Commit Graph

629 Commits

Author SHA1 Message Date
Benny Halevy
c16ec870da gms: pass endpoint_state_ptr to endpoint_state change subscribers
Now that the endpoint_state isn't change in place
we do not need to copy it to each subscriber.
We can rather just pass the lw_shared_ptr holding
a snapshot of it.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2023-08-31 09:35:15 +03:00
Kamil Braun
39ca07c49b Merge 'Gossiper endpoint locking' from Benny Halevy
This series cleans up and hardens the endpoint locking design and
implementation in the gossiper and endpoint-state subscribers.

We make sure that all notifications (expect for `before_change`, that
apparently can be dropped) are called under lock_endpoint, as well as
all calls to gossiper::replicate, to serialize endpoint_state changes
across all shards.

An endpoint lock gets a unique permit_id that is passed to the
notifications and passed back by them if the notification functions call
the gossiper back for the same endpoint on paths that modify the
endpoint_state and may acquire the same endpoint lock - to prevent a
deadlock.

Fixes scylladb/scylladb#14838
Refs scylladb/scylladb#14471

Closes #14845

* github.com:scylladb/scylladb:
  gossiper: replicate: ensure non-null permit
  gossiper: add_saved_endpoint: lock_endpoint
  gossiper: mark_as_shutdown: lock_endpoint
  gossiper: real_mark_alive: lock_endpoint
  gossiper: advertise_token_removed: lock_endpoint
  gossiper: do_status_check: lock_endpoint
  gossiper: remove_endpoint: lock_endpoint if needed
  gossiper: force_remove_endpoint: lock_endpoint if needed
  storage_service: lock_endpoint when removing node
  gossiper: use permit_id to serialize state changes while preventing deadlocks
  gossiper: lock_endpoint: add debug messages
  utils: UUID: make default tagged_uuid ctor constexpr
  gossiper: lock_endpoint must be called on shard 0
  gossiper: replicate: simplify interface
  gossiper: mark_as_shutdown: make private
  gossiper: convict: make private
  gossiper: mark_as_shutdown: do not call convict
2023-08-02 13:50:08 +02:00
Benny Halevy
f74d154fe3 gossiper: use permit_id to serialize state changes while preventing deadlocks
Pass permit_id to subscribers when we acquire one
via lock_endpoint.  The subscribers then pass it back to
gossiper for paths that acquire lock_endpoint for
the same endpoint, to detect nested locks when the endpoint
is locked with the same permit_id.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2023-08-01 17:41:57 +03:00
Botond Dénes
4a02865ea1 Merge 'Prevent invalidation of iterators over database::_column_families' from Aleksandra Martyniuk
Maps related to column families in database are extracted
to a column_families_data class. Access to them is possible only
through methods. All methods which may preempt hold rwlock
in relevant mode, so that the iterators can't become invalid.

Fixes: #13290

Closes #13349

* github.com:scylladb/scylladb:
  replica: make tables_metadata's attributes private
  replica: add methods to get a filtered copy of tables map
  replica: add methods to check if given table exists
  replica: add methods to get table or table id
  replica: api: return table_id instead of const table_id&
  replica: iterate safely over tables related maps
  replica: pass tables_metadata to phased_barrier_top_10_counts
  replica: add methods to safely add and remove table
  replica: wrap column families related maps into tables_metadata
  replica: futurize database::add_column_family and database::remove
2023-07-31 15:31:59 +03:00
Botond Dénes
5452fd1ce4 streaming: opt-in to compacting the stream
Use locally generated compaction time on each node. This could lead to
different nodes making different decisions on what is expired or not.
But this is already the case for streaming, as what exactly is expired
depends on when compaction last run.
2023-07-27 03:22:11 -04:00
Botond Dénes
42b0dd5558 replica/table: add optional compacting to make_streaming_reader()
Opt-in is possible by passing an engaged `compaction_time`
(gc_clock::time_point) to the method. When this new parameter is
disengaged, no compaction happens.
Note that there is a global override, via the
enable_compacting_data_for_streaming_and_repair config item, which can
force-disable this compaction.
Compaction done on the output of the streaming reader does *not*
garbage-collect tombstones!

All call-sites are adjusted (the new parameter is not defaulted), but
none opt in yet. This will be done in separate commit per user.
2023-07-27 03:22:11 -04:00
Tomasz Grabiec
6d545b2f9e storage_service: Implement stream_tablet RPC
Performs streaming of data for a single tablet between two tablet
replicas. The node which gets the RPC is the receiving replica.
2023-07-25 21:08:51 +02:00
Tomasz Grabiec
f88220aeee stream_transfer_task, multishard_writer: Work with table sharder
So that we can use it on tablet-based tables.
2023-07-25 21:08:51 +02:00
Aleksandra Martyniuk
cdbfa0b2f5 replica: iterate safely over tables related maps
Loops over _column_families and _ks_cf_to_uuid which may preempt
are protected by reader mode of rwlock so that iterators won't
get invalid.
2023-07-25 17:13:04 +02:00
Aleksandra Martyniuk
52afd9d42d replica: wrap column families related maps into tables_metadata
As a preparation for ensuring access safety for column families
related maps, add tables_metadata, access to members of which
would be protected by rwlock.
2023-07-25 16:13:00 +02:00
Kefu Chai
1eb76d93b7 streaming: cast the progress to a float before formatting it
before this change, we format a `long` using `{:f}`. fmtlib would
throw an exception when actually formatting it.

so, let's make the percentage a float before formatting it.

Fixes #14587
Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>

Closes #14588
2023-07-10 00:00:40 +03:00
Tomasz Grabiec
17d6163548 sstables: Generate sharding metadata using sharder from erm when writing
We need to keep sharding metadata consistent with tablet mapping to
shards in order for node restart to detect that those sstables belong
to a single shard and that resharding is not necessary. Resharding of
sstables based on tablet metadata is not implemented yet and will
abort after this series.

Keeping sharding metadata accurate for tablets is only necessary until
compaction group integration is finished. After that, we can use the
sstable token range to determine the owning tablet and thus the owning
shard. Before that, we can't, because a single sstable may contain
keys from different tablets, and the whole key range may overlap with
keys which belong to other shards.
2023-06-21 00:58:24 +02:00
Pavel Emelyanov
66e43912d6 code: Switch to seastar API level 7
In that level no io_priority_class-es exist. Instead, all the IO happens
in the context of current sched-group. File API no longer accepts prio
class argument (and makes io_intent arg mandatory to impls).

So the change consists of
- removing all usage of io_priority_class
- patching file_impl's inheritants to updated API
- priority manager goes away altogether
- IO bandwidth update is performed on respective sched group
- tune-up scylla-gdb.py io_queues command

The first change is huge and was made semi-autimatically by:
- grep io_priority_class | default_priority_class
- remove all calls, found methods' args and class' fields

Patching file_impl-s is smaller, but also mechanical:
- replace io_priority_class& argument with io_intent* one
- pass intent to lower file (if applicatble)

Dropping the priority manager is:
- git-rm .cc and .hh
- sed out all the #include-s
- fix configure.py and cmakefile

The scylla-gdb.py update is a bit hairry -- it needs to use task queues
list for IO classes names and shares, but to detect it should it checks
for the "commitlog" group is present.

Signed-off-by: Pavel Emelyanov <xemul@scylladb.com>

Closes #13963
2023-06-06 13:29:16 +03:00
Avi Kivity
26c8470f65 treewide: use #include <seastar/...> for seastar headers
We treat Seastar as an external library, so fix the few places
that didn't do so to use angle brackets.

Closes #14037
2023-06-06 08:36:09 +03:00
Pavel Emelyanov
678f8fb1b7 stream_manager: Add streaming sched group copy
The manager in question is responsible for maintaining the streaming
class IO bandwidth update. Nowadays it does it via priority manager's
global streaming IO priority class field, but it will need to switch to
streaming sched group.

Signed-off-by: Pavel Emelyanov <xemul@scylladb.com>
2023-05-23 14:31:23 +03:00
Gleb Natapov
7caf1d26fb migration manager: Make schema pull abortable.
Now which schema pull may issues raft read barrier it may stuck if
majority is not available. Make the operation abortable and abort it
during queries if timeout is reached.
2023-05-11 16:31:23 +03:00
Kefu Chai
a34e417069 streaming: remove unused operator==
since this operator is used nowhere, let's drop it.

Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>

Closes #13697
2023-04-28 12:39:17 +03:00
Kefu Chai
f5b05cf981 treewide: use defaulted operator!=() and operator==()
in C++20, compiler generate operator!=() if the corresponding
operator==() is already defined, the language now understands
that the comparison is symmetric in the new standard.

fortunately, our operator!=() is always equivalent to
`! operator==()`, this matches the behavior of the default
generated operator!=(). so, in this change, all `operator!=`
are removed.

in addition to the defaulted operator!=, C++20 also brings to us
the defaulted operator==() -- it is able to generated the
operator==() if the member-wise lexicographical comparison.
under some circumstances, this is exactly what we need. so,
in this change, if the operator==() is also implemented as
a lexicographical comparison of all memeber variables of the
class/struct in question, it is implemented using the default
generated one by removing its body and mark the function as
`default`. moreover, if the class happen to have other comparison
operators which are implemented using lexicographical comparison,
the default generated `operator<=>` is used in place of
the defaulted `operator==`.

sometimes, we fail to mark the operator== with the `const`
specifier, in this change, to fulfil the need of C++ standard,
and to be more correct, the `const` specifier is added.

also, to generate the defaulted operator==, the operand should
be `const class_name&`, but it is not always the case, in the
class of `version`, we use `version` as the parameter type, to
fulfill the need of the C++ standard, the parameter type is
changed to `const version&` instead. this does not change
the semantic of the comparison operator. and is a more idiomatic
way to pass non-trivial struct as function parameters.

please note, because in C++20, both operator= and operator<=> are
symmetric, some of the operators in `multiprecision` are removed.
they are the symmetric form of the another variant. if they were
not removed, compiler would, for instance, find ambiguous
overloaded operator '=='.

this change is a cleanup to modernize the code base with C++20
features.

Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>

Closes #13687
2023-04-27 10:24:46 +03:00
Kefu Chai
9215adee46 streaming: specialize fmt::formatter<stream_reason>
this is a part of a series to migrating from `operator<<(ostream&, ..)`
based formatting to fmtlib based formatting. the goal here is to enable
fmtlib to print `stream_reason` without the help of `operator<<`.

please note, because we still cannot use the generic formatter for
std::unordered_map provided by fmtlib, so in order to drop `operator<<`
for `stream_reason`, and to print `unordered_map<stream_reason>`,
`fmt::join()` is used as a temporary solution. we will audit all
`fmt::join()` calls, after removing the homebrew formatter of
`std::unordered_map`.

the corresponding `operator<<()` are dropped dropped in this change,
as all its callers are now using fmtlib for formatting now.

Refs #13245

Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>

Closes #13609
2023-04-21 09:44:23 +03:00
Botond Dénes
156e5d346d reader_permit: keep trace_state pointer on permit
And propagate it down to where it is created. This will be used to add
trace points for semaphore related events, but this will come in the
next patches.
2023-03-22 04:58:01 -04:00
Kamil Braun
fe14d14ce9 Merge 'Eliminate extraneous copies of dht::token_range_vector' from Benny Halevy
In several places we copy token range vectors where we could move them and eliminate unnecessary memory copies.

Ref #11005

Closes #12344

* github.com:scylladb/scylladb:
  dht/range_streamer: stream_async: move ranges_to_stream to do_streaming
  streaming: stream_session: maybe_yield
  streaming: stream_session: prepare: move token ranges to add_transfer_ranges
  streaming: stream_plan: transfer_ranges: move token ranges towards add_transfer_ranges
  dht/range_streamer: stream_async: do_streaming: move ranges downstream
  dht/range_streamer: add_ranges: clear_gently ranges_for_keyspace
  dht/range_streamer: get_range_fetch_map: reduce copies
  dht/range_streamer: add_ranges: move ranges down-stream
  dht/boot_strapper: move ranges to add_ranges
  dht/range_streamer: stream_async: incrementally update _nr_ranges_remaining
  dht/range_streamer: stream_async: erase from range_vec only after do_streaming success
2023-03-07 13:46:33 +01:00
Benny Halevy
1392c7e1cf streaming: stream_session: maybe_yield
To prevent reactor stalls when freeing many/long
token range vectors.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2023-02-28 17:32:44 +02:00
Benny Halevy
c4836ab9e9 streaming: stream_session: prepare: move token ranges to add_transfer_ranges
Reduce copies on the path to calling add_transfer_ranges.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2023-02-28 17:04:47 +02:00
Benny Halevy
12eb3d210f streaming: stream_plan: transfer_ranges: move token ranges towards add_transfer_ranges
Rather than copying the ranges vector.

Note that add_transfer_ranges itself cannot simply move the ranges
since it copies them for multiple tables.

While at it, move also the keyspace and column_family strings.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2023-02-28 17:03:51 +02:00
Kefu Chai
af3968bf6e build: cmake: extract mutation,db,replica,streaming out
Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>
2023-02-28 21:28:46 +08:00
Pavel Emelyanov
f51762c72a headers: Refine view_update_generator.hh and around
The initial intent was to reduce the fanout of shared_sstable.hh through
v.u.g.hh -> cql_test_env.hh chain, but it also resulted in some shots
around v.u.g.hh -> database.hh inclusion.

By and large:
- v.u.g.hh doesn't need database.hh
- cql_test_env.hh doesn't need v.u.g.hh (and thus -- the
  shared_sstable.hh) but needs database.hh instead
- few other .cc files need v.u.g.hh directly as they pulled it via
  cql_test_env.hh before
- add forward declarations in few other places

Signed-off-by: Pavel Emelyanov <xemul@scylladb.com>

Closes #12952
2023-02-22 09:32:30 +02:00
Kefu Chai
df63e2ba27 types: move types.{cc,hh} into types
they are part of the CQL type system, and are "closer" to types.
let's move them into "types" directory.

the building systems are updated accordingly.

the source files referencing `types.hh` were updated using following
command:

```
find . -name "*.{cc,hh}" -exec sed -i 's/\"types.hh\"/\"types\/types.hh\"/' {} +
```

the source files under sstables include "types.hh", which is
indeed the one located under "sstables", so include "sstables/types.hh"
instea, so it's more explicit.

Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>

Closes #12926
2023-02-19 21:05:45 +02:00
Kefu Chai
0cb842797a treewide: do not define/capture unused variables
these warnings are found by Clang-17 after removing
`-Wno-unused-lambda-capture` and '-Wno-unused-variable' from
the list of disabled warnings in `configure.py`.

Signed-off-by: Kefu Chai <kefu.chai@scylladb.com>
2023-02-15 22:57:18 +02:00
Avi Kivity
69a385fd9d Introduce schema/ module
Schema related files are moved there. This excludes schema files that
also interact with mutations, because the mutation module depends on
the schema. Those files will have to go into a separate module.

Closes #12858
2023-02-15 11:01:50 +02:00
Avi Kivity
c5e4bf51bd Introduce mutation/ module
Move mutation-related files to a new mutation/ directory. The names
are kept in the global namespace to reduce churn; the names are
unambiguous in any case.

mutation_reader remains in the readers/ module.

mutation_partition_v2.cc was missing from CMakeLists.txt; it's added in this
patch.

This is a step forward towards librarization or modularization of the
source base.

Closes #12788
2023-02-14 11:19:03 +02:00
Botond Dénes
84a69b6adb db/view/view_update_check: check_needs_view_update_path(): filter out non-member hosts
We currently don't clean up the system_distributed.view_build_status
table after removed nodes. This can cause false-positive check for
whether view update generation is needed for streaming.
The proper fix is to clean up this table, but that will be more
involved, it even when done, it might not be immediate. So until then
and to be on the safe side, filter out entries belonging to unknown
hosts from said table.

Fixes: #11905
Refs: #11836

Closes #11860
2023-01-27 17:12:45 +03:00
Asias He
b9e5e340aa streaming: Enable offstrategy for all classic streaming based node ops
This patch enables offstrategy compaction for all classic streaming
based node ops. We can use this method because tables are streamed one
after another. As long as there is still streamed data for a given
table, we update the automatic trigger timer. When all the streaming has
finished, the trigger timer will timeout and fire the offstrategy
compaction for the given table.

I checked with this patch, rebuild is 3X faster. There was no compaction
in the middle of the streaming. The streamed sstables are compacted
together after streaming is done.

Time Before:
INFO  2022-11-25 10:06:08,213 [shard 0] range_streamer - Rebuild
succeeded, took 67 seconds, nr_ranges_remaining=0

Time After:
INFO  2022-11-25 09:42:50,943 [shard 0] range_streamer - Rebuild
succeeded, took 23 seconds, nr_ranges_remaining=0

Compaciton Before:
88 sstables were written -> 88 sstables were added into main set

Compaction After:
88 sstables written ->  after offstretegy 2 sstables were added into main seet

Closes #11848
2022-12-28 11:12:02 +02:00
Asias He
9ed401c4b2 streaming: Add finished percentage metrics for node ops using streaming
We have added the finished percentage for repair based node operations.

This patch adds the finished percentage for node ops using the old
streaming.

Example output:

scylla_streaming_finished_percentage{ops="bootstrap",shard="0"} 1.000000
scylla_streaming_finished_percentage{ops="decommission",shard="0"} 1.000000
scylla_streaming_finished_percentage{ops="rebuild",shard="0"} 0.561945
scylla_streaming_finished_percentage{ops="removenode",shard="0"} 1.000000
scylla_streaming_finished_percentage{ops="repair",shard="0"} 1.000000
scylla_streaming_finished_percentage{ops="replace",shard="0"} 1.000000

In addition to the metrics, log shows the percentage is added.

[shard 0] range_streamer - Finished 2698 out of 2817 ranges for rebuild, finished percentage=0.95775646

Fixes #11600

Closes #11601
2022-09-22 14:19:34 +03:00
Benny Halevy
314e45d957 streaming: define plan_id as a strong tagged_uuid type
Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2022-08-22 19:45:30 +03:00
Benny Halevy
3554533e2c stream_manager: update_progress: rename cf_id param to plan_id
Before changing its type to streaming::plan_id
this patch clarifies that the parameter actually represents
the plan id and not the table id as its name suggests.

For reference, see the call to update_progress in
`stream_transfer_task::execute`, as well as the function
using _stream_bytes which map key is the plan id.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2022-08-21 16:56:41 +03:00
Benny Halevy
c1fc0672a5 streaming: add forward declarations in stream_fwd.hh
To be used for defining streaming::plan_id
in the next patcvh.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2022-08-21 16:00:02 +03:00
Benny Halevy
2b017ce285 schema, everywhere: define and use table_schema_version as a strong type
Define table_schema_version as a distinct tagged_uuid class,
So it can be differentiated from other uuid-class types,
in particular table_id.

Added reversed(table_schema_version) for convenience
and uniformity since the same logic is currently open coded
in several places.

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2022-08-08 08:09:45 +03:00
Benny Halevy
257d74bb34 schema, everywhere: define and use table_id as a strong type
Define table_id as a distinct utils::tagged_uuid modeled after raft
tagged_id, so it can be differentiated from other uuid-class types,
in particular from table_schema_version.

Fixes #11207

Signed-off-by: Benny Halevy <bhalevy@scylladb.com>
2022-08-08 08:09:41 +03:00
Pavel Emelyanov
96d6be7daf streaming: Maintain class bandwidth
Same as was done in b112a983 for compaction manager

Signed-off-by: Pavel Emelyanov <xemul@scylladb.com>
2022-07-19 12:19:56 +03:00
Pavel Emelyanov
a246b6d3eb streaming: Pass db::config& to manager constructor
The stream_manager will bookkeep the streaming bandwidth option, to
subscribe on its changes it needs the config reference. It would be
better if it was stream_manager::config, but currently subscription on
db::config::<stuff> updates is not very shard-friendly, so we need to
carry the config reference itself around.

Similar trouble is there for compaction_manager. The option is passed
through its own config, but the config is created on each shard by
database code. Stream manager config would be created once by main code
on shard 0.

Signed-off-by: Pavel Emelyanov <xemul@scylladb.com>
2022-07-19 12:18:08 +03:00
Asias He
e0aca10bcd streaming: Enable auto off strategy compaction trigger for all rbno ops
Since commit 3dc9a81d02 (repair: Repair
table by table internally), a table is always repaired one after
another. This means a table will be repaired in a continuous manner.

Unlike before a table will be repaired again after other tables have
finished the same range.

```
for range in ranges
  for table in tables
      repair(range, table)
```

The wait interval can be large so we can not utilize the assumption if
there is no repair traffic, the whole table is finished.

After commit 3dc9a81d02, we can utilize
the fact that a table is repaired continuously property and trigger off
strategy automatically when no repair traffic for a table is present.

This is especially useful for decommission operation with multiple
tables. Currently, we only notify the peer node the decommission is done
and ask the peer to trigger off strategy compaction. With this
patch, the peer node will trigger automatically after a table is
finished, reducing the number of temporary sstables on disk.

Refs #10462

Closes #10761
2022-06-09 17:10:14 +03:00
Michael Livshin
8305ac26ca stream_transfer_task: mutation_fragment_v1_stream() instead of downgrade_to_v1()
Signed-off-by: Michael Livshin <michael.livshin@scylladb.com>
2022-05-31 23:42:34 +03:00
Avi Kivity
528ab5a502 treewide: change metric calls from make_derive to make_counter
make_derive was recently deprecated in favor of make_counter, so
make the change throughput the codebase.

Closes #10564
2022-05-14 12:53:55 +02:00
Avi Kivity
5937b1fa23 treewide: remove empty comments in top-of-files
After fcb8d040 ("treewide: use Software Package Data Exchange
(SPDX) license identifiers"), many dual-licensed files were
left with empty comments on top. Remove them to avoid visual
noise.

Closes #10562
2022-05-13 07:11:58 +02:00
Asias He
953af38281 streaming: Allow drop table during streaming
Currently, if a table is dropped during streaming, the streaming would
fail with no_such_column_family error.

Since the table is dropped anyway, it makes more sense to ignore the
streaming result of the dropped table, whether it is successful or
failed.

This allows users to drop tables during node operations, e.g., bootstrap
or decommission a node.

This is especially useful for the cloud users where it is hard to
coordinate between a node operation by admin and user cql change.

This patch also fixes a possible user after free issue by not passing
the table reference object around.

Fixes #10395

Closes #10396
2022-04-24 17:43:20 +03:00
Botond Dénes
b029bd3db7 tree: remove mutation_reader.hh include
In most files it was unused. We should move these to the patch which
moved out the last interesting reader from mutation_reader.hh (and added
the corresponding new header include) but its probably not worth the
effort.
Some other files still relied on mutation_reader.hh to provide reader
concurrency semaphore and some other misc reader related definitions.
2022-03-30 15:42:51 +03:00
Botond Dénes
fcf15fda94 readers: generating_reader: use noncopyable_function<>
std::function<> requires the functor it wraps to be copyable, which is
an unnecessarily strict requirement. To relax this, we use
noncopyable_function<> instead. Since the former seems to lack some
disambiguation magic of the latter, we add `_v1` and `_v2` postfixes to
manually disambiguate.
2022-03-17 06:53:44 +02:00
Botond Dénes
35bbd54946 readers: merge generating.hh into generating_v2.hh
Both variants return a v2 reader and we are going to keep both for a
time to come.
2022-03-17 06:52:28 +02:00
Botond Dénes
7844ff9912 readers/generating.hh: return v2 reader from make_generating_reader()
For now, the (v1) reader is just upgraded to v2 behind the scenes.
2022-03-17 06:51:20 +02:00
Mikołaj Sielużycki
1d84a254c0 flat_mutation_reader: Split readers by file and remove unnecessary includes.
The flat_mutation_reader files were conflated and contained multiple
readers, which were not strictly necessary. Splitting optimizes both
iterative compilation times, as touching rarely used readers doesn't
recompile large chunks of codebase. Total compilation times are also
improved, as the size of flat_mutation_reader.hh and
flat_mutation_reader_v2.hh have been reduced and those files are
included by many file in the codebase.

With changes

real	29m14.051s
user	168m39.071s
sys	5m13.443s

Without changes

real	30m36.203s
user	175m43.354s
sys	5m26.376s

Closes #10194
2022-03-14 13:20:25 +02:00