Original commit message:
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Parallel IO: New collated file format
When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
mesh(es) has historically been stored in multiple files within separate
directories for each processor. Processor directories are named 'processorN',
where N is the processor number.
This commit introduces an alternative "collated" file format where the data for
each decomposed field (and mesh) is collated into a single file, which is
written and read on the master processor. The files are stored in a single
directory named 'processors'.
The new format produces significantly fewer files - one per field, instead of N
per field. For large parallel cases, this avoids the restriction on the number
of open files imposed by the operating system limits.
The file writing can be threaded allowing the simulation to continue running
while the data is being written to file. NFS (Network File System) is not
needed when using the the collated format and additionally, there is an option
to run without NFS with the original uncollated approach, known as
"masterUncollated".
The controls for the file handling are in the OptimisationSwitches of
etc/controlDict:
OptimisationSwitches
{
...
//- Parallel IO file handler
// uncollated (default), collated or masterUncollated
fileHandler uncollated;
//- collated: thread buffer size for queued file writes.
// If set to 0 or not sufficient for the file size threading is not used.
// Default: 2e9
maxThreadFileBufferSize 2e9;
//- masterUncollated: non-blocking buffer size.
// If the file exceeds this buffer size scheduled transfer is used.
// Default: 2e9
maxMasterFileBufferSize 2e9;
}
When using the collated file handling, memory is allocated for the data in the
thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that
is allocated. If the data exceeds this size, the write does not use threading.
When using the masterUncollated file handling, non-blocking MPI communication
requires a sufficiently large memory buffer on the master node.
maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the
data exceeds this size, the system uses scheduled communication.
The installation defaults for the fileHandler choice, maxThreadFileBufferSize
and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
the case controlDict file, like other parameters. Additionally the fileHandler
can be set by:
- the "-fileHandler" command line argument;
- a FOAM_FILEHANDLER environment variable.
A foamFormatConvert utility allows users to convert files between the collated
and uncollated formats, e.g.
mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
An example case demonstrating the file handling methods is provided in:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
This tutorial demonstrates moving mesh and AMI with a Lagrangian cloud.
It is very slow, as interaction lists (required to compute collisions)
are not optimised for moving meshes. The simulation time has therefore
been made very short, so that it finishes in a reasonable time. The
mixer only completes a small fraction of a rotation in this time. This
is still sufficient to test tracking and collisions in the presence of
AMI and mesh motion.
In order to generate a convincing animation, however, the end time must
be increased and the simulation run for a number of days.
and the continuous-phase simulation type
For LTS and steady-state simulations the transient option does not need to be
provided as only steady-state tracking is appropriate. For transient running
the Lagrangian tracking may be steady or transient.
terms of the local barycentric coordinates of the current tetrahedron,
rather than the global coordinate system.
Barycentric tracking works on any mesh, irrespective of mesh quality.
Particles do not get "lost", and tracking does not require ad-hoc
"corrections" or "rescues" to function robustly, because the calculation
of particle-face intersections is unambiguous and reproducible, even at
small angles of incidence.
Each particle position is defined by topology (i.e. the decomposed tet
cell it is in) and geometry (i.e. where it is in the cell). No search
operations are needed on restart or reconstruct, unlike when particle
positions are stored in the global coordinate system.
The particle positions file now contains particles' local coordinates
and topology, rather than the global coordinates and cell. This change
to the output format is not backwards compatible. Existing cases with
Lagrangian data will not restart, but they will still run from time
zero without any modification. This change was necessary in order to
guarantee that the loaded particle is valid, and therefore
fundamentally prevent "loss" and "search-failure" type bugs (e.g.,
2517, 2442, 2286, 1836, 1461, 1341, 1097).
The tracking functions have also been converted to function in terms
of displacement, rather than end position. This helps remove floating
point error issues, particularly towards the end of a tracking step.
Wall bounded streamlines have been removed. The implementation proved
incompatible with the new tracking algorithm. ParaView has a surface
LIC plugin which provides equivalent, or better, functionality.
Additionally, bug report <https://bugs.openfoam.org/view.php?id=2517>
is resolved by this change.
- although this has been supported for many years, the tutorials
continued to use "convertToMeters" entry, which is specific to blockMesh.
The "scale" is more consistent with other dictionaries.
ENH:
- ignore "scale 0;" (treat as no scaling) for blockMeshDict,
consistent with use elsewhere.
- allows configuration without an environment variable.
For compatibility still respect FOAM_SIGFPE and FOAM_SETNAN
env-variables
- The env-variables are now treated as true/false switch values.
Previously there was just a check for env exists or not, but this
can be fairly fragile for a user's environment.
Community contribution from Johan Roenby, DHI
IsoAdvector is a geometric Volume-of-Fluid method for advection of a
sharp interface between two incompressible fluids. It works on both
structured and unstructured meshes with no requirements on cell shapes.
IsoAdvector is as an alternative choice for the interface compression
treatment with the MULES limiter implemented in the interFoam family
of solvers.
The isoAdvector concept and code was developed at DHI and was funded
by a Sapere Aude postdoc grant to Johan Roenby from The Danish Council
for Independent Research | Technology and Production Sciences (Grant-ID:
DFF - 1337-00118B - FTP).
Co-funding is also provided by the GTS grant to DHI from the Danish
Agency for Science, Technology and Innovation.
The ideas behind and performance of the isoAdvector scheme is
documented in:
Roenby J, Bredmose H, Jasak H. 2016 A computational method for sharp
interface advection. R. Soc. open sci. 3: 160405.
[http://dx.doi.org/10.1098/rsos.160405](http://dx.doi.org/10.1098/rsos.160405)
Videos showing isoAdvector's performance with a number of standard
test cases can be found in this youtube channel:
https://www.youtube.com/channel/UCt6Idpv4C8TTgz1iUX0prAA
Project contributors:
* Johan Roenby <jro@dhigroup.com> (Inventor and main developer)
* Hrvoje Jasak <hrvoje.jasak@fsb.hr> (Consistent treatment of
boundary faces including processor boundaries, parallelisation,
code clean up
* Henrik Bredmose <hbre@dtu.dk> (Assisted in the conceptual
development)
* Vuko Vukcevic <vuko.vukcevic@fsb.hr> (Code review, profiling,
porting to foam-extend, bug fixing, testing)
* Tomislav Maric <tomislav@sourceflux.de> (Source file
rearrangement)
* Andy Heather <a.heather@opencfd.co.uk> (Integration into OpenFOAM
for v1706 release)
See the integration repository below to see the full set of changes
implemented for release into OpenFOAM v1706
https://develop.openfoam.com/Community/Integration-isoAdvector
Adding special alphaCourantNo for overlaping
Adding bounded term to UEq.H for overInterDyMFoam
Changing to NO_WRITE for the cellMask field
Changing twoSimpleRotors tutorial to open domain
