8959b8e00a
Improvements to existing functionality
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- MPI is initialised without thread support if it is not needed e.g. uncollated
- Use native c++11 threading; avoids problem with static destruction order.
- etc/cellModels now only read if needed.
- etc/controlDict can now be read from the environment variable FOAM_CONTROLDICT
- Uniform files (e.g. '0/uniform/time') are now read only once on the master only
(with the masterUncollated or collated file handlers)
- collated format writes to 'processorsNNN' instead of 'processors'. The file
format is unchanged.
- Thread buffer and file buffer size are no longer limited to 2Gb.
The global controlDict file contains parameters for file handling. Under some
circumstances, e.g. running in parallel on a system without NFS, the user may
need to set some parameters, e.g. fileHandler, before the global controlDict
file is read from file. To support this, OpenFOAM now allows the global
controlDict to be read as a string set to the FOAM_CONTROLDICT environment
variable.
The FOAM_CONTROLDICT environment variable can be set to the content the global
controlDict file, e.g. from a sh/bash shell:
export FOAM_CONTROLDICT=$(foamDictionary $FOAM_ETC/controlDict)
FOAM_CONTROLDICT can then be passed to mpirun using the -x option, e.g.:
mpirun -np 2 -x FOAM_CONTROLDICT simpleFoam -parallel
Note that while this avoids the need for NFS to read the OpenFOAM configuration
the executable still needs to load shared libraries which must either be copied
locally or available via NFS or equivalent.
New: Multiple IO ranks
----------------------
The masterUncollated and collated fileHandlers can now use multiple ranks for
writing e.g.:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)'
In this example ranks 0 ('processor0') and 3 ('processor3') now handle all the
I/O. Rank 0 handles 0,1,2 and rank 3 handles 3,4,5. The set of IO ranks should always
include 0 as first element and be sorted in increasing order.
The collated fileHandler uses the directory naming processorsNNN_XXX-YYY where
NNN is the total number of processors and XXX and YYY are first and last
processor in the rank, e.g. in above example the directories would be
processors6_0-2
processors6_3-5
and each of the collated files in these contains data of the local ranks
only. The same naming also applies when e.g. running decomposePar:
decomposePar -fileHandler collated -ioRanks '(0 3)'
New: Distributed data
---------------------
The individual root directories can be placed on different hosts with different
paths if necessary. In the current framework it is necessary to specify the
root per slave process but this has been simplified with the option of specifying
the root per host with the -hostRoots command line option:
mpirun -np 6 simpleFoam -parallel -ioRanks '(0 3)' \
-hostRoots '("machineA" "/tmp/" "machineB" "/tmp")'
The hostRoots option is followed by a list of machine name + root directory, the
machine name can contain regular expressions.
New: hostCollated
-----------------
The new hostCollated fileHandler automatically sets the 'ioRanks' according to
the host name with the lowest rank e.g. to run simpleFoam on 6 processors with
ranks 0-2 on machineA and ranks 3-5 on machineB with the machines specified in
the hostfile:
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler hostCollated
This is equivalent to
mpirun -np 6 --hostfile hostfile simpleFoam -parallel -fileHandler collated -ioRanks '(0 3)'
This example will write directories:
processors6_0-2/
processors6_3-5/
A typical example would use distributed data e.g. no two nodes, machineA and
machineB, each with three processes:
decomposePar -fileHandler collated -case cavity
# Copy case (constant/*, system/*, processors6/) to master:
rsync -a cavity machineA:/tmp/
# Create root on slave:
ssh machineB mkdir -p /tmp/cavity
# Run
mpirun --hostfile hostfile icoFoam \
-case /tmp/cavity -parallel -fileHandler hostCollated \
-hostRoots '("machineA" "/tmp" "machineB" "/tmp")'
Contributed by Mattijs Janssens
106 lines
3.2 KiB
Bash
Executable File
106 lines
3.2 KiB
Bash
Executable File
#!/bin/sh
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cd ${0%/*} || exit 1 # Run from this directory
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. $WM_PROJECT_DIR/bin/tools/RunFunctions # Tutorial run functions
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if isTest $@
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then
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# Reset the controlDict
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if [ -f system/controlDict.orig ]
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then
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echo "$0: restoring the controlDict from controlDict.orig"
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mv system/controlDict.orig system/controlDict
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fi
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fi
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runApplication blockMesh
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application=$(getApplication)
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#- Test writing collated format
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runApplication decomposePar -fileHandler collated
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runParallel $application -fileHandler collated
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runApplication reconstructPar -latestTime -fileHandler collated
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#- Test writing uncollated format
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runApplication -s uncollated decomposePar -fileHandler uncollated -force
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runParallel -s uncollated $application -fileHandler uncollated
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#- Test uncollated+distributed running: copy to different roots
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rm -rf machineA/fileHandler
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mkdir -p machineA/fileHandler
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( cd machineA/fileHandler && \
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cp -r ../../processor[0-1] . && \
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cp -r ../../system . && \
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mkdir -p constant && cp ../../constant/* constant
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)
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#- Note: slave node does not need constant&system since these are global
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rm -rf machineB/fileHandler
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mkdir -p machineB/fileHandler
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( cd machineB/fileHandler && \
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cp -r ../../processor[2-3] .
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)
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#- Run with different roots
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( d=$PWD && \
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cd machineA/fileHandler && \
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runParallel -s multiRoot $application \
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-fileHandler masterUncollated -ioRanks '(0 2)' \
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-roots "(\"$d/machineA\" \"$d/machineB\" \"$d/machineB\")"
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)
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#- Restart from uncollated
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runParallel -s collated $application -fileHandler collated
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runApplication -s collated reconstructPar -latestTime -fileHandler collated
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#- Convert the parallel format to uncollated
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runParallel foamFormatConvert -fileHandler uncollated
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#- Restart with multiple IO ranks
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runParallel -s multiCollated \
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$application -fileHandler collated -ioRanks '(0 2)'
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#- Reconstruct the multi-rank format. Delete the collated directory
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# since conflicts with the multi-collated directory
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rm -rf processors4
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runApplication -s multiCollated reconstructPar -latestTime \
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-fileHandler collated -ioRanks '(0 2)'
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#- Convert the multi-rank format to uncollated
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runParallel -s uncollated foamFormatConvert -fileHandler uncollated
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#- Restart from multiCollated using collated
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runParallel -s uncollated_from_multiCollated \
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$application -fileHandler uncollated
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#- Test collated+distributed running: copy to different roots
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# Important: make sure to copy uniform since we're copying it
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#- Delete all processor directories
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runApplication -s collated decomposePar \
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-fileHandler collated -force -copyUniform
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rm -rf machineA/fileHandler
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mkdir -p machineA/fileHandler
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( cd machineA/fileHandler && \
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cp -r ../../processor* . && \
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cp -r ../../system . && \
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mkdir -p constant && cp ../../constant/* constant
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)
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#- Note: slave node does not need constant&system since these are global
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rm -rf machineB/fileHandler
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mkdir -p machineB/fileHandler
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#- Run with different roots
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( d=$PWD && \
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cd machineA/fileHandler && \
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runParallel -s distributed_multiCollated $application \
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-fileHandler collated -ioRanks '(0 2)' \
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-roots "(\"$d/machineA\" \"$d/machineB\" \"$d/machineB\")"
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)
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#------------------------------------------------------------------------------
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