<div dir="ltr">I am working on fixing this. <div><br></div><div>It is indeed SQLite and NFS not talking to each other which is the problem. I am able to get jupyter to behave somewhat better by forcing the SQLite server to be in the scratch instead if the NFS. This requires changing some default flags for jupyter. </div><div><br></div><div>Its not completely fixed yet, but I will get back with an update soon. </div><div><br></div><div>Chirag</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Nov 6, 2018 at 8:39 PM, Predrag Punosevac <span dir="ltr"><<a href="mailto:predragp@andrew.cmu.edu" target="_blank">predragp@andrew.cmu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">Chirag Nagpal <<a href="mailto:chiragn@cs.cmu.edu">chiragn@cs.cmu.edu</a>> wrote:<br>
<br>
> Predrag: I am able to reproduce the error on the scratch directory too.<br>
> <br>
<br>
</span>I am sure you guys have a problem but one doesn't need Jupyter to do<br>
actual programming in Python. I am saying this because there are<br>
handful of you who are affected by this behavior (God knows what could<br>
have caused possibly even regressions by newer version of packages) and<br>
I am the only firefighter currently without bandwidth to deal with such<br>
wild fires.<br>
<span class=""><br>
> Vincent, Matt: are you using the anaconda jupyter? it could be an anaconda<br>
> upgrade thats responsible ?<br>
> <br>
> Chirag<br>
> <br>
> On Tue, Nov 6, 2018 at 4:45 PM, Vincent Jeanselme <<a href="mailto:vjeansel@andrew.cmu.edu">vjeansel@andrew.cmu.edu</a>><br>
> wrote:<br>
> <br>
> > Even after changing my bashrc with export IPYTHONDIR=/home/scratch/$<wbr>USER/.ipython<br>
> > and reinstalling my jupyter, it still does not seem to work. I also have an<br>
> > issue with git, I am no longer able to pull from the server.<br>
> ><br>
<br>
<br>
</span>The git issue is environmental variable issue which is caused by the<br>
fact that there is only one user on Gogs server (git) and all accounts<br>
are just aliases with their own ssh-keys to this account. I don't use<br>
and know enough about git but those nasty files in your<br>
<br>
reponame/.git <br>
<br>
folder <br>
<br>
which look like <br>
<br>
predragp@lov3$ ls<br>
branches description HEAD index logs ORIG_HEAD refs<br>
config FETCH_HEAD hooks info objects packed-refs<br>
<br>
apparently get populated in different ways depending on the login. So<br>
for example if I ssh to one of the computing nodes from home I get this<br>
<br>
<br>
predragp@lov3$ git pull<br>
Host key fingerprint is<br>
SHA256:<wbr>XEkrneUFkkAPyf0gMOQKa3amiAp3Qr<wbr>Xmu1x+sIJMcsA<br>
+---[ECDSA 256]---+<br>
| .++++o.o.. |<br>
| . .+=+B . |<br>
|. . . . ..Bo. |<br>
|.E + o . o . |<br>
| .= * S |<br>
|o=o* . |<br>
|+=+.o .o |<br>
|o.o+.+. . |<br>
|. +o.. |<br>
+----[SHA256]-----+<br>
remote: Enumerating objects: 34, done.<br>
remote: Counting objects: 100% (34/34), done.<br>
remote: Compressing objects: 100% (21/21), done.<br>
remote: Total 22 (delta 8), reused 0 (delta 0)<br>
Unpacking objects: 100% (22/22), done.<br>
>From ssh://git:/predragp/ansible<br>
cfc10cf..71a9aec master -> origin/master<br>
Updating cfc10cf..71a9aec<br>
Fast-forward<br>
Linux/autofs/etc/auto.nfs | 18<br>
+++++++++++++++++<br>
Linux/ldap/etc/openldap/{certs => cacerts}/ca.crt | 0<br>
Linux/ldap/etc/openldap/ldap.<wbr>conf | 6 +++---<br>
Linux/ldap/etc/sssd/sssd.conf | 2 +-<br>
Linux/ldap/ldap.yaml | 24<br>
+++++++++++++++--------<br>
5 files changed, 38 insertions(+), 12 deletions(-)<br>
rename Linux/ldap/etc/openldap/{certs => cacerts}/ca.crt (100%)<br>
<br>
<br>
If I ssh to my desktop I get <br>
<br>
predragp@lake$ git pull<br>
Host key fingerprint is<br>
SHA256:<wbr>XEkrneUFkkAPyf0gMOQKa3amiAp3Qr<wbr>Xmu1x+sIJMcsA<br>
+---[ECDSA 256]---+<br>
| .++++o.o.. |<br>
| . .+=+B . |<br>
|. . . . ..Bo. |<br>
|.E + o . o . |<br>
| .= * S |<br>
|o=o* . |<br>
|+=+.o .o |<br>
|o.o+.+. . |<br>
|. +o.. |<br>
+----[SHA256]-----+<br>
Password for <a href="mailto:git@git.int.autonlab.org">git@git.int.autonlab.org</a>:<br>
<br>
which is the indication that my .ssh/config file and the ssh-key were<br>
not read even though<br>
<br>
Host git <br>
HostName <a href="http://git.int.autonlab.org" rel="noreferrer" target="_blank">git.int.autonlab.org</a><br>
Port 2222<br>
User git <br>
IdentityFile /home/predragp/.ssh/git_rsa <br>
<br>
However if I log from the terminal to my desktop I don't have a Git<br>
issue. <br>
<br>
<br>
Best,<br>
Predrag<br>
<div><div class="h5"><br>
<br>
<br>
<br>
<br>
<br>
> ><br>
> > On 11/6/18 3:14 PM, Predrag Punosevac wrote:<br>
> ><br>
> >> Matthew Barnes <<a href="mailto:mbarnes1@andrew.cmu.edu">mbarnes1@andrew.cmu.edu</a>> wrote:<br>
> >><br>
> >> Also having this problem. Trying to create a new notebook hangs on<br>
> >>> "Creating new notebook in", and unable to open old notebooks. Anyone's<br>
> >>> setup currently working?<br>
> >>><br>
> >>> Jupyter Notebook is using sqlite database to store the info. Unless you<br>
> >> explicitly force Jupyter to create the database on the scratch directory<br>
> >> the database is stored on the NFS share. There is nothing worse one can<br>
> >> do in terms of data consistency than put a database or a private Git<br>
> >> repo (talking about the server) onto the NFS. The datebase was left in<br>
> >> inconsistent state after the file server was rebooted. You have to clear<br>
> >> it and possibly recreate the database to be able to use Jupyter<br>
> >> Notebook.<br>
> >><br>
> >> Best,<br>
> >> Predrag<br>
> >><br>
> >><br>
> >> On Tue, Nov 6, 2018 at 12:44 PM Vincent Jeanselme <<br>
> >>> <a href="mailto:vjeansel@andrew.cmu.edu">vjeansel@andrew.cmu.edu</a>><br>
> >>> wrote:<br>
> >>><br>
> >>> Hello,<br>
> >>>><br>
> >>>> Has anyone faced problems with running Jupyter Notebook since yesterday<br>
> >>>> ?<br>
> >>>> Did you remember what was the change to operate after the last reboot of<br>
> >>>> the sqlite database ?<br>
> >>>><br>
> >>>> Thank you,<br>
> >>>><br>
> >>>> Vincent<br>
> >>>><br>
> >>>> --<br>
> >>>> Vincent Jeanselme<br>
> >>>> -----------------<br>
> >>>> Analyst Researcher<br>
> >>>> Auton Lab - Robotics Institute<br>
> >>>> Carnegie Mellon University<br>
> >>>><br>
> >>>><br>
> >>>> --<br>
> > Vincent Jeanselme<br>
> > -----------------<br>
> > Analyst Researcher<br>
> > Auton Lab - Robotics Institute<br>
> > Carnegie Mellon University<br>
> ><br>
> ><br>
> <br>
> <br>
> -- <br>
> <br>
</div></div>> *Chirag Nagpal* Graduate Student, Language Technologies Institute<br>
<div class="HOEnZb"><div class="h5">> School of Computer Science<br>
> Carnegie Mellon University<br>
> <a href="http://cs.cmu.edu/~chiragn" rel="noreferrer" target="_blank">cs.cmu.edu/~chiragn</a><br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span><b>Chirag Nagpal<br></b>
Graduate Student, Language Technologies Institute<br>
School of Computer Science<br>
Carnegie Mellon University<br></span></span></span></div><div><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)"><span><a href="http://cs.cmu.edu/~chiragn" target="_blank">cs.cmu.edu/~chiragn</a><br></span></span></span></div></div></div></div></div></div>
</div>