When I use SSHOperator to execute the command on the remote server with the user. But it can't use the proper system environment, I think it didn't source the /etc/profile or ~/.bashrc.
This issue is kind of annoying, for example, I have to write the absolute path of the Python interpreter everywhere. Is there any ways to avoid this.
Related
I am trying to use Run/Debug Configurations on WebStorm, however it doesn't seem to source .zshrc and produces errors about not finding commands and environment variables. (An example of this would be yarn tauri dev when using Tauri)
I have installed Ubuntu 20.04 in WSL and the project I opened in WebStorm resides under the $HOME directory. WebStorm is installed in Windows.
For the interactive shell, I have made zsh the default by chsh -s $(which zsh), but when using Run/Debug Configurations it uses the default non-interactive shell, which is dash as far as I know. And my environment variables and PATH are all set in .zshrc, which is not sourced by dash.
It seems in CLion, it is possible to execute commands in the login shell according to this YouTrack issue, but such an option is not available on WebStorm.
Is it possible to use zsh instead of dash as the default non-interactive shell? If not, it would help me a lot to know what is the best practice in such situations.
There are several questions and points you make:
First, from the question title (and the summary at the end):
Can I use zsh as the default non-interactive shell for WSL2 Ubuntu?
Well, maybe (using symlinks), but it would be a really bad idea. So many built-in scripts rely on /bin/sh pointing to Dash, or at least Bash. While Zsh might be compatible with 99.9% of them, eventually there's a strong likelihood that some difference in Zsh would cause a system-level script to fail (or at least produce results inconsistent with those from Dash).
It is possible in Ubuntu to change the default non-interactive ("system" shell) from Dash to Bash with sudo dpkg-reconfigure dash. If you select "No" in the resulting dialog, then the system will be updated to point /bin/sh to bash instead of dash.
But not to Zsh, no.
when using Run/Debug Configurations it uses the default non-interactive shell, which is dash as far as I know
I don't run WebStorm myself, so I'm not sure on this exactly. Maybe #lena's answer (or another) will cover it for you, but if it doesn't, I'm noticing this doc page. It might be worth trying to specify Zsh in those settings, but again, I can't be sure.
And my environment variables and PATH are all set in .zshrc, which is not sourced by dash.
Hmm. I'm guessing you would need these set in a .profile/.zprofile equivalent regardless. I would assume that WebStorm is executing the shell as a non-interactive one, which means that it wouldn't even parse ~/.bashrc if Bash was your default shell.
... it would help me a lot to know what is the best practice in such situations.
Best practice is probably to make sure that your ~/.profile has any environment changes needed. Yes, this violates DRY (don't repeat yourself), but it's probably the best route.
Thanks to the answer here and the discussion below, I was able to figure it out. (Thank you, #NotTheDr01ds and #lena.)
The main problem is that WebStorm is installed on Windows and therefore knows only the environment variables in Windows. There are two ways to solve the problem as follows.
Sharing WSL's environment variable to Windows through WSLENV
Add the line below to .zshrc so that it sets $WSLENV when zsh starts.
export WSLENV=VAR_I_WANT_TO_SHARE:$WSLENV
# Don't forget to insert the colon
# And for some reason, appending the variable after $WSLENV didn't work well
In Windows, run
wsl -e zsh -lic powershell.exe
This runs WSL using zsh (logged-in and interactive), then runs powershell which brings you back to Windows. Although this doesn't seem to achieve anything, by going through zsh in WSL, .zshrc was sourced and therefore $WSLENV set as well. You can check if it worked well by running the below command after you've run the above.
$env:VAR_I_WANT_TO_SHARE
Run WebStorm from the PowerShell that was just created.
& 'C:\Program Files (x86)\JetBrains\WebStorm 2022.1.3\bin\webstorm64.exe'
When you run or debug any of the Run/Debug Configurations, you will see that the environment variable is shared successfully.
Setting the PATH in Windows
For most environment variables, the previous method works well. However, PATH is an exception. The Windows PATH is shared to WSL by default. The opposite doesn't work, probably because the PATH in WSL should not interfere with Windows.I've tried adding the $PATH of WSL into $WSLENV but it didn't seem to work.
In the end, what I did was manually adding each needed $PATH of WSL into the Windows PATH.
For example, if there was export PATH=$PATH:home/(username)/.cargo/bin in .zshrc, you can then add \\wsl$\Ubuntu\home\(username)\.cargo\bin to the Windows $env:Path using the Environment Variable window.
I might have made some mistakes, so feel free to leave an edit or comments.
You can try using npm config set script-shell command to set the shell for your scripts. Like npm config set script-shell "/usr/bin/zsh".
When npm run <script name> spawns a child process, the SHELL being used depends on NPM environment. Cм https://docs.npmjs.com/cli/run-script:
The actual shell your script is run within is platform dependent. By
default, on Unix-like systems it is the /bin/sh command, on Windows it
is the cmd.exe. The actual shell referred to by /bin/sh also depends
on the system. As of npm#5.1.0 you can customize the shell with the
script-shell configuration
See also https://github.com/npm/npm-lifecycle/blob/10c0c08fc25fea3c18c7c030d4618a401963355a/index.js#L293-L304
I am cannot figure out how to load MPI modules a user in Fedora.
I am using fish shell and I dont know if there will be any issues with loading a module compared to bash shell
How I am trying to load MPI modules is
lumx#localhost ~> sudo module load mpi
[sudo] password for lumx:
sudo: module: command not found
lumx#localhost ~>
Also is there a way to load them during start up so i wont have to worry about loading modules again.
Fedora distributes few MPI distributions: OpenMPI and MPICH at least.
If you just install the packages, your environment is not properly set so that you can directly use the software.
However, there is one package for each distribution, which loads the required module that sets up your environment properly. For the case of MPICH is mpich-autoload.
On the other side, module command is neither a binary nor a script file, so $PATH value should not affect. It does not require admin rights, so you can use it in user mode directly.
Finally, I recommend you to check which modules are available in your system by running
$ module avail
I managed to solve the problem.
I just added /usr/lib64/openmpi/bin/ to my user paths. I don't know if this is the right solution instead of loading modules.
set -U fish_user_paths /usr/lib64/openmpi/bin/ $fish_user_paths
I'm trying to understand how openmpi/mpirun handle script file associated with an external program, here a R process ( doMPI/Rmpi )
I can't imagine that I have to copy my script on each host before running something like :
mpirun --prefix /home/randy/openmpi -H clust1,clust2 -n 32 R --slave -f file.R
But, apparently it doesn't work until I copy the script 'file.R' on clusters, and then run mpirun. Then, when I do this, the results are written on cluster, but I expected that they would be returned to working directory of localhost.
Is there another way to send R job from localhost to multiple hosts, including the script to be evaluated ?
Thanks !
I don't think it's surprising that mpirun doesn't know details of how scripts are specified to commands such as "R", but the Open MPI version of mpirun does include the --preload-files option to help in such situations:
--preload-files <files>
Preload the comma separated list of files to the current working
directory of the remote machines where processes will be
launched prior to starting those processes.
Unfortunately, I couldn't get it to work, which may be because I misunderstood something, but I suspect it isn't well tested because very few use that option since it is quite painful to do parallel computing without a distributed file system.
If --preload-files doesn't work for you either, I suggest that you write a little script that calls scp repeatedly to copy the script to the cluster nodes. There are some utilities that do that, but none seem to be very common or popular, which I again think is because most people prefer to use a distributed file system. Another option is to setup an sshfs file system.
I have several buckets mounted using the awesome riofs and they work great, however I'm at a loss trying to get them to mount after a reboot. I have tried entering in the following to my /etc/fstab with no luck:
riofs#bucket-name /mnt/bucket-name fuse _netdev,allow_other,nonempty,config=/path/to/riofs.conf.xml 0 0
I have also tried adding a startup script to run the riofs commands to my rc.local file but that too fails to mount them.
Any idea's or recommendations?
Currently RioFS does not support fstab. In order to mount remote bucket at the startup time, consider adding corresponding command line to your startup script (rc.local, as you mentioned).
If for some reason it fails to start RioFS from startup script, please feel free to contact developers and/or fill issue report.
If you enter your access key and secret access key in the riofs config xml file, then you should be able to mount this via fstab or an init.d or rc.local script ..
See this thread
EDIT:
I tested this myself and this is what I find. Even with the AWS access details specified in the config file, there is no auto-matic mounting at boot. But to access the system, all one needs to do is to issue mount /mount/point/in-fstab .. and the fstab directive would work and persist like a standard fstab mounted filesystem.
So, it seems the riofs system is not ready at that stage of the boot process when filesystems are mounted. That's the only logical reason I can find so far. This can be solved with an rc.local or init.d script that just issues a mount command (at the worst)
But riofs does work well, even as the documentation seems sparse. It is certainly more reliable and less buggy than s3fs ..
Thanks all,
I was able to get them auto-mounting from rc.local with the syntax similar to:
sudo riofs --uid=33 --gid=33 --fmode=0777 --dmode=0777 -o "allow_other" -c ~/.config/riofs/riofs.conf.xml Bucket-Name /mnt/mountpoint
Thanks again!
OS: UNIX Solaries, Oracle Application Server 10g
To run shell script from Oracle Forms, I used the following host('/bin/bash /u01/compile.sh') and it works well
Now, I need to run unix command something like
host('mv form1.fmx FORM1.FMX') but it's not working
I tried to append the command mv form1.fmx FORM1.FMX' to the compile.sh shell script but also it's not working although the rest lines of the shell script is running well
The solution is to just add the full path of the mv command and it worked well, as follow
/bin/mv /u01/oracle/runtime/test/form1.fmx /u01/oracle/runtime/test/FORM1.FMX
In case anyone else encounters the same problem, the cause is that Forms process creates a subprocess to execute host() command, and that subprocess inherits environment variables of the parent process, which are derived from default.env (or other env file as defined in server config). There is a PATH variable defined in that file, but it doesn't contain usual /bin or /usr/bin, so the commands will not execute unless full path is specified.
The solution is to set the correct PATH variable either in the executed script (via export PATH=$PATH:...) or in default.env. I set it in the script, since, knowing Oracle, there's no guarantee that modifying default.env won't break something.