I have created an API using FLASK which I am trying to deploy on a linux server by creating a systemd service.
I have used direnv to setup input parameters to the app like database connections. Below is what the file looks like :
The uwsgi config is as below :
The systemd file has the following entries:
I get the follwing error in my uwsgi logs whenever I try to reach the service on my browser :
--- no python application found, check your startup logs for errors ---
[pid: 23791|app: -1|req: -1/3] 192.168.9.180 () {44 vars in 719 bytes} [Thu Oct 11 14:35:09 2018] GET / => generated 21 bytes in 0 msecs (HTTP/1.1 500) 2 headers in 83 bytes (1 switches on core 0)
My understanding is the ExecStart command in the systemd file is not able to invoke the direnv set variables , hence i added the ExecStartPre entry but even does not seem to work.
Any hints/ideas are appreciated.
Note: The application is accessible without errors when I run the uwsgi via command line from my python virtual environment :
uwsgi --socket 0.0.0.0:5000 --protocol=http -w app:app
i have a few advises that may help you, probably only the first one is the one you need...
1) Either move all your env variable defined in direnv to the systemd unit as Environment or move them into a special file (similar to the you already have) without the "source activate" line and the export, and then pass that file as EnvironmentFile , this is the doc for that https://www.freedesktop.org/software/systemd/man/systemd.exec.html#Environment
2) Your ExecStartPre does nothing really, even tho you do "cd" into the path, that is lost and is not persistent. you should remove it.
3) By setting your PATH to only that path, you are restricting your self, i would recommend see the value of your current PATH and then set it to that value. but otherwise at least add "/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin". now spoiler alert, you probably dont need to set it.
4) put the socket in /run//socket.socket directory and let systemd manage your /run/<yourapp> with RuntimeDirectory directive.
good luck!
Related
I want to deploy my Node.js application in Pivotal Cloud Foundry using manifest.yml. I need to update the PATH variable of the container before the application starts, to include the path of a directory in my application's src directory. Can this be achieved?
manifest.yml:
---
applications:
- name: node-apollo-graphql-server
command: npm start
instances: 1
memory: 512M
buildpack: dicf_nodejs_buildpack_rc
stack: cflinuxfs3
You cannot do this by setting env variables with cf push -e or the env: block in manifest.yml. If you set path using one of these methods, you'll override path when what you likely want to do is append to it.
To append to $PATH, add a file .profile to the root of your project (directory from which you're running cf push). In that file, put one line export PATH=$PATH:<new loc> where <new loc> is the path you want to append to the $PATH env variable.
The .profile file is sourced before your application starts so you can use this to dynamically set environment variables or apply configuration before your application starts up.
The only caveat is that this happens before your application starts so it blocks the starting of your application. As such, you should avoid running expensive/time-consuming processes here. Otherwise, you will delay the start of your application, or possibly even cause app failures if you exceed the startup timeout (cf push -t).
I have a basic "service unit" file like the following.
[Unit]
Description=Certprovider service
After=network.target
[Service]
Type=simple
Restart=always
RestartSec=5s
ExecStart=/home/mert/certprovider/certprovider
WorkingDirectory=/home/mert
User=root
Group=root
[Install]
WantedBy=multi-user.target
I have the .env file in the root of the project.
CA_DIR_URL=https://acme-v02.api.letsencrypt.org/directory
EMAIL=mertsmsk0#gmail.com
HOST=127.0.0.1
PORT=8557
I load this file with the following lines.
err := godotenv.Load()
if err != nil {
log.Fatalln("Error loading .env file")
}
Service has been working very well but I cannot reach the PORT environment variable. Thus I cannot start the webserver because that port cannot listen. I print all the environment variables that in the .env excluding PORT. I changed its name to APP_PORT but it same thing.
The mystery part is I can reach other variables in the .env file. In addition to that when I add the following line in the unit file, I can reach that variable but I don't understand that why should I add only the PORT variable in the unit file?
[Service]
Environment=PORT=8557
It's happening when I try to run it as a binary file. Because I can reach the variables with the following command.
go run .
If you call Load without any args it will default to loading env in the current path.
Your current path is configured here:
WorkingDirectory=/home/mert
And yet, you say (emphasis added)
I have the .env file in the root of the project.
But that's not the current working directory.
root of the project
That concept is not meaningful to the application runtime. Unlike interpreted languages like, say, PHP, Go compiles to a static binary that is functionally entirely distinct from the set of libraries and sources that define it. In PHP (or python, ruby, etc) those libraries have no other place to be, than the root of some project directory.
In go, that stuff is only relevant for development and testing. The fact that your executable appears to be in your "root of the project" is entirely incidental and completely meaningless.
If you really want to put the runtime configuration in tht particular file, in that particular place, just set that as the working directory:
ExecStart=/home/mert/certprovider/certprovider
WorkingDirectory=/home/mert/certprovider/certprovider
I would put that stuff in /usr/local so I didn't accidentally break my let's encrypt while fiddling with stuff in my home directory - doubly so for let's encrypt because it might take up to 90 days to realize your certs weren't being refreshed. I'd put the config outside of my home directory for the same reason.
Actually, for this case I'd probably put all the config in the unit file. Why not put it there? But of course, that's a matter of opinion. If you really want to use the automatic .env discovery then you should dedicate a directory to containing that hidden file. It doesn't make much sense to put a config specific to one application in ~/.env.
Wherever you put .env, make sure that's your working directory so it will be discovered.
I print all the environment variables that in the .env excluding PORT. I changed its name to APP_PORT but it same thing. [...]
The mystery part is I can reach other variables in the .env file.
Respectfully, that sounds like an assumption on your part. Without evidence to the contrary, it's easy to conclude that you have set defaults for these values or that they're coming from some other source or behavior. That's more parsimonious than concluding the godotenv library read some, but not all, the values from a file.
It's happening when I try to run it as a binary file. Because I can reach the variables with the following command. [go run .]
Go always runs as a binary. go run . simply automatically builds the binary in a temp location and then runs it. Why is it recommended to use `go build` instead of `go run` when running a Go app in production? talks about why go run is often contraindicated on SO.
I've been at it for days but could not solve my problem.
I am running:
mpiexec -hostfile ~/machines -nolocal -pernode mkdir -p $dstpath where $dstpath points to current directory and "machines" is a file containing:
node01
node02
node03
node04
This is the error output:
Failed to parse XML input with the minimalistic parser. If it was not
generated by hwloc, try enabling full XML support with libxml2.
[node01:06177] [[6421,0],0] ORTE_ERROR_LOG: Error in file base/plm_base_launch_support.c at line 891
--------------------------------------------------------------------------
ORTE was unable to reliably start one or more daemons.
This usually is caused by:
* not finding the required libraries and/or binaries on
one or more nodes. Please check your PATH and LD_LIBRARY_PATH
settings, or configure OMPI with --enable-orterun-prefix-by-default
* lack of authority to execute on one or more specified nodes.
Please verify your allocation and authorities.
* the inability to write startup files into /tmp (--tmpdir/orte_tmpdir_base).
Please check with your sys admin to determine the correct location to use.
* compilation of the orted with dynamic libraries when static are required
(e.g., on Cray). Please check your configure cmd line and consider using
one of the contrib/platform definitions for your system type.
* an inability to create a connection back to mpirun due to a
lack of common network interfaces and/or no route found between
them. Please check network connectivity (including firewalls
and network routing requirements).
--------------------------------------------------------------------------
[node01:06177] 1 more process has sent help message help-errmgr-base.txt / failed-daemon-launch
[node01:06177] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Failed to parse XML input with the minimalistic parser. If it was not
generated by hwloc, try enabling full XML support with libxml2.
[node01:06181] [[6417,0],0] ORTE_ERROR_LOG: Error in file base/plm_base_launch_support.c at line 891
I have 4 machines, node01 to node04. In order to log into these 4 nodes, I have to first log in to node00. I am trying to run some distributed graph functions. The graph software is installed in node01 and is supposed to be synchronised to the other nodes using mpiexec.
What I've done:
Made sure all passwordless login are setup, every machine can ssh to any other machine with no issues.
Have a hostfile in the home directory.
echo $PATH gives /home/myhome/bin:/home/myhome/.local/bin:/usr/include/openmpi:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
echo $LD_LIBRARY_PATH gives
/usr/lib/openmpi/lib
This has previously worked before, but it just suddenly started giving these errors. I got my administrator to install fresh machines but it still gave such errors. I've tried doing it one node at a time but it gave the same errors. I'm not entirely familiar with command line at all so please give me some suggestions. I've tried reinstalling OpenMPI from source and from sudo apt-get install openmpi-bin. I'm on Ubuntu 16.04 LTS.
You should focus on fixing:
Failed to parse XML input with the minimalistic parser. If it was not
generated by hwloc, try enabling full XML support with libxml2.
[node01:06177] [[6421,0],0] ORTE_ERROR_LOG: Error in file base/plm_base_launch_support.c at line 891
I recently deployed a node application with Phusion Passenger for nginx, and encountered a pretty quirky error in the process:
My code threw an error from trying to spawn a child_process. I did a bit of debugging and eventually concluded that the problem arose from the $PATH environment variable being undefined in node, and I could solve the problem with a passenger_env_var directive like this (showing an extract of my nginx config):
server {
listen 80;
server_name blargh.com;
root /home/user/blargh.com/build;
passenger_enabled on;
# For some reason $PATH isn't loaded into node, and we can't spawn child processes without it
passenger_env_var PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games;
}
I still haven't figured out what caused this problem though - setting passenger_load_shell_envvars on; didn't help, and the www-data user did have a $PATH envvar defined in the shell. Moreover, other environment variables (like $SHELL) seems to have been loaded by node, adding to the mystery of why $PATH was excluded.
Does anybody know what could cause this problem?
tl;dr
Specify global envvars that you expect to be defined at system boot (like PATH) in /etc/default/nginx. Use something like dotenv properly and write environment specific config for your app in a text file that's not checked in. Environment variables are pretty evil in general.
I felt this one deserved a fairly lengthy answer, since environment variables has caused recurring problems for me during the last couple of months.
Storing your config as environment variables is one of the rules that 12 factor app lays out for writing scalable web applications. They're good because they let you separate your config from your code in a flexible manner. However, a problem with them is that the way we encounter them normally, when we export MYVAR=myvalue or set them in our ~/.pam_environment or ~/.bashrc, the scope of them is our current terminal session.
This causes issues as we start to use solutions like Phusion Passenger to start our apps at system boot - their startup scripts don't care about user shell environments. They also don't care about the global /etc/environment apparently, which is what caused my problems with PATH being undefined.
Phusion Passenger actually has some documentation on making global environment variables persist:
If you installed Nginx through the Debian or Ubuntu packages, then you can define environment variables in /etc/default/nginx. This is a shell script so you must use the export FOO=bar syntax.
So by setting the PATH envvar in /etc/default/nginx, I could solve that issue. But I was still having trouble with the other environment variables - I had to set them in my nginx config to have them passed on to my node app. It was clear to me that this wasn't the right way to do it.
At this point I was already using dotenv, but I had misunderstood its purpose slightly. I had checked in the .env file and thought of it as a way to provide default values for envvars that would be overridden by the environment as needed. This isn't how the authors themselves envisioned this module to be used:
We strongly recommend against committing your .env file to version control. It should only include environment-specific values such as database passwords or API keys.
It started becoming clear to me that people often don't define the envvars for their apps in the actual environment. I found an article by Peter Lyons that suggests storing config in a text file instead of in envvars, and that's when it clicked for me.
My final solution was to uncommit my .env file, and write a specific one for each environment. I left a .env.template in my repo as a reference to what configuration my app expected to be defined at run-time.
I have an arch linux setup and installed neo4j through the arch user repository (yaourt -S neo4j), and I'm able to run the web console fine (sudo neo4j console with seemingly normal output and full functionality), however when trying to start the server (sudo neo4j start), I encounter the following error message:
/usr/share/neo4j/bin/utils: line 345: [: -lt: unary operator expected
Using additional JVM arguments: -server -XX:+DisableExplicitGC -Dorg.neo4j.server.properties=/etc/neo4j/neo4j-server.properties -Djava.util.logging.config.file=/etc/neo4j/logging.properties -Dlog4j.configuration=file:/etc/neo4j/log4j.properties -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled
Starting Neo4j Server...cat: /run/neo4j/neo4j-service.pid: No such file or directory
process []... waiting for server to be ready. Failed to start within 120 seconds.
Neo4j Server may have failed to start, please check the logs.
rm: cannot remove ‘/run/neo4j/neo4j-service.pid’: No such file or directory
There's no delay before the error message is printed, so it seems to be something other than the timeout. I'm quite new to neo4j (I worked through a fair bit of the user manual using the web console, but no development or server config experience), so I'm not really sure what else might be relevant. I tried looking through the utils script and the error appears to be where it attempts to su neo4j, but it also seems to proceed to attempt to start the server. I also tried changing the port it's starting on as in this question, but no change. The only log I can find just has this over and over (with appropriate timestamps):
Oct 15, 2014 1:33:49 AM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO: Initiating Jersey application, version 'Jersey: 1.9 09/02/2011 11:17 AM'
Any help at all would be appreciated!
EDIT:
The line 345 that it's failing on is the end of this snippet:
if [ $UID == 0 ] ; then
OPEN_FILES=`su $NEO4J_USER -c "ulimit -n"`
else
OPEN_FILES=`ulimit -n`
fi
if [ $OPEN_FILES -lt 40000 ]; then
From doing some echo debugging, it seems that su $NEO4J_USER is failing, probably because $NEO4J_USER is set to neo4j, a user that does not exist on my system. I tried setting that to root in one of the config files, but evidently that's not working properly. Arch is a continual learning experience for me, but I've not had to add a new user before to get software working.
The interesting line here is:
/usr/share/neo4j/bin/utils: line 345: [: -lt: unary operator expected
I assume that is caused by a wrong default shell for the neo4j user. What default is currently set for the neo4j system user? Try to switch that to bash. The startup scripts should work nicely with bash.