New nmr server (was Talos failed for 1brv)

google-code-export / cing

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New nmr server (was Talos failed for 1brv) #315

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

What steps will reproduce the problem?
1. Look for ERROR in:
https://cvca.cmbi.ru.nl/tmp/cing/ano/Lu5fTO/1brv_cs_pk_2mdl.cing/Logs/1brv_cs_pk
_2mdl_2011-11-29_11-31-29.txt

Probably misconfigured in the new server.

Original issue reported on code.google.com by jurge...@gmail.com on 29 Nov 2011 at 10:43

GoogleCodeExporter commented 9 years ago

Fixed configuration (did chmod a+x to a file) and tested to:
https://cvca.cmbi.ru.nl/tmp/cing/ano/Q46PuO/1brv_cs_pk_2mdl.cing/Logs/1brv_cs_pk
_2mdl_2011-11-29_12-08-41.txt

We'll reopen this issue for any easy-to-fix new ones that come up with the new 
nmr server.

Original comment by jurge...@gmail.com on 29 Nov 2011 at 11:11

Changed title: New nmr server (was Talos failed for 1brv)
Changed state: Verified

GoogleCodeExporter commented 9 years ago

BMRB id is missing from NRG-CING query interface and RDB

iLcvca/cingStable/ echo "SELECT name, bmrb_id FROM nrgcing.cingentry where 
name='1brv';" | psql pdbmlplus pdbj
 name | bmrb_id 
------+---------
 1brv |        
(1 row)

Original comment by jurge...@gmail.com on 29 Nov 2011 at 12:29

Changed title: New nmr server BMRB id missing (was Talos failed for 1brv)
Changed state: Accepted

GoogleCodeExporter commented 9 years ago

Fixed the above by running proper prep.

Original comment by jurge...@gmail.com on 29 Nov 2011 at 2:25

Changed title: New nmr server (was Talos failed for 1brv)
Changed state: Fixed

GoogleCodeExporter commented 9 years ago

No output ccpn file for assign step in:

https://cvca.cmbi.ru.nl/NRG-CING/data/l5/2l5v/log_nrgCing/2l5v_2011-11-29_14-56-
40.log

Original comment by jurge...@gmail.com on 29 Nov 2011 at 2:26

Changed state: Started

GoogleCodeExporter commented 9 years ago

Considering CVCA still has the CVS version checked out it is time to update to 
latest from SVN archive following 
http://code.google.com/p/nmrrestrntsgrid/wiki/UpdatingCCPNapiForDevelopment

Original comment by jurge...@gmail.com on 29 Nov 2011 at 2:39

GoogleCodeExporter commented 9 years ago

Reinstalling fixed bug.
Checked in:
https://cvca.cmbi.ru.nl/NRG-CING/prep/F/l5/2l5v/2l5v_FC_assign.log

Original comment by jurge...@gmail.com on 29 Nov 2011 at 3:10

Changed state: Fixed

GoogleCodeExporter commented 9 years ago

Even with -Xmx1800m java 32 bit had a hard time on Ubuntu.
Going back to 1500m.
See: https://cvca.cmbi.ru.nl/NRG-CING/prep/C/l5/2l5r/2l5r.log

Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.

Original comment by jurge...@gmail.com on 29 Nov 2011 at 5:51

Changed state: Started

GoogleCodeExporter commented 9 years ago

Fixed by reducing to 1500m in a neat way uniform over the CING python code.

Original comment by jurge...@gmail.com on 1 Dec 2011 at 10:57

Changed state: Fixed