Original commit message:
------------------------
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.
Initially the listSwitches functions depended directly on argList functionality
but this has now been factored out so that the listSwitches functions are more
general and require only debug functionality.
Provides better context for the available boundary conditions, fvOptions,
functionObjects etc. and thus returns only those available to and compatible
with the particular application.
e.g.
pimpleFoam -help
Usage: pimpleFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-listFunctionObjects
List functionObjects
-listFvOptions List fvOptions
-listRegisteredSwitches
List switches registered for run-time modification
-listScalarBCs List scalar field boundary conditions (fvPatchField<scalar>)
-listSwitches List switches declared in libraries but not set in
etc/controlDict
-listTurbulenceModels
List turbulenceModels
-listUnsetSwitches
List switches declared in libraries but not set in
etc/controlDict
-listVectorBCs List vector field boundary conditions (fvPatchField<vector>)
-noFunctionObjects
do not execute functionObjects
-parallel run in parallel
-postProcess Execute functionObjects only
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
pimpleFoam listTurbulenceModels
pimpleFoam -listTurbulenceModels
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: dev |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : dev-39c46019e44f
Exec : pimpleFoam -listTurbulenceModels
Date : Jun 10 2017
Time : 21:37:49
Host : "dm"
PID : 675
Case : /home/dm2/henry/OpenFOAM/OpenFOAM-dev
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Turbulence models
3
(
LES
RAS
laminar
)
RAS models
18
(
LRR
LamBremhorstKE
LaunderSharmaKE
LienCubicKE
LienLeschziner
RNGkEpsilon
SSG
ShihQuadraticKE
SpalartAllmaras
kEpsilon
kOmega
kOmegaSST
kOmegaSSTLM
kOmegaSSTSAS
kkLOmega
qZeta
realizableKE
v2f
)
LES models
10
(
DeardorffDiffStress
Smagorinsky
SpalartAllmarasDDES
SpalartAllmarasDES
SpalartAllmarasIDDES
WALE
dynamicKEqn
dynamicLagrangian
kEqn
kOmegaSSTDES
)
Further work will be needed to support the -listTurbulenceModels option in
multiphase solvers.
- some functionality similar to what the standary library <iterator>
provides.
* stdFoam::begin() and stdFoam::end() do type deduction,
which means that many cases it is possible to manage these types
of changes.
For example, when managing a number of indices:
Map<labelHashSet> lookup;
1) Longhand:
for
(
Map<labelHashSet>::const_iterator iter = lookup.begin();
iter != lookup.end();
++iter
)
{ .... }
1b) The same, but wrapped via a macro:
forAllConstIter(Map<labelHashSet>, lookup, iter)
{ .... }
2) Using stdFoam begin/end templates directly
for
(
auto iter = stdFoam::begin(lookup);
iter != stdFoam::end(lookup);
++iter
)
{ .... }
2b) The same, but wrapped via a macro:
forAllConstIters(lookup, iter)
{ .... }
Note that in many cases it is possible to simply use a range-based for.
Eg,
labelList myList;
for (auto val : myList)
{ ... }
for (const auto& val : myList)
{ ... }
These however will not work with any of the OpenFOAM hash-tables,
since the standard C++ concept of an iterator would return a key,value
pair when deferencing the *iter.
The deduction methods also exhibits some slightly odd behaviour with
some PtrLists (needs some more investigation).
- ensure proper and sensible handling of empty names.
Eg, isDir(""), isFile("") are no-ops, and avoid file-stat
- rmDir:
* optional 'silent' option to suppress messages.
* removes all possible sub-entries, instead of just giving up on
the first problem encountered.
- reduced code duplication in etcFiles
ENH: provide WM_USER_RESOURCE_DIRNAME define (in foamVersion.H)
- this is still a hard-coded value, but at least centrally available
- was previously only within string expansions, but cover dictionaries
as well for consistency
ENH: replace the never-used fileName::caseName() functionality
- stringOps::inplaceReplaceVar() is more general
stringOps::inplaceReplaceVar(myfile, "FOAM_CASE");
STYLE: relax parameter passing when calling some POSIX 'query' functions.
- A std::string is sufficient since the functions use a plain C-string.
Eg, getEnv("SOMETHING").
Retain more stringent Foam::word for things like setEnv, since this
could be useful.
- Cleanup/centralize handling of -decomposeParDict by relocating
common code into argList. Ensures that all processes receive
identical information about the -decomposeParDict opton.
- Only use alternative decomposeParDict for simpleFoam/motorBike
tutorial so that this will be included in the test loop for snappy.
- Added Mattijs' fix for surfaceRedistributePar.
This supports the abstraction of the set of fields from the field code
generation macros making it easier to change the set of fields supported
by OpenFOAM. This functionality is demonstrated in the updated
fvPatchFields macros and will be applied to the rest of the field code
generation macros in the future.
replace system() call with vfork/exec combination (issue #185)
Tested systemCall function object, dynamicCode, but should be rechecked with IB+openmpi
@Prashant
See merge request !55
The normal library system() command uses 'fork', which causes
problems on IB+OPENMPI.
STYLE: add Foam:: qualifier to system calls to make them easier to spot.
- this option overrides any controlDict settings as a convenient means
to selecting profiling without messing with the controlDict.
- provide Profiling::writeNow() to emit profiling for utilities that
don't have any natural time increment mechanism to trigger it.
with the more general and flexible 'postProcess' utility and '-postProcess' solver option
Rationale
---------
Both the 'postProcess' utility and '-postProcess' solver option use the
same extensive set of functionObjects available for data-processing
during the run avoiding the substantial code duplication necessary for
the 'foamCalc' and 'postCalc' utilities and simplifying maintenance.
Additionally consistency is guaranteed between solver data processing
and post-processing.
The functionObjects have been substantially re-written and generalized
to simplify development and encourage contribution.
Configuration
-------------
An extensive set of simple functionObject configuration files are
provided in
OpenFOAM-dev/etc/caseDicts/postProcessing
and more will be added in the future. These can either be copied into
'<case>/system' directory and included into the 'controlDict.functions'
sub-dictionary or included directly from 'etc/caseDicts/postProcessing'
using the '#includeEtc' directive or the new and more convenient
'#includeFunc' directive which searches the
'<etc>/caseDicts/postProcessing' directories for the selected
functionObject, e.g.
functions
{
#includeFunc Q
#includeFunc Lambda2
}
'#includeFunc' first searches the '<case>/system' directory in case
there is a local configuration.
Description of #includeFunc
---------------------------
Specify a functionObject dictionary file to include, expects the
functionObject name to follow (without quotes).
Search for functionObject dictionary file in
user/group/shipped directories.
The search scheme allows for version-specific and
version-independent files using the following hierarchy:
- \b user settings:
- ~/.OpenFOAM/\<VERSION\>/caseDicts/postProcessing
- ~/.OpenFOAM/caseDicts/postProcessing
- \b group (site) settings (when $WM_PROJECT_SITE is set):
- $WM_PROJECT_SITE/\<VERSION\>/caseDicts/postProcessing
- $WM_PROJECT_SITE/caseDicts/postProcessing
- \b group (site) settings (when $WM_PROJECT_SITE is not set):
- $WM_PROJECT_INST_DIR/site/\<VERSION\>/caseDicts/postProcessing
- $WM_PROJECT_INST_DIR/site/caseDicts/postProcessing
- \b other (shipped) settings:
- $WM_PROJECT_DIR/etc/caseDicts/postProcessing
An example of the \c \#includeFunc directive:
\verbatim
#includeFunc <funcName>
\endverbatim
postProcess
-----------
The 'postProcess' utility and '-postProcess' solver option provide the
same set of controls to execute functionObjects after the run either by
reading a specified set of fields to process in the case of
'postProcess' or by reading all fields and models required to start the
run in the case of '-postProcess' for each selected time:
postProcess -help
Usage: postProcess [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-field <name> specify the name of the field to be processed, e.g. U
-fields <list> specify a list of fields to be processed, e.g. '(U T p)' -
regular expressions not currently supported
-func <name> specify the name of the functionObject to execute, e.g. Q
-funcs <list> specify the names of the functionObjects to execute, e.g.
'(Q div(U))'
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
pimpleFoam -postProcess -help
Usage: pimpleFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-field <name> specify the name of the field to be processed, e.g. U
-fields <list> specify a list of fields to be processed, e.g. '(U T p)' -
regular expressions not currently supported
-func <name> specify the name of the functionObject to execute, e.g. Q
-funcs <list> specify the names of the functionObjects to execute, e.g.
'(Q div(U))'
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-postProcess Execute functionObjects only
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
The functionObjects to execute may be specified on the command-line
using the '-func' option for a single functionObject or '-funcs' for a
list, e.g.
postProcess -func Q
postProcess -funcs '(div(U) div(phi))'
In the case of 'Q' the default field to process is 'U' which is
specified in and read from the configuration file but this may be
overridden thus:
postProcess -func 'Q(Ua)'
as is done in the example above to calculate the two forms of the divergence of
the velocity field. Additional fields which the functionObjects may depend on
can be specified using the '-field' or '-fields' options.
The 'postProcess' utility can only be used to execute functionObjects which
process fields present in the time directories. However, functionObjects which
depend on fields obtained from models, e.g. properties derived from turbulence
models can be executed using the '-postProcess' of the appropriate solver, e.g.
pisoFoam -postProcess -func PecletNo
or
sonicFoam -postProcess -func MachNo
In this case all required fields will have already been read so the '-field' or
'-fields' options are not be needed.
Henry G. Weller
CFD Direct Ltd.
To compile with 64bit labels set
WM_LABEL_SIZE=64
in ~/OpenFOAM/dev/prefs.sh
source ~/.bashrc
then Allwmake in OpenFOAM-dev.
This will build into for example OpenFOAM-dev/platforms/linux64ClangDPInt64Opt
If WM_LABEL_SIZE is unset or set to 32:
WM_LABEL_SIZE=32
the build would be placed into OpenFOAM-dev/platforms/linux64ClangDPInt32Opt
Thus both 32bit and 64bit label builds can coexist without problem.
Links are followed in most cases, with some notable exceptions:
- mv, mvBak:
renames the link, not the underlying file/directory
- rmDir:
remove the symlink to a directory, does not recurse into the
underlying directory
- alternative to WM_PROJECT_INST_DIR/site for systems with locked down
installation paths (eg, when packaged as RPM or deb)
When "$WM_PROJECT_SITE" is defined, it is used in favour of
"$WM_PROJECT_INST_DIR/site"
