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MIT-LCP
Docker image error: LOG: invalid length of startup packet
Prerequisites
- [X] Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.physionet.org/about/mimic/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
Description
Greetings,
I'm having a little trouble setting up the docker image. I've followed the guide here: https://github.com/MIT-LCP/mimic-code/tree/master/buildmimic/docker
My System:
------------------
System Information
------------------
Operating System: Windows 10 Pro 64-bit (10.0, Build 18363) (18362.19h1_release.190318-1202)
Language: English (Regional Setting: English)
Processor: Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz (4 CPUs), ~2.9GHz
Memory: 16384MB RAM
Available OS Memory: 16080MB RAM
Page File: 14726MB used, 10058MB available
Windows Dir: C:\WINDOWS
My current folder tree at (D:):
.
|-- mimic_code
| |-- benchmark
| |-- buildmimic
| |-- concepts
| |-- notebooks
| |-- tests
| `-- tutorials
|-- mimic_data
| `-- csv
`-- mimic_pgdata
The folder at \mimic-data\csv contains the MIMIC-III .csv.gz data files. The folder mimic_pgdata is empty at the time of running the container. It's empty even after running the container. I assume this is because I do not execute any commands after the container is created.
The command I used (using the Git Bash terminal):
docker run \
--name mimic \
-p 5433:5432 \
-e BUILD_MIMIC=1 \
-e POSTGRES_PASSWORD=postgres \
-e MIMIC_PASSWORD=mimic \
-v //d/mimic_data/csv:/mimic_data \
-v //d/mimic_pgdata:/var/lib/postgresql/data \
-d postgres/mimic
My result from the Docker Dashboard:
PostgreSQL Database directory appears to contain a database; Skipping initialization
2020-02-04 15:23:25.966 UTC [1] LOG: starting PostgreSQL 12.1 (Debian 12.1-1.pgdg100+1) on x86_64-pc-linux-gnu, compiled by gcc (Debian 8.3.0-6) 8.3.0, 64-bit
2020-02-04 15:23:25.974 UTC [1] LOG: listening on IPv4 address "0.0.0.0", port 5432
2020-02-04 15:23:25.974 UTC [1] LOG: listening on IPv6 address "::", port 5432
2020-02-04 15:23:25.995 UTC [1] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
2020-02-04 15:23:26.014 UTC [25] LOG: database system was shut down at 2020-02-04 15:20:26 UTC
2020-02-04 15:23:26.020 UTC [1] LOG: database system is ready to accept connections
2020-02-04 15:23:26.034 UTC [32] LOG: invalid length of startup packet
2020-02-04 15:23:26.086 UTC [33] LOG: invalid length of startup packet
2020-02-04 15:23:27.219 UTC [34] LOG: invalid length of startup packet
2020-02-04 15:23:27.219 UTC [35] LOG: invalid length of startup packet
2020-02-04 15:23:28.257 UTC [36] LOG: invalid length of startup packet
2020-02-04 15:23:28.259 UTC [37] LOG: invalid length of startup packet
2020-02-04 15:23:29.264 UTC [38] LOG: invalid length of startup packet
2020-02-04 15:23:29.269 UTC [39] LOG: invalid length of startup packet
2020-02-04 15:23:29.795 UTC [40] LOG: invalid length of startup packet
2020-02-04 15:23:30.278 UTC [42] LOG: invalid length of startup packet
2020-02-04 15:23:30.278 UTC [41] LOG: invalid length of startup packet
2020-02-04 15:23:30.824 UTC [43] LOG: invalid length of startup packet
2020-02-04 15:23:31.287 UTC [44] LOG: invalid length of startup packet
2020-02-04 15:23:31.292 UTC [45] LOG: invalid length of startup packet
2020-02-04 15:23:31.834 UTC [46] LOG: invalid length of startup packet
2020-02-04 15:23:32.854 UTC [47] LOG: invalid length of startup packet
2020-02-04 15:23:33.863 UTC [48] LOG: invalid length of startup packet
2020-02-04 15:23:34.875 UTC [49] LOG: invalid length of startup packet
The output of docker images:
REPOSITORY TAG IMAGE ID CREATED SIZE
postgres/mimic latest 10d900d346ac 19 minutes ago 440MB
postgres latest cf879a45faaa 2 days ago 394MB
k8s.gcr.io/kube-apiserver v1.15.5 e534b1952a0d 3 months ago 207MB
k8s.gcr.io/kube-controller-manager v1.15.5 1399a72fa1a9 3 months ago 159MB
k8s.gcr.io/kube-proxy v1.15.5 cbd7f21fec99 3 months ago 82.4MB
k8s.gcr.io/kube-scheduler v1.15.5 fab2dded59dd 3 months ago 81.1MB
golang 1.11-alpine e116d2efa2ab 5 months ago 312MB
docker/kube-compose-controller v0.4.23 a8c3d87a58e7 8 months ago 35.3MB
docker/kube-compose-api-server v0.4.23 f3591b2cb223 8 months ago 49.9MB
alpine 3.5 f80194ae2e0c 12 months ago 4MB
k8s.gcr.io/coredns 1.3.1 eb516548c180 12 months ago 40.3MB
k8s.gcr.io/etcd 3.3.10 2c4adeb21b4f 14 months ago 258MB
k8s.gcr.io/pause 3.1 da86e6ba6ca1 2 years ago 742kB
I've tried:
- deleting the image and recreating it again but to no avail.
- different HOST port numbers but I still get the same output.
- using a single slash for addresses in running the container, but it failed despite using the Git Bash terminal.
Honestly not that familiar with Docker - but maybe @xiaosongz or @haobibo could comment since they both have recently been working with the build.
Hi @khalid-hussain , @xiaosongz has found a bug in the docker image build file setup.sh.
And I've created a PR https://github.com/MIT-LCP/mimic-code/pull/693 trying to fix that.
Could you please follow the updated setup.sh (or directly clone it from https://github.com/haobibo/mimic-code) to see if the updated code works or not.
I'm sorry, I got preoccupied with some other issues. I'll give it a try tomorrow. Thanks for the prompt replies.
UPDATE: I'm still having the same problem. I updated the setup.sh and the Dockerfile as well but it still gives me the same ouput.
Someone in the lab may take a look at fixing the the Docker image at some point, but we have limited resources and this is not one of our priorities. We would be happy to review a pull request from the community.
I'm facing same issue?
-03-11 08:31:31.885 UTC [1] LOG: starting PostgreSQL 13.2 (Debian 13.2-1.pgdg100+1) on x86_64-pc-linux-gnu, compiled by gcc (Debian 8.3.0-6) 8.3.0, 64-bit 2021-03-11 08:31:31.885 UTC [1] LOG: listening on IPv4 address "0.0.0.0", port 5432 2021-03-11 08:31:31.885 UTC [1] LOG: listening on IPv6 address "::", port 5432 2021-03-11 08:31:31.899 UTC [1] LOG: listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432" 2021-03-11 08:31:31.914 UTC [66] LOG: database system was shut down at 2021-03-11 08:31:31 UTC 2021-03-11 08:31:31.924 UTC [1] LOG: database system is ready to accept connections 2021-03-11 08:31:51.485 UTC [73] FATAL: password authentication failed for user "pgadmin" 2021-03-11 08:31:51.485 UTC [73] DETAIL: Role "pgadmin" does not exist. Connection matched pg_hba.conf line 99: "host all all all md5" 2021-03-11 08:32:00.969 UTC [74] FATAL: password authentication failed for user "pgadmin" 2021-03-11 08:32:00.969 UTC [74] DETAIL: Role "pgadmin" does not exist. Connection matched pg_hba.conf line 99: "host all all all md5" 2021-03-11 08:32:06.826 UTC [75] FATAL: password authentication failed for user "pgadmin" 2021-03-11 08:32:06.826 UTC [75] DETAIL: Role "pgadmin" does not exist. Connection matched pg_hba.conf line 99: "host all all all md5" 2021-03-11 08:33:38.128 UTC [78] FATAL: password authentication failed for user "pgadmin" 2021-03-11 08:33:38.128 UTC [78] DETAIL: Role "pgadmin" does not exist. Connection matched pg_hba.conf line 99: "host all all all md5" 2021-03-11 08:33:52.780 UTC [79] LOG: invalid length of startup packet 2021-03-11 08:33:52.783 UTC [80] LOG: invalid length of startup packet..........................................
Thanks everyone, we recognize that the issue exists and we would be happy to review a pull request with a fix. No need for +1s at this point.