DUMM3: Difference between revisions
No edit summary |
m (24 revisions) |
||
| (23 intermediate revisions by one other user not shown) | |||
| Line 1: | Line 1: | ||
== Attendees & Time== | == Attendees & Time== | ||
# Oliv Eidam | |||
# Sarah Boyce | |||
# Rafaela Ferreira | |||
# Gabe Rocklin | |||
# Peter Kolb | |||
# Pascal Wassam | |||
# Hao Fan | |||
# Matt Merski | |||
# Yu Chen | |||
# Denise Teotico | |||
# Francesco Colizzi | |||
# Michael Mysinger | |||
'''Next DUM on | Date: August 06, 2008, 4:00pm - 4:45pm | ||
'''Next DUM on Sept 3, 2008 ''' | |||
== Hardware updates== | == Hardware updates== | ||
''Pascal'': the write load on a disk even when the entire cluster is filled with DOCK jobs is negligible, i.e., it rarely happens that two jobs write to the same disk at the same time (cf. [[DUMM1]]). | |||
== Software updates == | == Software updates == | ||
''Oliv'' reports about a recent change in the docking workflow (when starting from <tt>startdockblaster5</tt>): tarted residues can now be found in the form of <tt>.prot2</tt> files, which should be appended to <tt>amb.crg.oxt</tt>. Find more information [[Preparing the protein#Tarting the protein|here]]. | |||
===Requests/Improvements=== | ===Requests/Improvements=== | ||
== Database updates == | |||
== Varia == | == Varia == | ||
''Oliv'' reports how to obtain a VPN account for the UCSF network: get an account via [http://oaais.ucsf.edu/OAAIS/service_catalog/networking/219-DSY.html http://oaais.ucsf.edu/OAAIS/service_catalog/networking/219-DSY.html] (students already have one (email account), others need to apply for one with their employee ID and SSN). Afterwards, the VPN client can be run directly from the browser.<br> | |||
''Peter'': there is a page describing [[How to use the QB3 cluster|docking on the QB3 cluster]].<br> | |||
''All'': how to find out about the current version of the docking environment? How can we make sure that dependencies in scripts don't get broken? Is there a way to maintain a certain flexibility in the docking scripts?<br> | |||
''Michael/Peter'' have started to develop their own versions of some key scripts, how can these be made available to the other users?<br> | |||
''Pascal'': a CVS/SVN system could be set up in such a way that all users are automatically notified upon change or addition of a script. | |||
== Action Items == | == Action Items == | ||
''Pascal:'' think about a structure for a potential docking development environment. | |||
[[Category:DUMM]] | |||
→ back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]] | |||
Latest revision as of 20:11, 8 October 2012
Attendees & Time
- Oliv Eidam
- Sarah Boyce
- Rafaela Ferreira
- Gabe Rocklin
- Peter Kolb
- Pascal Wassam
- Hao Fan
- Matt Merski
- Yu Chen
- Denise Teotico
- Francesco Colizzi
- Michael Mysinger
Date: August 06, 2008, 4:00pm - 4:45pm
Next DUM on Sept 3, 2008
Hardware updates
Pascal: the write load on a disk even when the entire cluster is filled with DOCK jobs is negligible, i.e., it rarely happens that two jobs write to the same disk at the same time (cf. DUMM1).
Software updates
Oliv reports about a recent change in the docking workflow (when starting from startdockblaster5): tarted residues can now be found in the form of .prot2 files, which should be appended to amb.crg.oxt. Find more information here.
Requests/Improvements
Database updates
Varia
Oliv reports how to obtain a VPN account for the UCSF network: get an account via http://oaais.ucsf.edu/OAAIS/service_catalog/networking/219-DSY.html (students already have one (email account), others need to apply for one with their employee ID and SSN). Afterwards, the VPN client can be run directly from the browser.
Peter: there is a page describing docking on the QB3 cluster.
All: how to find out about the current version of the docking environment? How can we make sure that dependencies in scripts don't get broken? Is there a way to maintain a certain flexibility in the docking scripts?
Michael/Peter have started to develop their own versions of some key scripts, how can these be made available to the other users?
Pascal: a CVS/SVN system could be set up in such a way that all users are automatically notified upon change or addition of a script.
Action Items
Pascal: think about a structure for a potential docking development environment.
→ back to DUMM main page