Troubleshooting (AEN 4.1.0) — Anaconda Enterprise 4.4 documentation

Anaconda Enterprise: Documentation

# Troubleshooting (AEN 4.1.0)

## Overview

This is a troubleshooting guide for a Anaconda Enterprise Notebooks deployment.

## Normal Operation

### Server

Anaconda Enterprise Notebooks Server is installed in `/opt/wakari/wakari-server`.

You can get the status of the server processes with:

    # service wakari-server status
    wk-server                        RUNNING    pid 20758, uptime 5 days, 0:30:23
    worker                           RUNNING    pid 20757, uptime 5 days, 0:30:23

or:

    root@server # ps -Hu wakari
      PID TTY          TIME CMD
    20756 ?        00:02:26 .supervisord
    20757 ?        00:05:58   mtq-worker
    20758 ?        00:00:08   wk-server
    20765 ?        00:02:00     wk-server
    20766 ?        00:01:55     wk-server
    20767 ?        00:02:20     wk-server
    20770 ?        00:02:02     wk-server

supervisord | details
--- | ---
description | Manages `wakari-worker` and multiple processes of `wk-server`
user | `wakari`
configuration | `/opt/wakari/wakari-server/etc/supervisord.conf`
log | `/opt/wakari/wakari-server/var/log/supervisord.log`
control | `service wakari-server`
ports | none

wk-server | details
--- | ---
description | Handles user interaction and passing jobs on to the wakari gateway. Access to it is managed by nginx.
user | `wakari`
command | `/opt/wakari/wakari-server/bin/wk-server`
configuration | `/opt/wakari/wakari-server/etc/wakari/`
control | `service wakari-server`
logs | `/opt/wakari/wakari-server/var/log/wakari/server.log`
ports | 5000 (only on localhost)

wakari-worker | details
--- | ---
description | Asynchronously executes tasks from `wk-server`
user | `wakari`
logs | `/opt/wakari/wakari-server/var/log/wakari/worker.log`
control | `service wakari-server`

nginx | details
--- | ---
description | Serves static files and acts as proxy for all other requests which are passed to wk-server process running on port 5000.
user | nginx
configuration | `/etc/nginx/nginx.conf` `/opt/wakari/wakari-server/etc/conf.d/www.enterprise.conf`
logs | `/var/log/nginx/woc.log` `/var/log/nginx/woc-error.log`
control | `service nginx status`
port | 80

Nginx runs at least two processes: - master process running as root user - worker processes running as nginx user

## Gateway

Anaconda Enterprise Notebooks Gateway is installed in `/opt/wakari/wakari-gateway`.

You can get the status of the gateway processes with:

    # service wakari-gateway status
    wk-gateway                       RUNNING    pid 1137, uptime 5 days, 1:59:28

or:

    root@gateway # ps -Hu wakari
      PID TTY          TIME CMD
     1136 ?        00:01:59 .supervisord
     1137 ?        00:00:02   wk-gateway

supervisord | details
--- | ---
description | Manages the `wk-gateway` process.
user | `wakari`
configuration | `/opt/wakari/wakari-gateway/etc/supervisord.conf`
log | `/opt/wakari/wakari-gateway/var/log/supervisord.log`
control | `service wakari-gateway`
ports | none

wakari-gateway | details
--- | ---
description | Passes requests from Anaconda Enterprise Notebooks Server to the Compute Nodes.
user | `wakari`
configuration | `/opt/wakari/wakari-gateway/etc/wakari/wk-gateway-config.json`
logs | `/opt/wakari/wakari-gateway/var/log/wakari/gateway.application.log` `/opt/wakari/wakari-gateway/var/log/wakari/gateway.log`
working dir | `/` (root)
port | 8089 (webcache)

## Compute Node

Anaconda Enterprise Notebooks Compute is installed in `/opt/wakari/wakari-compute`.

You can get the status of the compute node processes with:

    # service wakari-compute status
    wk-compute                       RUNNING    pid 22050, uptime 3 days, 1:03:19

or:

    root@compute # ps -Hu wakari
      PID TTY          TIME CMD
     1150 ?        00:02:01 .supervisord
     1152 ?        00:00:01   wk-compute

wk-compute will load each of these configuration files, in order:

- `/etc/wakari/config.json`
- `/etc/wakari/compute-launcher-config.json`
- `./compute-launcher-config.json`
- Config file specified by `-c` option

If an option is specified in multiple files, the last one encountered takes precedence.

supervisord | details
--- | ---
description | Manages the `wk-compute` process.
user | `wakari`
configuration | `/opt/wakari/wakari-compute/etc/supervisord.conf`
log | `/opt/wakari/wakari-compute/var/log/supervisord.log`
control | `service wakari-compute`
working dir | `/opt/wakari/wakari-compute/etc`
ports | none

wk-compute | details
--- | ---
description | Launches compute processes
user | `wakari`
configuration | `/opt/wakari/wakari-compute/etc/wakari/wk-compute-launcher-config.json` `/opt/wakari/wakari-compute/etc/wakari/scripts/config.json`
logs | `/opt/wakari/wakari-compute/var/log/wakari/compute-launcher.application.log` `/opt/wakari/wakari-compute/var/log/wakari/compute-launcher.log`
working dir | `/` (root)
control | `service wakari-compute`
port | 5002 (rfe)

### Projects and Permissions

Projects live in the projectRoot folder on the compute node (by default, /projects). The project directory is created the first time the project is started; the start-project script clones it from `/opt/wakari/wakari-compute/lib/node_modules/wakari-compute-launcher/skeleton`.

Project directory permissions are as follows:

    owner: rwx, user who created the project
    group: rwx, owner's group
    other: --x, to allow access to the Public folder
    ACL:   rwx for any other team members

Files and subdirectories within the project directory have the same permissions as the project directory, except:

1. The public folder and everything in it are world readable.
2. Any files hardlinked into the root anaconda environment (`/opt/wakari/anaconda`) remain owned by the `root` or `wakari` users.

Project file and directory permissions are maintained by the start-project script. All files and directories in the project will have their permissions set when the project is started, except for files owned by `root` or `wakari` (in order to avoid changing permissions of the linked files in `/opt/wakari/anaconda`). Because of this, the `wakari` user should not create projects that are intended to be shared with others, because the permissions system will not correctly manage project files owned by the `wakari` user.

## General Troubleshooting Steps

### Ensure that the Anaconda Enterprise Notebooks services are set to start at boot

(on all 3 components: Server, Gateway, and Compute nodes)

    chkconfig --list | grep wakari

If they are missing, you can try adding them with:

    chkconfig --add [wakari-server|wakari-gateway|wakari-compute]

Then services can be started safely with the `restart` command as follows:

    service wakari-server restart
    service wakari-gateway restart
    service wakari-compute restart

These commands need to be executed on the appropriate nodes.

### Ensure that all services are running

(see Normal Operation, above).

    # service wakari-server status
    wk-server                        RUNNING    pid 20758, uptime 5 days, 0:30:23
    worker                           RUNNING    pid 20757, uptime 5 days, 0:30:23

    root@server # service nginx status
    nginx (pid  26303) is running...

    # service wakari-gateway status
    wk-gateway                       RUNNING    pid 1137, uptime 5 days, 1:59:28

    # service wakari-compute status
    wk-compute                       RUNNING    pid 22050, uptime 3 days, 1:03:19

If any of the processes are missing, restart them using the commands above.

### Check for Extraneous Processes

Use `ps -Hu wakari` to get a complete list of the processes running under the `wakari` user account.

    root@server # ps -Hu wakari
      PID TTY          TIME CMD
    20756 ?        00:02:26 .supervisord
    20757 ?        00:05:58   mtq-worker
    20758 ?        00:00:08   wk-server
    20765 ?        00:02:00     wk-server
    20766 ?        00:01:55     wk-server
    20767 ?        00:02:20     wk-server
    20770 ?        00:02:02     wk-server

    root@server # ps -f -C nginx
    UID        PID  PPID  C STIME TTY          TIME CMD
    root     26303     1  0 12:18 ?        00:00:00 nginx: master process /usr/sbin/nginx -c /etc/nginx/nginx.conf
    nginx    26305 26303  0 12:18 ?        00:00:00 nginx: worker process

    root@gateway # ps -Hu wakari
      PID TTY          TIME CMD
     1136 ?        00:01:59 .supervisord
     1137 ?        00:00:02   wk-gateway

    root@compute # ps -Hu wakari
      PID TTY          TIME CMD
     1150 ?        00:02:01 .supervisord
     1152 ?        00:00:01   wk-compute

What’s normal:

- The wk-server, wk-gateway, and wk-compute processes should have the PIDs reported by `supervisorctl`.
- The nginx master process should have the PID reported by `service nginx status`.
- If you have installed more than one Anaconda Enterprise Notebooks component on a single machine, the processes from all of the installed components will show up on that machine.
- On the Compute node, any Anaconda Enterprise Notebooks applications currently being run by users will be present. For example:

    root@compute # ps -Hu wakari
      PID TTY          TIME CMD
     1150 ?        00:00:00 .supervisord
     1152 ?        00:00:00   wk-compute
     1340 ?        00:00:00 bash
     1341 ?        00:00:00   notebookwrapper

If extra wk-server, wk-gateway, wk-compute, or supervisord processes are present, use the `kill` command to remove them. Then restart the services using `service SERVICE_NAME restart` as described above.

### Check connectivity between the servers

#### Server to Gateways

On the Server, navigate to Admin/Data Centers. For each data center in the list, check connectivity from the server to that gateway (in this example, the gateway is `http://gateway.example.com:8089`):

    root@server # curl --connect-timeout 5 http://gateway.example.com:8089 > /dev/null

#### Gateways to Compute Nodes

On the Server, navigate to Admin/Enterprise Resources. For each compute resource in the list, open it and check the contents of the URL field to ensure that it begins with either “http” or “https”. Check connectivity to that URL from the corresponding Gateway. For example, if the URL is `http://compute.example.com:5002`:

    root@gateway # curl --connect-timeout 5 http://compute.example.com:5002 > /dev/null

#### Gateways to server

This path is used by the gateway configuration command `wk-gateway-configure`. First, ensure that the gateway is linked to the correct server in the configuration file and that the full server URL is specified. Then check connectivity to the server.

    root@gateway # grep WAKARI_SERVER /opt/wakari/wakari-gateway/etc/wakari/wk-gateway-config.json
      "WAKARI_SERVER": "http://wakari.example.com",

    root@gateway # curl --connect-timeout 5 http://wakari.example.com > /dev/null
    root@gateway # curl --connect-timeout 5 http://error.example.com > /dev/null
    curl: (7) Failed to connect to error.example.com port 80: Connection refused

If a connection fails, check the following items:

- Ensure that Gateways (Data Centers) and Compute nodes (Enterprise Resources) are correctly configured on the server.
- Verify that processes are listening on the configured ports:

    root@server # netstat -plt
    Active Internet connections (only servers)
    Proto Recv-Q Send-Q Local Address               Foreign Address             State       PID/Program name
    tcp        0      0 *:http                      *:*                         LISTEN      26409/nginx
    tcp        0      0 *:ssh                       *:*                         LISTEN      986/sshd
    tcp        0      0 localhost:smtp              *:*                         LISTEN      1063/master
    tcp        0      0 *:commplex-main             *:*                         LISTEN      26192/python
    tcp        0      0 localhost:27017             *:*                         LISTEN      29261/mongod
    tcp        0      0 *:ssh                       *:*                         LISTEN      986/sshd
    tcp        0      0 localhost:smtp              *:*                         LISTEN      1063/master

- Check firewall settings/logs on both hosts to ensure that packets are not being blocked or discarded.

### Check Configuration File Syntax

Use this command to verify that the configuration file contains valid JSON:

    root@server  # python -m json.tool /opt/wakari/wakari-server/etc/wakari/*.json
    root@gateway # python -m json.tool /opt/wakari/wakari-gateway/etc/wakari/*.json
    root@compute # python -m json.tool /opt/wakari/wakari-compute/etc/wakari/*.json

If the file is correct, the contents will be displayed. If there is a syntax error in the file, the message `No JSON object could be decoded` will be displayed instead. Edit the configuration file, ensuring correct JSON syntax.

### Check file ownership

Verify that all files in /opt/wakari/anaconda belong to user/group `wakari`:

    root@server # find /opt/wakari/anaconda \! -user wakari -print
    root@server # find /opt/wakari/anaconda \! -group wakari -print

If any files are listed in the output, fix their ownership:

    chown -R wakari:wakari /opt/wakari/anaconda

### Verify that POSIX ACLs are enabled

The `acl` option must be enabled on the filesystem containing the project root directory.

First, determine the project root directory. If a custom projectRoot is configured, you can determine it with:

    root@compute # grep projectRoot /opt/wakari/wakari-compute/etc/wakari/config.json

If not, the project root is `/projects`.

Either the `mount` options or default options listed by `tune2fs` should indicate the `acl` option is enabled.

    root@compute # fs=`df /projects | tail -1 | cut -d " " -f 1`
    root@compute # mount | grep $fs
    /dev/vda on / type ext4 (rw)
    root@compute # tune2fs -l $fs | grep options
    Default mount options:    user_xattr acl

### Clear Browser Cookies

When the Anaconda Enterprise Notebooks configuration changes, or the software is upgraded, cookies remaining in the browser can cause issues. Clearing cookies and logging in again can help to resolve problems.

## Specific Problems

Problem | Cause | Solution
--- | --- | ---
Browser indicates “too many redirects” | Cookies are out of date | Clear your browser’s cookies and cache, then try again.
supervisorctl error: “unix:////opt/wakari/wakari-server/etc/supervisor.sock no such file” | “supervisord” is not running on the Server | Ensure that supervisord is included in the crontab, as described above. Then start supervisord manually.
Data Center Not Found message when deleting a project | Datacenter has already been removed | As root, run `/opt/wakari/wakari-server/bin/wk-server-admin remove-project --db-only <user> <project>`
Forgotten administrator password |  | Use ssh to log into the server as root, and run the command `/opt/wakari/wakari-server/bin/wk-server-admin add-user wakari --admin -p <new password> -e <your email>`. You can then log into Anaconda Enterprise Notebooks as the `wakari` user with the new password you chose.

## Logs

The default location for the Anaconda Enterprise Notebooks log files is /opt/wakari/install/var/log.

The Anaconda Enterprise Notebooks installers log into /tmp/wakari_{server,gateway,compute}.log.

If log files grow too large they can be deleted. To set the logs to be more or less verbose, the Jupyter Notebook system has a setting ‘Application.log_level’. Setting ‘Application.log_level’ to ‘ERROR’ will make the logs less verbose than the default but still fairly informative.

## Killed supervisord and “Error: This socket is closed.”

When the supervisor daemon “supervisord” is killed, information sent to standard output “stdout” and standard error “stderr” is held in a pipe which eventually fills up. Then attempting to start any app fails with an error message saying “This socket is closed.”

To prevent this problem, always shut down and restart the processes cleanly and do not shut down or kill supervisord without first shutting down wk-compute and other processes that use it.

To recover from this problem, shut down the process “wk-compute” with `sudo kill -9`. Then restart the supervisord and wk-compute processes:

    sudo /etc/init.d/wakari-compute stop
    sudo /etc/init.d/wakari-compute start

## Service Error 502: Can not connect to the application manager

When a gateway node shows this error it means that a compute resource is not responding.

This error is caused when the process “wk-compute” has been shut down. To recover from this problem, restart the supervisord and wk-compute processes:

    sudo /etc/init.d/wakari-compute stop
    sudo /etc/init.d/wakari-compute start

## “502 Communication Error” on Amazon Web Services

If you see a page showing “502 Communication Error: This gateway could not communicate with the Wakari server” and the IP address of the Wakari server, configure the AEN gateway to use the DNS hostname of the server. On Amazon Web Services (AWS) this will be the DNS hostname of the Amazon Elastic Compute Cloud (EC2) instance.