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CVNRneuroimaging / infrastructure

Issue tracking, system documentation and configs for operations side of the neuroimaging core @ Atlanta VA CVNR / Emory University
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NEW IMAGE #133

Open kmcgregor123456 opened 8 years ago

kmcgregor123456 commented 8 years ago

Hello,

Allow me to introduce you to your new operating environment if I have not done so already.

From here on, we will be using a different setup to do data analysis on our machines. Previously, if you have been using pano and qball2 and 3, you were using the Emory Active DIrectory authentication setup.

The new data processing format uses virtual machines on the PC's that are in the lab already (lens, larry, ralph, rama) and any machine that has a BIRC DNS entry (e.g. monoamine, neuron, etc.). In fact, as long as you are connected to the Emory network on a high speed connection (gigE), the image can be run from your own hardware (pending my approval).

To get this setup, we had to create a new authentication scheme, this scheme is called LDAP or Lightweight Directory Access Protocol. Rob Melby spent a good amount of time getting this setup and tested, and it work pretty well now.

So what does this mean for you:

1) Contact me and tell me where you will be doing your work (which machine). 2) I will setup the Virtual Environment for you on that machine and give you your login 3) The login will mount /data/backup (hippoback's store) as read/write - you should do your data analysis here 4) The data will be backed up to Tripleback as the backup store as will your home directory. 5) All of your existing home directory data can be transferred from its backup on hippoback into your new LDAP configuration.

I will be updating this image on a periodic basis to accommodate software changes and potential security updates.

For those of you who are Bold and Brave, you can setup the VMWare environment yourself using the following instructions:

1) The VMWare image can be downloaded from the following links: https://my.vmware.com/web/vmware/free#desktop_end_user_computing/vmware_player/7_0 (PC) https://my.vmware.com/web/vmware/info/slug/desktop_end_user_computing/vmware_workstation/11_0 (MAC) 2) Our license code is: (for either MAC OR PC) 3) Download the new image from my GOOGLE DRIVE:

FYI: qbal1l.birc.emory.edu and qball4.birc.emory.edu both are setup to use this environment in native Linux mode. They also have X2Go servers on them which authenticate using the LDAP authentication. They can also be reached by SSH.

kmcgregor123456 commented 8 years ago

@simonero @smtran

stowler commented 8 years ago

Emailed Keith and Rob this moring:

OK, I can log in to qball1 and 4 (haven't tested others), but it doesn't look like my sudoer access is working:

[09:52:44]-[stephentowler]-at-[qball4]-in-[~]
$ vim .bash_profile
The program 'vim' can be found in the following packages:
 * vim
 * vim-gnome
 * vim-tiny
 * vim-athena
 * vim-gtk
 * vim-nox
Ask your administrator to install one of them

[09:53:12]-[stephentowler]-at-[qball4]-in-[~]
$ sudo aptitude
[sudo] password for stephentowler:
stephentowler is not in the sudoers file.  This incident will be reported.
stowler commented 8 years ago

Emailed request for in-person trouble-shooting ("for efficiency I'm suggesting a group maintenance session"), followed up with doodle: 

Hi all,

Keith (and maybe Rob too?) kindly spend time this weekend moving my account from dead hippostore to the new LDAP-based system. I'm able to log in but there is more configuration needed.

To resume productivity as quickly as possible I'd like to suggest that Keith and Rob join me in person for configuration and testing. It would help us avoid losing a bunch of time to email/messaging delays. Goals would be:

1) knock out all of the easy issues quickly and in-person (simple configuration changes, easy-to-resolve errors)
2) finish the session with a list of outstanding issues captured as maintenance tickets

If Stella and Simone aren't yet buried under the beginning of their semester it would make sense to include them so that they can bring their laptops and demonstrate their remote-access errors (and other outstanding issues) in person. Simone has especially unique GUI needs.

Maybe we could schedule a three-hour block in WMB sometime this week? (WMB would allow testing directly on Emory's wired network AND over their wireless to simulate remote-work).

I'll be happy to send out a doodle for scheduling as soon as I hear that there are no objections or better ideas.

Thanks,
Stephen
stowler commented 8 years ago

Keith and Rob @kmcgregor123456 @rrmm ,

FYI: I'm trying to collect as much information as possible before Friday group maintenance. You can find the results of my preliminary testing here:

https://github.com/CVNRneuroimaging/infrastructure/blob/master/config/notes/20150812-stowlerBircSystemTesting.md

...including my task list as it stands at the moment, excerpted here:

To-be-fixed list for Keith and Rob (details for each follow):

To-be-propagated list for Keith and Rob (details for each follow):

kmcgregor123456 commented 8 years ago

Let's work collectively on this. If you see low-hanging fruit on the image, then go ahead and make the change to your host environment and dump the .ova to your home directory. I can then export the updated image for testing and distribution.

Keith McGregor, PhD VA RR&D Atlanta CoE Emory University 352.359.8084 www.varrd.emory.edu

From: Stephen Towler [notifications@github.com] Sent: Wednesday, August 12, 2015 2:04 PM To: CVNRneuroimaging/infrastructure Cc: Keith McGregor Subject: Re: [infrastructure] NEW IMAGE (#133)

Keith and Rob @kmcgregor123456https://github.com/kmcgregor123456 @rrmmhttps://github.com/rrmm ,

FYI: I'm trying to collect as much information as possible before Friday group maintenance. You can find the results of my preliminary testing here:

https://github.com/CVNRneuroimaging/infrastructure/blob/master/stowlerBircSystemTesting.md

...including my task list as it stands at the moment:

To-be-fixed list for Keith and Rob (details for each follow):

To-be-propagated list for Keith and Rob (details for each follow):

— Reply to this email directly or view it on GitHubhttps://github.com/CVNRneuroimaging/infrastructure/issues/133#issuecomment-130394769.

This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.

If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

stowler commented 8 years ago

Keith and Rob @kmcgregor123456 @rrmm ,

I'm happy to help (which is why I'm documenting fixes on that "To-be-propagated" list), but I need some information on the existing build first...is there build documentation/scripts/ks somewhere?

If there aren't build docs/scripts/ks, these are examples of things that would be important for me to know so that I can avoid creating iatrogenic problems:

Thanks, Stephen

stowler commented 8 years ago

Keith and Rob @kmcgregor123456 @rrmm ,

Here are the results of the testing I completed today:

https://github.com/CVNRneuroimaging/infrastructure/blob/master/config/notes/20150812-stowlerBircSystemTesting.md

...including this excerpted task list which I won't have time to grow to before our Friday meeting:

To-be-fixed list for Keith and Rob (details for each follow):

To-be-propagated list for Keith and Rob (details for each follow):

stowler commented 8 years ago

Resolved some of the VM image install/config tasks today, but no performance or function testing.

RESOLVED FOR QBALLS:

COMPLETED FOR UPCOMING VM IMAGE:

STARTED TODAY BUT NOT RESOLVED:

kmcgregor123456 commented 8 years ago

I added ITKSNAP3 to the image. It MUST be called explicitly as itksnap3. itksnap will launch ITKSNAP 2.2

I installed in /usr/local

kmcgregor123456 commented 8 years ago

New Image can be downloaded from link sent in email

stowler commented 8 years ago

Just FYI: from my recent pano and rama 14.04 experiences I have neuroimaging app/config updates to contribute to lab image . Sometime after Sept 2nd I'll make time to link to those notes from this ticket.