The current implentation do not guarantee that the partitions are contiguous.

• Remove gmsh reader from src
• Add gmsh reader to example
• Output results as vtk

Run gencon + parRSB to generate a ma2 file.

Describe the bug
Sometime in the last month, something broke in parSB related to how the connectivity works for serial cases. When I run a case in serial, I get a negative Jacobian error for every element in the mesh, but this error disappears and the case runs as normal if I run in parallel.

The reason I'm sure the error lies somewhere in parSB is because if you pre-generate the .co2 file, there is no error. So something is wrong with the automatic .co2 file generation for serial problems.

To Reproduce
I've attached a few input files that run with nekRS for you to replicate the problem. Download these files and run the following:

This fails with negative Jacobian errors:

nrsmpi pyramid 1 

This works:

nrsmpi pyramid 2

This also works:

gencon
nrsmpi pyramid 1

Expected behavior
Cases should be able to run in serial.

Currently, we have hard coded gs_crystal in genmap-laplacian.c and gs_pairwise in
genmap-quality.c. We should select these method automatically. May be we do this once
at the top level ?

We can get rid of this O(n^2) loop:
https://github.com/Nek5000/parRSB/blob/master/src/con-periodic.c#L188

Currently, the following functions are not valgrind clean:

• rcb_local
• findSegments
• mg_setup

Tested on BGQ using fparRSB_partMesh()

• Remove type from struct rcb_element and struct rsb_element
• Remove globalId0 from struct rsb_element
• Replace GenmapMalloc by tmalloc when allocating structs
• Replace GenmapMalloc by buffer_reserve when allocating arrays
• Replace GenmapFree by free and buffer_free
• Replace GenmapX by gslib types where X is int, long, uint, ulong.

Our current bucket sort of the Fielder vector results in unbalanced bin sizes. Hence, we may run out of memory on some ranks.

Currently we're using a fixed iteration counts which is not robust and efficient.

POSIX has reserved these names.