Mimic-code: Docker image error: LOG: invalid length of startup packet

Created on 4 Feb 2020  ·  23Comments  ·  Source: MIT-LCP/mimic-code

Prerequisites

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:

  1. deleting the image and recreating it again but to no avail.
  2. different HOST port numbers but I still get the same output.
  3. using a single slash for addresses in running the container, but it failed despite using the Git Bash terminal.

Most helpful comment

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.

All 23 comments

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.

Hello, I have also found this problem. Is there any solution now?

+1

The same issue here.

+1

Did anybody has a solution! Same problem with our system.

+1

+1

+1

+1

+1

+1

+1

any solution?

God please help, i've been stuck here for hours

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.

Same issue here

same issue here

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..........................................

Same issue

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