Jupyter Notebooks

[Predrag Punosevac]

Chirag Nagpal <chiragn at cs.cmu.edu> wrote:

> Predrag: I am able to reproduce the error on the scratch directory too.
> 

I am sure you guys have a problem but one doesn't need Jupyter to do
actual programming in Python. I am saying this because there are
handful of you who are affected by this behavior (God knows what could
have caused possibly even regressions by newer version of packages) and
I am the only firefighter currently without bandwidth to deal with such
wild fires.

> Vincent, Matt:  are you using the anaconda jupyter? it could be an anaconda
> upgrade thats responsible ?
> 
> Chirag
> 
> On Tue, Nov 6, 2018 at 4:45 PM, Vincent Jeanselme <vjeansel at andrew.cmu.edu>
> wrote:
> 
> > Even after changing my bashrc with export IPYTHONDIR=/home/scratch/$USER/.ipython
> > and reinstalling my jupyter, it still does not seem to work. I also have an
> > issue with git, I am no longer able to pull from the server.
> >


The git issue is environmental variable issue which is caused by the
fact that there is only one user on Gogs server (git) and all accounts
are just aliases with their own ssh-keys to this account. I don't use
and know enough about git but those nasty files in your

reponame/.git 

folder 

which look like 

predragp at lov3$ ls
branches  description  HEAD   index  logs     ORIG_HEAD    refs
config    FETCH_HEAD   hooks  info   objects  packed-refs

apparently get populated in different ways depending on the login. So
for example if I ssh to one of the computing nodes from home I get this


predragp at lov3$ git pull
Host key fingerprint is
SHA256:XEkrneUFkkAPyf0gMOQKa3amiAp3QrXmu1x+sIJMcsA
+---[ECDSA 256]---+
|     .++++o.o..  |
|     . .+=+B .   |
|. . . . ..Bo.    |
|.E + o . o  .    |
| .= *   S        |
|o=o*  .          |
|+=+.o .o         |
|o.o+.+. .        |
|.   +o..         |
+----[SHA256]-----+
remote: Enumerating objects: 34, done.
remote: Counting objects: 100% (34/34), done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 22 (delta 8), reused 0 (delta 0)
Unpacking objects: 100% (22/22), done.
>From ssh://git:/predragp/ansible
   cfc10cf..71a9aec  master     -> origin/master
Updating cfc10cf..71a9aec
Fast-forward
 Linux/autofs/etc/auto.nfs                         | 18
+++++++++++++++++
 Linux/ldap/etc/openldap/{certs => cacerts}/ca.crt |  0
 Linux/ldap/etc/openldap/ldap.conf                 |  6 +++---
 Linux/ldap/etc/sssd/sssd.conf                     |  2 +-
 Linux/ldap/ldap.yaml                              | 24
+++++++++++++++--------
 5 files changed, 38 insertions(+), 12 deletions(-)
 rename Linux/ldap/etc/openldap/{certs => cacerts}/ca.crt (100%)


If I ssh to my desktop I get 

predragp at lake$ git pull
Host key fingerprint is
SHA256:XEkrneUFkkAPyf0gMOQKa3amiAp3QrXmu1x+sIJMcsA
+---[ECDSA 256]---+
|     .++++o.o..  |
|     . .+=+B .   |
|. . . . ..Bo.    |
|.E + o . o  .    |
| .= *   S        |
|o=o*  .          |
|+=+.o .o         |
|o.o+.+. .        |
|.   +o..         |
+----[SHA256]-----+
Password for git at git.int.autonlab.org:

which is the indication that my .ssh/config file and the ssh-key were
not read even though

Host git 
    HostName git.int.autonlab.org
    Port 2222
    User git 
    IdentityFile /home/predragp/.ssh/git_rsa 

However if I log from the terminal to my desktop I don't have a Git
issue. 


Best,
Predrag






> >
> > On 11/6/18 3:14 PM, Predrag Punosevac wrote:
> >
> >> Matthew Barnes <mbarnes1 at andrew.cmu.edu> wrote:
> >>
> >> Also having this problem. Trying to create a new notebook hangs on
> >>> "Creating new notebook in", and unable to open old notebooks. Anyone's
> >>> setup currently working?
> >>>
> >>> Jupyter Notebook is using sqlite database to store the info. Unless you
> >> explicitly force Jupyter to create the database on the scratch directory
> >> the database is stored on the NFS share. There is nothing worse one can
> >> do in terms of data consistency than put a database or a private Git
> >> repo (talking about the server) onto the NFS. The datebase was left in
> >> inconsistent state after the file server was rebooted. You have to clear
> >> it and possibly recreate the database to be able to use Jupyter
> >> Notebook.
> >>
> >> Best,
> >> Predrag
> >>
> >>
> >> On Tue, Nov 6, 2018 at 12:44 PM Vincent Jeanselme <
> >>> vjeansel at andrew.cmu.edu>
> >>> wrote:
> >>>
> >>> Hello,
> >>>>
> >>>> Has anyone faced problems with running Jupyter Notebook since yesterday
> >>>> ?
> >>>> Did you remember what was the change to operate after the last reboot of
> >>>> the sqlite database ?
> >>>>
> >>>> Thank you,
> >>>>
> >>>> Vincent
> >>>>
> >>>> --
> >>>> Vincent Jeanselme
> >>>> -----------------
> >>>> Analyst Researcher
> >>>> Auton Lab - Robotics Institute
> >>>> Carnegie Mellon University
> >>>>
> >>>>
> >>>> --
> > Vincent Jeanselme
> > -----------------
> > Analyst Researcher
> > Auton Lab - Robotics Institute
> > Carnegie Mellon University
> >
> >
> 
> 
> -- 
> 
> *Chirag Nagpal* Graduate Student, Language Technologies Institute
> School of Computer Science
> Carnegie Mellon University
> cs.cmu.edu/~chiragn