Is it possible to write a bash script that opens a remote node (i.e. through ssh and/or slurm) and starts an interactive session there after running some commands? I'm trying to automate the process of starting a jupyter session on a remote computing cluster, which currently looks like this:
ssh into a login node of the remote cluster, using a specific port
use slurm to request an interactive session on one of the compute nodes, including x11 forwarding through that port
change directory to the working directory
activate conda environment for my project
open jupyter from the command line, specifying the port I used previously
It's a lengthy process, and if I get something wrong at any step I usually have to go back and start from the beginning because the port I'm using is still tied up. So I'm looking for a way I can run a single script (possibly with arguments) from my local machine that jumps through all the hoops to get me a working jupyter session with a link I can paste to my browser.
Like #Diego Torres Milano said, you would need to write a script locally that could do the interactive part, then invoke that via a remote script.
But since your process is interactive, this gets tricky. Luckily, linux has a tool which can easily be installed via a package manager called expect which has the ability to write logic to execute multi-step interactive scripts.
So you would write an expect script which would "expect" certain prompts, then it can read those prompts and use conditional logic respond to those prompts appropriately.
Once you have this written and it works locally, it's just a matter of executing it via ssh from a remote server as:
ssh user#12.34.56.78 /path/to/script.ex
Related
I have a script that I normally launch using the following syntax:
ssh -Yq user#host "xterm -e '. /home/user/bin/prog1 $arg1;prog2'"
(note: I've removed some of the complexities of the command, so please excuse if there are any syntax errors in the ssh command; it should not be relevant to the question)
This launches an xterm window that runs prog1, and after completion runs prog2. prog2 is a console-style program that performs some setup, then several seconds later waits for user input.
Is there a way via bash script (preferably without downloading external packages) that I can send data to prog2 that's running on $host?
I've looked into << and expect, but it's way over my head. My intuition is that there's probably a straightforward way of doing this, but I can't figure out what terms to search for. I also understand that I can remotely send keystrokes to a host using xdotools or something similar, but I'm hesitant to request a new package installation unless I know that's the only reasonable solution.
Thanks!
I am trying to do some work on a remote machine and disconnect without terminating the work. I have tried both nohup and screen, unfortunately it is not working out. After I type exit to logout my work also terminates immediately.
I am trying to run 108 simulations on a remote machine. For that purpose I have written a script named batch.sh which runs one simulation after the other until all 108 are done. The program that actually runs a simulation launches 5 programs in 5 different terminals (using xterm -e). I run batch.sh using:
nohup bash batch.sh &
As long as I am connected everything works just fine. If I disconnect and then reconnect to check whether everything is working as it should...no joy :(
Are there any caveats I am overlooking? Possibly because my program launches other programs in external terminals?
UPDATE
If I use the suggestions of adding -oForwardX11=no to ssh and unset DISPLAY before launching my script I get these errors:
nohup: ignoring input and appending output to nohup.out
In nohup.out I have these messages:
xterm Xt error: Can't open display:
xterm: DISPLAY is not set
Apparently your script/program is trying to launch xterm on its own. These days many systems enable X11 forwarding for their SSH client by default - as a result the DISPLAY variable is set in your shell session but becomes invalid once you disconnect. Therefore, as long as you are connected to the remote system, the xterm processes can access the X server on your local machine through the SSH connection, but die once that connection is severed.
I have occasionally encountered the same issue with Java programs that use e.g. the Java AWT subsystem to generate image files, even when there is no actual graphical window. You should first see if your program will somehow adapt if there is no X server available. One option is to disable X11 forwarding with the -oForwardX11=no option to ssh:
$ ssh -oForwardX11=no user#server.host.name
You could also try unsetting the DISPLAY environment variable before starting your script and see what happens.
However, if your program is launching xterm windows indiscriminately then you'd have to make it e.g. use an output file on the server instead - by modifying it, if necessary. As an added advantage, you would get rid off the network load and timing overhead involved with forwarded X connections.
If you cannot change the way your program works and you do not actually care about the output in those xterm windows, then you could try launching a virtual framebuffer X server on the remote system and have your script use that for xterm.
I am using elastic map reduce from Amazon. I am sshing into hadoop master node and executing a script like.
$EMR_BIN/elastic-mapreduce --jobflow $JOBFLOW --ssh < hivescript.sh . It sshes me into the master node and runs the hive script. The hivescript contains the following lines
hive
add jar joda-time-1.6.jar;
add jar EmrHiveUtils-1.2.jar;
and some commands to create hive tables. The script runs fine and creates the hive tables and everything else, but comes back to the prompt from where I ran the script. How do I leave it sshed into hadoop master node at the hive prompt.
Consider using Expect, then you could do something along these lines and interact at the end:
/usr/bin/expect <<EOF
spawn ssh ... YourHost
expect "password"
send "password\n"
send javastuff
interact
EOF
These are the most common answers I've seen (with the drawbacks I ran into with them):
Use expect
This is probably the most well rounded solution for most people
I cannot control whether expect is installed in my target environments
Just to try this out anyway, I put together a simple expect script to ssh to a remote machine, send a simple command, and turn control over to the user. There was a long delay before the prompt showed up, and after fiddling with it with little success I decided to move on for the time being.
Eventually I came back to this as the final solution after realizing I had violated one of the 3 virtues of a good programmer -- false impatience.
Use screen / tmux to start the shell, then inject commands from an external process.
This works ok, but if the terminal window dies it leaves a screen/tmux instance hanging around. I could certainly try to come up with a way to just re-attach to prior instances or kill them; screen (and probably tmux) can make it die instead of auto-detaching, but I didn't fiddle with it.
If using gnome-terminal, use its -x or --command flag (I'm guessing xterm and others have similar options)
I'll go into more detail on problems I had with this on #4
Make a bash script with #!/bin/bash --init-file as the shebang; this will cause your script to execute, then leave an interactive shell running afterward
This and #3 had issues with some programs that required user interaction before the shell is presented to them. Some programs (like ssh) it worked fine with, others (telnet, vxsim) presented a prompt but no text was passed along to the program; only ctrl characters like ^C.
Do something like this: xterm -e 'commands; here; exec bash'. This will cause it to create an interactive shell after your commands execute.
This is fine as long as the user doesn't attempt to interrupt with ^C before the last command executes.
Currently, the only thing I've found that gives me the behavior I need is to use cmdtool from the OpenWin project.
/usr/openwin/bin/cmdtool -I 'commands; here'
# or
/usr/openwin/bin/cmdtool -I 'commands; here' /bin/bash --norc
The resulting terminal injects the list of commands passed with -I to the program executed (no parms means default shell), so those commands show up in that shell's history.
What I don't like is that the terminal cmdtool provides feels so clunky ... but alas.
I have the current scenario to deal with:
I have to schedule the backup of my company's Linux-based server (under Suse Linux) with ARCServe R15 (installed on Windows 2003R2SP2).
I know I have the ability in my backup software (ARCServe) to add pre/post execution scripts to my backup-jobs.
If failure of the script, ARCServe would be specified NOT to run the backup-job, and if success, specified to be run. I have no problem with this.
The problem is, I want to make a windows script (to be launched by ARCServe) for executing a Linux script on the cluster:
- If this Linux-script fails, I want my windows-script to fail, so my backup job in ARCServe wouldn't run
- If the Linux-script success, I want my windows-script to end normally with error code 0, so my ARCServe job would run normally.
I've tried creating this batch file (let's call it HPC.bat):
echo ON
start /wait "C:\Program Files\PUTTY\plink.exe" -v -l root -i "C:\IST\admin\scripts\HPC\pri.ppk" [cluster_name] /appli/admin/backup_admin
exit %errorlevel%
If I manually launch this .bat by double-clicking on it, or launching it in a command prompt under Windows, it executes normally and then ends.
If I make it being launched by ARCServe, the script seems never to end.
My job stays in "waiting" status, it seems the execution code of the linux script isn't returned to my batch file, and this one doesn't close.
In my mind, what's happening is plink just opens the connection to the Linux, send the sript execution signal, and then close the connection, so the execution code can't be returned to the batch. Am I right ?
Is what I want to do possible or am I trying something impossible to do ?
So, do I have to proceed differently ?
Do I have to use PUTTY or CygWin instead of plink ?
Please, it's giving me headaches ...
If you install Cygwin, you could do it exactly like you can do it on Linux to Linux, i.e. remotely run a command with ssh someuser#remoteserver.com somecommand
This command will return with the same return code on the calling client, as the command exited with on the remote end. If you use SSH shared keys for authentication instead of passwords, it can also be scripted without user interaction.
I'd like to run a test script on dozens of embedded Linux units; in manufacturing the authentication credentials are all the same.
The tests are about an hour, but I'd like each unit to loop continuously (over the weekend say) and report the current iteration of the test (on a per unit basis).
I'm thinking expect might be the way to go (it would certainly help with ssh login), but the online documentation is ... uh ... a bit too distributed for what seems to be a simple exercise.
I'm stuck at the trying to determine how to spawn my embedded tests in parallel. In BASH I'd use the & operator to put the process on the background, but then entering the authentication is a challenge.
Should I use expect or stick with BASH scripting?
What I did:
Using an expect script I placed an SSH authentication file on the DUT. THE DUT's have only a RAM file system to play with so this before the rest of the bash script is run. Then, a simple BASH for loop issues an ssh command inside a for loop to run the tests and put the session on a background thread. Comme ca:
for i in <IP devices to test> ;
do
ssh user#$i "echo - \"IP Address: $i :\" ; test-script" &
done
Voila!
Setup ssh public-key authentication (example: http://www.petefreitag.com/item/532.cfm) with blank public key password, then you can use ssh to run these scripts without entering any authorization credential, thus you can write bash scripts to execute them without user intervention