I am executing a code in sever with Docker and jupyter.
I set my container with a feature: restart=always.
But, the jupyter always show a same error: Kernel Restarting, The kernel appears to have died. It will restart automatically.
The code is based on Keras with TensorFlow.
In this way, I need to restart manually it. And I need to execute the code from beginning if I have no save the parameters. And I cann't find the error in time, so it is wasting time.
So, is there any way to set it automatically connect successfully.
Related
I have a NodeJS Express App that depends on MongoDB change streams. For them to be available, MongoDB has to be configured to run as a replica set (even if there is only one node in that set).
I'm working on Windows 10 pro.
I'm trying to dockerize this App, basing the MongoDB container off the official mongo:5 image.
For this to work, I want an automated way of initializing the DB as a replica set. Tutorials I've found rely on either execing into the container and running rs.initiate() from mongosh (or similar approaches), which is manual work I want to avoid. Or they use hacks like wait-for-it.sh as here.
I feel there must be a better solution, based somehow on the paragraph "Initializing a fresh instance", from the docs.
It describes that
When a container is started for the first time it will execute files with extensions .sh and .js that are found in /docker-entrypoint-initdb.d.
When exactly in the container lifecycle does that happen? After the container is initialized? Or after the DB is ready? Because this seems to be the perfect place for this initialization logic, which runs flawlessly when executed manually, from within the container.
However, placing
// initReplSet.js
print('Script running');
config={"_id":"rs0", "members":[{"_id":0,"host":"app-db:27017"}]};
print(JSON.stringify(rs.initiate(config)));
print('Script end');
fails with the error {"ok":0,"errmsg":"No host described in new configuration with {version: 1, term: 0} for replica set rs0 maps to this node","code":93,"codeName":"InvalidReplicaSetConfig"}, yet the database is available under the hostname app-db from other containers. This makes me feel that this code runs too early, before all other initialization logic (networking) is done.
Another approach is to place a bash script that executes code via mongosh. Here's what I've tried:
#!/bin/bash
mongosh "mongodb://app-db:27017/app_db" "initiateReplSet"
where initiateReplSet is
config={"_id":"rs0", "members":[{"_id":0,"host":"app-db:27017"}]}
rs.initiate(config)
exit
but this crashes the container with the error
/usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/initiateReplSetWrapper.sh
{"t":{"$date":"2022-02-15T11:31:23.353+00:00"},"s":"I", "c":"-", "id":4939300, "ctx":"monitoring-keys-for-HMAC","msg":"Failed to refresh key cache","attr":{"error":"NotYetInitialized: Cannot use non-local read concern until replica set is finished initializing.","nextWakeupMillis":600}}
Warning: Could not access file: EACCES: permission denied, mkdir '/home/mongodb'
Current Mongosh Log ID: 620b8f0b04b7ad69b446768d
Connecting to: mongodb://app-db:27017/app_db?directConnection=true&appName=mongosh+1.1.9
Only the first and the last three lines seem to really belong to the bash script, the second line is repeated constantly.
I'm not sure whether the error originates at the permission denied issue, or whether the DB really can't be accessed. However, specifying
RUN mkdir -p /home/mongodb/.mongodb
RUN chown -R 777 /home/mongodb
in the Dockerfile did not improve the situation (same error nevertheless).
Could you please explain either why this approach can not work, or how to make it work? Is there another, better, automated way to initialize the replica set? Could the docker image be improved to allow such initialization logic?
I just made it work with a wild experiment. Means I simply left out the config in my call to rs.initiate(), from the JS script. For some reason, the script then runs successfully and change streams become available to my NodeJS backend.
I will post everything that's needed to run a MongoDB docker with change streams enabled:
# Dockerfile
From mongo
WORKDIR .
COPY initiateReplSet.js ./docker-entrypoint-initdb.d/
CMD ["-replSet", "rs0"]
// initiateReplSet.js
rs.initiate()
The following command doesn't exit on my system:
gcloud compute project-info add-metadata --metadata=itemname=itemvalue
I am using powershell on windows, and I've also tested on a linux container in docker. In both environments, the metadata is updated, but the command never terminates.
If I provide an invalid key, or update to the existing value, I do get the output: No change requested; skipping update for [project]. and the program exits. Performing an actual update produces the hang.
I need this command to terminate so that I can use it in a script. I would like to be able to check the exit code to ensure the update occurred successfully.
You aren't patient enough. In large projects, this operation can take significant time to process. Give the script several minutes to complete.
I have ipython notebook running on a remote server, i.e.
ipython notebook --profile=nbserver
which I access from my local machine. Further, I ssh to the remote server from my machine, and start ipython console (terminal) on that server. I have found following command to work well:
ipython console --existing \
~/.config/ipython/profile_nbserver/security/kernel-*.json
Now I am connected to the same remote kernel from two different clients (lets call them browser and terminal). Everything works well, except one annoying detail:
1) in browser, I type a=1
2) in terminal, I type b=2
3) in both clients I can see both commands using %history. But when I want to cycle through the history (in terminal) using Up, it only shows the commands which have been typed in the terminal, (i.e b=2). Similarly, I am unable to use a + PageDown in the terminal, to go back in history and find the command starting with a.
From what I understand, my two clients are using two separate history files history.sqlite. But why does %history show all commands ?
Question:
Is there any way to configure using one history.sqlite for both clients ?
I find, having easy access to history is absolutely crucial. Moreover, I see using both terminal and browser as complementary, they both have tradeoffs and are best used combined.
You can set where the history gets loaded either by setting it at the terminal:
ipython --HistoryManager.hist_file=$HOME/ipython_hist.sqlite
or within the ipython config files:
import os
c.HistoryManager.hist_file=os.path.expanduser("~/ipython_hist.sqlite")
I am using helios Eclipse for debugging my code in postgresql.
My aim is to know how postgresql uses join algorithms during the join query, so I started to debug nodenestloop.c which is in the Executor folder.
I gave break points in that file, But whenever I try to debug that file, the control goes to main.c and never comes back,How do I constraint the control only to that particular file(nodenestloop.c)
Below are the following fields which I gave in Debug configurations of Helios Eclipse.
C/C++ Application - src/backend/postgres and
project - pgsql
I followed the steps given in the following link for running the program.
https://wiki.postgresql.org/wiki/Working_with_Eclipse#
I even uncheked the field "Start on Start up=main" , but When I do that, The step in and Step over buttons are not activated and the following problem has popped up.
Could not save master table to file '/home/ravi/workspace/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources'.
/home/ravi/workspace/.metadata/.plugins/org.eclipse.core.resources/.safetable/org.eclipse.core.resources (Permission denied)
So I started eclipse using sudo, but this time the following error has come in the console of eclipse.
"root" execution of the PostgreSQL server is not permitted.
The server must be started under an unprivileged user ID to prevent
possible system security compromise. See the documentation for
more information on how to properly start the server.
Could any one help me with this.
Thank you
Problem 1: User ID mismatch
Reading between the lines, it sounds like you're trying to debug a PostgreSQL instance that's running as the postgres user, or a different user ID to your own anyway. Hence your attempt to use sudo.
That's painful, especially when using an IDE like Eclipse. With plain gdb you can just sudo the gdb command to the desired uid, e.g. sudo -u postgres -p 12345 to attach to pid 12345 running as user postgres. This will not work with Eclipse. In fact, running it with sudo has probably left your workspace with some messed up file permissions; run:
sudo chown -R ravi /home/ravi/workspace/
to fix file ownership.
If you want to debug processes under other user IDs with Eclipse, you'll need to figure out how to make Eclipse run gdb with sudo. Do not just run all of Eclipse with sudo.
Problem 2: Trying to run PostgreSQL under the control of Eclipse
This:
"root" execution of the PostgreSQL server is not permitted. The server must be started under an unprivileged user ID to prevent possible system security compromise. See the documentation for more information on how to properly start the server.
suggests that you're also attempting to let Eclipse start postgres directly. That's very useful if you're trying to debug the postmaster, but since you're talking about the query planner it's clear you want to debug a particular backend. Launching the postmaster under Eclipse is useless for that, you'll be attached to the wrong process.
I think you probably need to read the documentation on PostgreSQL's internals:
Tour of PostgreSQL Internals
PostgreSQL internals through pictures
Documentation chapter - internals
Doing it right
Here's what you need to do - rough outline, since I've only used Eclipse for Java development and do my C development with vim and gdb:
Compile a debug build of PostgreSQL (compiled with ./configure --enable-debug and preferably also CFLAGS="-ggdb -Og -fno-omit-frame-pointer"). Specify a --prefix within your homedir, like --prefix=$HOME/postgres-debug
Put your debug build's bin directory first on your PATH, e.g. export PATH=$HOME/postgres-debug/bin:$PATH
initdb -U postgres -D $HOME/postgres-debug-data a new instance of PostgreSQL from your debug build
Start the new instance with PGPORT=5599 pg_ctl -D $HOME/postgres-debug-data -l $HOME/postgres-debug-data.log -w start
Connect with PGPORT=5599 psql postgres
Do whatever setup you need to do
Get the backend process ID with SELECT pg_backend_pid() in a psql session. Leave that session open; it's the one you'll be debugging.
Attach Eclipse's debugger to that process ID, using the Eclipse project that contains the PostgreSQL extension source code you're debugging. Make sure Eclipse is configured so it can find the PostgreSQL source code you compiled with too (no idea how to do that, see the manual).
Set any desired breakpoints and resume execution
In the psql session, do whatever you need to do to make your extension run and hit the breakpoint
When execution pauses at the breakpoint in Eclipse, debug as desired.
Basic misunderstandings?
Also, in case you're really confused about how all this works: PostgreSQL is a client/server application. If you are attempting to debug a client program that uses libpq or odbc, and expecting a breakpoint to trigger in some PostgreSQL backend extension code, that is not going to happen. The client application communicates with PostgreSQL over a TCP/IP socket. It's a separate program. gdb cannot set breakpoints in the PostgreSQL server when it's connected to the client, because they are separate programs. If you want to debug the server, you have to attach gdb to the server. PostgreSQL uses one process per connection, so you have to attach gdb to the correct server process. Which is why I said to use SELECT pg_backend_pid() above, and attach to the process ID.
See the internals documentation linked above, and:
PostgreSQL site - coding
PostgreSQL wiki - developer resources
Developer FAQ
Attaching gdb to a backend on linux/bsd/unix
I also faced similar issue and resolved it after some struggle
I misunderstood the following point under Debugging with child processes in the wiki (https://wiki.postgresql.org/wiki/Working_with_Eclipse).
5."Start postmaster & one instant of postgresql client (for creating one new postgres)"
The above step should be performed from terminal by starting postgres server and one client.
Hope this helps
Once this is done then debugger in eclipse needs to be started for C/C++ Attach to Application
I have a web app that uses postgresql 9.0 with some plperl functions that call custom libraries of mine. So, when I want to start fresh as if just released, my build process for my development area does basically this:
dumps data and roles from production
drops dev data and roles
restores production data and roles onto dev
restarts postgresql so that any cached versions of my custom libraries are flushed and newly-changed ones will be picked up
applies my dev delta
vacuums
Since switching my app's stack from win32 to CentOS, I now sometimes (i.e., it seems, only if and only if I haven't run this build process in "a while"--perhaps at least a day) get an error when my build script tries to apply the delta:
psql: could not connect to server: No such file or directory
Is the server running locally and accepting connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
Specifically, what's failing to execute at the shell level is this:
psql --host=$host -U $superuser -p $port -d $db -f "$delta_filename.sql"
If, immediately after seeing this error, I try to connect to the dev database with psql, I can do so with no trouble. Also, if I just re-run the build script, it works fine the second time, every time I've encountered this. Acceptable workaround, but is the underlying cause something to be concerned about?
So far in my attempts to debug this, I inserted a step just after the server restart (which of course reports OK shutdown, OK startup) whereby I check the results of service postgresql-dev status in a loop, waiting 2 seconds between tries if it fails. On my latest build script run, said loop succeeds on the first try--status returns "is running"--but then applying the delta still fails with the above connection error. Again, second try succeeds, as does connecting via psql outside the script just after it fails.
My next debug attempt was to sleep for 5 seconds before the first status check and see what happens. So far this seems to solve the problem.
So why is pgsql not listening on the socket after it starts [OK] and also has status running ok, for up to 5 seconds, unless it has "recently" been restarted?
The status check only checks whether the process is running. It doesn't check whether you can connect. There can be any amount of time between starting the process and the process being ready to accept connections. It's usually a few seconds, but it could be longer. If you need to cope with this, you need to script it so that it checks whether it is possible to connect before proceeding. You could argue that the CentOS package should do this for you, but it doesn't.
Actually, I think in your case there is no reason to do a full restart. Unless you are loading libraries with shared_preload_libraries, it is sufficient to restart the connection to pick up new libraries.