Merge pull request #141 from lynxkite/darabos-no-ordered-mapping

Ditch ordered mapping

build.sbt

@@ -94,8 +94,8 @@ libraryDependencies ++= Seq(
   // Used for working with AVRO files. 
   "org.apache.spark" %% "spark-avro" % sparkVersion.value,
   // For Neo4j tests.
-  "org.testcontainers" % "testcontainers" % "1.14.3" % Test,
-  "org.testcontainers" % "neo4j" % "1.14.3" % Test,
+  "org.testcontainers" % "testcontainers" % "1.15.2" % Test,
+  "org.testcontainers" % "neo4j" % "1.15.2" % Test,
   // Used for working with Delta tables.
   "io.delta" %% "delta-core" % "0.6.1"
 )

dependency-licenses/scala.md

@@ -41,7 +41,6 @@ Apache | [Apache License](LICENSE.txt) | org.apache.httpcomponents # httpmime #
 Apache | [Apache License 2.0](http://www.apache.org/licenses/LICENSE-2.0.html) | com.ning # async-http-client # 1.8.14 | <notextile></notextile>
 Apache | [Apache License Version 2.0](LICENSE.txt) | org.yaml # snakeyaml # 1.15 | <notextile></notextile>
 Apache | [Apache License v2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | net.java.dev.jna # jna # 5.5.0 | <notextile></notextile>
-Apache | [Apache License v2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | net.java.dev.jna # jna-platform # 5.5.0 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](https://aws.amazon.com/apache2.0) | com.amazonaws # aws-java-sdk # 1.7.4 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.clearspring.analytics # stream # 2.7.0 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.github.javaparser # javaparser-core # 3.2.5 | <notextile></notextile>
@@ -50,8 +49,6 @@ Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.google.cloud.bigdataoss # util # 1.6.1 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.google.cloud.bigdataoss # util-hadoop # 1.6.1-hadoop2 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | com.jamesmurty.utils # java-xmlbuilder # 1.1 | <notextile></notextile>
-Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.kohlschutter.junixsocket # junixsocket-common # 2.0.4 | <notextile></notextile>
-Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.kohlschutter.junixsocket # junixsocket-native-common # 2.0.4 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | com.typesafe # config # 1.2.1 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | com.typesafe.akka # akka-actor_2.11 # 2.3.4 | <notextile></notextile>
 Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | com.typesafe.akka # akka-slf4j_2.11 # 2.3.4 | <notextile></notextile>
@@ -103,10 +100,14 @@ Apache | [Similar to Apache License but with the acknowledgment clause removed](
 Apache | [The Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | io.opencensus # opencensus-api # 0.21.0 | <notextile></notextile>
 Apache | [The Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | io.opencensus # opencensus-contrib-grpc-metrics # 0.21.0 | <notextile></notextile>
 Apache | [The Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.spark-project.spark # unused # 1.0.0 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-annotations # 2.10.3 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-annotations # 2.6.5 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-core # 2.6.5 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-databind # 2.6.5 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.dataformat # jackson-dataformat-yaml # 2.6.5 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.github.docker-java # docker-java-api # 3.2.7 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.github.docker-java # docker-java-transport # 3.2.7 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.github.docker-java # docker-java-transport-zerodep # 3.2.7 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.google.api-client # google-api-client # 1.20.0 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.google.api-client # google-api-client-jackson2 # 1.20.0 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.google.api-client # google-api-client-java6 # 1.20.0 | <notextile></notextile>
@@ -132,7 +133,6 @@ Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licens
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.codehaus.jackson # jackson-mapper-asl # 1.9.13 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.ejml # ejml-core # 0.34 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.ejml # ejml-ddense # 0.34 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0.txt) | org.jetbrains # annotations # 19.0.0 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.seleniumhq.selenium # selenium-android-driver # 2.39.0 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.seleniumhq.selenium # selenium-api # 2.39.0 | <notextile></notextile>
 Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.seleniumhq.selenium # selenium-chrome-driver # 2.39.0 | <notextile></notextile>
@@ -204,7 +204,6 @@ BSD | [The BSD License](http://www.antlr.org/license.html) | org.antlr # antlr4-
 BSD | [Three-clause BSD-style](https://github.com/mpilquist/simulacrum/blob/master/LICENSE) | com.github.mpilquist # simulacrum_2.11 # 0.10.0 | <notextile></notextile>
 BSD | [Three-clause BSD-style](https://github.com/scodec/scodec-bits/blob/master/LICENSE) | org.scodec # scodec-bits_2.11 # 1.0.9 | <notextile></notextile>
 BSD | [Two-clause BSD-style license](http://github.com/sbt/junit-interface/blob/master/LICENSE.txt) | com.novocode # junit-interface # 0.11-RC1 | <notextile></notextile>
-CC0 | [CC0 1.0 Universal License](http://creativecommons.org/publicdomain/zero/1.0/) | org.scijava # native-lib-loader # 2.0.2 | <notextile></notextile>
 CDDL | [COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0](https://glassfish.dev.java.net/public/CDDLv1.0.html) | javax.activation # activation # 1.1.1 | <notextile></notextile>
 GPL | [                 Dual license consisting of the CDDL v1.1 and GPL v2             ](https://glassfish.java.net/public/CDDL+GPL_1_1.html) | org.glassfish # javax.json # 1.0.4 | <notextile></notextile>
 GPL | [GPL2 w/ CPE](https://www.gnu.org/software/classpath/license.html) | jakarta.ws.rs # jakarta.ws.rs-api # 2.1.6 | <notextile></notextile>
@@ -226,16 +225,15 @@ MIT | [MIT](http://opensource.org/licenses/MIT) | com.github.julien-truffaut # m
 MIT | [MIT](http://www.opensource.org/licenses/mit-license.html) | com.lihaoyi # fansi_2.11 # 0.2.4 | <notextile></notextile>
 MIT | [MIT](http://www.opensource.org/licenses/mit-license.html) | com.lihaoyi # pprint_2.11 # 0.5.2 | <notextile></notextile>
 MIT | [MIT](http://www.opensource.org/licenses/mit-license.html) | com.lihaoyi # sourcecode_2.11 # 0.1.4 | <notextile></notextile>
-MIT | [MIT](http://opensource.org/licenses/MIT) | org.rnorth # tcp-unix-socket-proxy # 1.0.2 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.rnorth.duct-tape # duct-tape # 1.0.8 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.rnorth.visible-assertions # visible-assertions # 2.1.2 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.scalaz.stream # scalaz-stream_2.11 # 0.8 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.spire-math # jawn-parser_2.11 # 0.10.4 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.spire-math # kind-projector_2.11 # 0.7.1 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.spire-math # spire-macros_2.11 # 0.13.0 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.spire-math # spire_2.11 # 0.13.0 | <notextile></notextile>
-MIT | [MIT](http://opensource.org/licenses/MIT) | org.testcontainers # neo4j # 1.14.3 | <notextile></notextile>
-MIT | [MIT](http://opensource.org/licenses/MIT) | org.testcontainers # testcontainers # 1.14.3 | <notextile></notextile>
+MIT | [MIT](http://opensource.org/licenses/MIT) | org.testcontainers # neo4j # 1.15.2 | <notextile></notextile>
+MIT | [MIT](http://opensource.org/licenses/MIT) | org.testcontainers # testcontainers # 1.15.2 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.typelevel # cats-core_2.11 # 0.9.0 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.typelevel # cats-kernel_2.11 # 0.9.0 | <notextile></notextile>
 MIT | [MIT](http://opensource.org/licenses/MIT) | org.typelevel # cats-macros_2.11 # 0.9.0 | <notextile></notextile>

sphynx/go.mod

@@ -5,6 +5,7 @@ go 1.14
 require (
 	github.com/apache/arrow/go/arrow v0.0.0-20200701075601-f25a014ab157
 	github.com/golang/protobuf v1.4.2
+	github.com/jfcg/sorty v1.0.12
 	github.com/juju/errors v0.0.0-20200330140219-3fe23663418f
 	github.com/juju/testing v0.0.0-20200608005635-e4eedbc6f7aa // indirect
 	github.com/xitongsys/parquet-go v1.5.2

sphynx/go.sum

@@ -92,6 +92,8 @@ github.com/hashicorp/golang-lru v0.5.0/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ
 github.com/hashicorp/golang-lru v0.5.1/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8=
 github.com/ianlancetaylor/demangle v0.0.0-20181102032728-5e5cf60278f6/go.mod h1:aSSvb/t6k1mPoxDqO4vJh6VOCGPwU4O0C2/Eqndh1Sc=
 github.com/jcmturner/gofork v0.0.0-20180107083740-2aebee971930/go.mod h1:MK8+TM0La+2rjBD4jE12Kj1pCCxK7d2LK/UM3ncEo0o=
+github.com/jfcg/sorty v1.0.12 h1:1Np/SBt2ODK981ZyadqOViwPrZ4ncRPp1y7C+JqWQms=
+github.com/jfcg/sorty v1.0.12/go.mod h1:+v4Q9+K64VQk8A8FTAw6hHg1WAnHwm07TROXBVtsjWY=
 github.com/jmespath/go-jmespath v0.3.0/go.mod h1:9QtRXoHjLGCJ5IBSaohpXITPlowMeeYCZ7fLUTSywik=
 github.com/jstemmer/go-junit-report v0.0.0-20190106144839-af01ea7f8024/go.mod h1:6v2b51hI/fHJwM22ozAgKL4VKDeJcHhJFhtBdhmNjmU=
 github.com/jstemmer/go-junit-report v0.9.1/go.mod h1:Brl9GWCQeLvo8nXZwPNNblvFj/XSXhF0NWZEnDohbsk=

sphynx/lynxkite-sphynx/entity_cache.go

@@ -4,7 +4,9 @@ package main
 
 import (
 	"fmt"
+	"log"
 	"os"
+	"runtime"
 	"sort"
 	"strconv"
 	"sync"
@@ -33,6 +35,7 @@ type cacheEntry struct {
 }
 
 var cachedEntitiesMaxMem = getNumericEnv("SPHYNX_CACHED_ENTITIES_MAX_MEM_MB", 1*1024) * 1024 * 1024
+var sphynxThreads = getNumericEnv("SPHYNX_THREADS", runtime.NumCPU())
 
 func (entityCache *EntityCache) Get(guid GUID) (Entity, bool) {
 	ts := ourTimestamp()
@@ -77,6 +80,13 @@ func (entityCache *EntityCache) Set(guid GUID, entity Entity) {
 	// But we do not want to update the timestamp for those.
 }
 
+func NotInCacheError(kind string, guid GUID) error {
+	// If we drop something from the cache it will be reloaded before the next use.
+	// The exception is when we drop it right after loading it. This generally means
+	// the cache is too small.
+	return fmt.Errorf("Could not fit %v %v into memory. Increase SPHYNX_CACHED_ENTITIES_MAX_MEM_MB?", kind, guid)
+}
+
 type entityEvictionItem struct {
 	guid      GUID
 	timestamp int64
@@ -108,12 +118,12 @@ func (entityCache *EntityCache) maybeGarbageCollect() {
 
 	for i := 0; i < len(evictionCandidates) && memEvicted < howMuchMemoryToRecycle; i++ {
 		guid := evictionCandidates[i].guid
-		fmt.Printf("Evicting: %v\n", evictionCandidates[i])
+		log.Printf("Evicting: %v\n", evictionCandidates[i])
 		delete(entityCache.cache, guid)
 		memEvicted += evictionCandidates[i].memUsage
 		itemsEvicted++
 	}
-	fmt.Printf("Evicted %d entities (out of %d), estimated size: %d time: %d\n",
+	log.Printf("Evicted %d entities (out of %d), estimated size: %d time: %d\n",
 		itemsEvicted, len(evictionCandidates), memEvicted, (ourTimestamp()-start)/1000000)
 	entityCache.totalMemUsage -= memEvicted
 }

sphynx/lynxkite-sphynx/entity_io.go

@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"github.com/apache/arrow/go/arrow"
 	"github.com/apache/arrow/go/arrow/array"
+	"github.com/jfcg/sorty"
 	"io/ioutil"
 	"os"
 	"reflect"
@@ -55,6 +56,7 @@ var vertexSetSchema = arrow.NewSchema(
 	}, nil)
 
 func (v *VertexSet) toOrderedRows() array.Record {
+	assertSorted(v.MappingToUnordered)
 	b := array.NewInt64Builder(arrowAllocator)
 	defer b.Release()
 	b.AppendValues(v.MappingToUnordered, nil)
@@ -69,6 +71,8 @@ func (v *VertexSet) readFromOrdered(rec array.Record) error {
 	for i, d := range data {
 		v.MappingToUnordered[i] = d
 	}
+	// For backward compatibility.
+	sorty.SortI8(v.MappingToUnordered)
 	return nil
 }
 

sphynx/lynxkite-sphynx/main.go

@@ -14,6 +14,8 @@ import (
 	"google.golang.org/grpc/credentials"
 	"log"
 	"net"
+	"net/http"
+	_ "net/http/pprof"
 	"os"
 	"strings"
 )
@@ -62,6 +64,7 @@ func (s *Server) CanCompute(ctx context.Context, in *pb.CanComputeRequest) (*pb.
 
 func (s *Server) Compute(ctx context.Context, in *pb.ComputeRequest) (*pb.ComputeReply, error) {
 	opInst := OperationInstanceFromJSON(in.Operation)
+	log.Printf("Computing %v.", shortOpName(opInst))
 	switch in.Domain {
 	case "SphynxMemory":
 		op, exists := operationRepository[shortOpName(opInst)]
@@ -117,7 +120,7 @@ func (s *Server) GetScalar(ctx context.Context, in *pb.GetScalarRequest) (*pb.Ge
 	log.Printf("Received GetScalar request with GUID %v.", guid)
 	entity, exists := s.entityCache.Get(guid)
 	if !exists {
-		return nil, fmt.Errorf("Guid %v is missing", guid)
+		return nil, NotInCacheError("scalar", guid)
 	}
 
 	switch scalar := entity.(type) {
@@ -138,7 +141,7 @@ func (s *Server) HasInSphynxMemory(ctx context.Context, in *pb.HasInSphynxMemory
 func (s *Server) getVertexSet(guid GUID) (*VertexSet, error) {
 	entity, exists := s.entityCache.Get(guid)
 	if !exists {
-		return nil, fmt.Errorf("Guid %v is missing", guid)
+		return nil, NotInCacheError("vertex set", guid)
 	}
 	switch vs := entity.(type) {
 	case *VertexSet:
@@ -186,6 +189,12 @@ func main() {
 	if port == "" {
 		log.Fatalf("Please set SPHYNX_PORT.")
 	}
+	debugPort := os.Getenv("SPHYNX_DEBUG_PORT")
+	if debugPort != "" {
+		go func() error {
+			return http.ListenAndServe(fmt.Sprintf(":%s", debugPort), nil)
+		}()
+	}
 	keydir := flag.String(
 		"keydir", "", "directory of cert.pem and private-key.pem files (for encryption)")
 	flag.Parse()

sphynx/lynxkite-sphynx/networkit_community_detection.go

@@ -38,12 +38,12 @@ func init() {
 			defer networkit.DeletePartition(p)
 			vs := &VertexSet{}
 			vs.MappingToUnordered = make([]int64, p.NumberOfSubsets())
-			vs.MappingToOrdered = make(map[int64]SphynxId)
+			mappingToOrdered := make(map[int64]SphynxId)
 			ss := p.GetSubsetIdsVector()
 			defer networkit.DeleteUint64Vector(ss)
 			for i := range vs.MappingToUnordered {
 				vs.MappingToUnordered[i] = int64(ss.Get(i))
-				vs.MappingToOrdered[int64(ss.Get(i))] = SphynxId(i)
+				mappingToOrdered[int64(ss.Get(i))] = SphynxId(i)
 			}
 			es := &EdgeBundle{}
 			es.EdgeMapping = make([]int64, p.NumberOfElements())
@@ -54,7 +54,7 @@ func init() {
 			for i := range es.EdgeMapping {
 				es.EdgeMapping[i] = int64(i)
 				es.Src[i] = SphynxId(i)
-				es.Dst[i] = SphynxId(vs.MappingToOrdered[int64(v.Get(i))])
+				es.Dst[i] = SphynxId(mappingToOrdered[int64(v.Get(i))])
 			}
 			ea.output("partitions", vs)
 			ea.output("belongsTo", es)

sphynx/lynxkite-sphynx/networkit_test.go

@@ -56,30 +56,6 @@ func TestNewVertexAttribute(t *testing.T) {
 	}
 }
 
-func TestGraphToSphynx(t *testing.T) {
-	c := networkit.NewBarabasiAlbertGenerator(uint64(2), uint64(5))
-	defer networkit.DeleteBarabasiAlbertGenerator(c)
-	g := c.Generate()
-	defer networkit.DeleteGraph(g)
-	vs, es := ToSphynx(g)
-	if len(vs.MappingToUnordered) != 5 {
-		t.Errorf("Vertex set is %v, expected 5.", vs.MappingToUnordered)
-	}
-	expectedSrc := []SphynxId{1, 1, 2, 2, 3, 3, 4, 4}
-	if len(es.Src) != len(expectedSrc) {
-		t.Errorf("Source list is %v, expected %v.", es.Src, expectedSrc)
-	}
-	if len(es.Dst) != len(expectedSrc) {
-		t.Errorf("Destination list is %v, expected length %v.", es.Dst, len(expectedSrc))
-	}
-	for i := range es.Src {
-		if es.Src[i] != expectedSrc[i] {
-			t.Errorf("Source list is %v, expected %v.", es.Src, expectedSrc)
-			break
-		}
-	}
-}
-
 func TestVectorVector(t *testing.T) {
 	c := networkit.NewBarabasiAlbertGenerator(uint64(3), uint64(10))
 	defer networkit.DeleteBarabasiAlbertGenerator(c)
@@ -93,7 +69,7 @@ func TestVectorVector(t *testing.T) {
 	for i := 0; i < int(points.Size()); i += 1 {
 		x := points.Get(i).At(0)
 		y := points.Get(i).At(1)
-		if x < -2 || x > 2 || x == 0 || y < -2 || y > 2 || y == 0 {
+		if x < -3 || x > 3 || x == 0 || y < -3 || y > 3 || y == 0 {
 			t.Errorf("Unexpected coordinates: %v %v", x, y)
 		}
 	}

sphynx/lynxkite-sphynx/operations.go

@@ -19,7 +19,7 @@ func collectInputs(server *Server, opInst *OperationInstance) (map[string]Entity
 	for name, guid := range opInst.Inputs {
 		entity, exists := server.entityCache.Get(guid)
 		if !exists {
-			return nil, fmt.Errorf("Guid %v is missing", guid)
+			return nil, NotInCacheError("input", guid)
 		}
 		inputs[name] = entity
 	}

sphynx/lynxkite-sphynx/sphynxdisk.go

@@ -38,8 +38,8 @@ func createEntity(typeName string) (Entity, error) {
 }
 
 func saveToOrderedDisk(e Entity, dataDir string, guid GUID) error {
-	log.Printf("saveToOrderedDisk guid %v", guid)
 	typeName := e.typeName()
+	log.Printf("Writing %v %v to ordered disk.", typeName, guid)
 	dirName := fmt.Sprintf("%v/%v", dataDir, guid)
 	_ = os.Mkdir(dirName, 0775)
 	typeFName := fmt.Sprintf("%v/type_name", dirName)
@@ -96,14 +96,14 @@ func saveToOrderedDisk(e Entity, dataDir string, guid GUID) error {
 }
 
 func loadFromOrderedDisk(dataDir string, guid GUID) (Entity, error) {
-	log.Printf("loadFromOrderedDisk: %v", guid)
 	dirName := fmt.Sprintf("%v/%v", dataDir, guid)
 	typeFName := fmt.Sprintf("%v/type_name", dirName)
 	typeData, err := ioutil.ReadFile(typeFName)
 	if err != nil {
 		return nil, fmt.Errorf("Failed to read type of %v: %v", dirName, err)
 	}
 	typeName := string(typeData)
+	log.Printf("Reading %v %v from ordered disk.", typeName, guid)
 	e, err := createEntity(typeName)
 	if err != nil {
 		return nil, err
@@ -160,7 +160,7 @@ func (s *Server) WriteToOrderedDisk(
 
 	e, exists := s.entityCache.Get(guid)
 	if !exists {
-		return nil, fmt.Errorf("Guid %v is missing", guid)
+		return nil, NotInCacheError("entity", guid)
 	}
 
 	if err := saveToOrderedDisk(e, s.dataDir, guid); err != nil {

sphynx/lynxkite-sphynx/strip_duplicate_edges_from_bundle.go

@@ -25,6 +25,7 @@ func doStripDuplicateEdgesFromBundle(es *EdgeBundle) *EdgeBundle {
 		uniqueBundle.EdgeMapping[i] = id
 		i++
 	}
+	uniqueBundle.Sort()
 	return uniqueBundle
 }