neo4j does not start due to ch-run error

[peterfriedl]

Initializing neo4j fails as the neo4-admin command cannot be found:

(beeflow-env) di46riq@dlr-login:~> beeflow core status
beeflow components:
redis ... RUNNING
scheduler ... RUNNING
celery ... RUNNING
wf_manager ... RUNNING
task_manager ... RUNNING
neo4j-database ... FAILED

(beeflow-env) di46riq@dlr-login:~> cat /dss/dsshome1/lxc0F/di46riq/.beeflow/logs/beeflow.log
Running on dlr-login
Launching components in order: ['redis', 'scheduler', 'celery', 'wf_manager', 'task_manager', 'neo4j-database']
ch-run[118860]: error: can't execve(2): neo4j-admin: No such file or directory (ch_core.c:570 2)
[2025-02-24 14:27:27,132] neo4j:create_credentials(): neo4j-admin set-initial-password failed
[2025-02-24 14:27:27,132] neo4j:create_credentials(): neo4j-admin set-initial-password failed
ERROR:neo4j:neo4j-admin set-initial-password failed
waiting 1s for GDB to come up
Component "neo4j-database" failed, check log "/dss/dsshome1/lxc0F/di46riq/.beeflow/logs/neo4j-database.log"
Attempting restart 0 of "neo4j-database"...

This indicates that the path to the binary isn't set correctly. However, running the charliecloud-image manually and loading the environment file as in neo4j:create_credentials() works:

(beeflow-env) di46riq@dlr-login:~> ch-run --set-env=/dss/dsshome1/lxc0F/di46riq/.beeflow/deps/neo4j_container/ch/environment --set-env=apoc.export.file.enabled=true /dss/dsshome1/lxc0F/di46riq/.beeflow/deps/neo4j_container -- neo4j-admin
Usage: neo4j-admin [-hV] [--expand-commands] [--verbose] [COMMAND]
Neo4j database administration tool.
      --expand-commands   Allow command expansion in config value evaluation.
  -h, --help              Show this help message and exit.
  -V, --version           Print version information and exit.
      --verbose           Prints additional information.
Commands:
  version   Print version information and exit.
  help      Display help information about the specified command.
  database  Database-specific administration tasks.
  dbms      DBMS-wide (for single and clustered environments) administration tasks.
  server    Server-wide administration tasks.

Environment variables:
  NEO4J_CONF    Path to directory which contains neo4j.conf.
  NEO4J_DEBUG   Set to anything to enable debug output.
  NEO4J_HOME    Neo4j home directory.
  HEAP_SIZE     Set JVM maximum heap size during command execution. Takes a number and a unit, for example 512m.
  JAVA_OPTS     Used to pass custom setting to Java Virtual Machine executing the command. Refer to JVM documentation
about the exact format. This variable is incompatible with HEAP_SIZE and takes precedence over HEAP_SIZE.

[pagrubel]

Would you mind posting your bee.conf file or sending it to [email protected]

[peterfriedl]

# BEE Configuration File

[DEFAULT]
bee_workdir = /dss/dsshome1/lxc0F/di46riq/.beeflow
bee_archive_dir = /dss/dsshome1/lxc0F/di46riq/.beeflow/archives
bee_droppoint = /dss/dsshome1/lxc0F/di46riq/.beeflow/droppoint
remote_api = False
remote_api_port = 14277
workload_scheduler = Slurm
delete_completed_workflow_dirs = True
neo4j_image = /dss/dsshome1/lxc0F/di46riq/neo4j.tar.gz
redis_image = /dss/dsshome1/lxc0F/di46riq/redis.tar.gz
max_restarts = 5

[task_manager]
container_runtime = Charliecloud
runner_opts = 
background_interval = 5

[charliecloud]
image_mntdir = /tmp/di46riq
chrun_opts = --home
setup = 

[job]
default_account = pn56su
default_time_limit = 
default_partition = hpda2_compute
default_qos = 
default_reservation = 

[graphdb]
hostname = localhost
dbpass = password
gdb_image_mntdir = /tmp/di46riq
sleep_time = 1

[builder]
deployed_image_root = /tmp
container_output_path = /tmp
container_archive = /dss/dsshome1/lxc0F/di46riq/.beeflow/container_archive
container_type = charliecloud

[slurm]
use_commands = True

[scheduler]
algorithm = fcfs
default_algorithm = fcfs