I am running IPython Notebook on a vagrant virtual machine, and port-forwarding to my local machine so that I can view the notebook in my web browser. I run a bootstrap script that sets an an environment variable JYTHON_HOME in my /etc/environment with:
sudo echo "JYTHON_HOME=/usr/lib/jvm/jython" | sudo tee -a /etc/environment
source /etc/environment
The boot script later starts up ipython notebook. When I open up the notebook,
%%bash
cat /etc/environment
yeilds
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games"
JYTHON_HOME=/usr/lib/jvm/jython
but
%%bash
echo $JYTHON_HOME
prints an empty line.
I have also tried to append the export line to ~/.profile, /.profile, ~/.bashrc, and etc/profile, all with the same result. I know that the notebook is operating as root, but I can't seem to be able to get it to see my environment variable. What can I include in my boostrapping script that will remedy this?
I needed to actually export the variable in the script itself.
sudo echo "JYTHON_HOME=/usr/lib/jvm/jython" | sudo tee -a /etc/environment
source /etc/environment
export JYTHON_HOME=/usr/lib/jvm/jython
Related
I would like to change my conda environment from a bash script.
I want to run bash script_yxz, where 'script_xyz' is like:
#!/bin/bash
conda activate my_env
and switch to my_env.
This already works if I run source script_yxz.
But I have the problem that I am not able to 'source' on remote machines with 'sshpass'.
To better understand my purposes, my goal is to run on my terminal
sshpass -p "password" ssh -o user#server "bash script_xyz"
and changing the environment on the server.
This is why I need to use bash instead of source.
I have read a lot of solutions on various forums but none of them works.
seems like the conda script is not imported by default so this should fix it
source ~/anaconda3/etc/profile.d/conda.sh
conda activate <env>
#!/bin/bash
eval "$(conda shell.bash hook)"
source ~/anaconda3/etc/profile.d/conda.sh
conda create -n testing python=3.10 -y
conda activate testing
python --version
#output
You can use bash,zsh or any shell aliases for this purposes. You just add
alias my_conda='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38'
line into the .bashrc,.zshrc or .any_other_shell_rc.
"N.B. My environment name is MyPy38". So,replace it according name as well as the path /home/$USER/anaconda3.
Also you can create separate file for aliases. Just create a file called .bash_aliases and add
if [ -f ~/.bash_aliases ]; then
. ~/.bash_aliases
fi
lines to .bashrc,.zshrc or .any_other_shell_rc and keep the command
alias my_conda='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38'
into the .bash_aliases. Now, source ~/.zshrc ~/.bashrc or just close and open a new terminal. Run the command my_conda and BOOM!
Also, you can add some other aliases for jupyter-notebook jupyter-lab spyder etc. like
# Just activate my conda
alias my_conda='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38'
# Open Jupyter Notebook in my Env
alias my_jupn='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && jupyter-notebook'
# Open Jupyter Lab in my Env
alias my_jupl='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && jupyter-lab'
# Open Spyder in my Env
alias my_spyder='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && spyder'
To confirm active environment name python code
import sys
print(sys.executable)
I have been trying to resolve problems to be able to run openmpi on multiple nodes.
Initially I had a problem with $PATH and $LD_LIBRARY_PATH variables not being updated from .bashrc file by openmpi session, so I manually added --prefix /path/to/openmpi to resolve this issue.
Turns out that even the anaconda path variables are not being loaded as well. So ultimately I need ~/.bashrc file to be sourced from my home directory. How can I do that? Can anyone help me out please?
UPDATE 01:
I wrote a simple shell script to check the version of python
python --version
and tried to run it with openmpi on local as well as remote machine as follows:
mpirun --prefix /home/usama/.openmpi --hostfile hosts -np 4 bash script
And it returns
Python 2.7.12
Python 3.6.8 :: Anaconda, Inc.
Python 3.6.8 :: Anaconda, Inc.
Python 2.7.12
Confirming my suspicion that whatever openmpi is doing to run remote processes doesn't invoke / set proper environment variables from the ~/.bashrc file. Any help from someone who has worked with multi-node openmpi?
UPDATE 02:
A simple ssh environment grep tell me that my environment variables are not updated which might be the cause of the problem. (I have even tried to set it up in ~/.ssh/environment file)
$ ssh remote-node env | grep -i path
It seems to be loading only the /etc/environment file with only basic paths setup. How to I rectify this?
maybe you should run like this.I guess.
two ways help you!
first:
mpirun --prefix /home/usama/.openmpi --hostfile hosts -np 4 . ~/.bashrc && bash script
second:
## 1. add this line to the script
. ~/.bashrc
## 2. run command as you do
mpirun --prefix /home/usama/.openmpi --hostfile hosts -np 4 bash script
I want to automate the installation of perlbrew into the vagrant box. I use .sh file to accomplish this.
provision.sh
apt-get update
sudo -H -u vagrant bash -c " \curl -kL https://install.perlbrew.pl | bash"
sudo -u vagrant bash -c "source ~/perl5/perlbrew/etc/bashrc"
After ssh into the vagrant i expect that
$ which perlbrew
will return
/home/vagrant/perl5/perlbrew/bin/perlbrew
but unfortunately it returns nothing.
There is no way the settings applied by your source ~/perl5/perlbrew/etc/bashrc command would be visible in another bash session (and a SSH session executes a new bash process).
You need to add the command source ~/perl5/perlbrew/etc/bashrc to one of the bash "rc" files.
For a single user with the following command:
echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bashrc
For all users with the following command:
echo "source ~/perl5/perlbrew/etc/bashrc" >> /etc/bash.bashrc
This way every time a new bash session is started, it will run source ~/perl5/perlbrew/etc/bashrc and apply the settings.
I am using Arch Linux with MATE as desktop environment. So terminal emulator is MATE Terminal. Recently I installed Jekyll with gem install jekyll. But when I ran jekyll -v it says bash: jekyll: command not found. So I tried to add path of Jekyll to PATH variable.
I ran PATH=$PATH/$HOME/.gem/ruby/2.2.0/bin and it worked perfectly. Now I can run jekyll commands. To add it permanently to PATH variable I edited the ~/.bash_profile file like following. It is not working after reboot. But
source ~/.bash_profile works perfectly.
#
# ~/.bash_profile
#
[[ -f ~/.bashrc ]] && . ~/.bashrc
export PATH="${PATH}:/home/heisenberg/.gem/ruby/2.2.0/bin"
According to ArchWiki this is the proper way to concat something permanantly to PATH. But it isn't working. Can somebody figure me out where the wrong is?
[N. B. : Adding the same line in ~/.bashrc is doing okay.]
Depending on the option it is given, bash can be run as an interactive shell or login shell. The default interactive shell mode does not read ~/.bash_profile. login shell bash do.
See:
First, some setup:
% cat ~/.bashrc
…
export BASHRC="yes"
…
% cat ~/.bash_profile
…
export BASH_PROFILE="yes"
…
Now run a regular (interactive) bash:
% bash
[galaux#magenta ~]$ echo $BASHRC
yes
[galaux#magenta ~]$ echo $BASH_PROFILE
Notice we did not get yes with this last one.
Now with a login shell:
% bash --login
[galaux#magenta ~]$ echo $BASHRC
yes
[galaux#magenta ~]$ echo $BASH_PROFILE
yes
See paragraph INVOCATION from man bash.
I'm Mac user.
I want to set PYTHONPATH env for root. so
$ sudo su -
# vi ~/.profile
and add to file 'export PYTHONPATH=/mypythonlib'
then
# env
I can see this line
PYTHONPATH=/Users/simpnet2/projects/meiji/src/hershey
but..
when I use sudo command, cannot find that
$ sudo env
.. there's no PYTHONPATH
My program has to run with sudo command and needs PYTHONPATH.
If you use sh try /etc/profile, bash try /etc/bashrc and if you use zsh try /etc/zshenv.
You can make PYTHONPATH visible to sudo be editing your sudoers file. Notice you should ONLY do this through visudo as explained here.
You should try sudo -i which will simulate logging in as root and source the ~root/.profile.
As of 10.8.5, putting my environment statements in the .profile path in the home of the root user (/var/root) worked. after quitting bash and coming back to the root user prompt with 'su -', I could see my new path, etc. with the 'env' command and my MacPorts installationw orking correctly.
MacBook-Pro:~ root# cat /var/root/.profile
export MANPATH=/opt/local/share/man:$MANPATH
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
MacBook-Pro:~ root# which port
/opt/local/bin/port
Well, in other Linux system, it is also right that 'sudo' does not use local environment variable. But you can declare the temporary environment variable along with 'sudo' command.
For example, in your case, you can add 'PYTHONPATH=/mypythonlib' in your command 'sudo env', and the final command is:
sudo PYTHONPATH=/mypythonlib env
You can also read this article: Using sudo. You can see how 'sudo' keep or ignore user-defined environment variables.
In the case of logging in as a normal user and invoking "su - root" I found that Mac OS 10.8.5's bash was ignoring .profile and .bash_profile; I was unable to change root's $PATH by editing those files. What did work was editing /etc/paths. After exiting the root shell and entering again with "su - root" the new path was present.