kenaz 0.3.3 → 0.3.6

package/core/.kenaz/knowledge/ladybug_926a0ba1_column_checkpoint.patch

@@ -1,412 +1,412 @@
-From 926a0ba10d221eb437add0885ff492e7576bb7c9 Mon Sep 17 00:00:00 2001
-From: kory-io <kory-io@users.noreply.github.com>
-Date: Thu, 24 Sep 2026 18:56:55 -0600
-Subject: [PATCH] fix(storage): keep segment on disk when an out-of-place
- checkpoint fails
-
-Column::checkpointColumnChunkOutOfPlace rewrote a segment by switching
-the persistent ColumnChunkData itself to IN_MEMORY (setToInMemory) and
-then resizing, scanning, writing, finalizing and flushing it. Any of
-those steps can throw, for example "Unable to allocate memory! The
-buffer pool is full" from the resize or the scan. The checkpoint is
-then rolled back, but Checkpointer::rollback only discards pending page
-frees and rolls back node-table indexes; it does not touch node group
-state. The node group keeps the half-rewritten segment, which stays
-IN_MEMORY, and with runtime checks enabled (Debug, or RUNTIME_CHECKS=1
-as in CI) every later checkpoint of that table fails the
-`segment->getResidencyState() == ResidencyState::ON_DISK` assertion in
-ColumnChunk::checkpoint, so the database can no longer checkpoint.
-
-Rewrite the segment into a new in-memory chunk of the same kind
-instead, and return it once it has been flushed, the same way split
-segments are already returned. The persistent segment object is not
-touched until the rewrite has succeeded, and its pages are only freed
-after that, so a failure leaves it on disk and unchanged and the next
-checkpoint starts from it again. Segments rewritten earlier in the
-same failed checkpoint stay replaced; their old pages are only
-reclaimed after the database is reopened.
-
-ColumnChunk::checkpoint already installs returned segments. The nested
-null, list offset and list size chunks, which are checkpointed without
-splitting, now install the returned chunk into their parent.
-StringColumn and StructColumn also call syncNumValues on the returned
-segments, as they already did on the persistent segment.
-
-Add FlakyCheckpointerTest.RecoverFromFailureDuringOutOfPlaceCheckpoint.
-It fails a checkpoint at the flush of an out-of-place rewrite, then
-checks that the data is intact and that the next checkpoint succeeds.
-Add an e2e case that checkpoints a list column in place while its
-offsets and nulls are rewritten out of place.
----
- src/include/storage/table/column.h            |   4 +-
- src/storage/table/column.cpp                  |  58 +++++++---
- src/storage/table/column_chunk.cpp            |   4 +-
- src/storage/table/list_column.cpp             |  15 ++-
- src/storage/table/string_column.cpp           |   3 +
- src/storage/table/struct_column.cpp           |   3 +
- .../transaction/set_node/set_empty.test       |  41 +++++++
- test/transaction/checkpoint_test.cpp          | 106 ++++++++++++++++++
- 8 files changed, 209 insertions(+), 25 deletions(-)
-
-diff --git a/src/include/storage/table/column.h b/src/include/storage/table/column.h
-index 16584cb027..d56fefbf5f 100644
---- a/src/include/storage/table/column.h
-+++ b/src/include/storage/table/column.h
-@@ -95,8 +95,8 @@ class Column {
-         return common::dynamic_cast_checked<TARGET&>(*this);
-     }
- 
--    // Return value is the new segments if segment splitting occurs during an out of place
--    // checkpoint
-+    // Return value is the new segment(s) replacing the persistent segment if it was checkpointed
-+    // out of place (more than one if it was split), or empty if it was checkpointed in place
-     virtual std::vector<std::unique_ptr<ColumnChunkData>> checkpointSegment(
-         ColumnCheckpointState&& checkpointState, PageAllocator& pageAllocator,
-         bool canSplitSegment = true) const;
-diff --git a/src/storage/table/column.cpp b/src/storage/table/column.cpp
-index 72b9a2f206..9d23776188 100644
---- a/src/storage/table/column.cpp
-+++ b/src/storage/table/column.cpp
-@@ -3,6 +3,7 @@
- #include <algorithm>
- #include <cstdint>
- #include <memory>
-+#include <tuple>
- 
- #include "common/assert.h"
- #include "common/data_chunk/sel_vector.h"
-@@ -439,42 +440,63 @@ void Column::checkpointNullData(const ColumnCheckpointState& checkpointState,
-             segmentCheckpointState.numRows);
-     }
-     DASSERT(checkpointState.persistentData.hasNullData());
--    nullColumn->checkpointSegment(
-+    auto newNullData = nullColumn->checkpointSegment(
-         ColumnCheckpointState(*checkpointState.persistentData.getNullData(),
-             std::move(nullSegmentCheckpointStates)),
-         pageAllocator, false);
-+    if (!newNullData.empty()) {
-+        DASSERT(newNullData.size() == 1);
-+        auto* nullChunk = &newNullData[0]->cast<NullChunkData>();
-+        std::ignore = newNullData[0].release();
-+        checkpointState.persistentData.setNullData(std::unique_ptr<NullChunkData>(nullChunk));
-+    }
-+}
-+
-+static std::unique_ptr<ColumnChunkData> createInMemoryChunkLike(const ColumnChunkData& chunk,
-+    uint64_t capacity) {
-+    if (dynamic_cast<const NullChunkData*>(&chunk) != nullptr) {
-+        return ColumnChunkFactory::createNullChunkData(chunk.getMemoryManager(),
-+            chunk.isCompressionEnabled(), capacity, ResidencyState::IN_MEMORY);
-+    }
-+    return ColumnChunkFactory::createColumnChunkData(chunk.getMemoryManager(),
-+        chunk.getDataType().copy(), chunk.isCompressionEnabled(), capacity,
-+        ResidencyState::IN_MEMORY, chunk.hasNullData());
- }
- 
- std::vector<std::unique_ptr<ColumnChunkData>> Column::checkpointColumnChunkOutOfPlace(
-     const SegmentState& state, const ColumnCheckpointState& checkpointState,
-     PageAllocator& pageAllocator, bool canSplitSegment) const {
-     const auto numRows = std::max(checkpointState.endRowIdxToWrite, state.metadata.numValues);
--    checkpointState.persistentData.setToInMemory();
--    checkpointState.persistentData.resize(numRows);
--    DASSERT(checkpointState.persistentData.getNumValues() == 0);
--    scanSegment(state, &checkpointState.persistentData, 0, state.metadata.numValues);
--    state.reclaimAllocatedPages(pageAllocator);
-+    // Rewrite the segment into a new chunk instead of converting persistentData to an in-memory
-+    // chunk in place. If the rewrite fails part way (e.g. the buffer pool is full), the checkpoint
-+    // is rolled back but the segment is kept, so it must still describe its on-disk pages for the
-+    // data to stay readable and for the next checkpoint to be able to rewrite it.
-+    auto newData = createInMemoryChunkLike(checkpointState.persistentData, numRows);
-+    DASSERT(newData->getNumValues() == 0);
-+    scanSegment(state, newData.get(), 0, state.metadata.numValues);
-     // TODO(bmwinger): for simple compression types, we can predict whether or not we will need to
-     // split the segment and avoid having to re-write it multiple times
-     for (auto& segmentCheckpointState : checkpointState.segmentCheckpointStates) {
--        checkpointState.persistentData.write(&segmentCheckpointState.chunkData,
--            segmentCheckpointState.startRowInData, segmentCheckpointState.offsetInSegment,
--            segmentCheckpointState.numRows);
-+        newData->write(&segmentCheckpointState.chunkData, segmentCheckpointState.startRowInData,
-+            segmentCheckpointState.offsetInSegment, segmentCheckpointState.numRows);
-     }
-     // Finalize is necessary prior to splitting for strings and lists so that pruned values don't
-     // have an impact on the number/size of segments It should not be necessary after splitting
-     // since the function is used to prune unused values (or duplicated dictionary entries in the
-     // case of strings) and those will never be introduced when splitting.
--    checkpointState.persistentData.finalize();
--    if (canSplitSegment && checkpointState.persistentData.shouldSplit()) {
--        auto newSegments = checkpointState.persistentData.split();
--        for (auto& segment : newSegments) {
--            segment->flush(pageAllocator);
--        }
--        return newSegments;
-+    newData->finalize();
-+    std::vector<std::unique_ptr<ColumnChunkData>> newSegments;
-+    if (canSplitSegment && newData->shouldSplit()) {
-+        newSegments = newData->split();
-+    } else {
-+        newSegments.push_back(std::move(newData));
-     }
--    checkpointState.persistentData.flush(pageAllocator);
--    return {};
-+    for (auto& segment : newSegments) {
-+        segment->flush(pageAllocator);
-+    }
-+    // Only free the old pages once the replacement is on disk.
-+    state.reclaimAllocatedPages(pageAllocator);
-+    return newSegments;
- }
- 
- bool Column::canCheckpointInPlace(const SegmentState& state,
-diff --git a/src/storage/table/column_chunk.cpp b/src/storage/table/column_chunk.cpp
-index 9adf90426d..4c0f277344 100644
---- a/src/storage/table/column_chunk.cpp
-+++ b/src/storage/table/column_chunk.cpp
-@@ -311,8 +311,8 @@ void ColumnChunk::checkpoint(Column& column,
-             }
-         }
-         auto segmentEnd = segmentStart + segment->getNumValues();
--        // If the segment was split during checkpointing we need to insert the new segments into the
--        // ColumnChunk
-+        // If the segment was rewritten out of place (and possibly split) during checkpointing we
-+        // need to replace it with the new segments in the ColumnChunk
-         auto newSegments = column.checkpointSegment(
-             ColumnCheckpointState(*segment, std::move(segmentCheckpointStates)), pageAllocator);
-         if (!newSegments.empty()) {
-diff --git a/src/storage/table/list_column.cpp b/src/storage/table/list_column.cpp
-index 0ac0465896..e4a1ece4e2 100644
---- a/src/storage/table/list_column.cpp
-+++ b/src/storage/table/list_column.cpp
-@@ -403,10 +403,14 @@ std::vector<std::unique_ptr<ColumnChunkData>> ListColumn::checkpointSegment(
-     }
- 
-     // We do not allow nested splitting of offset/size segments
--    offsetColumn->checkpointSegment(
-+    auto newOffsetChunk = offsetColumn->checkpointSegment(
-         ColumnCheckpointState(*persistentListChunk.getOffsetColumnChunk(),
-             std::move(offsetChunkCheckpointStates)),
-         pageAllocator, false);
-+    if (!newOffsetChunk.empty()) {
-+        DASSERT(newOffsetChunk.size() == 1);
-+        persistentListChunk.setOffsetColumnChunk(std::move(newOffsetChunk[0]));
-+    }
- 
-     // Checkpoint size data.
-     std::vector<SegmentCheckpointState> sizeChunkCheckpointStates;
-@@ -416,9 +420,14 @@ std::vector<std::unique_ptr<ColumnChunkData>> ListColumn::checkpointSegment(
-             segmentCheckpointState.startRowInData, segmentCheckpointState.offsetInSegment,
-             segmentCheckpointState.numRows});
-     }
--    sizeColumn->checkpointSegment(ColumnCheckpointState(*persistentListChunk.getSizeColumnChunk(),
--                                      std::move(sizeChunkCheckpointStates)),
-+    auto newSizeChunk = sizeColumn->checkpointSegment(
-+        ColumnCheckpointState(*persistentListChunk.getSizeColumnChunk(),
-+            std::move(sizeChunkCheckpointStates)),
-         pageAllocator, false);
-+    if (!newSizeChunk.empty()) {
-+        DASSERT(newSizeChunk.size() == 1);
-+        persistentListChunk.setSizeColumnChunk(std::move(newSizeChunk[0]));
-+    }
-     // Checkpoint null data.
-     Column::checkpointNullData(checkpointState, pageAllocator);
- 
-diff --git a/src/storage/table/string_column.cpp b/src/storage/table/string_column.cpp
-index b7f94dc3ea..38b508765a 100644
---- a/src/storage/table/string_column.cpp
-+++ b/src/storage/table/string_column.cpp
-@@ -116,6 +116,9 @@ std::vector<std::unique_ptr<ColumnChunkData>> StringColumn::checkpointSegment(
-     auto result =
-         Column::checkpointSegment(std::move(checkpointState), pageAllocator, canSplitSegment);
-     persistentData.syncNumValues();
-+    for (auto& segment : result) {
-+        segment->syncNumValues();
-+    }
-     return result;
- }
- 
-diff --git a/src/storage/table/struct_column.cpp b/src/storage/table/struct_column.cpp
-index b16e3d83ff..673cb6c468 100644
---- a/src/storage/table/struct_column.cpp
-+++ b/src/storage/table/struct_column.cpp
-@@ -114,6 +114,9 @@ std::vector<std::unique_ptr<ColumnChunkData>> StructColumn::checkpointSegment(
-     auto result =
-         Column::checkpointSegment(std::move(checkpointState), pageAllocator, canSplitSegment);
-     persistentStructChunk.syncNumValues();
-+    for (auto& segment : result) {
-+        segment->syncNumValues();
-+    }
-     return result;
- }
- 
-diff --git a/test/test_files/transaction/set_node/set_empty.test b/test/test_files/transaction/set_node/set_empty.test
-index 72dbeefd09..b6e1495e07 100644
---- a/test/test_files/transaction/set_node/set_empty.test
-+++ b/test/test_files/transaction/set_node/set_empty.test
-@@ -33,3 +33,44 @@
- ---- 2
- 0|1010101010.300000
- 1341|1010101010.200000
-+
-+-CASE ListInPlaceWithOutOfPlaceOffsetsAndNulls
-+-STATEMENT CALL auto_checkpoint=false;
-+---- ok
-+-STATEMENT CREATE NODE TABLE t2(id INT64 PRIMARY KEY, l INT64[]);
-+---- ok
-+-STATEMENT UNWIND range(0, 4094) AS i CREATE (:t2 {id: i, l: [0, 1]});
-+---- ok
-+-STATEMENT CHECKPOINT;
-+---- ok
-+-STATEMENT MATCH (a:t2) WHERE a.id = 5 SET a.l = [1,0,1,0,1,0,1,0,1,0];
-+---- ok
-+-STATEMENT MATCH (a:t2) WHERE a.id = 7 SET a.l = NULL;
-+---- ok
-+-STATEMENT CHECKPOINT;
-+---- ok
-+-STATEMENT MATCH (a:t2) RETURN COUNT(a.l);
-+---- 1
-+4094
-+-STATEMENT MATCH (a:t2) UNWIND a.l AS x RETURN COUNT(x), SUM(x);
-+---- 1
-+8196|4098
-+-STATEMENT MATCH (a:t2) WHERE a.id = 5 RETURN SIZE(a.l), a.l[1], a.l[2];
-+---- 1
-+10|1|0
-+-STATEMENT MATCH (a:t2) WHERE a.id = 6 RETURN SIZE(a.l), a.l[1], a.l[2];
-+---- 1
-+2|0|1
-+-RELOADDB
-+-STATEMENT MATCH (a:t2) RETURN COUNT(a.l);
-+---- 1
-+4094
-+-STATEMENT MATCH (a:t2) UNWIND a.l AS x RETURN COUNT(x), SUM(x);
-+---- 1
-+8196|4098
-+-STATEMENT MATCH (a:t2) WHERE a.id = 5 RETURN SIZE(a.l), a.l[1], a.l[2];
-+---- 1
-+10|1|0
-+-STATEMENT MATCH (a:t2) WHERE a.id = 4094 RETURN SIZE(a.l), a.l[1], a.l[2];
-+---- 1
-+2|0|1
-diff --git a/test/transaction/checkpoint_test.cpp b/test/transaction/checkpoint_test.cpp
-index 2777560616..2049d21d19 100644
---- a/test/transaction/checkpoint_test.cpp
-+++ b/test/transaction/checkpoint_test.cpp
-@@ -13,6 +13,8 @@
- #include "catalog/catalog_entry/table_catalog_entry.h"
- #include "common/exception/runtime.h"
- #include "storage/checkpointer.h"
-+#include "storage/page_allocator.h"
-+#include "storage/page_manager.h"
- #include "storage/storage_manager.h"
- #include "storage/table/node_table.h"
- #include "storage/table/string_chunk_data.h"
-@@ -235,6 +237,110 @@ TEST_F(FlakyCheckpointerTest, RecoverFromCheckpointClearingFilesFailure) {
-     runTest(flakyCheckpointer);
- }
- 
-+// Page allocator that fails the first page allocation. In-place checkpoints do not allocate
-+// pages, so during the storage phase of a checkpoint that only updates a node group with
-+// persistent data, the first allocation is the flush of an out-of-place column chunk rewrite and
-+// the failure lands in the middle of that rewrite.
-+class FailFirstAllocationPageAllocator final : public PageAllocator {
-+public:
-+    FailFirstAllocationPageAllocator(PageAllocator& inner, bool& failed)
-+        : PageAllocator(inner.getDataFH()), inner{inner}, failed{failed} {}
-+
-+    PageRange allocatePageRange(page_idx_t numPages) override {
-+        if (!failed) {
-+            failed = true;
-+            throw RuntimeException("checkpoint failed.");
-+        }
-+        return inner.allocatePageRange(numPages);
-+    }
-+    void freePageRange(PageRange block) override { inner.freePageRange(block); }
-+
-+private:
-+    PageAllocator& inner;
-+    bool& failed;
-+};
-+
-+class FlakyCheckpointerFailsDuringOutOfPlaceRewrite final : public Checkpointer {
-+public:
-+    FlakyCheckpointerFailsDuringOutOfPlaceRewrite(main::ClientContext& context, bool& failed)
-+        : Checkpointer(context), failed{failed} {}
-+
-+    bool checkpointStorage() override {
-+        for (const auto& target : checkpointTargets) {
-+            FailFirstAllocationPageAllocator pageAllocator(
-+                *target.storageManager->getDataFH()->getPageManager(), failed);
-+            const Transaction snapshotTxn(TransactionType::CHECKPOINT,
-+                Transaction::DUMMY_TRANSACTION_ID, snapshotTS);
-+            target.storageManager->checkpoint(&clientContext, *target.catalog, snapshotTxn,
-+                pageAllocator, tableEpochWatermarksByManager.at(target.storageManager));
-+        }
-+        throw RuntimeException("expected the injected page allocation failure to fire.");
-+    }
-+
-+private:
-+    bool& failed;
-+};
-+
-+// A checkpoint that fails while a column chunk segment is being rewritten out of place must
-+// leave that segment as it was, so that the data stays readable and later checkpoints succeed.
-+TEST_F(FlakyCheckpointerTest, RecoverFromFailureDuringOutOfPlaceCheckpoint) {
-+    if (inMemMode || systemConfig->checkpointThreshold == 0) {
-+        GTEST_SKIP();
-+    }
-+    conn->query("CALL force_checkpoint_on_close=false;");
-+    conn->query("CALL auto_checkpoint=false;");
-+    ASSERT_TRUE(
-+        conn->query("CREATE NODE TABLE test(id INT64 PRIMARY KEY, name STRING);")->isSuccess());
-+    constexpr int64_t numInitialRows = 3000;
-+    constexpr int64_t numRows = 6000;
-+    constexpr std::string_view namePrefix = "a longer name so the pages fill up ";
-+    auto nameOf = [&](int64_t i) { return std::format("{}{}", namePrefix, i); };
-+    auto insertRows = [&](int64_t start, int64_t end) {
-+        auto res = conn->query(std::format("UNWIND range({}, {}) AS i CREATE (a:test {{id: i, "
-+                                           "name: concat('{}', CAST(i AS STRING))}});",
-+            start, end - 1, namePrefix));
-+        ASSERT_TRUE(res->isSuccess()) << res->getErrorMessage();
-+    };
-+    auto checkRows = [&]() {
-+        auto res = conn->query("MATCH (a:test) RETURN COUNT(a), CAST(SUM(a.id) AS INT64), "
-+                               "CAST(SUM(SIZE(a.name)) AS INT64), MIN(a.name), MAX(a.name);");
-+        ASSERT_TRUE(res->isSuccess()) << res->getErrorMessage();
-+        auto row = res->getNext();
-+        ASSERT_EQ(row->getValue(0)->getValue<int64_t>(), numRows);
-+        ASSERT_EQ(row->getValue(1)->getValue<int64_t>(), numRows * (numRows - 1) / 2);
-+        int64_t totalNameSize = 0;
-+        for (auto i = 0; i < numRows; i++) {
-+            totalNameSize += nameOf(i).size();
-+        }
-+        ASSERT_EQ(row->getValue(2)->getValue<int64_t>(), totalNameSize);
-+        ASSERT_EQ(row->getValue(3)->getValue<std::string>(), nameOf(0));
-+        ASSERT_EQ(row->getValue(4)->getValue<std::string>(), nameOf(999));
-+    };
-+    insertRows(0, numInitialRows);
-+    ASSERT_TRUE(conn->query("CHECKPOINT;")->isSuccess());
-+    // Appending to the persistent node group outgrows the pages of its column chunks, so the
-+    // next checkpoint has to rewrite them out of place.
-+    insertRows(numInitialRows, numRows);
-+
-+    auto context = getClientContext(*conn);
-+    bool failed = false;
-+    FlakyCheckpointer flakyCheckpointer([&failed](main::ClientContext& ctx) {
-+        return std::make_unique<FlakyCheckpointerFailsDuringOutOfPlaceRewrite>(ctx, failed);
-+    });
-+    flakyCheckpointer.setCheckpointer(*context);
-+    auto res = conn->query("CHECKPOINT;");
-+    ASSERT_FALSE(res->isSuccess());
-+    ASSERT_TRUE(failed);
-+    checkRows();
-+
-+    FlakyCheckpointer defaultCheckpointer(
-+        [](main::ClientContext& ctx) { return std::make_unique<Checkpointer>(ctx); });
-+    defaultCheckpointer.setCheckpointer(*context);
-+    res = conn->query("CHECKPOINT;");
-+    ASSERT_TRUE(res->isSuccess()) << res->getErrorMessage();
-+    checkRows();
-+}
-+
- // Simulates a situation where a database attempts to replay a shadow file from an older database
- // with the same path
- TEST_F(FlakyCheckpointerTest, ShadowFileDatabaseIDMismatchExistingDB) {
+From 926a0ba10d221eb437add0885ff492e7576bb7c9 Mon Sep 17 00:00:00 2001
+From: kory-io <kory-io@users.noreply.github.com>
+Date: Thu, 24 Sep 2026 18:56:55 -0600
+Subject: [PATCH] fix(storage): keep segment on disk when an out-of-place
+ checkpoint fails
+
+Column::checkpointColumnChunkOutOfPlace rewrote a segment by switching
+the persistent ColumnChunkData itself to IN_MEMORY (setToInMemory) and
+then resizing, scanning, writing, finalizing and flushing it. Any of
+those steps can throw, for example "Unable to allocate memory! The
+buffer pool is full" from the resize or the scan. The checkpoint is
+then rolled back, but Checkpointer::rollback only discards pending page
+frees and rolls back node-table indexes; it does not touch node group
+state. The node group keeps the half-rewritten segment, which stays
+IN_MEMORY, and with runtime checks enabled (Debug, or RUNTIME_CHECKS=1
+as in CI) every later checkpoint of that table fails the
+`segment->getResidencyState() == ResidencyState::ON_DISK` assertion in
+ColumnChunk::checkpoint, so the database can no longer checkpoint.
+
+Rewrite the segment into a new in-memory chunk of the same kind
+instead, and return it once it has been flushed, the same way split
+segments are already returned. The persistent segment object is not
+touched until the rewrite has succeeded, and its pages are only freed
+after that, so a failure leaves it on disk and unchanged and the next
+checkpoint starts from it again. Segments rewritten earlier in the
+same failed checkpoint stay replaced; their old pages are only
+reclaimed after the database is reopened.
+
+ColumnChunk::checkpoint already installs returned segments. The nested
+null, list offset and list size chunks, which are checkpointed without
+splitting, now install the returned chunk into their parent.
+StringColumn and StructColumn also call syncNumValues on the returned
+segments, as they already did on the persistent segment.
+
+Add FlakyCheckpointerTest.RecoverFromFailureDuringOutOfPlaceCheckpoint.
+It fails a checkpoint at the flush of an out-of-place rewrite, then
+checks that the data is intact and that the next checkpoint succeeds.
+Add an e2e case that checkpoints a list column in place while its
+offsets and nulls are rewritten out of place.
+---
+ src/include/storage/table/column.h            |   4 +-
+ src/storage/table/column.cpp                  |  58 +++++++---
+ src/storage/table/column_chunk.cpp            |   4 +-
+ src/storage/table/list_column.cpp             |  15 ++-
+ src/storage/table/string_column.cpp           |   3 +
+ src/storage/table/struct_column.cpp           |   3 +
+ .../transaction/set_node/set_empty.test       |  41 +++++++
+ test/transaction/checkpoint_test.cpp          | 106 ++++++++++++++++++
+ 8 files changed, 209 insertions(+), 25 deletions(-)
+
+diff --git a/src/include/storage/table/column.h b/src/include/storage/table/column.h
+index 16584cb027..d56fefbf5f 100644
+--- a/src/include/storage/table/column.h
++++ b/src/include/storage/table/column.h
+@@ -95,8 +95,8 @@ class Column {
+         return common::dynamic_cast_checked<TARGET&>(*this);
+     }
+ 
+-    // Return value is the new segments if segment splitting occurs during an out of place
+-    // checkpoint
++    // Return value is the new segment(s) replacing the persistent segment if it was checkpointed
++    // out of place (more than one if it was split), or empty if it was checkpointed in place
+     virtual std::vector<std::unique_ptr<ColumnChunkData>> checkpointSegment(
+         ColumnCheckpointState&& checkpointState, PageAllocator& pageAllocator,
+         bool canSplitSegment = true) const;
+diff --git a/src/storage/table/column.cpp b/src/storage/table/column.cpp
+index 72b9a2f206..9d23776188 100644
+--- a/src/storage/table/column.cpp
++++ b/src/storage/table/column.cpp
+@@ -3,6 +3,7 @@
+ #include <algorithm>
+ #include <cstdint>
+ #include <memory>
++#include <tuple>
+ 
+ #include "common/assert.h"
+ #include "common/data_chunk/sel_vector.h"
+@@ -439,42 +440,63 @@ void Column::checkpointNullData(const ColumnCheckpointState& checkpointState,
+             segmentCheckpointState.numRows);
+     }
+     DASSERT(checkpointState.persistentData.hasNullData());
+-    nullColumn->checkpointSegment(
++    auto newNullData = nullColumn->checkpointSegment(
+         ColumnCheckpointState(*checkpointState.persistentData.getNullData(),
+             std::move(nullSegmentCheckpointStates)),
+         pageAllocator, false);
++    if (!newNullData.empty()) {
++        DASSERT(newNullData.size() == 1);
++        auto* nullChunk = &newNullData[0]->cast<NullChunkData>();
++        std::ignore = newNullData[0].release();
++        checkpointState.persistentData.setNullData(std::unique_ptr<NullChunkData>(nullChunk));
++    }
++}
++
++static std::unique_ptr<ColumnChunkData> createInMemoryChunkLike(const ColumnChunkData& chunk,
++    uint64_t capacity) {
++    if (dynamic_cast<const NullChunkData*>(&chunk) != nullptr) {
++        return ColumnChunkFactory::createNullChunkData(chunk.getMemoryManager(),
++            chunk.isCompressionEnabled(), capacity, ResidencyState::IN_MEMORY);
++    }
++    return ColumnChunkFactory::createColumnChunkData(chunk.getMemoryManager(),
++        chunk.getDataType().copy(), chunk.isCompressionEnabled(), capacity,
++        ResidencyState::IN_MEMORY, chunk.hasNullData());
+ }
+ 
+ std::vector<std::unique_ptr<ColumnChunkData>> Column::checkpointColumnChunkOutOfPlace(
+     const SegmentState& state, const ColumnCheckpointState& checkpointState,
+     PageAllocator& pageAllocator, bool canSplitSegment) const {
+     const auto numRows = std::max(checkpointState.endRowIdxToWrite, state.metadata.numValues);
+-    checkpointState.persistentData.setToInMemory();
+-    checkpointState.persistentData.resize(numRows);
+-    DASSERT(checkpointState.persistentData.getNumValues() == 0);
+-    scanSegment(state, &checkpointState.persistentData, 0, state.metadata.numValues);
+-    state.reclaimAllocatedPages(pageAllocator);
++    // Rewrite the segment into a new chunk instead of converting persistentData to an in-memory
++    // chunk in place. If the rewrite fails part way (e.g. the buffer pool is full), the checkpoint
++    // is rolled back but the segment is kept, so it must still describe its on-disk pages for the
++    // data to stay readable and for the next checkpoint to be able to rewrite it.
++    auto newData = createInMemoryChunkLike(checkpointState.persistentData, numRows);
++    DASSERT(newData->getNumValues() == 0);
++    scanSegment(state, newData.get(), 0, state.metadata.numValues);
+     // TODO(bmwinger): for simple compression types, we can predict whether or not we will need to
+     // split the segment and avoid having to re-write it multiple times
+     for (auto& segmentCheckpointState : checkpointState.segmentCheckpointStates) {
+-        checkpointState.persistentData.write(&segmentCheckpointState.chunkData,
+-            segmentCheckpointState.startRowInData, segmentCheckpointState.offsetInSegment,
+-            segmentCheckpointState.numRows);
++        newData->write(&segmentCheckpointState.chunkData, segmentCheckpointState.startRowInData,
++            segmentCheckpointState.offsetInSegment, segmentCheckpointState.numRows);
+     }
+     // Finalize is necessary prior to splitting for strings and lists so that pruned values don't
+     // have an impact on the number/size of segments It should not be necessary after splitting
+     // since the function is used to prune unused values (or duplicated dictionary entries in the
+     // case of strings) and those will never be introduced when splitting.
+-    checkpointState.persistentData.finalize();
+-    if (canSplitSegment && checkpointState.persistentData.shouldSplit()) {
+-        auto newSegments = checkpointState.persistentData.split();
+-        for (auto& segment : newSegments) {
+-            segment->flush(pageAllocator);
+-        }
+-        return newSegments;
++    newData->finalize();
++    std::vector<std::unique_ptr<ColumnChunkData>> newSegments;
++    if (canSplitSegment && newData->shouldSplit()) {
++        newSegments = newData->split();
++    } else {
++        newSegments.push_back(std::move(newData));
+     }
+-    checkpointState.persistentData.flush(pageAllocator);
+-    return {};
++    for (auto& segment : newSegments) {
++        segment->flush(pageAllocator);
++    }
++    // Only free the old pages once the replacement is on disk.
++    state.reclaimAllocatedPages(pageAllocator);
++    return newSegments;
+ }
+ 
+ bool Column::canCheckpointInPlace(const SegmentState& state,
+diff --git a/src/storage/table/column_chunk.cpp b/src/storage/table/column_chunk.cpp
+index 9adf90426d..4c0f277344 100644
+--- a/src/storage/table/column_chunk.cpp
++++ b/src/storage/table/column_chunk.cpp
+@@ -311,8 +311,8 @@ void ColumnChunk::checkpoint(Column& column,
+             }
+         }
+         auto segmentEnd = segmentStart + segment->getNumValues();
+-        // If the segment was split during checkpointing we need to insert the new segments into the
+-        // ColumnChunk
++        // If the segment was rewritten out of place (and possibly split) during checkpointing we
++        // need to replace it with the new segments in the ColumnChunk
+         auto newSegments = column.checkpointSegment(
+             ColumnCheckpointState(*segment, std::move(segmentCheckpointStates)), pageAllocator);
+         if (!newSegments.empty()) {
+diff --git a/src/storage/table/list_column.cpp b/src/storage/table/list_column.cpp
+index 0ac0465896..e4a1ece4e2 100644
+--- a/src/storage/table/list_column.cpp
++++ b/src/storage/table/list_column.cpp
+@@ -403,10 +403,14 @@ std::vector<std::unique_ptr<ColumnChunkData>> ListColumn::checkpointSegment(
+     }
+ 
+     // We do not allow nested splitting of offset/size segments
+-    offsetColumn->checkpointSegment(
++    auto newOffsetChunk = offsetColumn->checkpointSegment(
+         ColumnCheckpointState(*persistentListChunk.getOffsetColumnChunk(),
+             std::move(offsetChunkCheckpointStates)),
+         pageAllocator, false);
++    if (!newOffsetChunk.empty()) {
++        DASSERT(newOffsetChunk.size() == 1);
++        persistentListChunk.setOffsetColumnChunk(std::move(newOffsetChunk[0]));
++    }
+ 
+     // Checkpoint size data.
+     std::vector<SegmentCheckpointState> sizeChunkCheckpointStates;
+@@ -416,9 +420,14 @@ std::vector<std::unique_ptr<ColumnChunkData>> ListColumn::checkpointSegment(
+             segmentCheckpointState.startRowInData, segmentCheckpointState.offsetInSegment,
+             segmentCheckpointState.numRows});
+     }
+-    sizeColumn->checkpointSegment(ColumnCheckpointState(*persistentListChunk.getSizeColumnChunk(),
+-                                      std::move(sizeChunkCheckpointStates)),
++    auto newSizeChunk = sizeColumn->checkpointSegment(
++        ColumnCheckpointState(*persistentListChunk.getSizeColumnChunk(),
++            std::move(sizeChunkCheckpointStates)),
+         pageAllocator, false);
++    if (!newSizeChunk.empty()) {
++        DASSERT(newSizeChunk.size() == 1);
++        persistentListChunk.setSizeColumnChunk(std::move(newSizeChunk[0]));
++    }
+     // Checkpoint null data.
+     Column::checkpointNullData(checkpointState, pageAllocator);
+ 
+diff --git a/src/storage/table/string_column.cpp b/src/storage/table/string_column.cpp
+index b7f94dc3ea..38b508765a 100644
+--- a/src/storage/table/string_column.cpp
++++ b/src/storage/table/string_column.cpp
+@@ -116,6 +116,9 @@ std::vector<std::unique_ptr<ColumnChunkData>> StringColumn::checkpointSegment(
+     auto result =
+         Column::checkpointSegment(std::move(checkpointState), pageAllocator, canSplitSegment);
+     persistentData.syncNumValues();
++    for (auto& segment : result) {
++        segment->syncNumValues();
++    }
+     return result;
+ }
+ 
+diff --git a/src/storage/table/struct_column.cpp b/src/storage/table/struct_column.cpp
+index b16e3d83ff..673cb6c468 100644
+--- a/src/storage/table/struct_column.cpp
++++ b/src/storage/table/struct_column.cpp
+@@ -114,6 +114,9 @@ std::vector<std::unique_ptr<ColumnChunkData>> StructColumn::checkpointSegment(
+     auto result =
+         Column::checkpointSegment(std::move(checkpointState), pageAllocator, canSplitSegment);
+     persistentStructChunk.syncNumValues();
++    for (auto& segment : result) {
++        segment->syncNumValues();
++    }
+     return result;
+ }
+ 
+diff --git a/test/test_files/transaction/set_node/set_empty.test b/test/test_files/transaction/set_node/set_empty.test
+index 72dbeefd09..b6e1495e07 100644
+--- a/test/test_files/transaction/set_node/set_empty.test
++++ b/test/test_files/transaction/set_node/set_empty.test
+@@ -33,3 +33,44 @@
+ ---- 2
+ 0|1010101010.300000
+ 1341|1010101010.200000
++
++-CASE ListInPlaceWithOutOfPlaceOffsetsAndNulls
++-STATEMENT CALL auto_checkpoint=false;
++---- ok
++-STATEMENT CREATE NODE TABLE t2(id INT64 PRIMARY KEY, l INT64[]);
++---- ok
++-STATEMENT UNWIND range(0, 4094) AS i CREATE (:t2 {id: i, l: [0, 1]});
++---- ok
++-STATEMENT CHECKPOINT;
++---- ok
++-STATEMENT MATCH (a:t2) WHERE a.id = 5 SET a.l = [1,0,1,0,1,0,1,0,1,0];
++---- ok
++-STATEMENT MATCH (a:t2) WHERE a.id = 7 SET a.l = NULL;
++---- ok
++-STATEMENT CHECKPOINT;
++---- ok
++-STATEMENT MATCH (a:t2) RETURN COUNT(a.l);
++---- 1
++4094
++-STATEMENT MATCH (a:t2) UNWIND a.l AS x RETURN COUNT(x), SUM(x);
++---- 1
++8196|4098
++-STATEMENT MATCH (a:t2) WHERE a.id = 5 RETURN SIZE(a.l), a.l[1], a.l[2];
++---- 1
++10|1|0
++-STATEMENT MATCH (a:t2) WHERE a.id = 6 RETURN SIZE(a.l), a.l[1], a.l[2];
++---- 1
++2|0|1
++-RELOADDB
++-STATEMENT MATCH (a:t2) RETURN COUNT(a.l);
++---- 1
++4094
++-STATEMENT MATCH (a:t2) UNWIND a.l AS x RETURN COUNT(x), SUM(x);
++---- 1
++8196|4098
++-STATEMENT MATCH (a:t2) WHERE a.id = 5 RETURN SIZE(a.l), a.l[1], a.l[2];
++---- 1
++10|1|0
++-STATEMENT MATCH (a:t2) WHERE a.id = 4094 RETURN SIZE(a.l), a.l[1], a.l[2];
++---- 1
++2|0|1
+diff --git a/test/transaction/checkpoint_test.cpp b/test/transaction/checkpoint_test.cpp
+index 2777560616..2049d21d19 100644
+--- a/test/transaction/checkpoint_test.cpp
++++ b/test/transaction/checkpoint_test.cpp
+@@ -13,6 +13,8 @@
+ #include "catalog/catalog_entry/table_catalog_entry.h"
+ #include "common/exception/runtime.h"
+ #include "storage/checkpointer.h"
++#include "storage/page_allocator.h"
++#include "storage/page_manager.h"
+ #include "storage/storage_manager.h"
+ #include "storage/table/node_table.h"
+ #include "storage/table/string_chunk_data.h"
+@@ -235,6 +237,110 @@ TEST_F(FlakyCheckpointerTest, RecoverFromCheckpointClearingFilesFailure) {
+     runTest(flakyCheckpointer);
+ }
+ 
++// Page allocator that fails the first page allocation. In-place checkpoints do not allocate
++// pages, so during the storage phase of a checkpoint that only updates a node group with
++// persistent data, the first allocation is the flush of an out-of-place column chunk rewrite and
++// the failure lands in the middle of that rewrite.
++class FailFirstAllocationPageAllocator final : public PageAllocator {
++public:
++    FailFirstAllocationPageAllocator(PageAllocator& inner, bool& failed)
++        : PageAllocator(inner.getDataFH()), inner{inner}, failed{failed} {}
++
++    PageRange allocatePageRange(page_idx_t numPages) override {
++        if (!failed) {
++            failed = true;
++            throw RuntimeException("checkpoint failed.");
++        }
++        return inner.allocatePageRange(numPages);
++    }
++    void freePageRange(PageRange block) override { inner.freePageRange(block); }
++
++private:
++    PageAllocator& inner;
++    bool& failed;
++};
++
++class FlakyCheckpointerFailsDuringOutOfPlaceRewrite final : public Checkpointer {
++public:
++    FlakyCheckpointerFailsDuringOutOfPlaceRewrite(main::ClientContext& context, bool& failed)
++        : Checkpointer(context), failed{failed} {}
++
++    bool checkpointStorage() override {
++        for (const auto& target : checkpointTargets) {
++            FailFirstAllocationPageAllocator pageAllocator(
++                *target.storageManager->getDataFH()->getPageManager(), failed);
++            const Transaction snapshotTxn(TransactionType::CHECKPOINT,
++                Transaction::DUMMY_TRANSACTION_ID, snapshotTS);
++            target.storageManager->checkpoint(&clientContext, *target.catalog, snapshotTxn,
++                pageAllocator, tableEpochWatermarksByManager.at(target.storageManager));
++        }
++        throw RuntimeException("expected the injected page allocation failure to fire.");
++    }
++
++private:
++    bool& failed;
++};
++
++// A checkpoint that fails while a column chunk segment is being rewritten out of place must
++// leave that segment as it was, so that the data stays readable and later checkpoints succeed.
++TEST_F(FlakyCheckpointerTest, RecoverFromFailureDuringOutOfPlaceCheckpoint) {
++    if (inMemMode || systemConfig->checkpointThreshold == 0) {
++        GTEST_SKIP();
++    }
++    conn->query("CALL force_checkpoint_on_close=false;");
++    conn->query("CALL auto_checkpoint=false;");
++    ASSERT_TRUE(
++        conn->query("CREATE NODE TABLE test(id INT64 PRIMARY KEY, name STRING);")->isSuccess());
++    constexpr int64_t numInitialRows = 3000;
++    constexpr int64_t numRows = 6000;
++    constexpr std::string_view namePrefix = "a longer name so the pages fill up ";
++    auto nameOf = [&](int64_t i) { return std::format("{}{}", namePrefix, i); };
++    auto insertRows = [&](int64_t start, int64_t end) {
++        auto res = conn->query(std::format("UNWIND range({}, {}) AS i CREATE (a:test {{id: i, "
++                                           "name: concat('{}', CAST(i AS STRING))}});",
++            start, end - 1, namePrefix));
++        ASSERT_TRUE(res->isSuccess()) << res->getErrorMessage();
++    };
++    auto checkRows = [&]() {
++        auto res = conn->query("MATCH (a:test) RETURN COUNT(a), CAST(SUM(a.id) AS INT64), "
++                               "CAST(SUM(SIZE(a.name)) AS INT64), MIN(a.name), MAX(a.name);");
++        ASSERT_TRUE(res->isSuccess()) << res->getErrorMessage();
++        auto row = res->getNext();
++        ASSERT_EQ(row->getValue(0)->getValue<int64_t>(), numRows);
++        ASSERT_EQ(row->getValue(1)->getValue<int64_t>(), numRows * (numRows - 1) / 2);
++        int64_t totalNameSize = 0;
++        for (auto i = 0; i < numRows; i++) {
++            totalNameSize += nameOf(i).size();
++        }
++        ASSERT_EQ(row->getValue(2)->getValue<int64_t>(), totalNameSize);
++        ASSERT_EQ(row->getValue(3)->getValue<std::string>(), nameOf(0));
++        ASSERT_EQ(row->getValue(4)->getValue<std::string>(), nameOf(999));
++    };
++    insertRows(0, numInitialRows);
++    ASSERT_TRUE(conn->query("CHECKPOINT;")->isSuccess());
++    // Appending to the persistent node group outgrows the pages of its column chunks, so the
++    // next checkpoint has to rewrite them out of place.
++    insertRows(numInitialRows, numRows);
++
++    auto context = getClientContext(*conn);
++    bool failed = false;
++    FlakyCheckpointer flakyCheckpointer([&failed](main::ClientContext& ctx) {
++        return std::make_unique<FlakyCheckpointerFailsDuringOutOfPlaceRewrite>(ctx, failed);
++    });
++    flakyCheckpointer.setCheckpointer(*context);
++    auto res = conn->query("CHECKPOINT;");
++    ASSERT_FALSE(res->isSuccess());
++    ASSERT_TRUE(failed);
++    checkRows();
++
++    FlakyCheckpointer defaultCheckpointer(
++        [](main::ClientContext& ctx) { return std::make_unique<Checkpointer>(ctx); });
++    defaultCheckpointer.setCheckpointer(*context);
++    res = conn->query("CHECKPOINT;");
++    ASSERT_TRUE(res->isSuccess()) << res->getErrorMessage();
++    checkRows();
++}
++
+ // Simulates a situation where a database attempts to replay a shadow file from an older database
+ // with the same path
+ TEST_F(FlakyCheckpointerTest, ShadowFileDatabaseIDMismatchExistingDB) {