Database crashes after too many queries?

Hi,
I'm using Neo4j 4.0.4 with GraphDataScience 1.2.1 library, from python 3.8.3 using the official neo4j python driver.
I have a script to call Louvain algorithm from python, but my database keeps crashing with the following error :

Traceback (most recent call last):

  File "<ipython-input-1-4a6a01b5290f>", line 44, in <module>
    call_louvain_algo(subject, obj, clust, rel_name, nb_supports, driver)

  File "<ipython-input-1-4a6a01b5290f>", line 26, in call_louvain_algo
    results = [[record['id'], record['communityId']] for record in results]

  File "<ipython-input-1-4a6a01b5290f>", line 26, in <listcomp>
    results = [[record['id'], record['communityId']] for record in results]

  File "/home/briere/miniconda3/envs/ClustOmics/lib/python3.8/site-packages/neo4j/work/result.py", line 184, in __iter__
    self._connection.fetch_message()  # Receive at least one message from the server, if available.

  File "/home/briere/miniconda3/envs/ClustOmics/lib/python3.8/site-packages/neo4j/io/_bolt4x0.py", line 330, in fetch_message
    response.on_failure(summary_metadata or {})

  File "/home/briere/miniconda3/envs/ClustOmics/lib/python3.8/site-packages/neo4j/io/_bolt4x0.py", line 518, in on_failure
    raise Neo4jError.hydrate(**metadata)

TransientError: Database 'neo4j' unavailable

Here is my code :

import numpy as np
from neo4j import GraphDatabase

def call_louvain_algo(subject, obj, clust, rel_name, nb_supports, driver):
    with driver.session() as session:
        print("louvain")
        obj1_nodes = "(o1:"+ obj + ":" + subject + ")"
        obj2_nodes = "(o2:"+ obj + ":" + subject + ")"
    
        cat_graph_name = "_".join([rel_name, str(nb_supports)])
    
        objects =' MATCH ' + obj1_nodes + '-[r:' + rel_name + ']-' + obj2_nodes + \
        ' WHERE r.nb_supports >= ' + str(nb_supports) + ' RETURN DISTINCT id(o1) as id'
    
        relations = 'MATCH ' + obj1_nodes + '-[r:' + rel_name + ']->' + obj2_nodes + \
        ' WHERE r.nb_supports >= ' + str(nb_supports) + ' RETURN id(o1) as source, id(o2) as target, r.nb_supports as weight'
    
        make_graph_cat = "CALL gds.graph.create.cypher('" + cat_graph_name +\
            "', '" + objects + "', '" + relations + "')"
        session.run(make_graph_cat)

        call_louvain = "CALL gds.louvain.stream('" + cat_graph_name +\
            "',{relationshipWeightProperty:'weight', maxIterations:10})" +\
            "YIELD nodeId, communityId RETURN gds.util.asNode(nodeId).id as id, communityId"
        results = session.run(call_louvain)
        results = [[record['id'], record['communityId']] for record in results]

        remove_graph_cat = "CALL gds.graph.drop('" + cat_graph_name + "') YIELD graphName;"
        session.run(remove_graph_cat)

    return(np.array(results))

neo_id = 'neo4j'
neo_pwd = '4jneo'
neo_localhost = "bolt://localhost:7687"
subject = "SARC"
obj = "Patient"
clust = "Cluster"
rel_name = "SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL"
nb_supports = 2

driver = GraphDatabase.driver(uri=neo_localhost, auth=(neo_id, neo_pwd))
for i in range(0,8):
    call_louvain_algo(subject, obj, clust, rel_name, nb_supports, driver)
driver.close()

It runs fine for few iterations, but when executed multiple times in a row, then the database crashes.
Am I using session.run() wrong, is it a configuration issue ?

All tips appreciated,
Best regards,
GB

Hi galadriel.briere, Can you please check neo4j.log for any exceptions and share. Thanks

Thanks for taking a look :) That's the strange thing, I could'nt find anything in neo4j.log, it just seems to stop without any error message. Here's the tail of the file :

2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 87%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 88%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 89%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 90%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 90%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 91%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 92%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 93%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 93%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 94%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 95%
2020-06-25 11:25:11.828+0000 INFO  [gds-4] ModularityOptimization 96%
2020-06-25 11:25:11.829+0000 INFO  [gds-2] ModularityOptimization 96%
2020-06-25 11:25:11.829+0000 INFO  [gds-2] ModularityOptimization 97%
2020-06-25 11:25:11.829+0000 INFO  [gds-2] ModularityOptimization 98%
2020-06-25 11:25:11.829+0000 INFO  [gds-2] ModularityOptimization 99%
2020-06-25 11:25:11.829+0000 INFO  [gds-2] ModularityOptimization 100%
2020-06-25 11:25:11.836+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 5 :: Finished
2020-06-25 11:25:11.836+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Finished
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 1 :: Finished
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 2 :: Start
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Start
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Initialization :: Start
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Start
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 1 :: Start
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 1 :: Finished
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 2 :: Start
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 2 :: Finished
2020-06-25 11:25:11.838+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Finished
2020-06-25 11:25:11.839+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Initialization :: Finished
2020-06-25 11:25:11.839+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 1 :: Start
2020-06-25 11:25:11.845+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 1 :: Finished
2020-06-25 11:25:11.845+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 2 :: Start
2020-06-25 11:25:11.848+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 2 :: Finished
2020-06-25 11:25:11.848+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Finished
2020-06-25 11:25:11.849+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 2 :: Finished
2020-06-25 11:25:11.849+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain :: Finished
2020-06-25 11:25:11.849+0000 INFO  LouvainStreamProc: overall memory usage 1384 KiB
2020-06-25 11:25:12.014+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] LOADING 
2020-06-25 11:25:12.019+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain :: Start
2020-06-25 11:25:12.019+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 1 :: Start
2020-06-25 11:25:12.019+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Start
2020-06-25 11:25:12.020+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Initialization :: Start
2020-06-25 11:25:12.020+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Start
2020-06-25 11:25:12.020+0000 INFO  [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 1 :: Start
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 0%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 0%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 0%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 0%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 0%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 1%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 1%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 1%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 1%
2020-06-25 11:25:12.020+0000 INFO  [gds-4] K1Coloring 1%

I also checked in debug.log :

2020-06-25 11:25:12.258+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 3 :: Finished
2020-06-25 11:25:12.258+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Finished
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 2 :: Finished
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 3 :: Start
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Start
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Initialization :: Start
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Start
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 1 :: Start
2020-06-25 11:25:12.259+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Iteration 1 :: Finished
2020-06-25 11:25:12.260+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] K1Coloring :: Finished
2020-06-25 11:25:12.260+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Initialization :: Finished
2020-06-25 11:25:12.260+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 1 :: Start
2020-06-25 11:25:12.265+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 1 :: Finished
2020-06-25 11:25:12.265+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 2 :: Start
2020-06-25 11:25:12.268+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Iteration 2 :: Finished
2020-06-25 11:25:12.268+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] ModularityOptimization :: Finished
2020-06-25 11:25:12.268+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain Level 3 :: Finished
2020-06-25 11:25:12.269+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-5 [bolt] [/127.0.0.1:42254] ] Louvain :: Finished
2020-06-25 11:25:12.269+0000 INFO [o.n.k.a.p.GlobalProcedures] LouvainStreamProc: overall memory usage 1915 KiB
2020-06-25 11:25:12.285+0000 INFO [o.n.k.i.t.l.c.CheckPointerImpl] [neo4j] Checkpoint triggered by "Database shutdown" @ txId: 6406 checkpoint started...
2020-06-25 11:25:12.335+0000 INFO [o.n.k.i.t.l.c.CheckPointerImpl] [neo4j] Checkpoint triggered by "Database shutdown" @ txId: 6406 checkpoint completed in 50ms
2020-06-25 11:25:12.341+0000 INFO [o.n.k.i.t.l.p.LogPruningImpl] [neo4j] No log version pruned. The strategy used was '7 days'. Last checkpoint was made in log version 0.
2020-06-25 11:25:12.370+0000 INFO [c.n.d.DbmsReconciler] Database system is requested to transition from EnterpriseDatabaseState{databaseId=DatabaseId{00000000[system]}, operatorState=STARTED, failed=false} to EnterpriseDatabaseState{databaseId=DatabaseId{00000000[system]}, operatorState=STOPPED, failed=false}
2020-06-25 11:25:12.370+0000 INFO [c.n.d.d.EnterpriseMultiDatabaseManager] Stop 'system' database.
2020-06-25 11:25:12.370+0000 INFO [o.n.k.a.DatabaseAvailabilityGuard] [system] Requirement `Database unavailable` makes database system unavailable.
2020-06-25 11:25:12.370+0000 INFO [o.n.k.a.DatabaseAvailabilityGuard] [system] Database system is unavailable.
2020-06-25 11:25:12.372+0000 INFO [o.n.k.i.t.l.c.CheckPointerImpl] [system] Checkpoint triggered by "Database shutdown" @ txId: 40 checkpoint started...
2020-06-25 11:25:12.414+0000 INFO [o.n.k.i.t.l.c.CheckPointerImpl] [system] Checkpoint triggered by "Database shutdown" @ txId: 40 checkpoint completed in 41ms
2020-06-25 11:25:12.414+0000 INFO [o.n.k.i.t.l.p.LogPruningImpl] [system] No log version pruned. The strategy used was '7 days'. Last checkpoint was made in log version 0.

Also, I don't know if it helps, but here's the log from Neo4j Desktop (AppImage for Linux) :

[16:43:05.162] [info] Starting Neo4j Desktop 1.2.9 @ Linux 5.3.0-59-generic
(node:16981) DeprecationWarning: file property is deprecated and will be removed in v5.
(node:16981) DeprecationWarning: file property is deprecated and will be removed in v5.
[16:43:05.326] [info] GraphQL server is running @ http://localhost:11001
[16:43:05.347] [info] Initializing persistence
[16:43:05.347] [info] GraphQL server is running @ 127.0.0.1:11002
[16:43:05.389] [info] Configuring crash reporting
[16:43:05.390] [info] Reading settings
[16:43:05.392] [info] Reading bundled resources /tmp/.mount_neo4j-7K0XGr/resources
[16:43:05.392] [info] Distribution folder for java should exist
[16:43:07.500] [info] Will copy []
[16:43:07.505] [info] Distribution folder for neo4j should exist
[16:43:08.601] [info] Will copy []
[16:43:08.601] [info] Reading bundled resources /tmp/.mount_neo4j-7K0XGr/resources
[16:43:08.605] [info] Distribution folder for graphApps should exist
[16:43:08.608] [info] Will copy []
[16:43:08.609] [info] Configuring proxy: NO_PROXY
[16:43:09.148] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:43:09.354] [info] [1] Online check response: 200 version: 1.2.9
files
[16:43:09.357] [info] Stopping any running databases
[16:43:09.414] [info] Checking store_lock file for database-0442a08c-be95-4caa-8d23-46cffa5d9223
[16:43:09.415] [info] Checking store_lock file for database-1c408f3f-4b26-4852-9487-22eadaae0faf
[16:43:09.415] [info] Checking store_lock file for database-1c408f3f-4b26-4852-9487-22eadaae0faf
[16:43:09.415] [info] Checking store_lock file for database-1d3baed0-c0b6-435f-83a2-92142085c338
[16:43:09.415] [info] Checking store_lock file for database-2c6750b8-52ac-4bce-853e-ced285b768eb
[16:43:09.416] [info] Checking store_lock file for database-2c6750b8-52ac-4bce-853e-ced285b768eb
[16:43:09.416] [info] Checking store_lock file for database-3feb52b2-d6d1-4a4b-aa1d-cd44d3ae6dc7
[16:43:09.416] [info] Checking store_lock file for database-68002928-eeda-4733-9182-4fd53ab9bb84
[16:43:09.416] [info] Checking store_lock file for database-6eeacb6d-2673-4fe0-8821-f6a6430fd6a1
[16:43:09.417] [info] Checking store_lock file for database-9a11397a-f3cf-48d1-8ba8-14229a860967
[16:43:09.417] [info] Checking store_lock file for database-9a11397a-f3cf-48d1-8ba8-14229a860967
[16:43:09.417] [info] Checking store_lock file for database-b2098795-86b4-4097-9715-0ab82a5a4666
[16:43:09.417] [info] Checking store_lock file for database-b2098795-86b4-4097-9715-0ab82a5a4666
[16:43:09.417] [info] Checking store_lock file for database-d426f59b-0000-46af-85d6-8ee4569fab8e
[16:43:09.418] [info] Registering listener for protocolManager/arguments/changed
[16:43:09.433] [info] Opening main window
[16:43:09.437] [error] Protocol Manager type error: url must be string. url = undefined
[16:43:09.550] [info] Registering IPC listeners
[16:43:10.065] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:43:10.144] [info] [1] Online check response: 200 version: 1.2.9
files
[16:43:10.293] [info] Buffering metrics until application is online
[16:43:10.297] [info] Buffering metrics until application is online
(electron) 'getName function' is deprecated and will be removed. Please use 'name property' instead.
[16:43:11.200] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:43:11.354] [info] [1] Online check response: 200 version: 1.2.9
files
[16:43:11.947] [info] Retrieving status for database[database-0442a08c-be95-4caa-8d23-46cffa5d9223]
[16:43:11.948] [info] Retrieving status for database[database-3feb52b2-d6d1-4a4b-aa1d-cd44d3ae6dc7]
[16:43:11.948] [info] Retrieving status for database[database-d426f59b-0000-46af-85d6-8ee4569fab8e]
[16:43:11.958] [info] Retrieving status for database[database-1d3baed0-c0b6-435f-83a2-92142085c338]
[16:43:11.966] [info] Retrieving status for database[database-9a11397a-f3cf-48d1-8ba8-14229a860967]
[16:43:11.967] [info] Retrieving status for database[database-2c6750b8-52ac-4bce-853e-ced285b768eb]
[16:43:11.974] [info] Retrieving status for database[database-6eeacb6d-2673-4fe0-8821-f6a6430fd6a1]
[16:43:11.974] [info] Retrieving status for database[database-68002928-eeda-4733-9182-4fd53ab9bb84]
[16:43:11.980] [info] Retrieving status for database[database-b2098795-86b4-4097-9715-0ab82a5a4666]
[16:43:11.985] [info] Retrieving status for database[database-1c408f3f-4b26-4852-9487-22eadaae0faf]
[16:43:12.965] [warn] Failed to parse manifest file for Graph-App[neo4j-bloom]. {
  constructor: 'Error',
  stack: 'Error: Graph-App[neo4j-bloom] does not contain manifest.json\n' +
    '    at t.getManifest (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:37625)\n' +
    '    at N.resolveConfig (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:66478)\n' +
    '    at b (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:57402)\n' +
    '    at async Promise.all (index 1)\n' +
    '    at C.getGraphApps (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:60149)'
}
[16:43:13.198] [info] Graph Apps: Removing installed but not configured []
[16:43:13.201] [warn] Failed to parse manifest file for Graph-App[neo4j-bloom]. {
  constructor: 'Error',
  stack: 'Error: Graph-App[neo4j-bloom] does not contain manifest.json\n' +
    '    at t.getManifest (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:37625)\n' +
    '    at N.resolveConfig (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:66478)\n' +
    '    at b (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:57402)\n' +
    '    at async Promise.all (index 1)\n' +
    '    at C.getGraphApps (/tmp/.mount_neo4j-7K0XGr/resources/app.asar/dist/main.prod.js:1:60494)'
}
[16:43:13.796] [info] Graph App[037845f8-f21a-42db-aa76-6278554b6121]: Checking 1.5.0 for suitable desktop API version
[16:43:13.798] [info] Graph App[037845f8-f21a-42db-aa76-6278554b6121]: Version 1.5.0 satisfied. { desktopApiVersion: '1.4.0', packageDesktopApiVersion: '^1.4.0' }
[16:43:13.865] [info] Graph App[neo4j-browser-id]: Checking 4.0.11 for suitable desktop API version
[16:43:13.866] [info] Graph App[neo4j-browser-id]: Version 4.0.11 satisfied. { desktopApiVersion: '1.4.0', packageDesktopApiVersion: '^1.4.0' }
[16:43:13.965] [info] Graph App[neo4j-bloom-id]: Checking 1.3.2 for suitable desktop API version
[16:43:13.968] [info] Graph App[neo4j-bloom-id]: Version 1.3.2 satisfied. { desktopApiVersion: '1.4.0', packageDesktopApiVersion: '^1.4.0' }
[16:43:18.698] [info] Checking ports
[16:43:18.716] [info] Starting Neo4j
[16:43:18.717] [info] Starting db [database-1c408f3f-4b26-4852-9487-22eadaae0faf] 'v4.0.6'
[16:43:18.722] [info] Checking store_lock file for database-1c408f3f-4b26-4852-9487-22eadaae0faf
[16:43:18.723] [info] Executing '/home/briere/.config/Neo4j Desktop/Application/neo4jDatabases/database-1c408f3f-4b26-4852-9487-22eadaae0faf/installation-4.0.6/bin/neo4j' [ 'console' ]
[16:43:28.914] [info] Check if neo4j is available on { host: '127.0.0.1', path: '/', port: 7687 }
[16:43:28.915] [info] Check if neo4j is available on { host: '127.0.0.1', path: '/', port: 7474 }
[16:43:28.918] [info] Neo4j @ 7474 is down. connect ECONNREFUSED 127.0.0.1:7474
[16:43:29.011] [info] Neo4j @ 7687 is up and running!
[16:43:29.924] [info] Check if neo4j is available on { host: '127.0.0.1', path: '/', port: 7687 }
[16:43:29.924] [info] Check if neo4j is available on { host: '127.0.0.1', path: '/', port: 7474 }
[16:43:29.928] [info] Neo4j @ 7687 is up and running!
[16:43:30.011] [info] Neo4j @ 7474 is up and running!
[16:43:50.052] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:43:50.169] [info] [1] Online check response: 200 version: 1.2.9
files
[16:43:54.985] [info] Process [17091] exit with code '0', signal 'null'
[16:43:54.986] [info] DB [database-1c408f3f-4b26-4852-9487-22eadaae0faf] 'v4.0.6' exited with status 'STOPPED'
[16:44:30.052] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:44:30.133] [info] [1] Online check response: 200 version: 1.2.9
files
[16:45:10.054] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:45:10.225] [info] [1] Online check response: 200 version: 1.2.9
files
[16:45:50.055] [info] [1] Online check request: https://dist.neo4j.org/neo4j-desktop/win/latest.yml
[16:45:50.165] [info] [1] Online check response: 200 version: 1.2.9
files

I just noticed the warning on the manifest file for Graph-App[neo4j-bloom], but I'm not sure this is the issue here. Same for the Protocol Manager type error.

Also, for more context on this issue, the database always crashes on the 7th iteration, which makes me think it could be a configuration issue. I didn't changed the configuration file, so all parameters are set to default.

Turns out it was a Neo4j Desktop issue, starting Neo4j from the terminal fixed it !
The bug is reported here : https://github.com/neo4j/graph-data-science/issues/58

Problem solved !

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