I added an alias (alias homedir='cd /export/home/file/myNmae'
) to .bashrc in my home directory and restarted the session. When I run the alias it says homedir: command not found.
Please advice.
This is because .bashrc is not sourced everytime, only for interactive non login shells .bashrc is sourced.
From the bash man page.
When bash is invoked as an interactive login shell, or as a non-interactive shell with the --login option, it first reads and executes commands from the file /etc/pro-
file, if that file exists. After reading that file, it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile, in that order, and reads and executes commands from the
first one that exists and is readable. The --noprofile option may be used when the shell is started to inhibit this behavior.
When a login shell exits, bash reads and executes commands from the files ~/.bash_logout and /etc/bash.bash_logout, if the files exists.
When an interactive shell that is not a login shell is started, bash reads and executes commands from ~/.bashrc, if that file exists. This may be inhibited by using the
--norc option. The --rcfile file option will force bash to read and execute commands from file instead of ~/.bashrc.
i found the solution - i added it to the .profile file and restarted the session - it worked
Related
I want to run an R script using SLURM. I have created the R script, "test.R" as shown:
print("Running the test script")
write.csv(head(mtcars), "mtcars_data_test.csv")
I created a bash script to run this R script "submit.sh"
#!/bin/bash
#sbatch --job-name=test.job
#sbatch --output=.out/abc.out
Rscript /home/abc/job_sub_test/test.R
And I submitted the job on the cluster
sbatch submit.sh
I am not sure where my output is saved. I looked in the home directory but no output file.
Edit
I also set my working directory in test.R, but nothing different.
setwd("/home/abc")
print("Running the test script")
write.csv(head(mtcars), "mtcars_data_test.csv")
When I run the script without SLURM Rscript test.R, it worked fine and saved the output according to the set path.
Slurm will set the job working directory to the directory which was the working directory when the sbatch command was issued.
Assuming the /home directory is mounted on all compute nodes, you can change explicitly the working directory with cd in the submission script, or setwd() in the R syntax. But that should not be necessary.
Three possibilities:
either the job did not start at all because of a configuration or hardware issue ; that you can find out with the sacct command, looking at the state column.
either the file was indeed created but on the compute node on a filesystem that is not shared; in that case the best option is to SSH to the compute node (which you can find out with sacct) and look for the file there; or
the script crashed and the file was not created at all, in that case you should look into the output file of the job (.out/abc.out). Beware that the .out directory must be present before the job starts, and that, as it starts with a ., it will be a hidden file, revealed in ls only with the -a argument.
The --output argument to sbatch is relative to the folder you submitted the job from. setwd inside the R script wouldn't affect it, because Slurm has already parsed that argument and started piping output to the file by the time the R script is running.
First, if you want the output to go to /home/abc/.out/ make sure you're in your homedir when you submit the script, or specify the full path to the --output argument.
Second, the .out folder has to exist; I tested this and Slurm does not create it if it doesn't.
I have below two file to start and stop my spring-boot application. Is it possible to have this installed as server etc in unix? so that I can just type start app or stop app to start or stop my application from any location?
startApplication.sh
stopApplication.sh
You can always define alias in your bash, do as below:
sudo vim ~/.bashrc
go at the end of file and add this line
alias start-app='bash /<path-to-script>/startApplications.sh'
save and exit and resource it with source command
source ~/.bashrc
now if you type in your terminal start-app it will execute your script. create one for stop-app too.
I'm creating a script for users to run. I need to redirect the output to a file I'm creating from inside the script (hostname-date).
I have all the pieces except for how to copy the output of the script from inside the same script. All the examples I can find call the script and > it into the log, but this isn't an option.
-Alex
Add the following at the top of your script:
exec &> output.txt
It will make both stdin and stderr of the commands in the rest of your script go into the file output.txt.
exec in bash allows you to permanently redirect a FD (say, stdout) to a file.
A shell that calls a shell.
Have the first shell create the variable (hostname-date)
and call the second shell redirecting the output to the file.
Whenever I start a shell in vim using :sh, it doesn't source my ~/.bashrc file. How can I get it to do this automatically?
See :help 'shell'. You can set this string to include -l or --login, which will source your .bashrc file. So, you might have a line like this in your .vimrc:
set shell=bash\ --login
Note that this will alter everything that invokes the shell, including :!. This shouldn't be much of a problem, but you should be aware of it.
The value of this command can also be changed by setting the $SHELL environment variable.
If it doesn't source your .bashrc file, it may still source your .bash_profile file. I usually make one of them a symlink to the other. If your .bashrc performs some particularly odd one-time operations, you may have to edit it to only perform those operations with a login shell, but I've never had problems with it.
~/.vimrc
cmap sh<CR> !bash --login<CR>
If you quickly enter "sh<Enter>" in command-line, you can start bash with sourcing ~/.bashrc. So dirty.
When setting the export path in Unix, example:
export PATH=$PATH: $EC2_HOME/bin
If I quit terminal and open it back up to continue working, I have to go through all the steps again, setting up the paths each time.
I'm wondering how I can set the path and have it "stick" so my system knows where to find everything the next time I open terminal without having to do it all over again.
Thanks!
Open ~/.bashrc. This file is loaded every time you start up a new shell (if you're using Bash, which most people are). If you're using a different shell, the file may have a different name, like ~/.shrc.
Add the line you need to the bottom of the file:
export PATH=$PATH:$EC2_HOME/bi
Other info rolled up from elsewhere in the thread:
There are multiple places to put this, depending on your shell and your needs. All of these files are in your home directory:
For Bash:
.bashrc (executed when you shart a shell)
OR
.bash_profile (executed when you log in)
For csh and tcsh:
.cshrc
For sh and ksh:
.profile
Add it to your .cshrc file (for csh and tcsh), .profile file (for sh and ksh), or .bash_profile file (for bash)
You need to find your profile file and put that line in there. Suppose you use bash, the profile files are .bashrc and .bash_profile, found in ~. These files will vary depending on which shell you use.
You have to put those commands into one of the "autostart" files of your shell.
For bash this would be .bashrc in your homedirectory (create it if necessary)
add it to your .bashrc or another .bash startup file.
... and for ksh edit .profile.