I've just executed a script on a server and forgot to enable the logging of the output.
is it possible to record everything since i started the session after the script has finised executing? (baring in mind this script takes several hours to run)
Related
I've been trying to terminate my scripts but I've found that I usually lose these logs and I don't know why. Specifically they are the .xml, .log, and .report files that are produced after the running of a script. Is there someway I can ensure that the logs aren't deleted?
Looks like you are pressing CTRL+C Twice, making it force exit from test run. If you press once, it will create logs.
I'm executing a batch file inside an R script. I'd like to run this and another large section of the R script twice using a foreach loop.
foreach (i=1:2, .combine = rbind)%do%{
shell.exec("\\\\network\\path\\to\\batch\\script.ext")
*rest of the R script*
}
One silly problem though is that this batch file generates data and that data is connected to SQL Server localdb inside the loop. I thought at first that the script would execute the batch file, wait for it to finish and then move on. However, (seems obvious in hindsight) the script instead executes the batch file, tries to grab data that hasn't been created yet (because the file isn't finished running) and the executes the batch file again before it finishes the first time.
I've been trying to find away to delay the rest of the script from executing until the batch script has finished executing but have not come up with anything yet. I'd appreciate any insights anyone has.
Use system2 instead of shell.exe. system2 calls are blocking — meaning, the function waits until the external program has finished running. On most systems, this can be used directly to run scripts. On Windows, you may have to invoke rundll32 to execute a script:
cmd = c('rundll32.exe', 'Shell32.dll,ShellExecute', 'NULL', 'open', scriptpath)
system2(paste(shQuote(cmd), collapse = ' '))
Windows users may use shell, which by default has wait=TRUE, which will cause R to wait for its completion. You may choose whether or not to directly "intern" the result.
On unix-like systems, use system, which also defaults to wait=TRUE.
If your batch file simply launches another process and terminates, then it may need to be modified to either wait for completion or return a suitable process or file indicator that can be monitored.
I am calling child process from a process in Powershell.
The child process will not end, it will be running continuously in the background.
I need the logs entered by the child process continuously.
process.standardoutput.rradtoend() will enter the logs into file when the child process ends.
But i need the logs continuously.
Please help me in this regard.
You can redirect the log to files as below:
start-process your_executable -ArgumentList "your arguments" -RedirectStandardOutput the_path_you_want_to_put_your_log -RedirectStandardError the_path_to_put_error_log
the logs of the child process will be written to the log files continuously, you can open the files to check them from time to time.
Edit
And I think Unix tail equivalent command in windows Powershell will do you more help, which tell you how to monitor the log file in real time, like use the Get-FileTail Cmdlet from PowerShell Community Extensions
I have a few work flows where I would like R to halt the Linux machine it's running on after completion of a script. I can think of two similar ways to do this:
run R as root and then call system("halt")
run R from a root shell script (could run the R script as any user) then have the shell script run halt after the R bit completes.
Are there other easy ways of doing this?
The use case here is for scripts running on AWS where I would like the instance to stop after script completion so that I don't get charged for machine time post job run. My instance I use for data analysis is an EBS backed instance so I don't want to terminate it, simply suspend. Issuing a halt command from inside the instance is the same effect as a stop/suspend from AWS console.
I'm impressed that works. (For anyone else surprised that an instance can stop itself, see notes 1 & 2.)
You can also try "sudo halt", as you wouldn't need to run as a root user, as long as the user account running R is capable of running sudo. This is pretty common on a lot of AMIs on EC2.
Be careful about what constitutes an assumption of R quitting - believe it or not, one can crash R. It may be better to have a separate script that watches the R pid and, once that PID is no longer active, terminates the instance. Doing this command inside of R means that if R crashes, it never reaches the call to halt. If you call it from within another script, that can be dangerous, too. If you know Linux well, what you're looking for is the PID from starting R, which you can pass to another script that checks ps, say every 1 second, and then terminates the instance once the PID is no longer running.
I think a better solution is to use the EC2 API tools (see: http://docs.amazonwebservices.com/AWSEC2/latest/APIReference/ for documentation) to terminate OR stop instances. There's a difference between the two of these, and it matters if your instance is EBS backed or S3 backed. You needn't run as root in order to terminate the instance - the fact that you have the private key and certificate shows Amazon that you're the BOSS, way above the hoi polloi who merely have root access on your instance.
Because these credentials can be used for mischief, be careful about running API tools from a given server, you'll need your certificate and private key on the server. That's a bad idea in the event that you have a security problem. It would be better to message to a master server and have it shut down the instance. If you have messaging set up in any way between instances, this can do all the work for you.
Note 1: Eric Hammond reports that the halt will only suspend an EBS instance, so you still have storage fees. If you happen to start a lot of such instances, this can clutter things up. Your original question seems unclear about whether you mean to terminate or stop an instance. He has other good advice on this page
Note 2: A short thread on the EC2 developers forum gives advice for Linux & Windows users.
Note 3: EBS instances are billed for partial hours, even when restarted. (See this thread from the developer forum.) Having an auto-suspend close to the hour mark can be useful, assuming the R process isn't working, in case one might re-task that instance (i.e. to save on not restarting). Other useful tools to consider: setTimeLimit and setSessionTimeLimit, and various checkpointing tools (I have a Q that mentions a couple). Using an auto-kill is useful if one has potentially badly behaved code.
Note 4: I recently learned of the shutdown command in package fun. This is multi-platform. See this blog post for commentary, and code is here. Dangerous stuff, but it could be useful if you want to adapt to Windows. I haven't tried it, though.
Update 1. Three more ideas:
You could use .Last() and runLast = TRUE for q() and quit(), which could shut down the instance.
If using littler or a script that invokes the script via Rscript, the same command line functions could be used.
My favorite package of today, tcltk2 has a neat timer mechanism, called tclTaskSchedule() that can be used to schedule the execution of an expression. You could then go crazy with the execution of stuff just before a hourly interval has elapsed.
system("echo 'rootpassword' | sudo halt")
However, the downside is having your root password in plain text in the script.
AFAIK those ways you mentioned are the only ones. In any case the script will have to run as root to be able to shut down the machine (if you find a way to do it without root that's possibly an exploit). You ask for an easier way but system("halt") is just an additional line at the end of your script.
sudo is an option -- it allows you to run certain commands without prompting for any password. Just put something like this in /etc/sudoers
<username> ALL=(ALL) PASSWD: ALL, NOPASSWD: /sbin/halt
(of course replacing with the name of user running R) and system('sudo halt') should just work.
I have a local server insalled on my system and have to start that from within my R function.
here is how I start it:
cmd<-"sh start-server.sh"
system(cmd, wait=FALSE)
I have to perform computations after starting the server. Basically my function has to start the server and proceeds with further steps.
The server starts but the further steps of the program are not executed.The cursor keeps waiting after the server is started.
Please suggest how to go about this.
My problem is finally solved. I had to add Sys.sleep() and it runs after waiting for few seconds. Thank you for help.
You need to determine whether or not the problem is with the server script or with R's execution of the script. Try:
Running sh start-server.sh directly from a command prompt and seeing what happens.
Running something simple via R's system function, e.g., system("ls", wait = FALSE).
By default, system waits for the executed command to terminate before returning. Add wait=FALSE if you want it to return immediately.