I am trying to launch shiny application on server. I just followed instruction from Administering guide:
mkdir ~/ShinyApps
sudo cp -R /opt/shiny-server/samples/sample-apps/hello ~/ShinyApps/
Then tried to access the hello application through http://<server-address>:3838/<your_username>/hello But it shows this page can't be displayed error. Anyone has any idea about what can cause this problem? Thanks!
Cont.
Thanks Jeff, I used the exact same part in guide.
Here is the shiny-server.conf file:
server {
listen 3838;
# Define a location at the base URL
location /users {
#this is set up so that I can run apps sithout sudo
run_as :HOME_USER:
user_dirs;
}
location /apps {
run_as shiny;
# Host the directory of Shiny Apps stored in this directory
site_dir /srv/shiny-server;
# Log all Shiny output to files in this directory
log_dir /var/log/shiny-server;
# When a user visits the base URL rather than a particular application,
# an index of the applications available in this directory will be shown.
directory_index on;
}
}
shiny-server.log shows lots of error:
[32m[2014-04-28 11:04:42.871] [INFO] shiny-server - [39mShiny Server v1.1.0.10000 (Node.js v0.10.21)
[32m[2014-04-28 11:04:42.875] [INFO] shiny-server - [39mUsing pidfile /var/run/shiny-server.pid
[32m[2014-04-28 11:04:42.877] [INFO] shiny-server - [39mUsing config file "/etc/shiny-server/shiny-server.conf"
[33m[2014-04-28 11:04:42.973] [WARN] shiny-server - [39mRunning as root unnecessarily is a security risk! You could be running more securely as non-root.
[31m[2014-04-28 11:04:42.217] [ERROR] shiny-server - [39mError loading config: location directive must contain (or inherit) one of site_dir, user_apps, app_dir, or redirect (/etc/shiny-server/shiny-server.conf:10:3)
[32m[2014-04-28 11:04:42.218] [INFO] shiny-server - [39mShutting down worker processes
How can I fix those those error?
I assume you got that command from this portion of the guide? If so, did you also use the deploy-example script to change your configuration file? Did you get any errors when you ran that script?
Alternatively, edit your question to include your configuration file at /etc/shiny-server/shiny-server.conf and we'll be able to see if your server is properly configured to use user_dirs which would be needed for users to be able to host their own applications.
Also check for (and/or edit your question to include) any recent entries in the server's log at /var/log/shiny-server.log.
Try the URL http://<server-address>:4949/sample-apps/.
If not 4949, try 3838.
The reason is whether the port 3838 is open. If it's not open, maybe you should run the following directives in your server:
iptables -I INPUT -p tcp --dport 3838 -j ACCEPT
iptables -I INPUT -p gre -j ACCEPT
Related
I am trying to setup R Shiny Server on my Amazon Linux AWS EC2 instance and am getting the following error:
An error has occurred
The application failed to start.
The application exited during initialization.
I did a sudo shiny-server to see what happens and see the error EADDRINUSE:
$ sudo shiny-server
[2017-01-29 13:21:22.724] [INFO] shiny-server - Shiny Server v1.5.1.834 (Node.js v6.9.1)
[2017-01-29 13:21:22.728] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2017-01-29 13:21:22.764] [INFO] shiny-server - Starting listener on 0.0.0.0:80
[2017-01-29 13:21:22.771] [ERROR] shiny-server - HTTP server error (0.0.0.0:80): listen EADDRINUSE 0.0.0.0:80
[2017-01-29 13:21:22.771] [INFO] shiny-server - Shutting down worker processes
I have verified that Shiny, rmarkdown and, Shiny Server and R are properly installed on my instance:
R --version
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.
> library(shiny)
> library(rmarkdown)
>
I have also checked the network connection on my ec2 instance:
$ sudo netstat --tcp -nlpa | grep 80
tcp 0 0 0.0.0.0:80 0.0.0.0:* LISTEN 1875/shiny-server
My ec2 instance network security group:
$ aws ec2 describe-security-groups --group-name launch-wizard-7
{
"SecurityGroups": [
{
"IpPermissionsEgress": [
{
"IpProtocol": "-1",
"PrefixListIds": [],
"IpRanges": [
{
"CidrIp": "0.0.0.0/0"
}
],
"UserIdGroupPairs": [],
"Ipv6Ranges": []
}
],
"Description": "launch-wizard-7 created 2017-01-28T14:22:51.817-05:00",
"IpPermissions": [
{
"PrefixListIds": [],
"FromPort": 80,
"IpRanges": [
{
"CidrIp": "0.0.0.0/0"
}
],
"ToPort": 80,
"IpProtocol": "tcp",
"UserIdGroupPairs": [],
"Ipv6Ranges": []
},
(there's another entry but that ssh into my own machine so I won't put that information)
and here is my shiny-server.conf file from /etc/shiny-server/shiny-server.conf
$ cat /etc/shiny-server/shiny-server.conf
# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;
# Define a server that listens on port 3838
server {
listen 3838;
# Define a location at the base URL
location / {
# Host the directory of Shiny Apps stored in this directory
site_dir /srv/shiny-server;
# Log all Shiny output to files in this directory
log_dir /var/log/shiny-server;
# When a user visits the base URL rather than a particular application,
# an index of the applications available in this directory will be shown.
directory_index on;
}
}
Any help would be really appreciated. I tried to let AWS listen to request for port 80 for all ip addresses and for the shiny-server as I thought maybe both services shouldn't be listening to the same port but that didn't work. Am just trying to deploy the sample-app that came with shiny server.
url: http://34.198.107.126/sample-apps/hello/
nevermind, figured out what it was; everything was setup properly but my r packages were not installed as root but as ec2-user; installing as root worked as the webpages/folders permissions are mostly root.
I had the same error because the port was already in use (a crashed process could be hogging the port, or a legitimate program could be using it).
A simple solution could be to try on another port. Otherwise try some/all of the following:
To check to see if any process is using the port you're trying to use (change 3838 to the port you're interested in):
netstat -an | grep 3838
tcp46 0 0 *.3838 *.* LISTEN
If you see something there, you know the port is in use (a port that isn't in use won't return any result).
To see what process is using port 3838:
lsof -i tcp:3838
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
com.docke 23298 st 115u IPv6 0xfa130c123d3bd073 0t0 TCP *:sos (LISTEN)
If you're happy to kill the process (use the process ID found above):
kill -9 23298
After this the shiny app worked as expected.
I have an Nginx service that's configured to start automatically on my Windows 10; however, this morning, the service wouldn't start.
The error log says: nginx: [alert] could not open error log file: CreateFile() "C:\someForlderName\build\distribution\.\nginx/logs/error.log" failed (3: The system cannot find the path specified)
Looking at the path in the error log above, I do NOT have the /logs/ folder on my local system so it looks like Nginx doesn't have the proper permissions to create that folder?
I'm setup as an admin user and my service is set to Log On As - Local System Account
This only happens on Windows 10; but the service starts and works on
older Windows i.e 8.1
So does anyone know how to grant administrator's permissions to Nginx so that Nginx can create folders and files on Windows 10 ?
You need:
To install nginx/Windows, download the latest mainline version distribution (1.13.8), since the mainline branch of nginx contains all known fixes. Then unpack the distribution, go to the nginx-1.13.8 directory, and run nginx. Here is an example for the drive C: root directory: (Run cmd as administrator)
cd c:\
unzip nginx-1.13.8.zip
cd nginx-1.13.8
start nginx
Go to: http://localhost:80 -> test install
Goback to console cmd: "nginx -s stop"
Run for next time:
Config with file: "C:\nginx-1.13.8\conf\nginx.conf"
Open cmd as administrator
Run bash: "cd C:\nginx-1.13.8"
Run nginx with bash: "start nginx" . If you run with bash: "nginx", will get trouble for exit nginx.
And
nginx -s stop #fast shutdown
nginx -s quit #graceful shutdown
nginx -s reload #changing configuration, starting new worker processes with a new configuration, graceful shutdown of old worker processes
nginx -s reopen #re-opening log files
Under the directory that you run nginx.exe, try to create a directory named logs, and a file named error.log under log.
It should pass this error.
After downloading zip file, you have unzip.
Make sure that you dont have nested folder names. You have to copy your folder which has nginx.exe file in it, and paste it into C:/ folder.
While running commands, like nginx -s stop, make sure that current your working directory is same as the nginx.exe file.
enter image description here
Nginx start on default port 80, not 8080. Try localhost:80 on browser.
If you want to change port, open C:\nginx-1.16.1\conf\nginx.conf with text editor.
change port number what you want use default port.
server {
listen 80;
server_name localhost;
to:
server {
listen 8080;
server_name localhost;
I had a similar issue with starting the nginx server, but after looking at it closely and trying to run the command in different consoles, I realized it just a simple issue of a missing path.
How I solved it was to cd into the containing folder for the nginx.exe file (which actually contains error logs and all the necessary files) and then run the nginx command which started the server and fixed it for me.
I have installed the shiny server on another ubuntu ip and using it through putty on windows. But the application is failing to start as you can see on the right column (An error has occured in bold). What configuration should I make to start the application on the shiny server? Please help.
I have opened the whole path to the R file in linux and the permissions are granted to the R file. Still not working.
Moreover, when I try to open the shiny-server.config file in etc/shiny-server/shiny-server.config , it shows:
[2015-08-19 12:13:59.666] [INFO] shiny-server - Shiny Server v1.4.0.721 (Node.js v0.10.21)
[2015-08-19 12:13:59.669] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2015-08-19 12:13:59.750] [ERROR] shiny-server - Error loading config: The user 'hadoop' does not have permissions to run applications as one of the users in 'shiny'. Please restart shiny-server as one of the users in 'shiny'. (/etc/shiny-server/shiny-server.conf:2:1)
[2015-08-19 12:13:59.751] [INFO] shiny-server - Shutting down worker processes
The line Error loading config: The user 'hadoop' does not have permissions to run applications as one of the users in 'shiny'. Please restart shiny-server as one of the users in 'shiny'. (/etc/shiny-server/shiny-server.conf:2:1)
says that you are trying to start shiny-server as a user named hadoop and this is not possible because the only user who can start this shiny-server is shiny and this is written in the second line of /etc/shiny-server/shiny-server.conf file. Try to edit beggining of this file from
# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;
to
# Instruct Shiny Server to run applications as the user "shiny"
run_as hadoop shiny;
I am getting this error in my nginx-error.log file:
2014/02/17 03:42:20 [crit] 5455#0: *1 connect() to unix:/tmp/uwsgi.sock failed (13: Permission denied) while connecting to upstream, client: xx.xx.x.xxx, server: localhost, request: "GET /users HTTP/1.1", upstream: "uwsgi://unix:/tmp/uwsgi.sock:", host: "EC2.amazonaws.com"
The browser also shows a 502 Bad Gateway Error. The output of a curl is the same, Bad Gateway html
I've tried to fix it by changing permissions for /tmp/uwsgi.sock to 777. That didn't work. I also added myself to the www-data group (a couple questions that looked similar suggested that). Also, no dice.
Here is my nginx.conf file:
nginx.conf
worker_processes 1;
worker_rlimit_nofile 8192;
events {
worker_connections 3000;
}
error_log /var/log/nginx/error.log warn;
pid /var/run/nginx.pid;
http {
include /etc/nginx/mime.types;
default_type application/octet-stream;
log_format main '$remote_addr - $remote_user [$time_local] "$request" '
'$status $body_bytes_sent "$http_referer" '
'"$http_user_agent" "$http_x_forwarded_for"';
access_log /var/log/nginx/access.log main;
sendfile on;
#tcp_nopush on;
keepalive_timeout 65;
#gzip on;
include /etc/nginx/conf.d/*.conf;
include /etc/nginx/sites-enabled/*;
}
I am running a Flask application with Nginsx and Uwsgi, just to be thorough in my explanation. If anyone has any ideas, I would really appreciate them.
EDIT
I have been asked to provide my uwsgi config file. So, I never personally wrote my nginx or my uwsgi file. I followed the guide here which sets everything up using ansible-playbook. The nginx.conf file was generated automatically, but there was nothing in /etc/uwsgi except a README file in both apps-enabled and apps-available folders. Do I need to create my own config file for uwsgi? I was under the impression that ansible took care of all of those things.
I believe that ansible-playbook figured out my uwsgi configuration since when I run this command
uwsgi -s /tmp/uwsgi.sock -w my_app:app
it starts up and outputs this:
*** Starting uWSGI 2.0.1 (64bit) on [Mon Feb 17 20:03:08 2014] ***
compiled with version: 4.7.3 on 10 February 2014 18:26:16
os: Linux-3.11.0-15-generic #25-Ubuntu SMP Thu Jan 30 17:22:01 UTC 2014
nodename: ip-10-9-xxx-xxx
machine: x86_64
clock source: unix
detected number of CPU cores: 1
current working directory: /home/username/Project
detected binary path: /usr/local/bin/uwsgi
!!! no internal routing support, rebuild with pcre support !!!
*** WARNING: you are running uWSGI without its master process manager ***
your processes number limit is 4548
your memory page size is 4096 bytes
detected max file descriptor number: 1024
lock engine: pthread robust mutexes
thunder lock: disabled (you can enable it with --thunder-lock)
uwsgi socket 0 bound to UNIX address /tmp/uwsgi.sock fd 3
Python version: 2.7.5+ (default, Sep 19 2013, 13:52:09) [GCC 4.8.1]
*** Python threads support is disabled. You can enable it with --enable-threads ***
Python main interpreter initialized at 0x1f60260
your server socket listen backlog is limited to 100 connections
your mercy for graceful operations on workers is 60 seconds
mapped 72760 bytes (71 KB) for 1 cores
*** Operational MODE: single process ***
WSGI app 0 (mountpoint='') ready in 3 seconds on interpreter 0x1f60260 pid: 26790 (default app)
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI worker 1 (and the only) (pid: 26790, cores: 1)
The permission issue occurs because uwsgi resets the ownership and permissions of /tmp/uwsgi.sock to 755 and the user running uwsgi every time uwsgi starts.
The correct way to solve the problem is to make uwsgi change the ownership and/or permission of /tmp/uwsgi.sock such that nginx can write to this socket. Therefore, there are three possible solutions.
Run uwsgi as the www-data user so that this user owns the socket file created by it.
uwsgi -s /tmp/uwsgi.sock -w my_app:app --uid www-data --gid www-data
Change the ownership of the socket file so that www-data owns it.
uwsgi -s /tmp/uwsgi.sock -w my_app:app --chown-socket=www-data:www-data
Change the permissions of the socket file, so that www-data can write to it.
uwsgi -s /tmp/uwsgi.sock -w my_app:app --chmod-socket=666
I prefer the first approach because it does not leave uwsgi running as root.
The first two commands need to be run as root user. The third command does not need to be run as root user.
The first command leaves uwsgi running as www-data user. The second and third commands leave uwsgi running as the actual user that ran the command.
The first and second command allow only www-data user to write to the socket. The third command allows any user to write to the socket.
I prefer the first approach because it does not leave uwsgi running as root user and it does not make the socket file world-writeable .
While the accepted solution is true there might also SELinux be blocking the access. If you did set the permissions correctly and still get permission denied messages try:
sudo setenforce Permissive
If it works then SELinux was at fault - or rather was working as expected! To add the permissions needed to nginx do:
# to see what permissions are needed.
sudo grep nginx /var/log/audit/audit.log | audit2allow
# to create a nginx.pp policy file
sudo grep nginx /var/log/audit/audit.log | audit2allow -M nginx
# to apply the new policy
sudo semodule -i nginx.pp
After that reset the SELinux Policy to Enforcing with:
sudo setenforce Enforcing
Anyone who lands here from the Googles and is trying to run Flask on AWS using the default Ubuntu image after installing nginx and still can't figure out what the problem is:
Nginx runs as user "www-data" by default, but the most common Flask WSGI tutorial from Digital Ocean has you use the logged in user for the systemd service file. Change the user that nginx is running as from "www-data" (which is the default) to "ubuntu" in /etc/nginx/nginx.conf if your Flask/wsgi user is "ubuntu" and everything will start working. You can do this with one line in a script:
sudo sed -i 's/user www-data;/user ubuntu;/' /etc/nginx/nginx.conf
Trying to make Flask and uwsgi run as www-data did not work off the bat, but making nginx run as ubuntu worked just fine since all I'm running with this instance is Flask anyhow.
You have to set these permissions (chmod/chown) in uWSGI configuration.
It is the chmod-socket and the chown-socket.
http://uwsgi-docs.readthedocs.org/en/latest/Options.html#chmod-socket
http://uwsgi-docs.readthedocs.org/en/latest/Options.html#chown-socket
Nginx connect to .sock failed (13:Permission denied) - 502 bad gateway
change the name of the user on the first line in /etc/nginx/nginx.conf file.
the default user is www-data and change it to root or your username
I know it's too late, but it might helps to other. I'll suggest to follow Running flask with virtualenv, uwsgi, and nginx very simple and sweet documentation.
Must activate your environment if you run your project in virtualenv.
here is the yolo.py
from config import application
if __name__ == "__main__":
application.run(host='127.0.0.1')
And create uwsgi.sock file in /tmp/ directory and leave it blank.
As #susanpal answer said "The permission issue occurs because uwsgi resets the ownership and permissions of /tmp/uwsgi.sock to 755 and the user running uwsgi every time uwsgi starts." it is correct.
So you have to give permission to sock file whenever uwsgi starts.
so now follow the below command
uwsgi -s /tmp/uwsgi.sock -w yolo:application -H /var/www/yolo/env --chmod-socket=666
A little different command from #susanpal.
And for persist connection, simply add "&" end of command
uwsgi -s /tmp/uwsgi.sock -w yolo:app -H /var/www/yolo/env --chmod-socket=666 &
In my case changing some php permission do the trick
sudo chown user:group -R /run/php
I hope this helps someone.
You should post both nginx and uwsgi configuration file for your application (the ones in /etc/nginx/sites-enabled/ and /etc/uwsgi/ - or wherever you put them).
Typically check that you have a line similar to the following one in your nginx app configuration:
uwsgi_pass unix:///tmp/uwsgi.sock;
and the same socket name in your uwsgi config file:
socket=/tmp/uwsgi.sock
I noticed when I test my nginx config using nginx -t, it gives me a warning:
nginx: [alert] could not open error log file: open() "/var/logs/nginx/error.log" failed (2: No such file or directory)
Which makes sense, since the log path for nginx is actually set up to be /var/log/nginx/ not /var/logs/nginx.
I scanned the entire nginx config directory and there is nothing there referencing /var/logs. I'm at a loss as to where this log location could be written?
Run this command in a terminal (note: capital V):
nginx -V
Do you find /var/logs there? Your nginx might be compiled with that default file location.
[EDIT]
I guess that some of your server blocks don't have the "error_log" directive. So nginx tries the default one for them. Note that by default the error_log is always on.
To fix this issue, you can add this line on the main block (the top level) such that all child blocks can inherit the setting:
error_log /var/log/nginx/error.log;
You can create these missed files:
cd /var/log/nginx/
sudo touch error.log
sudo touch access.log
sudo chmod 750 *.log
Then trigger nginx service:
sudo systemctl daemon-relod
sudo service nginx restart
[NOTE]:
You can also disable nginx logging:
disable nginx logging (1)
disable nginx logging (2)
You have a bad compiled default. Anything nginx notices before loading the config goes to the path for the error log defined at compile time. Recompile nginx with sane path or symlink log to logs if you can't.