UM7.1 standard job failing to submit to queue

[jmarsham]

I'm at the UM turorial at the Met Office

I have copied the NCAS v7.1 standard global-NAE-4 job and am trying to run the global.

When I hit submit I get:

asked for pwd
CM_MAIN calling extract
pwd again
base extract OK
pwd again
model extract OK
pwd again
FCM_MAIN: Extract OK

FCM_MAIN: submitting
umui_runs/xelya-309163553/umuisubmit_clr

On PUMA I then have:

puma$ps -f
UID        PID  PPID  C STIME TTY          TIME CMD
jmarsham  1992  1991  0 16:34 pts/25   00:00:00 -bash
jmarsham  2013  1992  0 16:34 pts/25   00:00:00 /bin/sh
/usr/local/bin/umui
jmarsham  2014  2013  0 16:34 pts/25   00:00:00 /bin/sh
/home/umui/umui/ghui2.0/bin/ghui umui x
jmarsham  2015  2014  0 16:34 pts/25   00:00:00 /home/umui/bin/wish8.3
/home/umui/umui/ghui2.0/tcl/entry.tcl /home/umui/bin/wish8.3 rsh
/home/umui/umui/ghui
jmarsham  2018  2015  0 16:35 pts/25   00:00:01 /home/umui/bin/wish8.3
/home/umui/umui/ghui2.0/vn1.4/tcl/edit_job.tcl /home/umui/bin/wish8.3 rsh
umui 7.1 /h
jmarsham  2729  2018  0 16:36 pts/25   00:00:00 /usr/bin/ksh
/home/jmarsham/umui_jobs/xelya/FCM_MAIN_SCR 309163553
jmarsham  2730  2018  0 16:36 pts/25   00:00:00 cat
jmarsham  2900  2729  0 16:37 pts/25   00:00:00 ssh login.hector.ac.uk -l
jmarsham -n /opt/pbs/8.1.4/bin/qsub -S /bin/ksh
umui_runs/xelya-309163553/umuisubm
jmarsham  2904  1992  0 16:38 pts/25   00:00:00 ps -f

On hector: umui_runs/xelya-309163553 is created but nothing goes to the queue. Any ideas?

Thanks,
John

[jmarsham]

PS: PUMA is very slow, and repeatedly hangs. Others here don't appear to have this problem

[ros]

Hi John,

You need to set up ssh-agent so that you won't keep getting asked for you password. The second stage of the submit is hanging. Submission of UM jobs at 7.x will not work without first setting up ssh properly.

Please see instructions available at ​http://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/UmTutorial/SettingUp

I'm not aware of any problems with PUMA. However, I do know from other people that the link from the Met Office to PUMA can often be very slow.

Regards,
Ros.

[jmarsham]

Thanks. I'm aware of this and thought it was working. This system didn't appear to work, so Willie (he's here) so we thought we'd found a work around it. I'll try it again
John

Replying to ros:

Hi John,

You need to set up ssh-agent so that you won't keep getting asked for you password. The second stage of the submit is hanging. Submission of UM jobs at 7.x will not work without first setting up ssh properly.

Please see instructions available at ​http://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/UmTutorial/SettingUp

I'm not aware of any problems with PUMA. However, I do know from other people that the link from the Met Office to PUMA can often be very slow.

Regards,
Ros.

[jmarsham]

This is the same eror I had on Tuesday (below). Any ideas?
John

puma$ssh-keygen -f ~/.ssh/id_dsa -C "<username>@puma.nerc.ac.uk"
Generating public/private rsa key pair.
/home/jmarsham/.ssh/id_dsa already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/jmarsham/.ssh/id_dsa.
Your public key has been saved in /home/jmarsham/.ssh/id_dsa.pub.
The key fingerprint is:
d2:61:4d:47:1d:5b:a4:6f:02:d4:a4:ad:11:a3:db:e1 <username>@puma.nerc.ac.uk
puma$cat ~/.ssh/id_dsa.pub | ssh <username>@login.hector.ac.uk 'mkdir -p .ssh ; cat - >> ~/.ssh/authorized_keys'
-bash: username: No such file or directory
puma$

Replying to ros:

Hi John,

You need to set up ssh-agent so that you won't keep getting asked for you password. The second stage of the submit is hanging. Submission of UM jobs at 7.x will not work without first setting up ssh properly.

Please see instructions available at ​http://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/UmTutorial/SettingUp

I'm not aware of any problems with PUMA. However, I do know from other people that the link from the Met Office to PUMA can often be very slow.

Regards,
Ros.

[jmarsham]

Sorry, were errors in my attempt below. I have now worked through all this and it appears successful, except step 6:

puma$ssh-add
Could not open a connection to your authentication agent.

Again, I remember this from attempts on Tuesday

Replying to jmarsham:

This is the same eror I had on Tuesday (below). Any ideas?
John

puma$ssh-keygen -f ~/.ssh/id_dsa -C "<username>@puma.nerc.ac.uk"
Generating public/private rsa key pair.
/home/jmarsham/.ssh/id_dsa already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/jmarsham/.ssh/id_dsa.
Your public key has been saved in /home/jmarsham/.ssh/id_dsa.pub.
The key fingerprint is:
d2:61:4d:47:1d:5b:a4:6f:02:d4:a4:ad:11:a3:db:e1 <username>@puma.nerc.ac.uk
puma$cat ~/.ssh/id_dsa.pub | ssh <username>@login.hector.ac.uk 'mkdir -p .ssh ; cat - >> ~/.ssh/authorized_keys'
-bash: username: No such file or directory
puma$

Replying to ros:

Hi John,

You need to set up ssh-agent so that you won't keep getting asked for you password. The second stage of the submit is hanging. Submission of UM jobs at 7.x will not work without first setting up ssh properly.

Please see instructions available at ​http://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/UmTutorial/SettingUp

I'm not aware of any problems with PUMA. However, I do know from other people that the link from the Met Office to PUMA can often be very slow.

Regards,
Ros.

[jmarsham]

Needed to source my .kshrc even though I had logged off PUMA and back on.

UMUI submission is now not demanding password and there is a job in the Hector queue

Replying to jmarsham:

Sorry, were errors in my attempt below. I have now worked through all this and it appears successful, except step 6:

puma$ssh-add
Could not open a connection to your authentication agent.

Again, I remember this from attempts on Tuesday

Replying to jmarsham:

This is the same eror I had on Tuesday (below). Any ideas?
John

puma$ssh-keygen -f ~/.ssh/id_dsa -C "<username>@puma.nerc.ac.uk"
Generating public/private rsa key pair.
/home/jmarsham/.ssh/id_dsa already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/jmarsham/.ssh/id_dsa.
Your public key has been saved in /home/jmarsham/.ssh/id_dsa.pub.
The key fingerprint is:
d2:61:4d:47:1d:5b:a4:6f:02:d4:a4:ad:11:a3:db:e1 <username>@puma.nerc.ac.uk
puma$cat ~/.ssh/id_dsa.pub | ssh <username>@login.hector.ac.uk 'mkdir -p .ssh ; cat - >> ~/.ssh/authorized_keys'
-bash: username: No such file or directory
puma$

Replying to ros:

Hi John,

You need to set up ssh-agent so that you won't keep getting asked for you password. The second stage of the submit is hanging. Submission of UM jobs at 7.x will not work without first setting up ssh properly.

Please see instructions available at ​http://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/UmTutorial/SettingUp

I'm not aware of any problems with PUMA. However, I do know from other people that the link from the Met Office to PUMA can often be very slow.

Regards,
Ros.