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Add unit test for graph connectivity with data from the ECL_CC paper
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3
data/data/third_party/ecl_cc/README
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3
data/data/third_party/ecl_cc/README
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@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:6f5e6e3dc559fefc7990daaec071fcd620f620e5ab8652dddaa6b43ca4ba08e7
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size 222
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3
data/data/third_party/ecl_cc/internet.egr
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data/data/third_party/ecl_cc/internet.egr
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version https://git-lfs.github.com/spec/v1
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oid sha256:892470e152ccd46ddcca70e26bcd88816c247f08c496319cea80864b6b94ce46
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size 3596536
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3
data/data/third_party/ecl_cc/kron_g500-logn21.egr
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3
data/data/third_party/ecl_cc/kron_g500-logn21.egr
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version https://git-lfs.github.com/spec/v1
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oid sha256:1058d22553440f11d3077e70ac8d3a06c6f59107f2dee3fa889fb5933a2a2483
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size 1465043532
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@ -81,7 +81,7 @@ public:
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auto root_u = findRoot(parents, u);
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auto root_v = findRoot(parents, v);
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// There is a potential concurrent write data race as it is possible for
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// Case 3. There is a potential concurrent write data race as it is possible for
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// two threads to try to change the same old root to different new roots,
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// e.g. threadA calls parents.Set(root, rootB) while threadB calls
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// parents(root, rootB) where rootB < root and rootC < root (but the order
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@ -63,11 +63,14 @@ public:
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// Case 1, Two threads calling Unite(u, v) concurrently.
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// Problem: One thread might attach u to v while the other thread attach
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// v to u, causing a cycle in the Union-Find data structure.
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// Resolution: This is not necessary a data race issue. This is resolved by
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// "linking by index" as in SV Jayanti et.al. with less than as the total order.
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// Resolution: This is not so much a race condition as a problem with the
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// consistency of the algorithm that can also happen in serial. This is
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// resolved by "linking by index" as in SV Jayanti et.al. with less than
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// as the total order.
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// The two threads will make the same decision on how to Unite the two tree
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// (e.g. from root with larger id to root with smaller id.) This avoids cycles in
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// the resulting graph and maintains the rooted forest structure of Union-Find.
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// (e.g. from root with larger id to root with smaller id.) This avoids
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// cycles in the resulting graph and maintains the rooted forest structure
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// of Union-Find.
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// Case 2, T0 calling Unite(u, v), T1 calling Unite(u, w) and T2 calling
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// Unite(v, s) concurrently.
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@ -87,7 +90,7 @@ public:
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auto root_u = findRoot(parents, u);
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auto root_v = findRoot(parents, v);
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// There is a potential concurrent write data race as it is possible for
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// Case 3. There is a potential concurrent write data race as it is possible for
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// two threads to try to change the same old root to different new roots,
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// e.g. threadA calls parents.Set(root, rootB) while threadB calls
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// parents(root, rootB) where rootB < root and rootC < root (but the order
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@ -12,10 +12,108 @@
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#include <vtkm/worklet/connectivities/GraphConnectivity.h>
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class AdjacentDifference : public vtkm::worklet::WorkletMapField
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{
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public:
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using ControlSignature = void(FieldIn index, WholeArrayIn counts, FieldOut outputCount);
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using ExecutionSignature = void(_1, _2, _3);
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using InputDomain = _1;
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template <typename WholeArrayType>
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VTKM_EXEC void operator()(const vtkm::Id& index,
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const WholeArrayType& counts,
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int& difference) const
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{
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difference = counts.Get(index + 1) - counts.Get(index);
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}
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};
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class SameComponent : public vtkm::worklet::WorkletMapField
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{
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public:
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using ControlSignature = void(FieldIn start,
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FieldIn degree,
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WholeArrayIn conns,
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WholeArrayIn comps,
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AtomicArrayInOut same);
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using ExecutionSignature = void(WorkIndex, _1, _2, _3, _4, _5);
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template <typename Conn, typename Comp, typename AtomicSame>
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VTKM_EXEC void operator()(vtkm::Id index,
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int start,
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int degree,
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const Conn& conns,
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const Comp& comps,
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AtomicSame& same) const
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{
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for (vtkm::Id offset = start; offset < start + degree; ++offset)
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{
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vtkm::Id neighbor = conns.Get(offset);
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if (comps.Get(index) != comps.Get(neighbor))
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{
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same.Set(0, 0);
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}
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}
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}
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};
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class TestGraphConnectivity
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{
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public:
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void operator()() const
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void TestECL_CC(const std::string& filename, int ncomps) const
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{
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auto pathname =
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vtkm::cont::testing::Testing::GetTestDataBasePath() + "/third_party/ecl_cc/" + filename;
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std::ifstream stream(pathname, std::ios_base::in | std::ios_base::binary);
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int nnodes;
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stream.read(reinterpret_cast<char*>(&nnodes), sizeof(nnodes));
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int nedges;
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stream.read(reinterpret_cast<char*>(&nedges), sizeof(nedges));
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// CSR, there is one more element in offsets thant the actual number of nodes.
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std::vector<int> offsets(nnodes + 1);
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std::vector<int> conns(nedges);
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stream.read(reinterpret_cast<char*>(offsets.data()), (nnodes + 1) * sizeof(int));
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stream.read(reinterpret_cast<char*>(conns.data()), nedges * sizeof(int));
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vtkm::cont::ArrayHandle<int> counts_h;
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vtkm::cont::Invoker invoke;
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invoke(AdjacentDifference{},
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vtkm::cont::make_ArrayHandleCounting(0, 1, nnodes),
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vtkm::cont::make_ArrayHandle<int>(offsets, vtkm::CopyFlag::On),
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counts_h);
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offsets.pop_back();
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vtkm::cont::ArrayHandle<int> offsets_h =
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vtkm::cont::make_ArrayHandle(offsets, vtkm::CopyFlag::On);
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vtkm::cont::ArrayHandle<int> conns_h = vtkm::cont::make_ArrayHandle(conns, vtkm::CopyFlag::Off);
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vtkm::cont::ArrayHandle<vtkm::Id> comps_h;
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vtkm::worklet::connectivity::GraphConnectivity().Run(counts_h, offsets_h, conns_h, comps_h);
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VTKM_TEST_ASSERT(vtkm::cont::Algorithm::Reduce(comps_h, 0, vtkm::Maximum{}) == ncomps - 1,
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"number of components mismatch");
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vtkm::cont::ArrayHandle<vtkm::UInt32> atomicSame;
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atomicSame.Allocate(1);
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atomicSame.WritePortal().Set(0, 1);
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invoke(SameComponent{}, offsets_h, counts_h, conns_h, comps_h, atomicSame);
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VTKM_TEST_ASSERT(atomicSame.ReadPortal().Get(0) == 1,
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"Neighboring nodes don't have the same component id");
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}
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void TestECL_CC_DataSets() const
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{
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TestECL_CC("internet.egr", 1);
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TestECL_CC("kron_g500-logn21.egr", 553159);
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}
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void TestSimpleGraph() const
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{
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vtkm::cont::ArrayHandle<vtkm::Id> counts_h =
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 1, 1, 2, 2, 2 });
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@ -32,6 +130,12 @@ public:
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VTKM_TEST_ASSERT(comps.ReadPortal().Get(i) == 0, "Components has unexpected value.");
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}
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}
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void operator()() const
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{
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TestSimpleGraph();
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TestECL_CC_DataSets();
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}
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};
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int UnitTestGraphConnectivity(int argc, char* argv[])
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