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Kill the leftover orphan processes in the login nodes

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If users are performing a regular check for orphan processes, then they will need to traverse along all access the login and data-mover nodes individually and check for orphan processes on each of them. Currently there are 4 login nodes available to users going from -01 to -04.

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At any given time, the set of login and data-mover nodes that are accessible may be determined by running the following commands from a terminal session on whichever login or data-mover node you have logged into

username@setonix-06:~> dig @150.229.2.5 setonix.pawsey.org.au

...

  +noall +answer
setonix.pawsey.org.au.  3600    IN      A       146.118.12.26
setonix.pawsey.org.au.  3600    IN      A       146.118.12.27
setonix.pawsey.org.au.  3600    IN      A       146.118.12.22
username@setonix-06:~>
username@setonix-06:~> nslookup 146.118.12.26 150.229.2.5
26.12.118.146.in-addr.arpa      name = setonix-05.pawsey.org.au.
username@setonix-06:~>
username@setonix-06:~> nslookup 146.118.12.27 150.229.2.5
27.12.118.146.in-addr.arpa      name = setonix-06.pawsey.org.au.
username@setonix-06:~>
username@setonix-06:~> nslookup 146.118.12.22 150.229.2.5
22.12.118.146.in-addr.arpa      name = setonix-01.pawsey.org.au.
username@setonix-06:~>

Here, having logged into setonix-06, we obtain the list of IP addresses for the currently accessible login nodes, and then convert those IP addresses back into the individual nodes names.
in this instance, we can see that we should also check for leftover processe on setonix-01 and setonix-05

The following example shows the commands to obtain the list of names for the currently available data-mover nodes, having logged into setonix-dm01

username@setonix-dm01:~> dig @150.229.2.5 data-mover.pawsey.org.au  +noall +answer
data-mover.pawsey.org.au. 3600  IN      A       146.118.74.161
data-mover.pawsey.org.au. 3600  IN      A       146.118.74.160
data-mover.pawsey.org.au. 3600  IN      A       146.118.74.163
data-mover.pawsey.org.au. 3600  IN      A       146.118.74.162
username@setonix-dm01:~>
username@setonix-dm01:~> nslookup 146.118.74.161 150.229.2.5
161.74.118.146.in-addr.arpa      name = setonix-dm02.pawsey.org.au.
username@setonix-dm01:~>
username@setonix-dm01:~> nslookup 146.118.74.160 150.229.2.5
160.74.118.146.in-addr.arpa      name = setonix-dm01.pawsey.org.au.
username@setonix-dm01:~>
username@setonix-dm01:~> nslookup 146.118.74.163 150.229.2.5
163.74.118.146.in-addr.arpa      name = setonix-dm04.pawsey.org.au.
username@setonix-dm01:~>
username@setonix-dm01:~> nslookup 146.118.74.162 150.229.2.5
162.74.118.146.in-addr.arpa      name = setonix-dm03.pawsey.org.au.
username@setonix-dm01:~>

Once the user has logged into the desired login node, execute the ps command together with "filtering" with the grep command acting repeatedly on the output to narrow it down to only those processes owned by the user and related to "vscode":

$ ps -fea | head -n 1 ; ps -fea | grep ${USER} | grep -i "vscode" | grep -v "grep"
matilda | grep -i "vscode" | grep -v "grep"
UID         PID   PPID  C STIME TTY          TIME CMD
matilda  236771      1  0 11:55 ?        00:00:00 sh /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/bin/code-server --start-server --host=127.0.0.1 --accept-server-license-terms --enable-remote-auto-shutdown --port=0 --telemetry-level all --connection-token-file /home/matilda/.vscode-server/.fdb98833154679dbaa7af67a5a29fe19e55c2b73.token
matilda  236784 236771  0 11:55 ?        00:00:02 /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/node /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/out/server-main.js --start-server --host=127.0.0.1 --accept-server-license-terms --enable-remote-auto-shutdown --port=0 --telemetry-level all --connection-token-file /home/matilda/.vscode-server/.fdb98833154679dbaa7af67a5a29fe19e55c2b73.token
matilda  237900 236784 99 11:55 ?        02:37:53 /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/node --dns-result-order=ipv4first /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/out/bootstrap-fork --type=extensionHost --transformURIs --useHostProxy=false
matilda  237945 236784  0 11:55 ?        00:00:00 /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/node /home/matilda/.vscode-server/bin/fdb98833154679dbaa7af67a5a29fe19e55c2b73/out/bootstrap-fork --type=ptyHost --logsPath /home/matilda/.vscode-server/data/logs/20231003T115510

...

 --logsPath /home/matilda/.vscode-server/data/logs/20231003T115510

(Note that the first part of the command above (before the semicolon ";") is to keep displaying the header of the ps command.)

As the user has already disconnected from any VS Code active session, and the "cleaning" connection is being performed outside VS Code, then users can visually confirm that those processes are indeed only the orphan processes of interest, . Now they can proceed to kill them by extending the command to extract a list of the process IDs and passing that list to the kill command:

$ ps -fea | grep ${USER} | grep -i "vscode" | grep -v "grep" | awk '{print $2}' | xargs kill -9

#Confirm that after killing, no vscode process exist:
$ ps -fea | head -n 1 ; ps -fea | grep ${USER} | grep -i "vscode" | grep -v "grep"
UID $

...

        PID   PPID  C STIME TTY          TIME CMD
$

Now that users are taking some time to relief clean the login nodes from their orphan processes then, as recommended above, it is a good idea to go through all the active login nodes and perform a check on all of them (and kill if neededthe orphan processes that are identified).

If you find that after killing orphan processes in all the login nodes is still giving you problems to login using VS code. Then, you may need to purge the Visual Studio Code directory on Setonix using the following:

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# Create the settings.json file

$ touch ~/.vscode-server/data/Machine/settings.json

# add the following information to settings.json with your favourite text editor

"files.watcherExclude": {
  "**/.git/objects/**": true,
  "**/.git/subtree-cache/**": true,     
  "**/node_modules/*/**": true,
  "/usr/local/**": true,
  "/scratch/**": true},

"search.followSymlinks": false,

"search.exclude": {     
  "**/.git/objects/**": true,
  "**/.git/subtree-cache/**": {true,     
  "**/.git/objectsnode_modules/*/**": true,
  "/usr/local/**/.git/subtree-cache/**": true,     
  "**/node_modules/*/**": true,
  "/usr/local/**": true,
  "/scratch/**": true},

Note that we are explicitly telling VS Code not to watch or search in directories named as indicated nor in the whole /scratch file system. And, if you know of some other directory in your files that contain a large number of files and on which you really don't need VS Code to pay attention to its contents and changes, then it is highly recommended to add its name within the settings as "**/knownDirectoryWithLotsOfFiles/**".

Disable TypeScript and JavaScript Language Services

It's also important to disable the TypeScript and JavaScript Language Services. 

1. Hit the extensions button in VS Code (which looks like building blocks on the left toolbar)
2. Search for ‘@builtin TypeScript’.
3. Disable the TypeScript and Javascript Language Features extension
4. Reload

Image Removed

Preventing Visual Studio Code to consume your quota in the $HOME file system

Home is often used by a variety of programs use store configuration files and directories along with some cached information. These directories can contain many files and use up quite a bit of storage. An example is vscode, which stores quite a bit of data within the .vscode-server  directory located in $HOME . This directory can contain upwards of 1000 files and use on the order of 100 MB. This will impact your quota on home. We recommend moving such directories to /software/projects/<project>/<username>  and generating a symbolic link in $HOME.

$ mv .vscode-server $MYSOFTWARE/ # if .vscode_server already exists 
$ mkdir $MYSOFTWARE/.vscode-server # if the directory does not exist yet
$ cd $HOME
$ ln -s $MYSOFTWARE/.vscode-server # generate a symbolic link, make sure you are in $HOME": true,
  "/scratch/**": true},

Note that we are explicitly telling VS Code not to watch or search in directories named as indicated nor in the whole /scratch file system. And, if you know of some other directory in your files that contain a large number of files and on which you really don't need VS Code to pay attention to its contents and changes, then it is highly recommended to add its name within the settings as "**/knownDirectoryWithLotsOfFiles/**".

Disable TypeScript and JavaScript Language Services

It's also important to disable the TypeScript and JavaScript Language Services. 

1. Hit the extensions button in VS Code (which looks like building blocks on the left toolbar)
2. Search for ‘@builtin TypeScript’.
3. Disable the TypeScript and Javascript Language Features extension
4. Reload

Image Added

Preventing Visual Studio Code to consume your quota in the $HOME file system

$ mkdir -p $MYSOFTWARE/fakeHome
$ cp -r $HOME/.vscode-server $MYSOFTWARE/fakeHome   # if .vscode_server dir initially exists in $HOME
$ rm -r $HOME/.vscode-server                        # if .vscode_server dir initially exists in $HOME
$ mkdir -p $MYSOFTWARE/fakeHome/.vscode-server      # if .vscode_server did not initially existed in $HOME
$ ln -s $MYSOFTWARE/fakeHome/.vscode-server $HOME/.vscode-server       # generate a symbolic link

Further explanation of quotas can be found in Pawsey Filesystems and their Use.

Related pages

• Connecting to a Supercomputer
• Login nodes policy
• Pawsey Filesystems and their Use

External links

• Visual Studio Code
• git
• Remote Development using SSH