I tried to execute pbrun using JSch. But it gets into infinite loop. I tried the same program using the JSch site examples to execute the command. I even tried session.setPty(true) before session. connect(). Still, its not working. Please help.
I've found a solution by my own research. We can use pbrun with -c option so that we launch pbrun and get the command output in one shot. In my case, i have passwordless connectivity. So It is like pbrun su - username -c 'command'
From what I read about pbrun, it seems like it starts a new shell (similarly to su).
So if by "inifinite loop" you mean that pbrun never finishes, it is (might be) correct. It never finishes, the same way su never finishes (until you issue an exit command).
Related
I'm using singularity to run python in an environnement deprived of python. I'm also running a mysql instance as explained by the IOWA state university (running an instance of mysql, and closing it when done).
For clarity, I'm using a bash script to open mysql, then do what i have to do (a python script) and close mysql, and it works fine. But Python's only way to stop if an error occured is sys.exit([value]) and this not only stops the python script, but also the bash script that ran it. This makes it impossible for me to manage the errors and close the instance of mysql if the python script exits.
My question is : Is there a way for me to execute a 'singularity instance stop mysql' while being in the python sandbox. Something to tell singularity "hey, this command here must be used on the host !" ?
I keep searching but can't find anything.
I only tried to execute it with subprocess like any other command, but it returned an error message because I don't have this instance inside the python sandbox. I don't even have singularity in this sandbox.
For any clarifications, just ask me, I'm trying to be clear but I'm pretty sure it's not very clear.
Thanks a lot !
Generally speaking, it would be a big security issue if a process could be initiated from inside a container (docker or singularity) but run in the host OS's namespace.
If the bash script is exiting on the python failure, it sounds like you're using set -e or #!/bin/bash -e. This causes the script to abort if any command returns non-zero. It's commonly recommended for safer processing, but can cause problems like this at times. To bypass that for the python step you can modify your script:
# start mysql, do some stuff
set +x # disable abort on non-zero return
python my_script.py
set -x # re-enable abort on non-zero
# shut down mysql, do other stuff
I have a unique problem using jmeter SSH command.
I use this step to run spark jobs.
the problem is that one of the commands not working, to clarify it connects and not get response and just wait and wait for hours, and nothing displayed on screen.
I know how to work with the tool, and this behavior is special for this script alone.
All other script worked, I duplicate one that worked for example
sudo /run_stg.sh this command worked
sudo /run_off2-stg.sh this command not worked
if I run the job manually via jenkins it worked
if I entered to command line and use plik ssh it worked,
the problem is just Jmeter, that is waiting and waiting and I can not understand for what?
the job is about 3 minutes, and I wait for response in Jmeter for 4 hours and nothing Jmeter just waiting.
in the console log I set to trace level and nothing, absolutely no idea how to start handle this issue in Jmeter.
an anyone please assists how to make Jmeter to write what happened?
or just to know if he connect or anything
since this behavior all the test can not be performed
Most probably you are as usual misconfiguring the SSH Command sampler.
The idea is not to run the script per se, you need to delegate the script execution to the Unix Shell, for example Bash this way you will be able to combine several commands together, see the output, amend debugging level, etc.
So I would recommend setting your command to something like /bin/bash -c -x /your/script.sh
Another guess, given you use sudo it might be the case that the sudo command simply waits for the password (which JMeter never provides), if this is the case try amending your script permissions using chmod command and allowing your user its execution without root privileges.
And finally, given you're able to run your command using "plik ssh" (whatever it is) you can run it using OS Process Sampler
More information: How to Run External Commands and Programs Locally and Remotely from JMeter
I just started using fugitive in my workflow... very useful! But I've seem to have run into a weird annoyance that I'm hoping someone might have a solution to:
When I run :Gpush, sometimes control never returns to vi. Vi hangs on the output of git push until I Ctrl+C to kill "it". I've also tried installing vim-dispatch and, within tmux, the result is that the git push pane never closes. This is even more annoying because I've got to switch down to that pane to Ctrl+C it.
Oddly, if I ps, I do not see any git processes running, so I'm not sure what is hanging, exactly... but Ctrl+C does kill "it", whatever "it" is, and control returns to vi.
I've found a closed github issue that mentions similar behavior, but a solution was never posted... it appears the problem eventually just "went away" for the OP, so the issue was closed.
However, a second person replied to the issue some time later saying he was having a similar problem and it seemed to happen when git spawned some kind of "credential cache daemon". I'm not using a credential helper as he is, so that's not my exact issue... but that caused me to notice something else:
I have ssh configured to keep connections open for 5 minutes (ControlPersist 5m in my ~/.ssh/config). If I haven't pushed in a while, git push causes ssh to spawn a process to persist the connection. This triggers the issue. After 5 minutes, ssh exits, which will fix the problem and cause the tmux pane to close. If I do another push while the connection is still open, it works fine.
So, the problem seems to be when git spawns another process. This obviously doesn't cause any issues when I run git on the command-line, so why does it cause an issue here? And what can I do about it? I don't want to disable the ssh persistent connections because that's useful...
For anyone who stumbles upon this in the future, I've come up with a solution for my particular case where the ssh process is hanging vim: I disable the ControlPersist option, but only for git commands run inside vim via fugitive by setting the following option in my .vimrc:
let g:fugitive_git_executable = "env GIT_SSH_COMMAND='ssh -o ControlPersist=no' git"
It's ugly, and I'm sad that I have to disable the persistent connections, but it works.
I'm having a confusing problem running a variety of programs from a tcl script. Here's the story: I have a script (in tcl) which executes plink to establish a remote connection on a Linux computer. I basically use eval for calling plink, sending as parameters some ssh commands and info, and also a bash file to be executed on the Linux computer.
So far, that works fine, or at least it does what I intend it to do. The issue here is that after calling this procedure, my prompt stops working the normal way. I can type, but it doesn't appear on screen unless the command I send is "echo" (without ""). If so, I get the "ECHO is on" message and the prompt continues to work normally.
Does anyone have any idea why this could be happening? I thought about just patch it and add the "echo" command inside my script, but it says that it's an invalid command in this case...
Well, thanks for the help!
I'm trying to restart a custom IRC bot. I tried various commands :
load.php
daemon load.php
daemon load.php &&
But that makes the script execute inside the console (I see all the output) and when I quit the bot quits as well.
The bot author only taught me the IRC commands so I'm a bit lost.
You can install a package called screen. Then, run screen -dm php load.php and resume with screen -dR
This will allow you to run the script in the background, and still be able to use your current SSH terminal. You can also logout and the process will still be running.
Chances are good the shell is sending the HUP signal to all its running children when you log out to indicate that "the line has been hung up" (a plain old telephone system modem reference to a line being "hung up" when disconnected. You know, because you "hang" the handset on the hook...)
The HUP signal will ask all programs to die conveniently.
Try this:
nohup load.php &
The nohup asks for the next program executed to ignore the HUP signal. See signal(7) and the nohup(1) manpages for details. The & asks the shell to execute the program in the background.
Clay's answer of using screen(1) is pretty awesome, definitely look into screen(1) or tmux(1), but I don't think that they are necessary for this problem.
This line might help you
php load.php &