I have made a script that uses a program called Diascope, its a video slideshow program.
I am trying to run this command in encodeVideo.sh
echo "Running diascope -clean /mnt/videos/video$1.txt..."
diascope -clean /mnt/videos/video$1.txt > /var/www/html/video/encodeVideo.log
echo "Removing old deploy dir, and making new one..."
And I am running this script from rc.local so that it runs every time I boot the instance.
All I need is to get the output of the "diascope" command, in rc.local I run encodeVideo:
/bin/bash /var/www/html/video/encodeVideo.sh > /var/www/html/video/newlog
and in newlog I can see this
Running diascope -clean /mnt/videos/video7.txt...
Removing old deploy dir, and making new one...
and /var/www/html/video/encodeVideo.log is completely empty! Diascope uses gawk, and btw I can see the output of the processing when I manually run the encodeVideo.sh script. Why can I not capture it in this log?
Is it possible that it's not standard output, so ">" doesn't actually capture it?
Any ideas would be helpful, thanks!
try redirecting stderr and stdout to filename
diascope -clean /mnt/videos/video$1.txt 1> /var/www/html/video/encodeVideo.log 2>&1
Is it possible that it's not standard output, so ">" doesn't actually capture it?
Absolutely: it could be standard error, in which case you'd have to use 2> instead of >.
Related
I have a bash script, which when it's finished running, it going to write some files into a directory.
It prints a lot of warnings, which slows down the process, I'm looking for an effective way to prevent printing the warnings in the shell.
I added 2> /dev/null to end of my command at mybash.sh:
#!/bin/bash
command -f file 2> /dev/null
the original command:
java -mx28000M -jar ChromHMM.jar BinarizeBam CHROMSIZES/hg19.txt /Volumes/Control/ /primary_bam_files/FCX/Control/Marks_Run1.txt /Volumes/Control/output1/
When I run my mybash.sh, it will write 20 different output files in a directory.
However, when I use 2>/dev/null, it does not print any warning in the shell which is great but also does not write anything in the output directory which in principle should those 20 files.
Can anyone help me to solve this problem?
What I know and what I've tried: I have a script in R (called GAM.R) that I want to run in the background that outputs .rdata, .pdf, and .jpg files. Running this from the command line is relatively simple:
$ Rscript GAM.R
However, this code takes a very long time to run so I would love to send it to the background and let it work even after I have logged out and turned the computer off. I understand this is pretty easy, as well, and my code would look like this:
$ nohup Rscript GAM.R >/dev/null 2>&1 &
I used this to see if it was working:
$ fg
nohup Rscript GAM.R > /dev/null 2>&1
The problem: I don't know how to check if the code is working (is there a way I can see its progress?) and I don't know where the outputs are going. I can see the progress and output with the first code so I must not be too far off. It doesn't seem that the second code's outputs are going where the first code's outputs went.
Your command line is diverting all output to /dev/null aka, The Bit Bucket.
Consider diverting it to a temporary file:
$ nohup Rscript GAM.R >/tmp/GAM.R.output 2>&1 &
Then you can tail /tmp/GAM.R.output to see the results, it will show the last 10 lines of the file by default. You can use tail -f to show the end of the file, plus new output in real time.
Note, the /tmp/ filesystem is not guaranteed to exist between reboots. You can put the file somewhere else (like ~/GAM.R.output if you need to be sure.
Note, however, that if you turn your computer off, then all processing gets aborted. For this to work your machine must continue to run and not go to sleep, or shutdown.
What you are doing is that with the > you are redirecting the output of your script to /dev/null and by doing 2>&1 you are redirecting the error output to the same place. Finally nohup executes your process and detach it from the current terminal.
So to sum up what you are doing is creating a process and redirecting its output and error output to a file called null that is stored under /dev.
To answer your question I suggest you redirect your outputs to a folder that you can access as normal user and not super user. Then to make sure that everything is ok you can print this file.
For example you can do :
nohup Rscript GAM.R >/home/username/documents/output_file 2>&1 &
and then to see the file from a terminal you can do:
cat /home/username/documents/output_file
Lastly I don't think that your program will keep on running if your turn off your pc and I don't think there is a way to do that.
If you want to run your program in the background and access the output of the program you can easily do that by writing
exec 3< <(Rscript GAM.R)
And then when you wish to check the output of the program run
cat <&3 # or you can use 'cat /dev/fd/3'
Excellent! Thanks everyone for your helpful answers, particularly #Greg Tarsa. Ultimately I needed to use:
$ nohup Rscript GAM.R >/usr/emily/gams/2017_03_14 2>&1 &
The above is used to run the script and save the screen output to emily/gams (called "2017_03_14", a file to be made by the command, not a folder as I had origionally thought). This also outputs my .rdata, .pdf, and .jpg output filesf from the script to usr/emily.
Then I can see progress and running programs using:
$ tail -f 2017_03_14 #Shows the last 10 lines of the program's progress
$ ps #shows your running projects
$ ps -fu emily #see running projects regardless of session, where username==emily
In the spirit of completeness, I can also note here that to cancel a process, you can use:
$ kill -HUP processid #https://kb.iu.edu/d/adqw
I've downloaded and "installed" VSCode for Linux. I have placed the app in /home/Christian/Apps/VSCode/ and symlinked the executable to /usr/bin/code.
When I use this method to start Code it hijacks the terminal (expected I guess) and also dumps a lot of STDERR stuff at the same time.
If I redirect STDERR to a file, for example like
code 2> ~/.logs/VSCode-`date +%Y%m%d%H%M%S.log` &
Then I can get it to give me back my prompt, and it's silent (logging everything to the filename I gave it).
I was thinking of making this an alias, but then I realized I can't inject arguments ($1 $2 $3) in an alias. And I usually want to start code with code filename.js or code ..
What is the correct way to launch an application like this "in the background"?
Instead of making a symlink to the executable, create a bash script like this:
#!/bin/bash
/path/to/VSCode/Code "$#" 2>/dev/null &
I want to run a program from perl by using system command(or any other ways ).
system("samtools");
I think it should pass this to shell but it complains ,Can't exec "samtools" file or directory does not exist , when I run it.I have tried many other different program for example
system("velveth");
and it works properly but not this one (samtools). Is any of you facing this problem before?
I am really puzzled.
You can give the full path to that file location.
example:
system( "/usr/bin/perl -de 1");
Try putting Linux command inside `` characters. Will work as well.
Did you modify $path for samtools in the current shell manually?
Since system starts a new sub-shell to run your command, you have to append search path for samtools yourself if doesn't exist in your .bashrc. Check it by:
perl -e 'system("echo \$PATH")'
and
echo $PATH
to see if there's any difference.
I'm trying to run a script which stops and starts Tomcat on linux.
When I run it from the command line it works fine. But it does not seem to work when I run the same script from the "Execute Shell" build step in a Jenkins/Hudson job. Jenkins doesn't report any errors but if I try going to the tomcat page then I get a page not found error.
So Jenkins seems able to stop the server, but not bringing it back up.
I'd be grateful for any help.
Try unsetting the BUILD_ID in your 'shell execute' block. You might even not need to use nohup in this case
BUILD_ID=
./your_hudson_script_that_starts_tomcat.sh
Without seeing your script it is difficult to give an exact answer. However you could try adding the following to the start of your script (assuming it is a bash script):
# Trace executed commands.
set -x
# Save stdout / stderr in files
exec >/tmp/my_script.stdout
exec 2>/tmp/my_script.stderr
You could also try adding
set -e
to make the shell exit immediately if a command returns an error status.
If it looks as though Hudson is killing off Tomcat then you might want to run it within nohup (if you're not already doing that):
nohup bin/startup.sh >/dev/null 2>&1 &