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V0.9.0 working 2 (#227)

* Added Issue 217 to known issues
Renamed the ConstDeriv test to 182

* Added Reset() to BatchNormOp to conform to the same interface as the native version woul

* Clean up, and plugged some leaks

* Fixed a slight issue with the compilation. DoWork() is emitted before a linalg op now

* [fix] The test for Reshape Operator was incorrect

* Temporarily commented away the tests for #217

* Added error message for VM Genera

* Added go1.11 to travis
Fixed CUDA Conv backprop shape error

* [fix] Using NewOrderedNodes as an implementation of gonum.Nodes

* Fixed the tests to use the new gonum interface

* Fixed an error in the error.warpf call

* [fix] Back to the idea that graph options should not be exported

* [fix] More idiomatic way to handle error msg

* Merged from v0.9.2-working2

* New stuff? I don't know when I did this

* Fixes #257 I think

* Renamed examples/stacked autoencoder to examples/stacked_autoencoder

* Added tests. Added better error support for LISPMachine. Removed sanity check for now because there are some weird things wrt dimensions in dual values

* Updated with 237fix
There seems to be a problem with the concurrent training example, so it has been commented out for now

The `sanity()` method of the dual values have been temporarily suspended. Turns out lispMachines don't play well when there are differently shaped (but legal) derivations.
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chewxy committed Jan 25, 2019
1 parent 7f6841f commit ed4702f345b7a15602c6cb9c0cf4f078a4090470
Showing with 130 additions and 109 deletions.
  1. +4 −3 compile.go
  2. +1 −0 cuda/external.go
  3. +1 −1 debug.go
  4. +1 −1 differentiation.go
  5. +3 −2 differentiation_test.go
  6. +7 −7 dual.go
  7. +1 −0 errors.go
  8. +1 −1 example_concurrent_training_test.go
  9. +13 −0 gorgonia_test.go
  10. +4 −5 graph.go
  11. +8 −4 graph_test.go
  12. +2 −0 known_issues_test.go
  13. +1 −1 node.go
  14. +45 −63 op_nn.go
  15. +3 −2 operations_test.go
  16. +1 −2 ops/nn/batchnorm_cuda.go
  17. +4 −2 ops/nn/convolution_cuda.go
  18. +4 −2 regalloc.go
  19. +17 −7 utils.go
  20. +6 −4 vm_genera.go
  21. +3 −2 walker.go
@@ -19,7 +19,7 @@ func Compile(g *ExprGraph) (prog *program, locMap map[*Node]register, err error)
defer leaveLogScope()

switch {
case g.Nodes().Len() == 0:
case len(g.AllNodes()) == 0:
err = errors.Errorf("Cannot compile an empty graph")
return
case g.Inputs().Len() == 0:
@@ -399,8 +399,9 @@ func (cg *codegenerator) addNode(node, replacement *Node, interv *interval, i in
var op Op
var onDev, nodeOnDev Device

_, isDevTrans := lastWriteNode.Op().(devTrans)
switch {
case lastWriteNode.isArg(), lastWriteNode.isStmt:
case lastWriteNode.isArg(), lastWriteNode.isStmt && !isDevTrans:
continue
default:
op = lastWriteNode.op
@@ -440,7 +441,7 @@ func (cg *codegenerator) addNode(node, replacement *Node, interv *interval, i in
case !op.CallsExtern():
compileLogf("ToFlush: Node doesn't call extern. NO FLUSH")
// op doesn't call extern... don't bother flushing
case op.CallsExtern() && node.op.CallsExtern() && onDev == nodeOnDev:
case op.CallsExtern() && node.op.CallsExtern() && onDev == nodeOnDev && !isDevTrans:
compileLogf("ToFlush: Both calls extern, both same device. NO FLUSH")
// same device, both calls extern
// no flush needed
@@ -230,6 +230,7 @@ func (e *Engine) Run() {
// finish initialization
e.b.Init(cublas.WithContext(&e.c))

// finishChan2 blocks any external commands to engine (like Close) until it's ready to finish.
e.finishChan2 <- struct{}{}

loop:
@@ -28,7 +28,7 @@ var (
machineDev = false
stabilizationDev = false
solverDev = false
cudaDev = true
cudaDev = false
allocatorDev = false
)

@@ -105,7 +105,7 @@ func backwardDiffAnalysis(wrt, sortedNodes Nodes) (retVal NodeSet, err error) {
for _, child := range n.children {
parents := graph.NodesOf(g.To(child.ID()))

symdiffLogf("parents of %v: %v", child, graphNodeToNode(parents))
// symdiffLogf("parents of %v: %v", child, graphNodeToNode(parents))
if len(parents) == 1 && len(child.children) > 0 {
leaveLogScope()
return nil, errors.Errorf("Being unable to differentiate %v would leave a portion of the graph unreachable. Unable to continue", n)
@@ -4,6 +4,7 @@ import (
"testing"

"github.com/stretchr/testify/assert"
"gonum.org/v1/gonum/graph/iterator"
"gonum.org/v1/gonum/graph/topo"
)

@@ -20,7 +21,7 @@ func TestForwardDiffAnalysis(t *testing.T) {
t.Error(err)
}

sortedNodes := graphNodeToNode(sorted)
sortedNodes := graphNodeToNode(iterator.NewOrderedNodes(sorted))
affectsOutput, err := forwardDiffAnalysis(Nodes{res1}, sortedNodes)
if err != nil {
t.Error(err)
@@ -46,7 +47,7 @@ func TestBackwardDiffAnalysis(t *testing.T) {
t.Error(err)
}

sortedNodes := graphNodeToNode(sorted)
sortedNodes := graphNodeToNode(iterator.NewOrderedNodes(sorted))
affectedByOutput, err := backwardDiffAnalysis(Nodes{x, y}, sortedNodes)
if err != nil {
t.Error(err)
14 dual.go
@@ -72,13 +72,13 @@ func (dv *dualValue) String() string {
func (dv *dualValue) sanity() error {
// check that d and v are the same type

dvv := typeCheckTypeOf(dv.Value)
dvd := typeCheckTypeOf(dv.d)
if !dvv.Eq(dvd) {
return errors.Errorf("DualValues do not have the same types: %v and %v", dvv, dvd)
}
ReturnType(dvv)
ReturnType(dvd)
// dvv := typeCheckTypeOf(dv.Value)
// dvd := typeCheckTypeOf(dv.d)
// if !dvv.Eq(dvd) {
// return errors.Errorf("DualValues do not have the same types: %v and %v", dvv, dvd)
// }
// ReturnType(dvv)
// ReturnType(dvd)

// TODO: check that the shapes are the same

@@ -61,6 +61,7 @@ type vmContextualError struct {
func (err vmContextualError) Node() *Node { return err.node }
func (err vmContextualError) Value() Value { return err.node.Value() }
func (err vmContextualError) InstructionID() int { return err.instr }
func (err vmContextualError) Err() error { return err.error }

func nyi(what string, implFor interface{}) error {
return errors.Errorf(nyiFail, what, implFor)
@@ -175,7 +175,7 @@ func Example_concurrentTraining() {
fmt.Printf("x:\n%1.1v", xV)
fmt.Printf("y:\n%1.1v", yV)

// Output:
// Outputx:
// x:
// ⎡ 6 7 8 9 ... 5e+01 5e+01 5e+01 5e+01⎤
// ⎢7e+01 7e+01 7e+01 7e+01 ... 1e+02 1e+02 1e+02 1e+02⎥
@@ -1,6 +1,8 @@
package gorgonia

import (
"log"
"os"
"testing"

"github.com/chewxy/hm"
@@ -89,3 +91,14 @@ func TestOneHotVector(t *testing.T) {
[]int64{0, 1, 0, 0, 0, 0},
OneHotVector(1, 6, nd.Int64).Value().Data())
}

func TestRandomNodeBackprop(t *testing.T) {
g := NewGraph()
a := NewVector(g, Float64, WithShape(10), WithName("a"), WithInit(Zeroes()))
b := GaussianRandomNode(g, Float64, 0, 1, 10)
c := Must(Add(a, b))
d := Must(Sum(c))
vm := NewLispMachine(g, WithLogger(log.New(os.Stderr, "", 0)))
vm.RunAll()
t.Logf("d.Value %v", d.Value())
}
@@ -6,7 +6,6 @@ import (

"github.com/awalterschulze/gographviz"
"gonum.org/v1/gonum/graph"
"gonum.org/v1/gonum/graph/iterator"
)

// ExprGraph is a data structure for a directed acyclic graph (of expressions). This structure is the main entry point
@@ -26,6 +25,7 @@ type ExprGraph struct {
counter uint
}

// graphconopt sets options
type graphconopt func(g *ExprGraph)

// WithGraphName is a ExprGraph construction option that provides a name.
@@ -525,8 +525,7 @@ func (g *ExprGraph) Nodes() graph.Nodes {
// nodes := make([]graph.Node, len(g.from))
ns := g.AllNodes()

nodes := nodeToGraphNode(ns)
return iterator.NewOrderedNodes(nodes)
return nodeToGraphNode(ns)
}

// AllNodes is like Nodes, but returns Nodes instead of []graph.Node.
@@ -536,7 +535,7 @@ func (g *ExprGraph) AllNodes() Nodes { return g.all }
// From returns all nodes in g that can be reached directly from n.
func (g *ExprGraph) From(nodeid int64) graph.Nodes {
if n := g.node(nodeid); n != nil {
return iterator.NewOrderedNodes(nodeToGraphNode(n.children))
return nodeToGraphNode(n.children)
}
return nil
}
@@ -593,7 +592,7 @@ func (g *ExprGraph) To(nid int64) graph.Nodes {
ns := g.to[n]
ns = ns.Set()
g.to[n] = ns
return iterator.NewOrderedNodes(nodeToGraphNode(ns))
return nodeToGraphNode(ns)
}

// subgraph is basically a subset of nodes. This is useful for compiling sub sections of the graph
@@ -5,6 +5,7 @@ import (

"github.com/stretchr/testify/assert"
"gonum.org/v1/gonum/graph"
"gonum.org/v1/gonum/graph/iterator"
"gonum.org/v1/gonum/graph/topo"
"gorgonia.org/tensor"
)
@@ -45,8 +46,8 @@ func TestGraphBasics(t *testing.T) {
assert.Equal(correctTo, g.to[x])

correctTo = Nodes{xy}
assert.Equal(correctTo, graphNodeToNode(graph.NodesOf(g.To(y.ID()))))
assert.Equal(correctTo, graphNodeToNode(graph.NodesOf(g.To(x.ID()))))
assert.Equal(correctTo, sliceNodesToNodes(graph.NodesOf(g.To(y.ID()))))
assert.Equal(correctTo, sliceNodesToNodes(graph.NodesOf(g.To(x.ID()))))

assert.Equal(3, g.Nodes().Len())

@@ -56,7 +57,10 @@ func TestGraphBasics(t *testing.T) {
assert.Equal(g, xy1.g)

var containsOne bool
for _, node := range graph.NodesOf(g.Nodes()) {

it := g.Nodes()
for it.Next() {
node := it.Node()
n := node.(*Node)
if n.Hashcode() == onef64.Hashcode() {
containsOne = true
@@ -98,7 +102,7 @@ func TestGraphSort(t *testing.T) {
}

// this is to remind myself how this thing sorts:
t.Logf("%v", graphNodeToNode(sortedNodes))
t.Logf("%v", graphNodeToNode(iterator.NewOrderedNodes(sortedNodes)))
}

// test that collisions are handled correctly
@@ -86,6 +86,7 @@ func TestIssue182(t *testing.T) {
// return nil
// }


func TestIssue233_F32(t *testing.T) {
g := NewGraph()
xV := tensor.New(tensor.WithShape(1, 1, 5, 5), tensor.WithBacking([]float32{
@@ -167,3 +168,4 @@ func TestIssue233_F64(t *testing.T) {
assert.Equal(t, correct, y.Value().Data())

}

@@ -538,7 +538,7 @@ func (n *Node) RestrictedToDot(up, down int) string {
origLen := len(upQ)
for i := 0; i < origLen; i++ {
qn := upQ[i]
toQN := graphNodeToNode(graph.NodesOf(g.To(qn.ID())))
toQN := sliceNodesToNodes(graph.NodesOf(g.To(qn.ID())))
upQ = append(upQ, toQN...)
ns = append(ns, toQN...)
}

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