add an example program to try reproduce odb errors due to parallelism.

A motivating example is here: praetorian-inc/noseyparker#179

gitoxide-core/src/repository/odb.rs

@@ -1,4 +1,5 @@
 use std::io;
+use std::sync::atomic::Ordering;
 
 use anyhow::bail;
 
@@ -50,6 +51,8 @@ pub mod statistics {
     pub struct Options {
         pub format: OutputFormat,
         pub thread_limit: Option<usize>,
+        /// A debug-flag that triggers looking up the headers of all objects again, but without indices preloaded
+        pub extra_header_lookup: bool,
     }
 }
 
@@ -59,7 +62,11 @@ pub fn statistics(
     mut progress: impl gix::Progress,
     out: impl io::Write,
     mut err: impl io::Write,
-    statistics::Options { format, thread_limit }: statistics::Options,
+    statistics::Options {
+        format,
+        thread_limit,
+        extra_header_lookup,
+    }: statistics::Options,
 ) -> anyhow::Result<()> {
     use bytesize::ByteSize;
     use gix::odb::{find, HeaderExt};
@@ -76,6 +83,10 @@ pub fn statistics(
     #[cfg_attr(feature = "serde", derive(serde::Serialize))]
     #[derive(Default)]
     struct Statistics {
+        /// All objects that were used to produce these statistics.
+        /// Only `Some` if we are doing an extra round of header queries on a repository without loaded indices.
+        #[cfg_attr(feature = "serde", serde(skip_serializing))]
+        ids: Option<Vec<gix::ObjectId>>,
         total_objects: usize,
         loose_objects: usize,
         packed_objects: usize,
@@ -135,14 +146,17 @@ pub fn statistics(
     }
 
     impl gix::parallel::Reduce for Reduce {
-        type Input = Result<Vec<gix::odb::find::Header>, anyhow::Error>;
+        type Input = Result<Vec<(gix::ObjectId, gix::odb::find::Header)>, anyhow::Error>;
         type FeedProduce = ();
         type Output = Statistics;
         type Error = anyhow::Error;
 
         fn feed(&mut self, items: Self::Input) -> Result<Self::FeedProduce, Self::Error> {
-            for item in items? {
+            for (id, item) in items? {
                 self.stats.consume(item);
+                if let Some(ids) = self.stats.ids.as_mut() {
+                    ids.push(id);
+                }
             }
             Ok(())
         }
@@ -154,9 +168,9 @@ pub fn statistics(
     }
 
     let cancelled = || anyhow::anyhow!("Cancelled by user");
-    let object_ids = repo.objects.store_ref().iter()?.filter_map(Result::ok);
+    let object_ids = repo.objects.iter()?.filter_map(Result::ok);
     let chunk_size = 1_000;
-    let stats = if gix::parallel::num_threads(thread_limit) > 1 {
+    let mut stats = if gix::parallel::num_threads(thread_limit) > 1 {
         gix::parallel::in_parallel(
             gix::interrupt::Iter::new(
                 gix::features::iter::Chunks {
@@ -166,19 +180,30 @@ pub fn statistics(
                 cancelled,
             ),
             thread_limit,
-            move |_| (repo.objects.clone().into_inner(), counter),
+            {
+                let objects = repo.objects.clone();
+                move |_| (objects.clone().into_inner(), counter)
+            },
             |ids, (handle, counter)| {
                 let ids = ids?;
-                counter.fetch_add(ids.len(), std::sync::atomic::Ordering::Relaxed);
+                counter.fetch_add(ids.len(), Ordering::Relaxed);
                 let out = ids
                     .into_iter()
-                    .map(|id| handle.header(id))
+                    .map(|id| handle.header(id).map(|hdr| (id, hdr)))
                     .collect::<Result<Vec<_>, _>>()?;
                 Ok(out)
             },
-            Reduce::default(),
+            Reduce {
+                stats: Statistics {
+                    ids: extra_header_lookup.then(Vec::new),
+                    ..Default::default()
+                },
+            },
         )?
     } else {
+        if extra_header_lookup {
+            bail!("extra-header-lookup is only meaningful in threaded mode");
+        }
         let mut stats = Statistics::default();
 
         for (count, id) in object_ids.enumerate() {
@@ -193,6 +218,39 @@ pub fn statistics(
 
     progress.show_throughput(start);
 
+    if let Some(mut ids) = stats.ids.take() {
+        // Critical to re-open the repo to assure we don't have any ODB state and start fresh.
+        let start = std::time::Instant::now();
+        let repo = gix::open_opts(repo.git_dir(), repo.open_options().to_owned())?;
+        progress.set_name("re-counting".into());
+        progress.init(Some(ids.len()), gix::progress::count("objects"));
+        let counter = progress.counter();
+        counter.store(0, Ordering::Relaxed);
+        let errors = gix::parallel::in_parallel_with_slice(
+            &mut ids,
+            thread_limit,
+            {
+                let objects = repo.objects.clone();
+                move |_| (objects.clone().into_inner(), counter, false)
+            },
+            |id, (odb, counter, has_error), _threads_left, _stop_everything| -> anyhow::Result<()> {
+                counter.fetch_add(1, Ordering::Relaxed);
+                if let Err(err) = odb.header(id) {
+                    *has_error = true;
+                    gix::trace::error!(err = ?err, "Object that is known to be present wasn't found");
+                }
+                Ok(())
+            },
+            || Some(std::time::Duration::from_millis(100)),
+            |(_, _, has_error)| has_error,
+        )?;
+
+        progress.show_throughput(start);
+        if errors.contains(&true) {
+            bail!("At least one object couldn't be looked up even though it must exist");
+        }
+    }
+
     #[cfg(feature = "serde")]
     {
         serde_json::to_writer_pretty(out, &stats)?;

gix-odb/src/store_impls/dynamic/load_index.rs

@@ -119,7 +119,7 @@ impl super::Store {
                         let slot = &self.files[index.slot_indices[slot_map_index]];
                         let _lock = slot.write.lock();
                         if slot.generation.load(Ordering::SeqCst) > index.generation {
-                            // There is a disk consolidation in progress which just overwrote a slot that cold be disposed with some other
+                            // There is a disk consolidation in progress which just overwrote a slot that could be disposed with some other
                             // index, one we didn't intend to load.
                             // Continue with the next slot index in the hope there is something else we can do…
                             continue 'retry_with_next_slot_index;
@@ -134,7 +134,9 @@ impl super::Store {
                                     slot.files.store(bundle);
                                     break 'retry_with_next_slot_index;
                                 }
-                                Err(_) => {
+                                #[allow(unused_variables)]
+                                Err(err) => {
+                                    gix_features::trace::error!(err=?err, "Failed to load index file - some objects may seem to not exist");
                                     slot.files.store(bundle);
                                     continue 'retry_with_next_slot_index;
                                 }

src/plumbing/main.rs

@@ -1153,7 +1153,7 @@ pub fn main() -> Result<()> {
             ),
         },
         Subcommands::Odb(cmd) => match cmd {
-            odb::Subcommands::Stats => prepare_and_run(
+            odb::Subcommands::Stats { extra_header_lookup } => prepare_and_run(
                 "odb-stats",
                 trace,
                 auto_verbose,
@@ -1166,7 +1166,11 @@ pub fn main() -> Result<()> {
                         progress,
                         out,
                         err,
-                        core::repository::odb::statistics::Options { format, thread_limit },
+                        core::repository::odb::statistics::Options {
+                            format,
+                            thread_limit,
+                            extra_header_lookup,
+                        },
                     )
                 },
             ),

src/plumbing/options/mod.rs

@@ -586,7 +586,11 @@ pub mod odb {
         Info,
         /// Count and obtain information on all, possibly duplicate, objects in the database.
         #[clap(visible_alias = "statistics")]
-        Stats,
+        Stats {
+            /// Lookup headers again, but without preloading indices.
+            #[clap(long)]
+            extra_header_lookup: bool,
+        },
     }
 }