipv6-by-default.sh

percona_1        | 2021-05-27T15:00:43.922862Z 1 [System] [MY-013577] [InnoDB] InnoDB initialization has ended.

nginx_1          | 10-listen-on-ipv6-by-default.sh: info: Getting the checksum of /etc/nginx/conf.d/default.conf

nginx_1          | 10-listen-on-ipv6-by-default.sh: info: Enabled listen on IPv6 in /etc/nginx/conf.d/default.conf

nginx_1          | /docker-entrypoint.sh: Launching /docker-entrypoint.d/20-envsubst-on-templates.sh

nginx_1          | /docker-entrypoint.sh: Launching /docker-entrypoint.d/30-tune-worker-processes.sh

nginx_1          | /docker-entrypoint.sh: Configuration complete; ready for start up

percona_1        | 2021-05-27T15:00:44.117539Z 0 [System] [MY-011323] [Server] X Plugin ready for connections. Bind-address: '::' port: 33060, socket: /var/lib/mysql/mysqlx.sock

percona_1        | 2021-05-27T15:00:44.274416Z 0 [Warning] [MY-010068] [Server] CA certificate ca.pem is self signed.

percona_1        | 2021-05-27T15:00:44.274663Z 0 [System] [MY-013602] [Server] Channel mysql_main configured to support TLS. Encrypted connections are now supported for this channel.

percona_1        | 2021-05-27T15:00:44.308475Z 0 [System] [MY-010931] [Server] /usr/sbin/mysqld: ready for connections. Version: '8.0.23-14'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  Percona Server (GPL), Release 14, Revision 3558242.

elasticsearch_1  | [2021-05-27T15:00:44,540][INFO ][o.e.n.Node               ] [] initializing ...

elasticsearch_1  | [2021-05-27T15:00:44,653][INFO ][o.e.e.NodeEnvironment    ] [s5B6fNd] using [1] data paths, mounts [[/usr/share/elasticsearch/data (/dev/xvda4)]], net usable_space [39.7gb], net total_space [44.4gb], spins? [possibly], types [xfs]

elasticsearch_1  | [2021-05-27T15:00:44,654][INFO ][o.e.e.NodeEnvironment    ] [s5B6fNd] heap size [618.6mb], compressed ordinary object pointers [true]

elasticsearch_1  | [2021-05-27T15:00:44,655][INFO ][o.e.n.Node               ] node name [s5B6fNd] derived from node ID [s5B6fNdSSmitqi1DAJ2ttA]; set [node.name] to override

elasticsearch_1  | [2021-05-27T15:00:44,656][INFO ][o.e.n.Node               ] version[5.6.16], pid[1], build[3a740d1/2019-03-13T15:33:36.565Z], OS[Linux/5.11.15-300.fc34.x86_64/amd64], JVM[Oracle Corporation/OpenJDK 64-Bit Server VM/1.8.0_201/25.201-b09]

elasticsearch_1  | [2021-05-27T15:00:44,656][INFO ][o.e.n.Node               ] JVM arguments [-Xms2g, -Xmx2g, -XX:+UseConcMarkSweepGC, -XX:CMSInitiatingOccupancyFraction=75, -XX:+UseCMSInitiatingOccupancyOnly, -XX:+AlwaysPreTouch, -Xss1m, -Djava.awt.headless=true, -Dfile.encoding=UTF-8, -Djna.nosys=true, -Djdk.io.permissionsUseCanonicalPath=true, -Dio.netty.noUnsafe=true, -Dio.netty.noKeySetOptimization=true, -Dio.netty.recycler.maxCapacityPerThread=0, -Dlog4j.shutdownHookEnabled=false, -Dlog4j2.disable.jmx=true, -Dlog4j.skipJansi=true, -XX:+HeapDumpOnOutOfMemoryError, -Des.cgroups.hierarchy.override=/, -Xms640m, -Xmx640m, -Des.path.home=/usr/share/elasticsearch]

elasticsearch_1  | [2021-05-27T15:00:46,351][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [aggs-matrix-stats]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [ingest-common]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [lang-expression]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [lang-groovy]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [lang-mustache]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [lang-painless]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [parent-join]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [percolator]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [reindex]

elasticsearch_1  | [2021-05-27T15:00:46,352][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [transport-netty3]

elasticsearch_1  | [2021-05-27T15:00:46,353][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded module [transport-netty4]

elasticsearch_1  | [2021-05-27T15:00:46,353][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded plugin [ingest-geoip]

elasticsearch_1  | [2021-05-27T15:00:46,353][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded plugin [ingest-user-agent]

elasticsearch_1  | [2021-05-27T15:00:46,353][INFO ][o.e.p.PluginsService     ] [s5B6fNd] loaded plugin [x-pack]

elasticsearch_1  | [2021-05-27T15:00:48,840][INFO ][o.e.x.m.j.p.l.CppLogMessageHandler] [controller/68] [Main.cc@128] controller (64 bit): Version 5.6.16 (Build 9ed4c28f2a8755) Copyright (c) 2019 Elasticsearch BV

elasticsearch_1  | [2021-05-27T15:00:48,887][INFO ][o.e.d.DiscoveryModule    ] [s5B6fNd] using discovery type [zen]

elasticsearch_1  | [2021-05-27T15:00:49,758][INFO ][o.e.n.Node               ] initialized

elasticsearch_1  | [2021-05-27T15:00:49,759][INFO ][o.e.n.Node               ] [s5B6fNd] starting ...

elasticsearch_1  | [2021-05-27T15:00:49,977][INFO ][o.e.t.TransportService   ] [s5B6fNd] publish_address {172.20.0.2:9300}, bound_addresses {0.0.0.0:9300}

elasticsearch_1  | [2021-05-27T15:00:49,990][INFO ][o.e.b.BootstrapChecks    ] [s5B6fNd] bound or publishing to a non-loopback address, enforcing bootstrap checks

elasticsearch_1  | ERROR: [2] bootstrap checks failed

elasticsearch_1  | [1]: max file descriptors [1024] for elasticsearch process is too low, increase to at least [65536]

elasticsearch_1  | [2]: max virtual memory areas vm.max_map_count [65530] is too low, increase to at least [262144]

elasticsearch_1  | [2021-05-27T15:00:50,012][INFO ][o.e.n.Node               ] [s5B6fNd] stopping ...

elasticsearch_1  | [2021-05-27T15:00:50,090][INFO ][o.e.n.Node               ] [s5B6fNd] stopped

elasticsearch_1  | [2021-05-27T15:00:50,090][INFO ][o.e.n.Node               ] [s5B6fNd] closing ...

elasticsearch_1  | [2021-05-27T15:00:50,107][INFO ][o.e.n.Node               ] [s5B6fNd] closed

elasticsearch_1  | [2021-05-27T15:00:50,111][INFO ][o.e.x.m.j.p.NativeController] Native controller process has stopped - no new native processes can be started

docker_elasticsearch_1 exited with code 78

gearmand_1       |    INFO 2021-05-27 15:00:53.000000 [  main ] Accepted connection from 172.20.0.8:36896

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arFindingAidJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arInheritRightsJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arUpdateEsActorRelationsJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arCalculateDescendantDatesJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arObjectMoveJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arInformationObjectCsvExportJob

atom_worker_1    | 2021-05-27 08:00:54 > Ability not defined: qtSwordPluginWorker. Please ensure the job is in the lib/task/job directory or that the plugin is enabled.

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arUpdatePublicationStatusJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arFileImportJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arInformationObjectXmlExportJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arXmlExportSingleFileJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arGenerateReportJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arActorCsvExportJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arActorXmlExportJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arRepositoryCsvExportJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arUpdateEsIoDocumentsJob

atom_worker_1    | 2021-05-27 08:00:54 > New ability: arPhysicalObjectCsvHoldingsReportJob

atom_worker_1    | 2021-05-27 08:00:54 > Running worker...

atom_worker_1    | 2021-05-27 08:00:54 > PID 1

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "NOTICE: PHP message: Empty module and/or action after parsing the URL "/" (/)."

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "NOTICE: PHP message: PHP Fatal error:  Uncaught Zend_Acl_Exception: addRole() expects $role to be of type Zend_Acl_Role_Interface in /atom/src/plugins/qbAclPlugin/lib/vendor/Zend/Acl.php:124"

atom_1           | 172.20.0.5 -  27/May/2021:15:01:06 +0000 "GET /index.php" 500

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "Stack trace:"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#0 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(618): Zend_Acl->addRole(NULL)"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#1 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(59): QubitAcl->buildUserRoleList(Object(myUser))"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#2 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(65): QubitAcl->__construct()"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#3 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(175): QubitAcl::getInstance()"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#4 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(124): QubitAcl::isAllowed(Object(myUser), 'userInterface', 'translate', Array)"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#5 /atom/src/apps/qubit/templates/_footer.php(3): QubitAcl::check('userInterface', Array)"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#6 /atom/src/cache/qubit/prod/config/config_core_compile.yml.php(3896): require('/atom/src/apps/...')"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#7 /atom/src/vendor/symfony/lib/view/sfPartialView.class.php(124): sfPHPView->renderFile('/atom/src/apps/...')"

atom_1           | [27-May-2021 15:01:06] WARNING: [pool atom] child 16 said into stderr: "#8 /atom/src/ven..."

nginx_1          | 2021/05/27 15:01:06 [error] 31#31: *1 FastCGI sent in stderr: "PHP message: Empty module and/or action after parsing the URL "/" (/).PHP message: PHP Fatal error:  Uncaught Zend_Acl_Exception: addRole() expects $role to be of type Zend_Acl_Role_Interface in /atom/src/plugins/qbAclPlugin/lib/vendor/Zend/Acl.php:124

nginx_1          | Stack trace:

nginx_1          | #0 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(618): Zend_Acl->addRole(NULL)

nginx_1          | #1 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(59): QubitAcl->buildUserRoleList(Object(myUser))

nginx_1          | #2 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(65): QubitAcl->__construct()

nginx_1          | #3 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(175): QubitAcl::getInstance()

nginx_1          | #4 /atom/src/plugins/qbAclPlugin/lib/QubitAcl.class.php(124): QubitAcl::isAllowed(Object(myUser), 'userInterface', 'translate', Array)

nginx_1          | #5 /atom/src/apps/qubit/templates/_footer.php(3): QubitAcl::check('userInterface', Array)

nginx_1          | #6 /atom/src/cache/qubit/prod/config/config_core_compile.yml.php(3896): require('/atom/src/apps/...')

nginx_1          | #7 /atom/src/vendor/symfony/lib/view/sfPartialView.class.php(124): sfPHPView->renderFile('/atom/src/apps/...')

nginx_1          | #8 /atom/src/ven" while reading response header from upstream, client: 192.168.10.212, server: _, request: "GET / HTTP/1.1", upstream: "fastcgi://172.20.0.7:9000", host: "194.126.225.141:63001"

nginx_1          | 192.168.10.212 - - [27/May/2021:15:01:06 +0000] "GET / HTTP/1.1" 500 5 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/90.0.4430.212 Safari/537.36" "-"



^CGracefully stopping... (press Ctrl+C again to force)

Stopping docker_atom_worker_1   ... done

Stopping docker_nginx_1         ... done

Stopping docker_atom_1          ... done

Stopping docker_percona_1       ... done

Stopping docker_memcached_1     ... done

Stopping docker_gearmand_1      ... done

jesus san miguel

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May 27, 2021, 1:01:39 PM5/27/21
to AtoM Users
I was able to fix elasticsearch container tweaking the yml file:

  elasticsearch:

    image: docker.elastic.co/elasticsearch/elasticsearch:5.6.16

    env_file: etc/environment

    ulimits:

      memlock:

        soft: -1

        hard: -1

      nofile:

        soft: 65536

        hard: 65536

    volumes:

      - elasticsearch_data:/usr/share/elasticsearch/data

    ports:

      - "127.0.0.1:63002:9200"


...and the ignition files section:

        { "filesystem": "root", "path": "/etc/sysctl.d/vm.conf", "contents": { "source": "data:,vm.max_map_count%3D262144%0A", "verification": {} }, "mode":420 }

Any idea on the atom fatal error? It seems to be a permissions issue, but I have already tried with SELINUX disabled.

Best,
Jesus

José Raddaoui

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May 27, 2021, 1:46:51 PM5/27/21
to AtoM Users
Hi Jesús,

Good thing you found the solution for the Elasticsearch issues! About the AtoM error, that may be caused by an empty database, I'd suggest to run the purge task and restart the containers to see if that makes it.

Best regards,
Radda.

jesus san miguel

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May 27, 2021, 3:11:48 PM5/27/21
to AtoM Users
Yeah, you rock man:

[core@atom docker]$ docker-compose exec atom php -d memory_limit=-1 symfony tools:purge --demo

and after restarting the containers, smooth working now!

Best,
Jesus
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