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3550. By Adam Candy on 2011-08-02

Bringing partition.cpp back - effectively revoking r3549 (apologies for the break in history).

3549. By Adam Candy on 2011-08-02

Automatic sync to launchpad

3548. By Jon Hill on 2011-08-02

Apparently ar -q does add new object files into the archive if they alreadt exist there on some systems (i.e. Ubuntu). This means when you chnage existing code it doesn't get built into the binary. Switching to -r

3547. By Jon Hill on 2011-08-02

Adding the missing hyperlight back in

3546. By Jon Hill on 2011-08-02

For for the ext3_build fix. The line ar -cr lib/libfluidity.a */*.o was including all .o files in all directories.
Some of these contained a main() function (e.g. climatology) which was being used for some binaries (e.g. periodise)
This fix now lists explicitly the directories which are to have their .o files included in libfluidity.a

Note that listing each ar -cr seperately was very slow (~45 seconds for a build where no files are touched). The current
fix takes ~9 seconds on rubik for such a build.

3545. By Rhodri Nelson on 2011-08-01

When generating a sigma layered mesh undesirable elements near the bottom of the mesh should no longer be created. The mesh should now be nicely layered.

This is done through first creating the mesh using a dummy vector field from a single chain to get the desired topological properties. This node locations are then over written with the correct ones.

3544. By Tim Bond on 2011-08-01

Various changes supplied by James Maddison based on his work over the last
year, comprising:

Bugfixes and obsolete code removal:

* Updated bibliography for the manual, correcting reference errors
* Removing unused 'decomp' directory
* Correcting misleading (wrong!) ewrite messages
* Removing unused old-adjoint code
* Various small but important bugfixes
* Removing legacy shallow water codes
* Removing broken diagnostic

And a new addition:

* Adding boundary conditions to diagnostic field algorithms

3543. By Paul Woodhams on 2011-08-01

Fix for bugs #798736 and #799658 where Zoltan produces empty partitions. Within Zoltan we now check for whether an empty partition would be created prior to migrating any data. If an empty partition would be created we tighten the load imbalance tolerance and try again.

3542. By Jon Hill on 2011-08-01

Fix the build system for filsesystems that have 1 second or poorer temporal resolution.

libfluidity.a is now built *after* all subdirectories.

3541. By Rhodri Nelson on 2011-07-27

Updating the NetCDF reader so that it can handle files in a similar form to the CF-1.0 convention but with missing attributes. The manual and schema have also been updated to hopefully be a little more clear about the format of the data required.