fix segfault issues

codex/merkletree/codex/codex.nim

@@ -191,7 +191,7 @@ proc init*(
   var tree = CodexTree(compress: compressor, zero: Zero, mcodec: mcodec)
 
   var task =
-    CodexTreeTask(tree: cast[ptr ByteTree](addr tree), leaves: @leaves, signal: signal)
+    CodexTreeTask(tree: cast[ptr ByteTree](addr tree), leaves: leaves, signal: signal)
 
   doAssert tp.numThreads > 1,
     "Must have at least one separate thread or signal will never be fired"
@@ -208,10 +208,10 @@ proc init*(
   if not task.success.load():
     return failure("merkle tree task failed")
 
-  defer:
-    task.layers = default(Isolated[seq[seq[ByteHash]]])
+  # defer:
+  #   task.layers = default(Isolated[seq[seq[ByteHash]]])
 
-  tree.layers = task.layers.extract
+  tree.layers = extractValue(task.layers)
 
   success tree
 

codex/merkletree/merkletree.nim

@@ -17,6 +17,68 @@ import pkg/chronos/threadsync
 
 import ../errors
 
+type UniqueSeq*[T] = object
+  ## A unique pointer to a seq[seq[T]] in shared memory
+  ## Can only be moved, not copied
+  data: ptr seq[seq[T]]
+
+proc newUniqueSeq*[T](data: sink Isolated[seq[seq[T]]]): UniqueSeq[T] =
+  ## Creates a new unique sequence in shared memory
+  ## The memory is automatically freed when the object is destroyed
+  result.data = cast[ptr seq[seq[T]]](allocShared0(sizeof(seq[seq[T]])))
+
+  result.data[] = extract(data)
+
+proc `=destroy`*[T](p: var UniqueSeq[T]) =
+  ## Destructor for UniqueSeq
+  if p.data != nil:
+    # Clear the sequence to release inner sequences
+    p.data[].setLen(0)
+    echo "destroying unique seq"
+    deallocShared(p.data)
+    p.data = nil
+
+proc `=copy`*[T](
+  dest: var UniqueSeq[T], src: UniqueSeq[T]
+) {.error: "UniqueSeq cannot be copied, only moved".}
+
+proc `=sink`*[T](dest: var UniqueSeq[T], src: UniqueSeq[T]) =
+  ## Move constructor for UniqueSeq
+  if dest.data != nil:
+    `=destroy`(dest)
+  dest.data = src.data
+  # We need to nil out the source data to prevent double-free
+  # This is handled by Nim's destructive move semantics
+
+proc `[]`*[T](p: UniqueSeq[T]): lent seq[seq[T]] =
+  ## Access the data (read-only)
+  if p.data == nil:
+    raise newException(NilAccessDefect, "accessing nil UniqueSeq")
+  p.data[]
+
+proc `[]`*[T](p: var UniqueSeq[T]): var seq[seq[T]] =
+  ## Access the data (mutable)
+  if p.data == nil:
+    raise newException(NilAccessDefect, "accessing nil UniqueSeq")
+  p.data[]
+
+proc isNil*[T](p: UniqueSeq[T]): bool =
+  ## Check if the UniqueSeq is nil
+  p.data == nil
+
+proc extractValue*[T](p: var UniqueSeq[T]): seq[seq[T]] =
+  ## Extract the value from the UniqueSeq and release the memory
+  if p.data == nil:
+    raise newException(NilAccessDefect, "extracting from nil UniqueSeq")
+
+  # Move the value out
+  var isolated = isolate(p.data[])
+  result = extract(isolated)
+
+  # Free the shared memory
+  deallocShared(p.data)
+  p.data = nil
+
 type
   CompressFn*[H, K] = proc(x, y: H, key: K): ?!H {.noSideEffect, raises: [].}
 
@@ -36,7 +98,7 @@ type
     tree*: ptr MerkleTree[H, K]
     leaves*: seq[H]
     signal*: ThreadSignalPtr
-    layers*: Isolated[seq[seq[H]]]
+    layers*: UniqueSeq[H]
     success*: Atomic[bool]
 
 func depth*[H, K](self: MerkleTree[H, K]): int =
@@ -171,6 +233,12 @@ proc merkleTreeWorker*[H, K](task: ptr MerkleTask[H, K]) {.gcsafe.} =
     task[].success.store(false)
     return
 
-  var isolatedLayers = isolate(res.get())
-  task[].layers = isolatedLayers
+  var l = res.get()
+  var newOuterSeq = newSeq[seq[H]](l.len)
+  for i in 0 ..< l.len:
+    var isoInner = isolate(l[i])
+    newOuterSeq[i] = extract(isoInner)
+
+  var isolatedLayers = isolate(newOuterSeq)
+  task[].layers = newUniqueSeq(isolatedLayers)
   task[].success.store(true)

codex/merkletree/poseidon2.nim

@@ -118,10 +118,10 @@ proc init*(
   if not task.success.load():
     return failure("merkle tree task failed")
 
-  defer:
-    task.layers = default(Isolated[seq[seq[Poseidon2Hash]]])
+  # defer:
+  #   task.layers = default(Isolated[seq[seq[Poseidon2Hash]]])
 
-  tree.layers = task.layers.extract
+  tree.layers = extractValue(task.layers)
 
   success tree
 

codex/slots/builder/builder.nim

@@ -191,11 +191,11 @@ proc getBlockDigest*[T, H](
   if blk.isEmpty:
     return self.emptyDigestTree.root
 
-  without digest =? (await T.digest(self.taskPool, blk.data, self.cellSize.int)), err:
+  without dg =? (await T.digest(self.taskPool, blk.data, self.cellSize.int)), err:
     error "Failed to create digest for block", err = err.msg
     return failure(err)
 
-  return success digest
+  return success dg
 
 proc getCellHashes*[T, H](
     self: SlotsBuilder[T, H], slotIndex: Natural

codex/utils/poseidon2digest.nim

@@ -23,7 +23,7 @@ type DigestTask* = object
   bytes: seq[byte]
   chunkSize: int
   success: Atomic[bool]
-  digest: Isolated[Poseidon2Hash]
+  digest: ptr Poseidon2Hash
 
 export DigestTask
 
@@ -85,7 +85,8 @@ proc digestWorker(tp: Taskpool, task: ptr DigestTask) {.gcsafe.} =
     task[].success.store(false)
     return
 
-  task[].digest = isolate(res.get())
+  var isolatedDigest = isolate(res.get())
+  task[].digest[] = extract(isolatedDigest)
   task[].success.store(true)
 
 proc digest*(
@@ -93,14 +94,18 @@ proc digest*(
 ): Future[?!Poseidon2Hash] {.async: (raises: [CancelledError]).} =
   without signal =? ThreadSignalPtr.new():
     return failure("Unable to create thread signal")
-
   defer:
     signal.close().expect("closing once works")
 
   doAssert tp.numThreads > 1,
     "Must have at least one separate thread or signal will never be fired"
 
-  var task = DigestTask(signal: signal, bytes: bytes, chunkSize: chunkSize)
+  var task = DigestTask(
+    signal: signal,
+    bytes: bytes,
+    chunkSize: chunkSize,
+    digest: cast[ptr Poseidon2Hash](allocShared(sizeof(Poseidon2Hash))),
+  )
 
   tp.spawn digestWorker(tp, addr task)
 
@@ -114,11 +119,10 @@ proc digest*(
   if not task.success.load():
     return failure("digest task failed")
 
+  var isolatedDigest = isolate(task.digest[])
+  var digest = extract(isolatedDigest)
   defer:
-    task.digest = default(Isolated[Poseidon2Hash])
-
-  var digest = task.digest.extract
-
+    deallocShared(task.digest)
   success digest
 
 func digestMhash*(

tests/codex/node/testnode.nim

@@ -178,12 +178,14 @@ asyncchecksuite "Test Node - Basic":
     check string.fromBytes(data) == testString
 
   test "Setup purchase request":
+    echo "Here the tedt"
     let
       erasure = Erasure.new(store, leoEncoderProvider, leoDecoderProvider, taskPool)
       manifest = await storeDataGetManifest(localStore, chunker)
       manifestBlock =
         bt.Block.new(manifest.encode().tryGet(), codec = ManifestCodec).tryGet()
       protected = (await erasure.encode(manifest, 3, 2)).tryGet()
+    let
       builder = Poseidon2Builder.new(localStore, protected, taskPool).tryGet()
       verifiable = (await builder.buildManifest()).tryGet()
       verifiableBlock =

tests/codex/node/testslotrepair.nim

@@ -52,7 +52,6 @@ asyncchecksuite "Test Node - Slot Repair":
     )
   var
     manifest: Manifest
-    taskPool: Taskpool
     builder: Poseidon2Builder
     verifiable: Manifest
     verifiableBlock: bt.Block
@@ -102,7 +101,7 @@ asyncchecksuite "Test Node - Slot Repair":
     (await localStore.putBlock(manifestBlock)).tryGet()
 
     protected = (await erasure.encode(manifest, ecK, ecM)).tryGet()
-    builder = Poseidon2Builder.new(localStore, protected, taskPool).tryGet()
+    builder = Poseidon2Builder.new(localStore, protected, cluster.taskpool).tryGet()
     verifiable = (await builder.buildManifest()).tryGet()
     verifiableBlock =
       bt.Block.new(verifiable.encode().tryGet(), codec = ManifestCodec).tryGet()