Local host web interface stuck at loading

yijietseng · June 16, 2022, 1:39pm

Hi all,

Our cryosparc stop working yesterday. I think it starts properly, but the local host web interface just stuck at the loading page forever (shown as below picture).

Here is the output of cryosparcm status:

CryoSPARC process status:

app RUNNING pid 28900, uptime 0:11:25
app_dev STOPPED Not started
command_core RUNNING pid 28616, uptime 0:11:52
command_rtp RUNNING pid 28701, uptime 0:11:37
command_vis RUNNING pid 28694, uptime 0:11:38
database RUNNING pid 28500, uptime 0:11:57
liveapp STOPPED Not started
liveapp_dev STOPPED Not started
webapp RUNNING pid 28890, uptime 0:11:27
webapp_dev STOPPED Not started

License is valid

Any suggestions to fix this?

wtempel · June 16, 2022, 5:06pm

Welcome to the forum @yijietseng.
Please could you share the following logs with us:

webapp
command_core
database

You can capture the logs with commands like
cryosparcm log webapp > webapp_$(date +%F).log

I will send you a forum direct message for more details.

In addition, we are also interested in messages that appear in the browser console while you visit the url of your cryoSPARC instance. Details of accessing the browser console may vary by browser and platform. On the chrome browser (on MS windows), I can access the browser console via the menu:
More tools | Developer tools (Console tab)

parag · June 16, 2022, 5:26pm

I am working with @yijietseng.

Now it just says:

# This page isn’t working

**localhost** didn’t send any data.

ERR_EMPTY_RESPONSE

Here is the command_core log:

2022-06-16 11:09:55,403 COMMAND.MAIN         start                INFO     |  === STARTED ===
2022-06-16 11:09:55,404 COMMAND.BG_WORKER    background_worker    INFO     |  === STARTED ===
2022-06-16 11:09:55,404 COMMAND.CORE         run                  INFO     | === STARTED TASKS WORKER ===
 * Serving Flask app "command_core" (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: off
2022-06-16 11:09:56,984 COMMAND.SCHEDULER    get_gpu_info         INFO     | UPDATING WORKER GPU INFO
2022-06-16 11:09:56,984 COMMAND.JOBS         update_all_job_sizes INFO     | UPDATING ALL JOB SIZES IN 10s
2022-06-16 11:09:56,985 COMMAND.DATA         export_all_projects  INFO     | EXPORTING ALL PROJECTS IN 60s...
2022-06-16 11:10:07,684 COMMAND.USER         create_user          INFO     | Creating User: xxxxxxxxxxx@gmail.com

Here is what it says in webapp log:

cryoSPARC
(node:266418) DeprecationWarning: current Server Discovery and Monitoring engine is deprecated, and will be removed in a future version. To use the new Server Discover and Monitoring engine, pass option { useUnifiedTopology: true } to the MongoClient constructor.
Ready to serve GridFS

parag · June 16, 2022, 5:26pm

Here is the database log:

2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] MongoDB starting : pid=265670 port=39001 dbpath=/zhome/pgajjar/software/cryosparc_database 64-bit host=login02.rc.byu.edu
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] db version v3.4.10
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] git version: 078f28920cb24de0dd479b5ea6c66c644f6326e9
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] allocator: tcmalloc
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] modules: none
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] build environment:
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten]     distarch: x86_64
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten]     target_arch: x86_64
2022-06-16T11:09:51.649-0600 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/zhome/pgajjar/software/cryosparc_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2022-06-16T11:09:51.685-0600 I STORAGE  [initandlisten] wiredtiger_open config: create,cache_size=4096M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),,log=(enabled=false),
2022-06-16T11:09:51.721-0600 I CONTROL  [initandlisten]
2022-06-16T11:09:51.721-0600 I CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database.
2022-06-16T11:09:51.721-0600 I CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2022-06-16T11:09:51.721-0600 I CONTROL  [initandlisten]
2022-06-16T11:09:51.722-0600 I CONTROL  [initandlisten]
2022-06-16T11:09:51.722-0600 I CONTROL  [initandlisten] ** WARNING: You are running on a NUMA machine.
2022-06-16T11:09:51.722-0600 I CONTROL  [initandlisten] **          We suggest launching mongod like this to avoid performance problems:
2022-06-16T11:09:51.722-0600 I CONTROL  [initandlisten] **              numactl --interleave=all mongod [other options]
2022-06-16T11:09:51.722-0600 I CONTROL  [initandlisten]
2022-06-16T11:09:51.732-0600 I FTDC     [initandlisten] Initializing full-time diagnostic data capture with directory '/zhome/pgajjar/software/cryosparc_database/diagnostic.data'
2022-06-16T11:09:51.742-0600 I REPL     [initandlisten] Did not find local voted for document at startup.
2022-06-16T11:09:51.743-0600 I REPL     [initandlisten] Did not find local replica set configuration document at startup;  NoMatchingDocument: Did not find replica set configuration document in local.system.replset
2022-06-16T11:09:51.743-0600 I NETWORK  [thread1] waiting for connections on port 39001
2022-06-16T11:09:52.934-0600 I NETWORK  [thread1] connection accepted from 127.0.0.1:54876 #1 (1 connection now open)
2022-06-16T11:09:52.935-0600 I NETWORK  [conn1] received client metadata from 127.0.0.1:54876 conn1: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:09:52.935-0600 I NETWORK  [thread1] connection accepted from 127.0.0.1:54878 #2 (2 connections now open)
2022-06-16T11:09:52.935-0600 I NETWORK  [conn2] received client metadata from 127.0.0.1:54878 conn2: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:09:53.442-0600 I -        [conn1] end connection 127.0.0.1:54876 (2 connections now open)
2022-06-16T11:09:53.442-0600 I -        [conn2] end connection 127.0.0.1:54878 (2 connections now open)
2022-06-16T11:09:53.496-0600 I NETWORK  [thread1] connection accepted from 127.0.0.1:55180 #3 (1 connection now open)
2022-06-16T11:09:53.497-0600 I NETWORK  [conn3] received client metadata from 127.0.0.1:55180 conn3: { application: { name: "MongoDB Shell" }, driver: { name: "MongoDB Internal Client", version: "3.4.10" }, os: { type: "Linux", name: "Red Hat Enterprise Linux Server release 7.9 (Maipo)", architecture: "x86_64", version: "Kernel 3.10.0-1160.53.1.el7.x86_64" } }
2022-06-16T11:09:53.497-0600 I REPL     [conn3] replSetInitiate admin command received from client
2022-06-16T11:09:53.499-0600 I REPL     [conn3] replSetInitiate config object with 1 members parses ok
2022-06-16T11:09:53.499-0600 I REPL     [conn3] ******
2022-06-16T11:09:53.499-0600 I REPL     [conn3] creating replication oplog of size: 64MB...
2022-06-16T11:09:53.506-0600 I STORAGE  [conn3] Starting WiredTigerRecordStoreThread local.oplog.rs
2022-06-16T11:09:53.506-0600 I STORAGE  [conn3] The size storer reports that the oplog contains 0 records totaling to 0 bytes
2022-06-16T11:09:53.506-0600 I STORAGE  [conn3] Scanning the oplog to determine where to place markers for truncation
2022-06-16T11:09:53.513-0600 I REPL     [conn3] ******
2022-06-16T11:09:53.551-0600 I INDEX    [conn3] build index on: admin.system.version properties: { v: 2, key: { version: 1 }, name: "incompatible_with_version_32", ns: "admin.system.version" }
2022-06-16T11:09:53.551-0600 I INDEX    [conn3]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:53.553-0600 I INDEX    [conn3] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:53.553-0600 I COMMAND  [conn3] setting featureCompatibilityVersion to 3.4
2022-06-16T11:09:53.553-0600 I REPL     [conn3] New replica set config in use: { _id: "meteor", version: 1, protocolVersion: 1, members: [ { _id: 0, host: "localhost:39001", arbiterOnly: false, buildIndexes: true, hidden: false, priority: 1.0, tags: {}, slaveDelay: 0, votes: 1 } ], settings: { chainingAllowed: true, heartbeatIntervalMillis: 2000, heartbeatTimeoutSecs: 10, electionTimeoutMillis: 10000, catchUpTimeoutMillis: 60000, getLastErrorModes: {}, getLastErrorDefaults: { w: 1, wtimeout: 0 }, replicaSetId: ObjectId('62ab63e1777141f6e61babe6') } }
2022-06-16T11:09:53.553-0600 I REPL     [conn3] This node is localhost:39001 in the config
2022-06-16T11:09:53.553-0600 I REPL     [conn3] transition to STARTUP2
2022-06-16T11:09:53.553-0600 I REPL     [conn3] Starting replication storage threads
2022-06-16T11:09:53.554-0600 I REPL     [conn3] Starting replication fetcher thread
2022-06-16T11:09:53.554-0600 I REPL     [conn3] Starting replication applier thread
2022-06-16T11:09:53.554-0600 I REPL     [conn3] Starting replication reporter thread
2022-06-16T11:09:53.554-0600 I REPL     [rsSync] transition to RECOVERING
2022-06-16T11:09:53.554-0600 I REPL     [rsSync] transition to SECONDARY
2022-06-16T11:09:53.554-0600 I REPL     [rsSync] conducting a dry run election to see if we could be elected
2022-06-16T11:09:53.555-0600 I REPL     [ReplicationExecutor] dry election run succeeded, running for election
2022-06-16T11:09:53.556-0600 I -        [conn3] end connection 127.0.0.1:55180 (1 connection now open)
2022-06-16T11:09:53.576-0600 I REPL     [ReplicationExecutor] election succeeded, assuming primary role in term 1
2022-06-16T11:09:53.576-0600 I REPL     [ReplicationExecutor] transition to PRIMARY
2022-06-16T11:09:53.576-0600 I REPL     [ReplicationExecutor] Entering primary catch-up mode.
2022-06-16T11:09:53.576-0600 I REPL     [ReplicationExecutor] Exited primary catch-up mode.
2022-06-16T11:09:53.954-0600 I NETWORK  [thread1] connection accepted from 127.0.0.1:55454 #4 (1 connection now open)
2022-06-16T11:09:53.955-0600 I NETWORK  [conn4] received client metadata from 127.0.0.1:55454 conn4: { application: { name: "MongoDB Shell" }, driver: { name: "MongoDB Internal Client", version: "3.4.10" }, os: { type: "Linux", name: "Red Hat Enterprise Linux Server release 7.9 (Maipo)", architecture: "x86_64", version: "Kernel 3.10.0-1160.53.1.el7.x86_64" } }
2022-06-16T11:09:53.956-0600 I -        [conn4] end connection 127.0.0.1:55454 (1 connection now open)
2022-06-16T11:09:55.555-0600 I REPL     [rsSync] transition to primary complete; database writes are now permitted
2022-06-16T11:09:56.665-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:60878 #5 (1 connection now open)
2022-06-16T11:09:56.666-0600 I NETWORK  [conn5] received client metadata from 128.187.49.41:60878 conn5: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:09:56.667-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:60880 #6 (2 connections now open)
2022-06-16T11:09:56.667-0600 I NETWORK  [conn6] received client metadata from 128.187.49.41:60880 conn6: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:09:56.744-0600 I INDEX    [conn6] build index on: meteor.projects properties: { v: 2, unique: true, key: { uid: 1 }, name: "uid_1", ns: "meteor.projects" }
2022-06-16T11:09:56.744-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.745-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.761-0600 I INDEX    [conn6] build index on: meteor.workspaces properties: { v: 2, unique: true, key: { project_uid: 1, uid: 1 }, name: "project_uid_1_uid_1", ns: "meteor.workspaces" }
2022-06-16T11:09:56.761-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.762-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.768-0600 I INDEX    [conn6] build index on: meteor.workspaces properties: { v: 2, key: { created_at: 1 }, name: "created_at_1", ns: "meteor.workspaces" }
2022-06-16T11:09:56.768-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.769-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.774-0600 I INDEX    [conn6] build index on: meteor.workspaces properties: { v: 2, key: { project_uid: 1, session_uid: 1 }, name: "project_uid_1_session_uid_1", ns: "meteor.workspaces" }
2022-06-16T11:09:56.774-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.776-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.791-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, unique: true, key: { project_uid: 1, uid: 1 }, name: "project_uid_1_uid_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.791-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.792-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.798-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, key: { created_at: 1 }, name: "created_at_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.798-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.799-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.804-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, key: { workspace_uids: 1 }, name: "workspace_uids_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.804-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.806-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.811-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, key: { status: 1 }, name: "status_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.811-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.812-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.818-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, key: { heartbeat_at: 1 }, name: "heartbeat_at_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.818-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.819-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.824-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, key: { deleted: 1 }, name: "deleted_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.824-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.825-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.830-0600 I INDEX    [conn6] build index on: meteor.jobs properties: { v: 2, key: { children: 1 }, name: "children_1", ns: "meteor.jobs" }
2022-06-16T11:09:56.830-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.831-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.847-0600 I INDEX    [conn6] build index on: meteor.events properties: { v: 2, key: { project_uid: 1 }, name: "project_uid_1", ns: "meteor.events" }
2022-06-16T11:09:56.847-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.848-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.853-0600 I INDEX    [conn6] build index on: meteor.events properties: { v: 2, key: { job_uid: 1 }, name: "job_uid_1", ns: "meteor.events" }
2022-06-16T11:09:56.853-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.855-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.860-0600 I INDEX    [conn6] build index on: meteor.events properties: { v: 2, key: { created_at: 1 }, name: "created_at_1", ns: "meteor.events" }
2022-06-16T11:09:56.860-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.861-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.866-0600 I INDEX    [conn6] build index on: meteor.events properties: { v: 2, key: { project_uid: 1, job_uid: 1, created_at: 1 }, name: "project_uid_1_job_uid_1_created_at_1", ns: "meteor.events" }
2022-06-16T11:09:56.866-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.867-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.883-0600 I INDEX    [conn6] build index on: meteor.fs.files properties: { v: 2, key: { project_uid: 1, job_uid: 1 }, name: "project_uid_1_job_uid_1", ns: "meteor.fs.files" }
2022-06-16T11:09:56.883-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.884-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.898-0600 I INDEX    [conn6] build index on: meteor.cache_files properties: { v: 2, unique: true, key: { hostname: 1, key: 1 }, name: "hostname_1_key_1", ns: "meteor.cache_files" }
2022-06-16T11:09:56.899-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.900-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.906-0600 I INDEX    [conn6] build index on: meteor.cache_files properties: { v: 2, key: { in_use_by: 1 }, name: "in_use_by_1", ns: "meteor.cache_files" }
2022-06-16T11:09:56.906-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.907-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.912-0600 I INDEX    [conn6] build index on: meteor.cache_files properties: { v: 2, key: { last_requested: 1 }, name: "last_requested_1", ns: "meteor.cache_files" }
2022-06-16T11:09:56.912-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.913-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.918-0600 I INDEX    [conn6] build index on: meteor.cache_files properties: { v: 2, key: { status: 1 }, name: "status_1", ns: "meteor.cache_files" }
2022-06-16T11:09:56.918-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.920-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.935-0600 I INDEX    [conn6] build index on: meteor.exposures properties: { v: 2, unique: true, key: { project_uid: 1, session_uid: 1, uid: 1 }, name: "project_uid_1_session_uid_1_uid_1", ns: "meteor.exposures" }
2022-06-16T11:09:56.935-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.936-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.942-0600 I INDEX    [conn6] build index on: meteor.exposures properties: { v: 2, key: { discovered_at: 1 }, name: "discovered_at_1", ns: "meteor.exposures" }
2022-06-16T11:09:56.942-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.943-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.948-0600 I INDEX    [conn6] build index on: meteor.exposures properties: { v: 2, key: { created_at: 1 }, name: "created_at_1", ns: "meteor.exposures" }
2022-06-16T11:09:56.948-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.950-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.964-0600 I INDEX    [conn6] build index on: meteor.file_index properties: { v: 2, key: { parent_path_abs: 1 }, name: "parent_path_abs_1", ns: "meteor.file_index" }
2022-06-16T11:09:56.964-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.966-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.981-0600 I INDEX    [conn6] build index on: meteor.sched_queued properties: { v: 2, key: { queued_job_hash: 1 }, name: "queued_job_hash_1", ns: "meteor.sched_queued" }
2022-06-16T11:09:56.981-0600 I INDEX    [conn6]          building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:09:56.982-0600 I INDEX    [conn6] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:09:56.987-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:60934 #7 (3 connections now open)
2022-06-16T11:09:56.988-0600 I NETWORK  [conn7] received client metadata from 128.187.49.41:60934 conn7: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:09:59.310-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:33688 #8 (4 connections now open)
2022-06-16T11:09:59.310-0600 I NETWORK  [conn8] received client metadata from 128.187.49.41:33688 conn8: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:10:04.206-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:35686 #9 (5 connections now open)
2022-06-16T11:10:04.206-0600 I NETWORK  [conn9] received client metadata from 128.187.49.41:35686 conn9: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:10:04.207-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:35688 #10 (6 connections now open)
2022-06-16T11:10:04.208-0600 I NETWORK  [conn10] received client metadata from 128.187.49.41:35688 conn10: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:10:04.688-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:35878 #11 (7 connections now open)
2022-06-16T11:10:04.688-0600 I NETWORK  [conn11] received client metadata from 128.187.49.41:35878 conn11: { driver: { name: "PyMongo", version: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-06-16T11:10:05.478-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36152 #12 (8 connections now open)
2022-06-16T11:10:05.482-0600 I NETWORK  [conn12] received client metadata from 128.187.49.41:36152 conn12: { driver: { name: "nodejs", version: "2.2.34" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE, mongodb-core: 2.1.18" }
2022-06-16T11:10:05.489-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36159 #13 (9 connections now open)
2022-06-16T11:10:05.490-0600 I NETWORK  [conn13] received client metadata from 128.187.49.41:36159 conn13: { driver: { name: "nodejs", version: "2.2.34" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE, mongodb-core: 2.1.18" }
2022-06-16T11:10:05.511-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36160 #14 (10 connections now open)
2022-06-16T11:10:05.511-0600 I NETWORK  [conn14] received client metadata from 128.187.49.41:36160 conn14: { driver: { name: "nodejs", version: "2.2.34" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE, mongodb-core: 2.1.18" }
2022-06-16T11:10:05.542-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, unique: true, key: { username: 1 }, name: "username_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.542-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.543-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.552-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, unique: true, key: { emails.address: 1 }, name: "emails.address_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.552-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.554-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.561-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, unique: true, key: { services.resume.loginTokens.hashedToken: 1 }, name: "services.resume.loginTokens.hashedToken_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.561-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.562-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.569-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, unique: true, key: { services.resume.loginTokens.token: 1 }, name: "services.resume.loginTokens.token_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.569-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.570-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.578-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, key: { services.resume.haveLoginTokensToDelete: 1 }, name: "services.resume.haveLoginTokensToDelete_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.578-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.579-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.586-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, key: { services.resume.loginTokens.when: 1 }, name: "services.resume.loginTokens.when_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.586-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.587-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.594-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, key: { services.password.reset.when: 1 }, name: "services.password.reset.when_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.594-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.595-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.613-0600 I INDEX    [conn12] build index on: meteor.roles properties: { v: 2, unique: true, key: { name: 1 }, name: "name_1", ns: "meteor.roles" }
2022-06-16T11:10:05.614-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.615-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.758-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, unique: true, key: { services.email.verificationTokens.token: 1 }, name: "services.email.verificationTokens.token_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.758-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.759-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:05.765-0600 I INDEX    [conn12] build index on: meteor.users properties: { v: 2, unique: true, key: { services.password.reset.token: 1 }, name: "services.password.reset.token_1", ns: "meteor.users", sparse: 1 }
2022-06-16T11:10:05.765-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:05.767-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:06.434-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36272 #15 (11 connections now open)
2022-06-16T11:10:06.436-0600 I NETWORK  [conn15] received client metadata from 128.187.49.41:36272 conn15: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-06-16T11:10:06.447-0600 I INDEX    [conn12] build index on: meteor.meteor_accounts_loginServiceConfiguration properties: { v: 2, unique: true, key: { service: 1 }, name: "service_1", ns: "meteor.meteor_accounts_loginServiceConfiguration" }
2022-06-16T11:10:06.447-0600 I INDEX    [conn12]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:06.448-0600 I INDEX    [conn12] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:06.942-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36318 #16 (12 connections now open)
2022-06-16T11:10:06.945-0600 I NETWORK  [conn16] received client metadata from 128.187.49.41:36318 conn16: { driver: { name: "nodejs-core", version: "3.2.7" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v14.15.1, LE" }
2022-06-16T11:10:06.955-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36320 #17 (13 connections now open)
2022-06-16T11:10:06.955-0600 I NETWORK  [conn17] received client metadata from 128.187.49.41:36320 conn17: { driver: { name: "nodejs-core", version: "3.2.7" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v14.15.1, LE" }
2022-06-16T11:10:06.959-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36322 #18 (14 connections now open)
2022-06-16T11:10:06.959-0600 I NETWORK  [conn18] received client metadata from 128.187.49.41:36322 conn18: { driver: { name: "nodejs-core", version: "3.2.7" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v14.15.1, LE" }
2022-06-16T11:10:07.065-0600 I INDEX    [conn16] build index on: meteor.meteor_oauth_pendingCredentials properties: { v: 2, unique: true, key: { key: 1 }, name: "key_1", ns: "meteor.meteor_oauth_pendingCredentials" }
2022-06-16T11:10:07.065-0600 I INDEX    [conn16]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:07.066-0600 I INDEX    [conn16] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:07.074-0600 I INDEX    [conn16] build index on: meteor.meteor_oauth_pendingCredentials properties: { v: 2, key: { credentialSecret: 1 }, name: "credentialSecret_1", ns: "meteor.meteor_oauth_pendingCredentials" }
2022-06-16T11:10:07.074-0600 I INDEX    [conn16]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:07.076-0600 I INDEX    [conn16] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:07.083-0600 I INDEX    [conn16] build index on: meteor.meteor_oauth_pendingCredentials properties: { v: 2, key: { createdAt: 1 }, name: "createdAt_1", ns: "meteor.meteor_oauth_pendingCredentials" }
2022-06-16T11:10:07.083-0600 I INDEX    [conn16]         building index using bulk method; build may temporarily use up to 500 megabytes of RAM
2022-06-16T11:10:07.084-0600 I INDEX    [conn16] build index done.  scanned 0 total records. 0 secs
2022-06-16T11:10:08.291-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36526 #19 (15 connections now open)
2022-06-16T11:10:08.294-0600 I NETWORK  [thread1] connection accepted from 128.187.49.41:36528 #20 (16 connections now open)
2022-06-16T11:10:08.298-0600 I NETWORK  [conn19] received client metadata from 128.187.49.41:36526 conn19: { driver: { name: "nodejs", version: "3.6.2" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "'Node.js v14.15.1, LE (unified)" }
2022-06-16T11:10:08.299-0600 I NETWORK  [conn20] received client metadata from 128.187.49.41:36528 conn20: { driver: { name: "nodejs-core", version: "3.2.7" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.53.1.el7.x86_64" }, platform: "Node.js v14.15.1, LE" }

parag · June 16, 2022, 5:27pm

From the Chrome Developer tool:
(index):6772 crbug/1173575, non-JS module files deprecated.

jucastil · June 17, 2022, 8:20am

Hi @yijietseng ,
I had this before.
I don’t know the reason - maybe a big database - but it was fixed by:

cryosparcm stop
cryosparcm start

If you can reboot the server after the “stop” even better.
Best,

Juan

yijietseng · June 17, 2022, 8:39am

Hi @jucastil ,

Thanks for your suggestion. But we tried rebooting several times, but the problem is still not fixed.

wtempel · June 29, 2022, 3:14pm

We are still not sure what is causing this problem. May we ask for this additional information:

Have you successfully processed data using this cryoSPARC instance prior to the occurrence of this problem?
What is the output of this command, run in a shell on the cryoSPARC master host:
host localhost
Have host or network-level firewalls been reconfigured after your latest successful processing jobs?
Does the command
cryosparcm listusers
output an accurate table of cryoSPARC users’ Name, Email, Admin fields?

gdodge · July 7, 2022, 5:56pm

I encountered this error once when the drive containing my cryosparc database was almost empty.