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Published 20 hours ago • verified publisher icon lucapinello

This looks awesome! Orchestra configuration is tricky

Open dylanmmarshall opened this issue 7 years ago • 3 comments

I just tried to configure this code towards HMS's Orchestra HPC, but ran into some subprocess issues that are outside of my domain. I would really like to get something like this going because as seen here - current instructions for Jupyter notebook use on Orchestra require many steps - (https://wiki.med.harvard.edu/Orchestra/SSHPortForwarding#Example_IPython_Notebook_setup).

The two screen shots are the bugs I ran into.

I had to alter the code a bit and am unsure whether my edits are the source of the bugs -

commandline

localhostissues

I created a pull request from my fork's "hms_orchestra" branch to show my implementation but of course, no merge necessary.

Any help would be appreciated! No rush.

dylanmmarshall avatar Oct 16 '17 22:10 dylanmmarshall

Thanks for trying it and happy to take a look, I have an account and I tried with my current version and I get :

bash: bsub: command not found

But when I login in the main node I can execute bsub. Any idea on what is happening?

Do you have anything set in bash_profile that append the bsub path?

lucapinello avatar Oct 17 '17 18:10 lucapinello

Hi Luca, thank you for getting back to me! I have a suffix appended on for my $HOME/bin directory - { PATH=$PATH:$HOME/bin }, but that's it. You can also see { ls -la /home/dmm57/ }. I wonder if the minor changes I wrote in ~ around line 140 make a difference to the bsub command.

dylanmmarshall avatar Oct 18 '17 14:10 dylanmmarshall

I'm gonna mess w/ the code this weekend to see if I can get this working in some other format.

Also, awesome paper yesterday! https://www.biorxiv.org/content/early/2017/10/17/204685

dylanmmarshall avatar Oct 18 '17 15:10 dylanmmarshall