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DistLocalGraph switch to LS_LC_CSR graph (#28)
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* changes to switch to LC_LS_CSR graph

* fixing debug err

* fixing pre-commit issues

* changing api calls for wf4

* Added data.001.csv using lfs

* fixing getEdgeData api

* fix for getEdgeData()

* ci fix

* data.001.csv

* changing test dataset

* quickfix

* fixing precommit

* fixing graph deallocate()

* fixing test

* Update workflows to be realistic

* CPU set

* Try this again

* Try this again

* Slight refactor

---------

Co-authored-by: AdityaAtulTewari <adityaatewari@gmail.com>
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@divija95 @AdityaAtulTewari
divija95 and AdityaAtulTewari authored Apr 14, 2024
1 parent 3262256 commit 2785392
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2 changes: 2 additions & 0 deletions .gitattributes
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@@ -0,0 +1,2 @@
*.csv filter=lfs diff=lfs merge=lfs -text
inputs/wmd/data.001.csv filter=lfs diff=lfs merge=lfs -text
22 changes: 21 additions & 1 deletion .github/workflows/build-and-test.yml
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Expand Up @@ -46,7 +46,6 @@ jobs:
CONTAINER_BUILD_DIR: "/pando-galois/build"
CONTAINER_WORK_DIR: "/pando-galois"
GALOIS_CONTAINER_ENV: "-e=GALOIS_BUILD_TOOL=Ninja"
GALOIS_CONTAINER_FLAGS: "--cpus=8"
INTERACTIVE: ""
defaults:
run:
Expand Down Expand Up @@ -77,6 +76,27 @@ jobs:
if [ ${{ matrix.sanitizer-type }} == 'san' ]; then
echo "GALOIS_CONTAINER_ENV=$GALOIS_CONTAINER_ENV -e=GALOIS_EXTRA_CXX_FLAGS='\"-fsanitize=address -fsanitize=undefined\"'" >> $GITHUB_ENV
fi
if [ ${{ matrix.build-type }} == 'Debug' ]; then
echo "GALOIS_CONTAINER_ENV=$GALOIS_CONTAINER_ENV -e=GALOIS_EXTRA_CXX_FLAGS='-O3'" >> $GITHUB_ENV
fi
if [ ${{ runner.name }} == 'zerberus-0' ]; then
echo "CONTAINER_CPUSET='--cpuset-cpus=0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30'" >> $GITHUB_ENV
fi
if [ ${{ runner.name }} == 'zerberus-1' ]; then
echo "CONTAINER_CPUSET='--cpuset-cpus=1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31'" >> $GITHUB_ENV
fi
if [ ${{ runner.name }} == 'languedoc-0' ]; then
echo "CONTAINER_CPUSET='--cpuset-cpus=0,1,2,3,4,5,6,7,32,33,34,35,36,37,38,39'" >> $GITHUB_ENV
fi
if [ ${{ runner.name }} == 'languedoc-1' ]; then
echo "CONTAINER_CPUSET='--cpuset-cpus=16,17,18,19,20,21,22,23,48,49,50,51,52,53,54,55'" >> $GITHUB_ENV
fi
if [ ${{ runner.name }} == 'languedoc-2' ]; then
echo "CONTAINER_CPUSET='--cpuset-cpus=8,9,10,11,12,13,14,15,40,41,42,43,44,45,46,47'" >> $GITHUB_ENV
fi
if [ ${{ runner.name }} == 'languedoc-3' ]; then
echo "CONTAINER_CPUSET='--cpuset-cpus=24,25,26,27,28,29,30,31,56,57,58,59,60,61,62,63'" >> $GITHUB_ENV
fi
cat $GITHUB_ENV
- name: Configure
Expand Down
2 changes: 2 additions & 0 deletions Makefile
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Expand Up @@ -14,6 +14,7 @@ CONTAINER_BUILD_DIR ?= /pando-galois/build
CONTAINER_WORKDIR ?= ${CONTAINER_SRC_DIR}
CONTAINER_CONTEXT ?= default
CONTAINER_OPTS ?=
CONTAINER_CPUSET ?=
CONTAINER_CMD ?= bash -l
INTERACTIVE ?= i

Expand Down Expand Up @@ -91,6 +92,7 @@ docker:
${GALOIS_CONTAINER_MOUNTS} \
${GALOIS_CONTAINER_ENV} \
${GALOIS_CONTAINER_FLAGS} \
${CONTAINER_CPUSET} \
--privileged \
--workdir=${CONTAINER_WORKDIR} \
${CONTAINER_OPTS} \
Expand Down
3 changes: 3 additions & 0 deletions inputs/wmd/data.001.csv
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Git LFS file not shown
69 changes: 33 additions & 36 deletions libcusp/include/galois/graphs/DistributedLocalGraph.h
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Expand Up @@ -31,7 +31,7 @@
#include <fstream>

#include "galois/graphs/DistributedGraph.h"
#include "galois/graphs/LS_LC_CSR_64_Graph.h"
#include "galois/graphs/LS_LC_CSR_Graph.h"
#include "galois/graphs/BufferedGraph.h"
#include "galois/runtime/DistStats.h"
#include "galois/graphs/OfflineGraph.h"
Expand All @@ -56,7 +56,7 @@ class DistLocalGraph {
//! Graph name used for printing things
constexpr static const char* const GRNAME = "dGraph";

using GraphTy = galois::graphs::LS_LC_CSR_64_Graph<NodeTy, EdgeTy, true>;
using GraphTy = galois::graphs::LS_LC_CSR_Graph<NodeTy, EdgeTy>;

// vector for determining range objects for master nodes + nodes
// with edges (which includes masters)
Expand All @@ -83,7 +83,7 @@ class DistLocalGraph {

protected:
//! The internal graph used by DistLocalGraph to represent the graph
GraphTy graph;
GraphTy* graph;

//! Marks if the graph is transposed or not.
bool transposed;
Expand Down Expand Up @@ -476,15 +476,11 @@ class DistLocalGraph {

public:
//! Type representing a node in this graph
using GraphNode = typename GraphTy::GraphNode;
//! Expose EdgeTy to other classes
using GraphNode = typename GraphTy::VertexTopologyID;
//! Type representing an edge data in this graph
using EdgeType = EdgeTy;
//! iterator type over nodes
using iterator = typename GraphTy::iterator;
//! constant iterator type over nodes
using const_iterator = typename GraphTy::const_iterator;
//! iterator type over edges
using edge_iterator = typename GraphTy::edge_iterator;
using edge_iterator = typename GraphTy::EdgeIterator;

/**
* Constructor for DistLocalGraph. Initializes metadata fields.
Expand Down Expand Up @@ -529,6 +525,7 @@ class DistLocalGraph {

public:
virtual ~DistLocalGraph() {}
void initGraph(uint64_t numNodes) { graph = new GraphTy(numNodes); }
//! Determines which host has the master for a particular node
//! @returns Host id of node in question
inline unsigned getHostID(uint64_t gid) const { return getHostIDImpl(gid); }
Expand Down Expand Up @@ -575,10 +572,8 @@ class DistLocalGraph {
* @param mflag access flag for node data
* @returns A node data object
*/
inline typename GraphTy::node_data_reference
getData(GraphNode N,
galois::MethodFlag mflag = galois::MethodFlag::UNPROTECTED) {
auto& r = graph.getData(N, mflag);
inline NodeTy& getData(GraphNode N) {
auto& r = graph->getData(N);
return r;
}

Expand All @@ -589,10 +584,14 @@ class DistLocalGraph {
* @param mflag access flag for edge data
* @returns The edge data for the requested edge
*/
inline typename GraphTy::edge_data_reference
getEdgeData(edge_iterator ni,
galois::MethodFlag mflag = galois::MethodFlag::UNPROTECTED) {
auto& r = graph.getEdgeData(ni, mflag);
inline EdgeTy& getEdgeData(GraphNode src, edge_iterator ni) {
GraphNode dst = getEdgeDst(ni);
auto& r = graph->getEdgeData(std::make_pair(src, getGID(dst)));
return r;
}

inline EdgeTy& getEdgeData(edge_iterator ni) {
auto& r = graph->getEdgeData(*ni);
return r;
}

Expand All @@ -602,7 +601,9 @@ class DistLocalGraph {
* @param ni edge id to get destination of
* @returns Local ID of destination of edge ni
*/
GraphNode getEdgeDst(edge_iterator ni) { return graph.getEdgeDst(ni); }
GraphNode getEdgeDst(edge_iterator ni) {
return getGID(graph->getEdgeDst(*ni));
}

/**
* Gets the first edge of some node.
Expand All @@ -611,7 +612,7 @@ class DistLocalGraph {
* @returns iterator to first edge of N
*/
inline edge_iterator edge_begin(GraphNode N) {
return graph.edge_begin(N, galois::MethodFlag::UNPROTECTED);
return graph->edges(N).begin();
}

/**
Expand All @@ -621,14 +622,12 @@ class DistLocalGraph {
* @returns iterator to the end of the edges of node N, i.e. the first edge
* of the next node (or an "end" iterator if there is no next node)
*/
inline edge_iterator edge_end(GraphNode N) {
return graph.edge_end(N, galois::MethodFlag::UNPROTECTED);
}
inline edge_iterator edge_end(GraphNode N) { return graph->edges(N).end(); }

/**
* Return the degree of the edge in the local graph
**/
inline uint64_t localDegree(GraphNode N) { return graph.getDegree(N); }
inline uint64_t localDegree(GraphNode N) { return graph->getDegree(N); }

/**
* Returns an iterable object over the edges of a particular node in the
Expand All @@ -647,14 +646,14 @@ class DistLocalGraph {
*
* @returns number of nodes present in this (local) graph
*/
inline size_t size() const { return graph.size(); }
inline size_t size() const { return graph->size(); }

/**
* Gets number of edges on this (local) graph.
*
* @returns number of edges present in this (local) graph
*/
inline size_t sizeEdges() const { return graph.sizeEdges(); }
inline size_t sizeEdges() { return graph->sizeEdges(); }

/**
* Gets number of nodes on this (local) graph.
Expand Down Expand Up @@ -746,7 +745,7 @@ class DistLocalGraph {
*/
inline void determineThreadRanges() {
allNodesRanges = galois::graphs::determineUnitRangesFromPrefixSum(
galois::runtime::activeThreads, graph.getEdgePrefixSum());
galois::runtime::activeThreads, graph->getEdgePrefixSum());
}

/**
Expand All @@ -770,9 +769,8 @@ class DistLocalGraph {
} else {
galois::gDebug("Manually det. master thread ranges");
masterRanges = galois::graphs::determineUnitRangesFromGraph(
graph, galois::runtime::activeThreads, beginMaster,
beginMaster + numOwned, 0,
(galois::graphs::is_LS_LC_CSR_64_Graph<decltype(graph)>::value == 1));
*graph, galois::runtime::activeThreads, beginMaster,
beginMaster + numOwned, 0, true);
}
}

Expand All @@ -797,7 +795,7 @@ class DistLocalGraph {
} else {
galois::gDebug("Manually det. with edges thread ranges");
withEdgeRanges = galois::graphs::determineUnitRangesFromGraph(
graph, galois::runtime::activeThreads, 0, numNodesWithEdges, 0);
*graph, galois::runtime::activeThreads, 0, numNodesWithEdges, 0);
}
}

Expand Down Expand Up @@ -869,19 +867,18 @@ class DistLocalGraph {
*/
void deallocate() {
galois::gDebug("Deallocating CSR in DistLocalGraph");
graph.deallocate();
graph->deallocate();
}

/**
* Sort the underlying LC_CSR_Graph by ID (destinations)
* It sorts edges of the nodes by destination.
*/
void sortEdgesByDestination() {
using GN = typename GraphTy::GraphNode;
galois::do_all(
galois::iterate(graph),
[&](GN n) { graph.sortEdges(n, IdLess<GN, EdgeTy>()); },
galois::no_stats(), galois::loopname("CSREdgeSort"), galois::steal());
galois::iterate(graph->vertices().begin(), graph->vertices().end()),
[&](GraphNode n) { graph->sortEdges(n); }, galois::no_stats(),
galois::loopname("CSREdgeSort"), galois::steal());
}

//! Used by substrate to determine if some stats are to be reported
Expand Down
9 changes: 5 additions & 4 deletions libgalois/include/galois/graphs/GraphHelpers.h
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Original file line number Diff line number Diff line change
Expand Up @@ -262,10 +262,11 @@ void determineUnitRangesLoopGraph(GraphTy& graph, uint32_t unitsToSplit,

// cannot use edge_end/begin on log strcutred CSR since its edges are not
// consecutive.
uint64_t numEdgesInRange = (is_LS_LC_CSR) ? graph.sizeEdges()
: graph.edge_end(endNode - 1) -
graph.edge_begin(beginNode);
uint64_t edgeOffset = (is_LS_LC_CSR) ? 0 : *graph.edge_begin(beginNode);
uint64_t numEdgesInRange = (is_LS_LC_CSR)
? graph.sizeEdges()
: std::distance(graph.edge_end(beginNode),
graph.edge_begin(endNode - 1));
uint64_t edgeOffset = (is_LS_LC_CSR) ? 0 : graph[beginNode];

returnRanges[0] = beginNode;
std::vector<unsigned int> dummyScaleFactor;
Expand Down
8 changes: 6 additions & 2 deletions libgalois/include/galois/graphs/LS_LC_CSR_Graph.h
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@
* Documentation, or loss or inaccuracy of data of any kind.
*/

#ifndef GALOIS_GRAPHS_LC_CSR_GRAPH_H
#define GALOIS_GRAPHS_LC_CSR_GRAPH_H
#ifndef GALOIS_GRAPHS_LS_LC_CSR_GRAPH_H
#define GALOIS_GRAPHS_LS_LC_CSR_GRAPH_H

#include <unordered_set>
#include <iterator>
Expand Down Expand Up @@ -205,6 +205,10 @@ class LS_LC_CSR_Graph : private boost::noncopyable {
return m_edge_data[handle];
}

template <typename E = EdgeData, typename = std::enable_if<HasEdgeData>>
inline E& getEdgeData(EdgeIterator const& it) {
return m_edge_data[*it];
}
/*
* Count the total number of edges in parallel.
*/
Expand Down
9 changes: 5 additions & 4 deletions libwmd/include/galois/wmd/WMDGraph.h
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Original file line number Diff line number Diff line change
Expand Up @@ -1142,7 +1142,8 @@ class WMDBufferedGraph : public BufferedGraph<EdgeDataType> {
&addedData
#endif
](size_t j) {
dstGraph.getData(GIDtoLID[NodeData[j].id]) = NodeData[j];
dstGraph->getData(GIDtoLID[NodeData[j].id]) =
NodeData[j];
});
NodeData.clear();
}
Expand All @@ -1153,7 +1154,7 @@ class WMDBufferedGraph : public BufferedGraph<EdgeDataType> {
&addedData
#endif
](size_t i) {
dstGraph.getData(GIDtoLID[nodesToSend[hostID][i].id]) =
dstGraph->getData(GIDtoLID[nodesToSend[hostID][i].id]) =
nodesToSend[hostID][i];
#ifndef NDEBUG
addedData++;
Expand All @@ -1172,7 +1173,7 @@ class WMDBufferedGraph : public BufferedGraph<EdgeDataType> {
if (i != hostID) {
for (uint64_t j = 0; j < proxiesOnHosts[i].size(); j++) {
auto& r =
dstGraph.getData(globalToLocalMap[proxiesOnHosts[i][j]]);
dstGraph->getData(globalToLocalMap[proxiesOnHosts[i][j]]);
nodesToSend[i].push_back(r);
};
}
Expand Down Expand Up @@ -1216,7 +1217,7 @@ class WMDBufferedGraph : public BufferedGraph<EdgeDataType> {
galois::iterate((size_t)0, IDofNodeRecv.size()),
[this, &nodeRecv, &IDofNodeRecv, &dstGraph,
&globalToLocalMap](size_t j) {
dstGraph.getData(globalToLocalMap[IDofNodeRecv[j]]) = nodeRecv[j];
dstGraph->getData(globalToLocalMap[IDofNodeRecv[j]]) = nodeRecv[j];
},
galois::steal());
nodeRecv.clear();
Expand Down
28 changes: 12 additions & 16 deletions libwmd/include/galois/wmd/WMDPartitioner.h
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Original file line number Diff line number Diff line change
Expand Up @@ -234,9 +234,7 @@ class WMDGraph : public DistLocalGraph<NodeTy, EdgeTy> {
// Graph construction related calls
base_DistGraph::beginMaster = 0;
// Allocate and construct the graph
base_DistGraph::graph.allocateFrom(base_DistGraph::numNodes,
base_DistGraph::numEdges);
base_DistGraph::graph.constructNodes();
base_DistGraph::initGraph(base_DistGraph::numNodes);

// construct edges
// not need to move edges from other host since all edges is already ready
Expand All @@ -250,10 +248,10 @@ class WMDGraph : public DistLocalGraph<NodeTy, EdgeTy> {
for (auto dst : edgeDst) {
dstData.emplace_back(base_DistGraph::globalToLocalMap[dst]);
}
auto edgeData = bufGraph.edgeDataPtr(globalID);
base_DistGraph::graph.addEdgesUnSort(
true, (globalID - bufGraph.globalNodeOffset[base_DistGraph::id]),
dstData.data(), edgeData, bufGraph.edgeNum(globalID), false);
std::vector<EdgeTy> edgeData(bufGraph.edgeNum(globalID));
base_DistGraph::graph->addEdges(
(globalID - bufGraph.globalNodeOffset[base_DistGraph::id]),
dstData, edgeData);
},
galois::steal());

Expand All @@ -269,10 +267,10 @@ class WMDGraph : public DistLocalGraph<NodeTy, EdgeTy> {
"] LS_CSR graph local nodes: ", base_DistGraph::numNodes);
galois::gInfo("[", base_DistGraph::id,
"] LS_CSR graph master nodes: ", base_DistGraph::numOwned);
galois::gInfo("[", base_DistGraph::id, "] LS_CSR graph local edges: ",
base_DistGraph::graph.sizeEdges());
assert(base_DistGraph::graph.sizeEdges() == base_DistGraph::numEdges);
assert(base_DistGraph::graph.size() == base_DistGraph::numNodes);
galois::gInfo("[", base_DistGraph::id,
"] LS_CSR graph local edges: ", base_DistGraph::sizeEdges());
assert(base_DistGraph::sizeEdges() == base_DistGraph::numEdges);
assert(base_DistGraph::graph->size() == base_DistGraph::numNodes);

bufGraph.resetAndFree();

Expand Down Expand Up @@ -471,14 +469,14 @@ class WMDGraph : public DistLocalGraph<NodeTy, EdgeTy> {
}

galois::gInfo("[", base_DistGraph::id, "] Start building projected graph.");
newGraph->graph.allocateFrom(newGraph->numNodes, newGraph->numEdges);
newGraph->initGraph(newGraph->numNodes);

galois::do_all(
galois::iterate(uint64_t(0), uint64_t(newGraph->numNodes)),
[&](auto& node) {
NodeLID oldGraphLID =
base_DistGraph::getLID(newGraph->localToGlobalVector[node]);
newGraph->graph.getData(node) = projection.ProjectNode(
newGraph->graph->getData(node) = projection.ProjectNode(
*this, base_DistGraph::getData(oldGraphLID), oldGraphLID);

uint64_t numEdges = newTopology[node].size();
Expand All @@ -490,9 +488,7 @@ class WMDGraph : public DistLocalGraph<NodeTy, EdgeTy> {
for (NodeGID gid : newTopology[node]) {
localDsts.emplace_back(newGraph->getLID(gid));
}
newGraph->graph.addEdgesUnSort(true, node, localDsts.data(),
newEdgeData[node].data(), numEdges,
false);
newGraph->graph->addEdges(node, localDsts, newEdgeData[node]);

newTopology[node].clear();
newEdgeData[node].clear();
Expand Down
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