grobid connection error

Question

grobid connection error

flckv opened this issue 2 months ago · comments

great work, thank you for sharing.

I think the grobid is running :

but the

api-1 | File "/api/app/api/document.py", line 41, in get_figures
api-1 | paragraphs, metadata = PDF2TextService().parse_paragraphs(pdf_path)
api-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
api-1 | File "/api/app/services/pdf2text.py", line 105, in parse_paragraphs
api-1 | response = requests.post(url, files=files)

File "/usr/local/lib/python3.11/site-packages/requests/adapters.py", line 519, in send
api-1 | raise ConnectionError(e, request=request)
api-1 | requests.exceptions.### ConnectionError: HTTPConnectionPool(host='grobid', port=8070):

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Max retries exceeded with url: /api/processFulltextDocument (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0xffff4caec710>: Failed to establish a new connection: [Errno -2] Name or service not known'))
api-1 | 192.168.65.1 - - [08/Jun/2024:14:24:59 +0000] "POST /backendapi/document/getfigures HTTP/1.0" 500 190 "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/125.0.0.0 Safari/537.36"
proxy-1 | {"time": "2024-06-08T14:27:12+00:00","request_method": "GET","request_uri": "http://localhost/_next/webpack-hmr","status": 101,"request_length": 813,"body_bytes_sent": 6535,"user_agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/125.0.0.0 Safari/537.36","ip": "192.168.65.1","realip": "192.168.65.1","referer": "","host": "localhost","scheme": "http","forwarded-for": ""}
proxy-1 | {"time": "2024-06-08T14:29:12+00:00","request_method": "GET","request_uri": "http://localhost/_next/webpack-hmr","status": 101,"request_length": 813,"body_bytes_sent": 166,"user_agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/125.0.0.0 Safari/537.36","ip": "192.168.65.1","realip": "192.168.65.1","referer": "","host": "localhost","scheme": "http","forwarded-for": ""}

any suggestions on this?

Nikhil Singh · Answer 1 · Sat Jun 08 2024 23:46:31 GMT+0800 (China Standard Time)

Hi @flckv,

Thanks for the issue!

I haven't been able to reproduce this quickly (though I'll keep trying), but in the meantime, you could try the following steps to diagnose the issue:

Open an interactive shell in the api container:
```
docker exec -it <container-id> /bin/bash
```
Check GROBID service response, to see if it is reachable from the api container.
```
curl -v http://grobid:8070/api/version
```
Check docker network configuration:
```
docker network ls # ID for 'figura11y-default'
docker network inspect <network-id>
```
Ensure that the grobid container is on the same network as the api container.

Let me know what you find; glad to help debug further.

flckv · Answer 2 · Sun Jun 09 2024 16:26:59 GMT+0800 (China Standard Time)

Thank you, @nikhilsinghmus

docker network ls
NETWORK ID NAME DRIVER SCOPE
27642bad6499 bridge bridge local
0d84bfa12447 figura11y_default bridge local
24285f91f8d9 host host local
f97d5204b0d7 none null local

docker network inspect 0d84bfa12447

[
{
"Name": "figura11y_default",
"Id": "0d84bfa12447f3b734dcb0f0842a70affef9b2e52cf466b973900f03b8d0acf1",
"Created": "2024-06-08T13:58:58.702392502Z",
"Scope": "local",
"Driver": "bridge",
"EnableIPv6": false,
"IPAM": {
"Driver": "default",
"Options": null,
"Config": [
{
"Subnet": "172.19.0.0/16",
"Gateway": "172.19.0.1"
}
]
},
"Internal": false,
"Attachable": false,
"Ingress": false,
"ConfigFrom": {
"Network": ""
},
"ConfigOnly": false,
"Containers": {
"36b7284bfca535e779d099c7173c50ac953e6b98e76a4296f217e90f382380de": {
"Name": "figura11y-ui-1",
"EndpointID": "0a5cb7f7df8de563d211ae7417cf5a63153fbd5f21dd282705a9d1c1c666accc",
"MacAddress": "02:42:ac:13:00:04",
"IPv4Address": "172.19.0.4/16",
"IPv6Address": ""
},
"3e001f128dd8054d2168a313083317fb8af36964111d804250828ac67047a642": {
"Name": "figura11y-db-1",
"EndpointID": "ed03ccfcf14004148a2b70311afeecc8c74b872447dc9b9758c55e45c2b6e98f",
"MacAddress": "02:42:ac:13:00:03",
"IPv4Address": "172.19.0.3/16",
"IPv6Address": ""
},
"76644cc8a8bee5da86d12c113bfba2d02fae3d496c7d85309d19839bba04e942": {
"Name": "figura11y-api-1",
"EndpointID": "727bbdcb03d48cb21c593b29312d38e981eff528fbb236443dc1cc2cf01b18da",
"MacAddress": "02:42:ac:13:00:02",
"IPv4Address": "172.19.0.2/16",
"IPv6Address": ""
},
"92048cacbab52f9a59262d3cc7b17ce764e1b61126bdfc8462be96879080df75": {
"Name": "figura11y-proxy-1",
"EndpointID": "f48547c4f60b887530475e391d137fa73061b3d97ffdc49ba3768fa9bec04b82",
"MacAddress": "02:42:ac:13:00:06",
"IPv4Address": "172.19.0.6/16",
"IPv6Address": ""
}
},
"Options": {},
"Labels": {
"com.docker.compose.network": "default",
"com.docker.compose.project": "figura11y",
"com.docker.compose.version": "2.27.0"
}
}
]

GROBID STILL RUNNING but no connection:

GROBID STOPPED:

Nikhil Singh · Answer 3 · Mon Jun 10 2024 02:09:01 GMT+0800 (China Standard Time)

Thank you for the update, @flckv! I wonder if the GROBID container is running out of memory, perhaps? Could you try increasing the memory for Docker, and seeing if that resolves it?

flckv · Answer 4 · Sun Jun 23 2024 23:01:46 GMT+0800 (China Standard Time)

Thank you @nikhilsinghmus, I switched to a larger RAM (24GB) hardware. I am using the same figura11y repo setup, but face different issue: I face issue with the the db and sqlalchemy:

podman start -a figura11y_db_1
2024-06-23 14:37:35.766 UTC [1] LOG: starting PostgreSQL 15.7 (Debian 15.7-1.pgdg120+1) on x86_64-pc-linux-gnu, compiled by gcc (Debian 12.2.0-14) 12.2.0, 64-bit
2024-06-23 14:37:35.767 UTC [1] LOG: listening on IPv4 address "0.0.0.0", port 5432
2024-06-23 14:37:35.767 UTC [1] LOG: listening on IPv6 address "::", port 5432
2024-06-23 14:37:35.768 UTC [1] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
2024-06-23 14:37:35.771 UTC [24] LOG: database system was shut down at 2024-06-23 14:37:26 UTC
2024-06-23 14:37:35.782 UTC [1] LOG: database system is ready to accept connections
podman start -a figura11y_api_1
Error: Could not import 'api.db'.

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Usage: flask [OPTIONS] COMMAND [ARGS]...
Try 'flask --help' for help.

Error: No such command 'db'.
Error: Could not import 'api.db'.

Usage: flask [OPTIONS] COMMAND [ARGS]...
Try 'flask --help' for help.

Error: No such command 'db'.
Error: Could not import 'api.db'.

Usage: flask [OPTIONS] COMMAND [ARGS]...
Try 'flask --help' for help.

Error: No such command 'db'.

podman start -a figura11y_grobid_1

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[2024-06-23 14:37:37 +0000] [1] [INFO] Starting gunicorn 22.0.0
[2024-06-23 14:37:37 +0000] [1] [INFO] Listening at: http://0.0.0.0:8000 (1)
[2024-06-23 14:37:37 +0000] [1] [INFO] Using worker: sync
[2024-06-23 14:37:37 +0000] [5] [INFO] Booting worker with pid: 5
podman start -a figura11y_ui_1
podman start -a figura11y_proxy_1

warn Invalid next.config.js options detected:
warn The root value has an unexpected property, maxBodyLength, which is not in the list of allowed properties (amp, analyticsId, assetPrefix, basePath, cleanDistDir, compiler, compress, configOrigin, crossOrigin, devIndicators, distDir, env, eslint, excludeDefaultMomentLocales, experimental, exportPathMap, generateBuildId, generateEtags, headers, httpAgentOptions, i18n, images, modularizeImports, onDemandEntries, optimizeFonts, output, outputFileTracing, pageExtensions, poweredByHeader, productionBrowserSourceMaps, publicRuntimeConfig, reactProductionProfiling, reactStrictMode, redirects, rewrites, sassOptions, serverRuntimeConfig, skipMiddlewareUrlNormalize, skipTrailingSlashRedirect, staticPageGenerationTimeout, swcMinify, target, trailingSlash, transpilePackages, typescript, useFileSystemPublicRoutes, webpack).
warn See more info here: https://nextjs.org/docs/messages/invalid-next-config
warn You have enabled experimental feature (proxyTimeout) in next.config.js.
warn Experimental features are not covered by semver, and may cause unexpected or broken application behavior. Use at your own risk.

2024/06/23 14:37:39 [emerg] 1#1: host not found in upstream "ui" in /etc/nginx/conf.d/default.conf:10
nginx: [emerg] host not found in upstream "ui" in /etc/nginx/conf.d/default.conf:10
podman start -a figura11y_sonar_1
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/affiliation-address/model.wapiti"
Model path: /opt/grobid/grobid-home/models/affiliation-address/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/name/header/model.wapiti"
Model path: /opt/grobid/grobid-home/models/name/header/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/name/citation/model.wapiti"
Model path: /opt/grobid/grobid-home/models/name/citation/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/header/model.wapiti"

Error: unable to start container 47115bdcaad81c8b1462865db84a2499fcf7fb18f7ab7995fe74000a8d0f5233: generating dependency graph for container 47115bdcaad81c8b1462865db84a2499fcf7fb18f7ab7995fe74000a8d0f5233: container aa79618ce092122dddfeec9b97259295146b14c951de24e5b2f064ab36fef562 depends on container 396de865c1e8ed1ed96cd5014090652544ed3db20df2da88b87c5a80475b8786 not found in input list: no such container
exit code: 1
exit code: 125
Neither CUDA nor MPS are available - defaulting to CPU. Note: This module is much faster with a GPU.

[Wapiti] Loading model: "/opt/grobid/grobid-home/models/citation/model.wapiti"

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Downloading recognition model, please wait. This may take several minutes depending upon your network connection.
Model path: /opt/grobid/grobid-home/models/citation/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/fulltext/model.wapiti"
Model path: /opt/grobid/grobid-home/models/fulltext/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/segmentation/model.wapiti"
Downloading config.json: 100%|██████████| 4.94k/4.94k [00:00<00:00, 27.7MB/s]
Downloading pytorch_model.bin: 48%|████▊ | 388M/809M [00:01<00:01, 288MB/s]Model path: /opt/grobid/grobid-home/models/segmentation/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/reference-segmenter/model.wapiti"
Downloading pytorch_model.bin: 88%|████████▊ | 713M/809M [00:02<00:00, 285MB/s]Model path: /opt/grobid/grobid-home/models/reference-segmenter/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/figure/model.wapiti"
Model path: /opt/grobid/grobid-home/models/figure/model.wapiti
[Wapiti] Loading model: "/opt/grobid/grobid-home/models/table/model.wapiti"
Downloading pytorch_model.bin: 93%|█████████▎| 755M/809M [00:02<00:00, 305MB/s]Model path: /opt/grobid/grobid-home/models/table/model.wapiti
Downloading pytorch_model.bin: 100%|██████████| 809M/809M [00:02<00:00, 297MB/s]
Downloading generation_config.json: 100%|██████████| 186/186 [00:00<00:00, 1.51MB/s]
Downloading (…)rocessor_config.json: 100%|██████████| 420/420 [00:00<00:00, 3.52MB/s]
Downloading tokenizer_config.json: 100%|██████████| 510/510 [00:00<00:00, 4.22MB/s]
Downloading (…)tencepiece.bpe.model: 100%|██████████| 1.30M/1.30M [00:00<00:00, 432MB/s]
Downloading tokenizer.json: 100%|██████████| 4.01M/4.01M [00:00<00:00, 7.00MB/s]
Downloading added_tokens.json: 100%|██████████| 235/235 [00:00<00:00, 2.26MB/s]
Downloading (…)cial_tokens_map.json: 100%|██████████| 355/355 [00:00<00:00, 4.09MB/s]
Neither CUDA nor MPS are available - defaulting to CPU. Note: This module is much faster with a GPU.

[2024-06-23 14:38:07 +0000] [5] [ERROR] Exception in worker process
Traceback (most recent call last):
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 145, in init
self._dbapi_connection = engine.raw_connection()
^^^^^^^^^^^^^^^^^^^^^^^

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File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3288, in raw_connection
return self.pool.connect()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 452, in connect
return _ConnectionFairy._checkout(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1267, in _checkout
fairy = _ConnectionRecord.checkout(pool)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 716, in checkout
rec = pool._do_get()
^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 169, in _do_get
with util.safe_reraise():
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 147, in exit
raise exc_value.with_traceback(exc_tb)
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 167, in _do_get
return self._create_connection()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 393, in _create_connection
return _ConnectionRecord(self)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 678, in init
self.__connect()
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 902, in __connect
with util.safe_reraise():
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 147, in exit
raise exc_value.with_traceback(exc_tb)
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 898, in __connect
self.dbapi_connection = connection = pool._invoke_creator(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 637, in connect
return dialect.connect(*cargs, **cparams)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 615, in connect
return self.loaded_dbapi.connect(*cargs, **cparams)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/psycopg2/init.py", line 122, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
psycopg2.OperationalError: could not translate host name "db" to address: Name or service not known

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/lib/python3.11/site-packages/gunicorn/arbiter.py", line 609, in spawn_worker
worker.init_process()

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File "/usr/local/lib/python3.11/site-packages/gunicorn/workers/base.py", line 134, in init_process
self.load_wsgi()
File "/usr/local/lib/python3.11/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
self.wsgi = self.app.wsgi()
^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/gunicorn/app/base.py", line 67, in wsgi
self.callable = self.load()
^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
return self.load_wsgiapp()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
return util.import_app(self.app_uri)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/gunicorn/util.py", line 424, in import_app
app = app(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^
File "/api/start.py", line 50, in create_app
create_app_db_api(app),
^^^^^^^^^^^^^^^^^^^^^^
File "/api/app/api/db.py", line 86, in create_app_db_api
SerializableBase.metadata.create_all(db.engine)
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/sql/schema.py", line 5822, in create_all
bind._run_ddl_visitor(
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3238, in _run_ddl_visitor
with self.begin() as conn:
File "/usr/local/lib/python3.11/contextlib.py", line 137, in enter
return next(self.gen)
^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3228, in begin
with self.connect() as conn:
^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3264, in connect
return self._connection_cls(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 147, in init
Connection._handle_dbapi_exception_noconnection(
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 2426, in _handle_dbapi_exception_noconnection
raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 145, in init
self._dbapi_connection = engine.raw_connection()
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3288, in raw_connection
return self.pool.connect()
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 452, in connect
return _ConnectionFairy._checkout(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1267, in _checkout
fairy = _ConnectionRecord.checkout(pool)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 716, in checkout
rec = pool._do_get()
^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 169, in _do_get
with util.safe_reraise():
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 147, in exit
raise exc_value.with_traceback(exc_tb)
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 167, in _do_get
return self._create_connection()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 393, in _create_connection
return _ConnectionRecord(self)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 678, in init
self.__connect()
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 902, in __connect
with util.safe_reraise():
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 147, in exit
raise exc_value.with_traceback(exc_tb)
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 898, in __connect
self.dbapi_connection = connection = pool._invoke_creator(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 637, in connect
return dialect.connect(*cargs, **cparams)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 615, in connect
return self.loaded_dbapi.connect(*cargs, **cparams)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/psycopg2/init.py", line 122, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) could not translate host name "db" to address: Name or service not known

(Background on this error at: https://sqlalche.me/e/20/e3q8)

[2024-06-23 14:38:07 +0000] [5] [INFO] Worker exiting (pid: 5)
[2024-06-23 14:38:10 +0000] [1] [ERROR] Worker (pid:5) exited with code 3
[2024-06-23 14:38:10 +0000] [1] [ERROR] Shutting down: Master
[2024-06-23 14:38:10 +0000] [1] [ERROR] Reason: Worker failed to boot.
exit code: 3
2024-06-23 14:42:35.863 UTC [22] LOG: checkpoint starting: time
2024-06-23 14:42:35.870 UTC [22] LOG: checkpoint complete: wrote 3 buffers (0.0%); 0 WAL file(s) added, 0 removed, 0 recycled; write=0.001 s, sync=0.002 s, total=0.008 s; sync files=2, longest=0.002 s, average=0.001 s; distance=0 kB, estimate=0 kB

Nikhil Singh · Answer 5 · Mon Jun 24 2024 04:19:42 GMT+0800 (China Standard Time)

Hi @flckv, thanks for the update! It looks like there's a difference in our setups; the project is designed and tested using Docker with docker compose up --build, but it looks like you're using podman and starting containers individually?

I think this difference is likely causing the problems. To resolve this, if possible, could you try installing Docker and Docker Compose, then run docker compose up --build?

Or alternatively, it might work with Podman Compose with podman-compose up --build; I did a quick test of this, and found that it worked.

Let me know if this might resolve it, or if I might have misinterpreted something.

flckv · Answer 6 · Mon Jun 24 2024 22:37:34 GMT+0800 (China Standard Time)

Thank you @nikhilsinghmus.

True I run the podman-compose(rootless setup) in combination with podman(root setup) file with podman-compose that initiates command e.g.:podman create --name=figura11y_db_1 ... The setup is because of:

Root Access for podman only:

`podman`

is setup on root

More: why not docker-compose

docker compose up --build

Emulate Docker CLI using podman. Create /usr/etc/containers/nodocker to quiet msg.
Error: unknown flag: --build
See 'podman --help'

`podman-compose`

is NOT setup on root

More: Permission denied

curl -o /usr/local/bin/podman-compose https://raw.githubusercontent.com/containers/podman-compose/main/podman_compose.py
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file /usr/local/bin/podman-compose:
Permission
Warning: denied
13 121k 13 16375 0 0 47394 0 0:00:02 --:--:-- 0:00:02 47326
curl: (23) Failure writing output to destination

Commands used to run docker-compose.yaml:

cd figura11y
loginctl enable-linger 2030

`podman-compose up --build`

podman-compose version: 1.0.6
['podman', '--version', '']
using podman version: 4.5.1

** excluding: set()
['podman', 'ps', '--filter', 'label=io.podman.compose.project=figura11y', '-a', '--format', '{{ index .Labels "io.podman.compose.config-hash"}}']

podman volume inspect figura11y_pgdata || podman volume create figura11y_pgdata
['podman', 'volume', 'inspect', 'figura11y_pgdata']
['podman', 'network', 'exists', 'figura11y_default']

podman create --name=figura11y_db_1 --label io.podman.compose.config-hash=974349d38b18b6c57d47a8f580bf50ad1f4ff0ff17dcc88aea2734fe44b756bb --label io.podman.compose.project=figura11y --label io.podman.compose.version=1.0.6 --label PODMAN_SYSTEMD_UNIT=podman-compose@figura11y.service --label com.docker.compose.project=figura11y --label com.docker.compose.project.working_dir=/home/felicia.kovacs/figura11y --label com.docker.compose.project.config_files=docker-compose.yaml --label com.docker.compose.container-number=1 --label com.docker.compose.service=db -e POSTGRES_USER=foo -e POSTGRES_PASSWORD=bar -e POSTGRES_DB=writealttext -v figura11y_pgdata:/var/lib/postgresql/data --net figura11y_default --network-alias db -p 5432:5432 --restart always postgres:15
exit code: 0
['podman', 'network', 'exists', 'figura11y_default']

podman create --name=figura11y_api_1 .....
...

DB gets stuck - Errors:

1.Error: Could not import 'api.db' (on the left)

podman-compose ps says api.db is running (on the right)

2.Error: unable to start container 4b57d08de04a (on the left)

podman-compose ps shows that both sonar and proxy are not listed in the compose (on the right)

3.LAST Errors: DB - Sqlalchemy related:

psycopg2.OperationalError: could not translate host name "db" to address: Name or service not known (on the left)
podman-compose ps says api.db is running (on the right)

sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) could not translate host name "db" to address: Name or service not known (on the left)
podman-compose ps says api.db is running (on the right)

Nikhil Singh · Answer 7 · Tue Jun 25 2024 00:04:05 GMT+0800 (China Standard Time)

Hi @flckv, thanks for following up! Would you mind running the network checks I mentioned initially, here in podman? E.g. podman network ls and podman network inspect <network-id>. Another thing you could try is podman exec figura11y_api_1 getent hosts db to see if it's able to resolve the db hostname.

I'm not able to reproduce the issue with podman==5.1.1 and podman-compose==1.0.6. Can you confirm what versions you are using?

flckv · Answer 8 · Tue Jun 25 2024 19:05:03 GMT+0800 (China Standard Time)

Thank you @nikhilsinghmus,

podman-compose ps
podman-compose version: 1.0.6
['podman', '--version', '']
using podman version: 4.5.1

podman network ls

podman network inspect figura11y_default

                "subnet": "10.89.0.0/24",
                "gateway": "10.89.0.1"

podman inspect figura11y_api_1
figura11y_api_1 EXITED (left)
figura11y_api_1 RUNNING for few second (right)

figura11y_api_1 getent hosts db

Nikhil Singh · Answer 9 · Thu Jun 27 2024 06:10:14 GMT+0800 (China Standard Time)

Thank you, @flckv! I tried testing with that version of Podman, but ran into some issues on my machine (though I'll try again). Would you be able to try upgrading and testing with a newer version?

Additionally, one other thing to check might be your installation of netavark (default network stack) and aardvark-dns (DNS server). I think podman-compose will rely on these for name resolution between containers (e.g. db, where the issue seems to be). I'm still getting familiar with the Podman ecosystem, so I appreciate your patience while working through this!

flckv · Answer 10 · Sun Jun 30 2024 19:40:51 GMT+0800 (China Standard Time)

Thank you @nikhilsinghmus,

no ROOT access

sudo apt-get -y install podman
Permission denied

find . -type f -name 'netavark'
find: ‘./opt/TrendMicro’: Permission denied

find . -type f -name 'aardvark-dns'
find: ‘./opt/TrendMicro’: Permission denied

cd /opt/ds_agent/netagent
ls
pattern tm_netagent tm_netagent.version
cat tm_netagent.version
1.0.140-e6154b

I noticed that figura11y_proxy_1 exists immediately:

More:

      "NetworkSettings": {
           "EndpointID": "",
           "Gateway": "",
           "IPAddress": "",
           "IPPrefixLen": 0,
           "IPv6Gateway": "",
           "GlobalIPv6Address": "",
           "GlobalIPv6PrefixLen": 0,
           "MacAddress": "",
           "Bridge": "",
           "SandboxID": "",
           "HairpinMode": false,
           "LinkLocalIPv6Address": "",
           "LinkLocalIPv6PrefixLen": 0,
           "Ports": {
                "80/tcp": null,
                "8080/tcp": [
                     {
                          "HostIp": "",
                          "HostPort": "8080"
                     }
                ]
           },
           "SandboxKey": "",
           "Networks": {
                "figura11y_default": {
                     "EndpointID": "",
                     "Gateway": "",
                     "IPAddress": "",
                     "IPPrefixLen": 0,
                     "IPv6Gateway": "",
                     "GlobalIPv6Address": "",
                     "GlobalIPv6PrefixLen": 0,
                     "MacAddress": "",
                     "NetworkID": "figura11y_default",
                     "DriverOpts": null,
                     "IPAMConfig": null,
                     "Links": null,
                     "Aliases": [
                          "proxy",
                          "4a2e86782c2a"
                     ]
                }
           }
      },

...

       "CreateCommand": [
                "podman",
                "create",
                "--name=figura11y_proxy_1",

               ...

            "figura11y_default",
                "--network-alias",
                "proxy",
                "-p",
                "8080:8080",
                "figura11y_proxy"
           ],
           "Umask": "0022",

I have seen in this video umask being changed from 22
...

          "NetworkMode": "bridge",
           "PortBindings": {
                "8080/tcp": [
                     {
                          "HostIp": "",
                          "HostPort": "8080"
                     }
                ]
           },

right after few second later the figura11y_api_1 exists too

I also noticed that upon command:

podman images

podman inspect <image id>
there the proxy is on port 80 that is less than 1024:

butsonar
exposes ports:
"3000/tcp": {},
"8000/tcp": {},
"8080/tcp": {}

because I added lines:

" Podman can not create containers that bind to ports < 1024." from rootless.md

events {
worker_connections 1024;
}

ports 3000, 8000 and 8080 do not seem to be accessible by proxy only 5432 and 8070 :

How is it possible that the figura11y_db_1 keeps running on port 0.0.0.0:5432->5432/tcp but the error is related to db ?
Is unprivileged ping needed for this project I saw the sonar was using command ping.py?

flckv · Answer 11 · Sun Jul 14 2024 00:26:20 GMT+0800 (China Standard Time)

I have run it on a third computer and I noticed that the very first issue is the api.db is not imported. Then I rerun it in the previous two machines and I noticed that I overlooked that that is the first issue on those machines too.

Do you also see this error log on your end ?

Nikhil Singh · Answer 12 · Sun Jul 14 2024 00:48:58 GMT+0800 (China Standard Time)

Hi @flckv, sorry for the slow response! Re: the api.db issue, I think that's related to the flask-migrate commands in dev.sh/start.sh. I think you may not need them, so if you comment out the lines beginning with flask db, it should avoid that. The flask server and db connection should still run either way though, so I'm not sure it will resolve the main issue!

Did you find that the whole setup runs on the third machine, or are you running into the same issue?