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MPI examples

This page contains a collection of MPI examples of running the framework on test data.

Homogeneous graph

Example 1: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, saturation at default value (1.0), virtual nodes granularity set to type

mpirun -np 2 ./build/c2c-sepia-MPI --fUniqueGraph data/testdata/testHomogeneousGraph/edges-Graph1-general.tsv \
            --fInitialPerturbation data/testdata/testHomogeneousGraph/initialValues-general.tsv \
            --typeInteractionFolder data/testdata/testHomogeneousGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --saturation \
            --outputFolder outputs/testingMPIsingle

Example 2: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, saturation at default value (1.0), virtual nodes granularity set to type and node

mpirun -np 2 ./build/c2c-sepia-MPI --fUniqueGraph data/testdata/testHomogeneousGraph/edges-Graph1-general.tsv \
            --fInitialPerturbation data/testdata/testHomogeneousGraph/initialValues-general.tsv \
            --typeInteractionFolder data/testdata/testHomogeneousGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --virtualNodesGranularity typeAndNode \
            --saturation \
            --outputFolder outputs/testingMPISingleGranular

Example 3: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, saturation at default value (1.0), virtual nodes granularity set to type and node, using a folder for the initial perturbation values

mpirun -np 2 ./build/c2c-sepia-MPI --fUniqueGraph data/testdata/testHomogeneousGraph/edges-Graph1-general.tsv \
            --initialPerturbationPerTypeFolder data/testdata/testHomogeneousGraph/initialValues \
            --typeInteractionFolder data/testdata/testHomogeneousGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --virtualNodesGranularity typeAndNode \
            --saturation \
            --outputFolder outputs/testingMPISingleGranular

Heterogeneous temporal graph

Example 1: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, saturation at default value (1.0)

mpirun -np 2 ./build/c2c-sepia-MPI --graphsFilesFolder data/testdata/testHeterogeneousGraph/graphs \
            --initialPerturbationPerTypeFolder data/testdata/testHeterogeneousTemporalGraph/initialValuesPartialTypes \
            --typeInteractionFolder data/testdata/testHeterogeneousTemporalGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --virtualNodesGranularity typeAndNode \
            --saturation \
            --outputFolder outputs/testingMPIgranularDifferentProcessors

Example 2: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, saturation at default value (1.0), node description folder provided to get the nodes in the graph

mpirun -np 2 ./build/c2c-sepia-MPI --graphsFilesFolder data/testdata/testHeterogeneousGraph/graphs \
            --initialPerturbationPerTypeFolder data/testdata/testHeterogeneousTemporalGraph/initialValuesPartialTypes \
            --typeInteractionFolder data/testdata/testHeterogeneousTemporalGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --virtualNodesGranularity typeAndNode \
            --saturation \
            --nodeDescriptionFolder data/testdata/testHeterogeneousGraph/nodesDescriptionDifferentStructure \
            --outputFolder outputs/testingMPIgranularDifferentProcessors

Example 3: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, saturation at default value (1.0), node description folder provided to get the nodes in the graph, using temporal contact information between types

mpirun -np 2 ./build/c2c-sepia-MPI --graphsFilesFolder data/testdata/testHeterogeneousTemporalGraph/graphs \
            --initialPerturbationPerTypeFolder data/testdata/testHeterogeneousTemporalGraph/initialValuesPartialTypes \
            --typeInteractionFolder data/testdata/testHeterogeneousTemporalGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --virtualNodesGranularity typeAndNode \
            --saturation \
            --nodeDescriptionFolder data/testdata/testHeterogeneousGraph/nodesDescriptionDifferentStructure \
            --outputFolder outputs/testingMPIgranularDifferentProcessors

Example 3: custom propagation model (neighbors if the code in src/propagationModelCustom.cxx is unmodified), scaled dissipation and conservation models set at constants, no saturation, node description folder provided to get the nodes in the graph, using temporal contact information between types

mpirun -np 2 ./build/c2c-sepia-MPI --graphsFilesFolder data/testdata/testHeterogeneousTemporalGraph/graphs \
            --initialPerturbationPerTypeFolder data/testdata/testHeterogeneousTemporalGraph/initialValuesPartialTypes \
            --typeInteractionFolder data/testdata/testHeterogeneousTemporalGraph/interactions \
            --dissipationModel scaled \
            --dissipationModelParameters 0.2 \
            --conservationModel scaled \
            --conservationModelParameters 0.2 \
            --propagationModel customPropagation \
            --propagationModelParameters 0.2 \
            --virtualNodesGranularity typeAndNode \
            --nodeDescriptionFolder data/testdata/testHeterogeneousGraph/nodesDescriptionDifferentStructure \
            --outputFolder outputs/testingMPIgranularDifferentProcessors