No longer works so is just crufting up the code

 Conflict: examples/main.c resolved

Multi time step warnings and stop condition

Solves the issues #111 flagged by @alepper 

We now explicitly check the time-step sizes given in input are sensible.

We now have a function to test whether we have reached the end of the simulation or not. 

Branch can be removed.

See merge request !104

Pedro naming scheme, clockstime->clocks_time, cpufreq->clocks_cpufreq, estimate_cpufreq->clocks_estimate_cpufreq

Make sure CPU frequency is initialised once (per rank), allow user to define it and report the frequency used

functions. CPU_TPS is now only found in one Makefile.am and one
file, clocks.c.

Many of the uses are commented out or protected by TIMER_VERBOSE.
TIMER_VERBOSE no longer compiles, so these changes are untested
and just aim to guide the future...

After tests prefer sleep() cpu freq estimate, that works well on i7 (with constant_tsc), sys maxfreq looks like the turbo boost value so not as good

Simplest possible version. Still reports tick value for comparison.

This reverts commit 4654968d.

Teach me to do more than one thing at a time...

Simplest possible version. Still reports tick value for comparison.

Nicer summary message for METIS

Prints "yes" instead of the full path to metis in the configure summary.

See merge request !102

Add new initial partition schemes and extend repartition ones.

Add new schemes for the initial partition of cells for MPI.

The initial cell distribution can now be based on a METIS partition of the cell
graph using particle counts per cell and a simple unweighted version. The distribution
can also be based on a vectorised selection of seed cells. This is guaranteed
to work for all cases when the number of MPI nodes is less than the number of 
cells (the grid and METIS based ones do not guarantee this), so is the fallback
method when the others fail.

Repartition is also extended to offer particle count based weights, as well the
existing task times weights for edges and vertices, which is extended to allow
weighting by edges only and a hybrid particle count vertices and times for edges.

A failure to repartition is handled by continuing with the existing partition.

The new options are handled by flags:

   * `-R`  - reparition type: 'n', 'b', 'v', 'e', 'x'
   * `-P`  - initial Partition type: 'g', 'm', 'w', 'v'

note the old '-g' flag is removed, use '-P g' or '-P g n n n' now. 

The repartition types are:
   * 'n' None, for completeness.
   * 'b' both, task time weighted vertices and edges (as as current).
   * 'v' vertex particle count weighted vertices, no edge weights.
   * 'e' task time weighted edges, no vertex weights.
   * 'x' task time weighted edges, particle count weighted vertices.

And the initial partition types:
   * 'g' geometric grid partition (as now)
   * 'm' METIS partition without any weights
   * 'w' METIS partition with particle count weighted vertices
   * 'v' vectorised cell array positions used as seeds for partition

Not giving any options just gives the existing behaviour, i.e. grid initial
partition and task time weighted redistribution.


See merge request !76

Compressed i/o

This adds gzip compression to the datasets within the HDF5 outputs. That can save a lot of storage space for arrays that are constant (mass,...) or similar/regular (IDs, h, ...).

We can play with the chunk sizes and compression levels later on, when we have "real" runs and a parameter file.

It "solves" issue #106.

Feel free to remove the source branch.

See merge request !98

Repartition type is always none, but initial partitions can be based on grid and vector

Sort some headers into alphabetic order

Inter procedural optimization

These patches enable inter procedural optimization for the GCC and
Intel compilers. They may also work for the LLVM/clang.

Further response to #104.

Matthieu, I tried these and didn't see any improvements.
Can you also check please.

See merge request !101

Autotools update

Updates autotools to include support for avx2, plus some smaller
updates to scripts.

See merge request !96

It is probably the case that the -x<code> option from AX_CC_MAXOPT is sufficient to get AVX support

Remove unused define and make check static