hdf5/doxygen/dox/MetadataCachingInHDF5.dox

/** \page TNMDC Metadata Caching in HDF5

\todo Revise this!

\section intro Introduction

In the 1.6.4 release, we introduced a re-implementation of the metadata
cache. That release contained an incomplete version of the cache which could not
be controlled via the API. The version in the 1.8 release is more mature and
includes new API calls that allow the user program to configure the metadata
cache both on file open and at run time.

From the user perspective, the most striking effect of the new cache should be a
large reduction in the cache memory requirements when working with complex HDF5
files.

Those working with such files may also notice a reduction in file close time.

Those working with HDF5 files with a simple structure shouldn't notice any
particular changes in most cases. In rare cases, there may be a significant
improvement in performance.

The remainder of this document contains an architectural overview of the old and
new metadata caches, a discussion of algorithms used to automatically adjust
cache size to circumstances, and a high-level discussion of the cache
configuration controls. It can be safely skipped by anyone who works only with
HDF5 files with relatively simple structure (i.e. no huge groups, no datasets
with large numbers of chunks, and no objects with large numbers of attributes.)

On the other hand, it is mandatory reading if you want to use something other
than the default metadata cache configuration. The documentation on the metadata
cache-related API calls will not make much sense without this background.

\section oldnew Old and New Metadata Cache

\subsection old The Old Metadata Cache

The old metadata cache indexed the cache with a hash table with no provision for
collisions. Instead, collisions were handled by evicting the existing entry to
make room for the new entry. Aside from flushes, there was no other mechanism
for evicting entries, so the replacement policy could best be described as
"Evict on Collision".

As a result, if two frequently used entries hashed to the same location, they
would evict each other regularly. To decrease the likelihood of this situation,
the default hash table size was set fairly large -- slightly more than
10,000. This worked well, but since the size of metadata entries is not bounded,
and since entries were only evicted on collision, the large hash table size
allowed the cache size to explode when working with HDF5 files with complex
structure.

The "Evict on Collision" replacement policy also caused problems with the
parallel version of the HDF5 library, as a collision with a dirty entry could
force a write in response to a metadata read. Since all metadata writes must be
collective in the parallel case while reads need not be, this could cause the
library to hang if only some of the processes participated in a metadata read
that forced a write. Prior to the implementation of the new metadata cache, we
dealt with this issue by maintaining a shadow cache for dirty entries evicted by
a read.

\subsection new The New Metadata Cache

The new metadata cache was designed to address the above issues. After
implementation, it became evident that the working set size for HDF5 files
varies widely depending on both structure and access patterns. Thus it was
necessary to add support for cache size adjustment under either automatic or
user program control (see section 2.3 for details).

When the cache is operating under direct user program control, it is also
possible to temporarily disable evictions from the metadata cache so as to
maximize raw data throughput at the expense of allowing the cache to grow
without bound until evictions are enabled again.

Structurally, the new metadata cache can be thought of as a heavily modified
version of the UNIX buffer cache as described in chapter three of M. J. Bach's
"The Design of the UNIX Operating System" In essence, the UNIX buffer cache uses
a hash table with chaining to index a pool of fixed-size buffers. It uses the
LRU replacement policy to select candidates for eviction.

Since HDF5 metadata entries are not of fixed size and may grow arbitrarily
large, the size of the new metadata cache cannot be controlled by setting a
maximum number of entries. Instead, the new cache keeps a running sum of the
sizes of all entries and attempts to evict entries as necessary to stay within a
user-specified maximum size. (Note the use of the word "attempts" here -- as
will be seen, it is possible for the cache to exceed its currently specified
maximum size.) At present, the LRU replacement policy is the only option for
selecting candidates for eviction.

Per the standard Unix buffer cache, dirty entries are given two passes through
the LRU list before being evicted. The first time they reach the end of the LRU
list, they are flushed, marked as clean, and moved to the head of the LRU
list. When a clean entry reaches the end of the LRU list, it is simply evicted
if space is needed.

The cache cannot evict entries that are locked, and thus it will temporarily
grow beyond its maximum size if there are insufficient unlocked entries
available for eviction.

In the parallel version of the library, only the cache running under process 0
of the file communicator is allowed to write metadata to file. All the other
caches must retain dirty metadata until the process 0 cache tells them that the
metadata is clean.

Since all operations modifying metadata must be collective, all caches see the
same stream of dirty metadata. This fact is used to allow them to synchronize
every n bytes of dirty metadata, where n is a user-configurable value that
defaults to 256 KB.

To avoid sending the other caches messages from the future, process 0 must not
write any dirty entries until it reaches a synchronization point. When it
reaches a synchronization point, it writes entries as needed, and then
broadcasts the list of flushed entries to the other caches. The caches on the
other processes use this list to mark entries clean before they leave the
synchronization point, allowing them to evict those entries as needed.

The caches will also synchronize on a user-initiated flush.

To minimize overhead when running in parallel, the cache maintains a "clean" LRU
list in addition to the regular LRU list. This list contains only clean entries
and is used as a source of candidates for eviction when flushing dirty entries
is not allowed.

Since flushing entries is forbidden most of the time when running in parallel,
the caches can be forced to exceed their maximum sizes if they run out of clean
entries to evict.

To decrease the likelihood of this event, the new cache allows the user to
specify a minimum clean size -- which is a minimum total size of all the entries
on the clean LRU plus all unused space in the cache.

While the clean LRU list is only maintained in the parallel version of the HDF5
library, the notion of a minimum clean size still applies in the serial
case. Here it is used to force a mix of clean and dirty entries in the cache
even in the write-only case.

This, in turn, reduces the number of redundant flushes by avoiding the case in
which the cache fills with dirty metadata and all entries must be flushed before
a clean entry can be evicted to make room for a new entry.

Observe that in both the serial and parallel cases, the maintenance of a minimum
clean size modifies the replacement policy, as dirty entries may be flushed
earlier than would otherwise be the case so as to maintain the desired amount of
clean and/or empty space in the cache.

While the new metadata cache only supports the LRU replacement policy at
present, that may change. Support for multiple replacement policies was very
much in mind when the cache was designed, as was the ability to switch
replacement policies at run time. The situation has been complicated by the
later addition of the adaptive cache resizing requirement, as two of the
resizing algorithms piggyback on the LRU list. However, if there is a need for
additional replacement policies, it shouldn't be too hard to implement them.

\section adapt Adaptive Cache Resizing in the New Metadata Cache

As mentioned earlier, the metadata working set size for an HDF5 file varies
wildly depending on the structure of the file and the access pattern. For
example, a 2MB limit on metadata cache size is excessive for an H5repack of
almost all HDF5 files we have tested. However, I have a file submitted by one of
our users that will run a 13% hit rate with this cache size and will lock up one
of our Linux boxes using the old metadata cache. Increase the new metadata cache
size to 4 MB, and the hit rate exceeds 99%.

In this case, the main culprit is a root group with more than 20,000 entries in
it. As a result, the root group heap exceeds 1 MB, which tends to crowd out the
rest of the metadata in a 2 MB cache

This case and a number of synthetic tests convinced us that we needed to modify
the new metadata cache to expand and contract according to need within
user-specified bounds.

I was unable to find any previous work on this problem, so I invented solutions
as I went along. If you are aware of prior work, please send me references. The
closest I was able to come was a group of embedded CPU designers who were
turning off sections of their cache to conserve power.

\subsection increasing Increasing the Cache Size

In the context of the HDF5 library, the problem of increasing the cache size as
necessary to contain the current working set turns out to involve two rather
different issues.

The first of these, which was recognized immediately, is the problem of
recognizing long term changes in working set size, and increasing the cache size
accordingly, while not reacting to transients.

The second, which I recognized the hard way, is to adjust the cache size for
sudden, dramatic increases in working set size caused by requests for large
pieces of metadata which may be larger than the current metadata cache size.

The algorithms for handling these situations are discussed below. These problems
are largely orthogonal to each other, so both algorithms may be used
simultaneously.

\subsubsection hrtcsi  Hit Rate Threshold Cache Size Increment

Perhaps the most obvious heuristic for identifying cases in which the cache is
too small involves monitoring the hit rate. If the hit rate is low for a while,
and the cache is at its current maximum size, the current maximum cache size is
probably too small.

The hit rate threshold algorithm for increasing cache size applies this
intuition directly.

Hit rate statistics are collected over a user-specified number of cache
accesses. This period is known as an epoch.

At the end of each epoch, the hit rate is computed, and the counters are
reset. If the hit rate is below a user-specified threshold and the cache is at
its current maximum size, the maximum size of the cache is increased by a
user-specified multiple. If required, the new cache maximum size is clipped to
stay within the user-specified upper bound on the maximum cache size, and
optionally, within a user-specified maximum increment.

My tests indicate that this algorithm works well in most cases. However, in a
synthetic test in which hit rate increased slowly with cache size, and load
remained steady for many epochs, I observed a case in which cache size increased
until the hit rate just exceeded the specified minimum and then stalled. This is
a problem, as to avoid volatility, it is necessary to set the minimum hit rate
threshold well below the desired hit rate. Thus we may find ourselves with a
cache running with a 91% hit rate when we really want it to increase its size
until the hit rate is about 99%.

If this case occurs frequently in actual use, I will have to come up with an
improved algorithm. Please let me know if you see this behavior. However, I had
to work rather hard to create it in my synthetic tests, so I would expect it to
be uncommon.

\subsubsection fcsi Flash Cache Size Increment

A fundamental problem with the above algorithm is that contains the hidden
assumption that cache entries are relatively small in comparison to the cache
itself. While I knew this assumption was not generally true when I developed the
algorithm, I thought that cases, where it failed, would be so rare as to not be
worth considering, as even if they did occur, the above algorithm would rectify
the situation within an epoch or two.

While it is true that such occurrences are rare, and it is true that the hit
rate threshold cache size increment algorithm will rectify the situation
eventually, the performance degradation experienced by users while waiting for
the epoch to end was so extreme that some way of accelerating response to such
situations was essential.

To understand the problem, consider the following use case:

Suppose we create a group, and then repeatedly create a new data set in the
group, write some data to it and then close it.

In some versions of the HDF5 file format, the names of the datasets will be
stored in a local heap associated with the group, and the space for that heap
will be allocated in a single, contiguous chunk. When this local heap is full,
we allocate a new chunk twice the size of the old, copy the data from the old
local heap into the new, and discard the old local heap.

By default, the minimum metadata cache size is set to 2 MB. Thus in this use
case, our hit rate will be fine as long as the local heap is no larger than a
little less than 2 MB, as the group related metadata is accessed frequently and
never evicted, and the data set related metadata is never accessed once the data
set is closed, and thus is evicted smoothly to make room for new data sets.

All this changes abruptly when the local heap finally doubles in size to a value
above the slightly less than 2 MB limit. All of a sudden, the local heap is the
size of the metadata cache, and the cache must constantly swap it in to access
it, and then swap it out to make room for other metadata.

The hit rate threshold-based algorithm for increasing the cache size will fix
this problem eventually, but performance will be very bad until it does, as the
metadata cache will largely ineffective until its size is increased.

An obvious heuristic for addressing this "big rock in a small pond" issue is to
watch for large "incoming rocks", and increase the size of the "pond" if the
rock is so big that it will force most of the "water" out of the "pond".

The add space flash cache size increment algorithm applies this intuition
directly:

Let x be either the size of a newly inserted entry, a newly loaded entry, or the
number of bytes by which the size of an existing entry has been increased
(i.e. the size of the "rock").

If x is greater than some user-specified fraction of the current maximum cache
size, increase the current maximum cache size by x times some user-specified
multiple, less any free space that was in the cache, to begin with. Further, to
avoid confusing the other cache size increment/decrement code, start a new
epoch.

At present, this algorithm pays no attention to any user-specified limit on the
maximum size of any single cache size increase, but it DOES stay within the
user-specified upper bound on the maximum cache size.

While it should be easy to see how this algorithm could be fooled into
inactivity by a large number of entries that were not quite large enough to
cross the threshold, in practice it seems to work reasonably well.

Needless to say, I will revisit the issue should this cease to be the case.

\subsection decreasing Decreasing the Cache Size

Identifying cases in which the maximum cache size is larger than necessary
turned out to be more difficult.

\subsubsection hrtcsr Hit Rate Threshold Cache Size Reduction

One obvious heuristic is to monitor the hit rate and guess that we can safely
decrease cache size if the hit rate exceeds some user-supplied threshold (say
.99995). The hit rate threshold size decrement algorithm implemented in the new
metadata cache implements this intuition as follows:

At the end of each epoch (this is the same epoch that is used in the cache size
increment algorithm), the hit rate is compared with the user-specified
threshold. If the hit rate exceeds that threshold, the current maximum cache
size is decreased by a user-specified factor. If required, the size of the
reduction is clipped to stay within a user-specified lower bound on the maximum
cache size, and optionally, within a user-specified maximum decrement.

In my synthetic tests, this algorithm works poorly. Even with a very high
threshold and a small maximum reduction, it results in cache size
oscillations. The size increment code typically increments the maximum cache
size above the working set size. This results in a high hit rate, which causes
the threshold size decrement code to reduce the maximum cache size below the
working set size, which causes the hit rate to crash causing the cycle to
repeat. The resulting average hit rate is poor.

It remains to be seen if this behavior will be seen in the field. The algorithm
is available for use, but it wouldn't be my first choice. If you use it, please
report back.

\subsubsection acsr Ageout Cache Size Reduction

Another heuristic for dealing with oversized cache conditions is to look for
entries that haven't been accessed for a long time, evict them, and reduce the
cache size accordingly.

The age out cache size reduction applies this intuition as follows: At the end
of each epoch (again the same epoch as used in the cache size increment
algorithm), all entries that haven't been accessed for a user-configurable
number of epochs (1 - 10 at present) are evicted. The maximum cache size is then
reduced to equal the sum of the sizes of the remaining entries. The size of the
reduction is clipped to stay within a user-specified lower bound on maximum
cache size, and optionally, within a user-specified maximum decrement.

In addition, the user may specify a minimum fraction of the cache which must be
empty before the cache size is reduced. Thus if an empty reserve of 0.1 was
specified on a 10 MB cache, there would be no cache size reduction unless the
eviction of aged out entries resulted in more than 1 MB of empty space. Further,
even after the reduction, the cache would be one-tenth empty.

In my synthetic tests, the age out algorithm works rather well, although it is
somewhat sensitive to the epoch length and age out period selection.

\subsubsection awhrtcsr Ageout With Hit Rate Threshold Cache Size Reduction

To address these issues, I combined the hit rate threshold and age out
heuristics.

Age out with threshold works just like age out, except that the algorithm is not
run unless the hit rate exceeded a user-specified threshold in the previous
epoch.

In my synthetic tests, age out with threshold seems to work nicely, with no
observed oscillation. Thus I have selected it as the default cache size
reduction algorithm.

For those interested in such things, the age out algorithm is implemented by
inserting a marker entry at the head of the LRU list at the beginning of each
epoch. Entries that haven't been accessed for at least n epochs are simply
entries that appear in the LRU list after the n-th marker at the end of an
epoch.

\section configuring Configuring the New Metadata Cache

Due to a lack of resources, the design work on the automatic cache size
adjustment algorithms was done hastily, using primarily synthetic tests. I don't
think I spent more than a couple weeks writing and running performance tests --
most time went into coding and functional testing.

As a result, while I think the algorithms provided for adaptive cache resizing
will work well in actual use, I don't really know (although preliminary results
from the field are promising). Fortunately, the issue shouldn't arise for the
vast majority of HDF5 users, and those for whom it may arise should be savvy
enough to recognize problems and deal with them.

For this latter class of users, I have implemented a number of new API calls
allowing the user to select and configure the cache resize algorithms, or to
turn them off and control cache size directly from the user program. There are
also API calls that allow the user program to monitor hit rate and cache size.

From the user perspective, all the cache configuration data for a given file is
contained in an instance of the \ref H5AC_cache_config_t structure -- the definition
of which is given below:

\snippet H5ACpublic.h H5AC_cache_config_t_snip

This structure is defined in \c H5ACpublic.h. Each field is discussed below and in
the associated header comment.

The C API allows you to get and set this structure directly. Unfortunately, the
Fortran API has to do this with individual parameters for each of the fields
(with the exception of version).

While the API calls are discussed individually in the reference manual, the
following high-level discussion of what fields to change for different purposes
should be useful.

\subsection gconfig General Configuration

The \c version field is intended to allow \THG to change the \c
H5AC_cache_config_t structure without breaking old code. For now, this field
should always be set to \c H5AC__CURR_CACHE_CONFIG_VERSION, even when you are
getting the current configuration data from the cache. The library needs the
version number to know where fields are located with reference to the supplied
base address.

The \ref H5AC_cache_config_t.rpt_fcn_enabled "rpt_fcn_enabled" field is a
boolean flag that allows you to turn on and off the resize reporting function
that reports the activities of the adaptive cache resize code at the end of each
epoch -- assuming that it is enabled.

The report function is unsupported, so you are on your own if you use it. Since
it dumps status data to stdout, you should not attempt to use it with Windows
unless you modify the source. You may find it useful if you want to experiment
with different adaptive resize configurations. It is also a convenient way of
diagnosing poor cache configuration. Finally, if you do lots of runs with
identical behavior, you can use it to determine the metadata cache size needed
in each phase of your program so you can set the required cache sizes manually.

The trace file fields are also unsupported. They allow one to open and close a
trace file in which all calls to the metadata cache are logged in a
user-specified file for later analysis. The feature is intended primarily for
THG use in debugging or optimizing the metadata cache in cases where users in
the field observe obscure failures or poor performance that we cannot re-create
in the lab. The trace file will allow us to re-create the exact sequence of
cache operations that are triggering the problem.

At present we do not have a playback utility for trace files, although I imagine
that we will write one quickly when and if we need it.

To enable the trace file, you load the full path of the desired trace file into
\ref H5AC_cache_config_t.trace_file_name "trace_file_name", and set \ref
H5AC_cache_config_t.open_trace_file "open_trace_file" to \c TRUE. In the
parallel case, an ASCII representation of the rank of each process is appended
to the supplied trace file name to create a unique trace file name for that
process.

To close an open trace file, set \ref H5AC_cache_config_t.close_trace_file
"close_trace_file" to \c TRUE.

It must be emphasized that you are on your own if you play with the trace file
feature absent a request from \THG. Needless to say, the trace file feature is
disabled by default. If you enable it, you will take a large performance hit and
generate huge trace files.

The \ref H5AC_cache_config_t.evictions_enabled "evictions_enabled" field is a
boolean flag allowing the user to disable the eviction of entries from the
metadata cache. Under normal operation conditions, this field will always be set
to \c TRUE.

In rare circumstances, the raw data throughput requirements may be so high that
the user wishes to postpone metadata writes so as to reserve I/O throughput for
raw data. The \ref H5AC_cache_config_t.evictions_enabled "evictions_enabled"
field exists to allow this -- although the user is to be warned that the
metadata cache will grow without bound while evictions are disabled. Thus
evictions should be re-enabled as soon as possible, and it may be wise to
monitor cache size and statistics (to see how to enable statistics, see the
debugging facilities section below).

Evictions may only be disabled when the automatic cache resize code is disabled
as well. Thus to disable evictions, not only must the user set the \ref
H5AC_cache_config_t.evictions_enabled "evictions_enabled" field to \c FALSE, but
he must also set \ref H5AC_cache_config_t.incr_mode "incr_mode" to
#H5C_incr__off, set \ref H5AC_cache_config_t.flash_incr_mode "flash_incr_mode"
to #H5C_flash_incr__off, and set \ref H5AC_cache_config_t.decr_mode "decr_mode"
to #H5C_decr__off.

To re-enable evictions, just set \ref H5AC_cache_config_t.evictions_enabled
"evictions_enabled" back to \c TRUE.

Before passing on to other subjects, it is worth re-iterating that disabling
evictions is an extreme step. Before attempting it, you might consider setting a
large cache size manually, and flushing the cache just before high raw data
throughput is required. This may yield the desired results without the risks
inherent in disabling evictions.

The \ref H5AC_cache_config_t.set_initial_size "set_initial_size" and \ref
H5AC_cache_config_t.initial_size "initial_size" fields allow you to specify an
initial maximum cache size. If \ref H5AC_cache_config_t.set_initial_size
"set_initial_size" is \c TRUE, \ref H5AC_cache_config_t.initial_size
"initial_size" must lie in the interval [\ref H5AC_cache_config_t.min_size
"min_size", \ref H5AC_cache_config_t.max_size "max_size"] (see below for a
discussion of the \ref H5AC_cache_config_t.min_size "min_size" and \ref
H5AC_cache_config_t.max_size "max_size" fields).

If you disable the adaptive cache resizing code (done by setting \ref
H5AC_cache_config_t.incr_mode "incr_mode" to #H5C_incr__off, \ref
H5AC_cache_config_t.flash_incr_mode "flash_incr_mode" to #H5C_flash_incr__off,
and \ref H5AC_cache_config_t.decr_mode "decr_mode" to #H5C_decr__off), you can
use these fields to control maximum cache size manually, as the maximum cache
size will remain at the initial size.

Note, that the maximum cache size is only modified when \ref
H5AC_cache_config_t.set_initial_size "set_initial_size" is \c TRUE. This allows
the use of configurations specified at compile time to change resize
configuration without altering the current maximum size of the cache. Without
this feature, an additional call would be required to get the current maximum
cache size so as to set the \ref H5AC_cache_config_t.initial_size "initial_size"
to the current maximum cache size, and thereby avoid changing it.

The \ref H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" sets the
current minimum clean size as a fraction of the current max cache size. While
this field was originally used only in the parallel version of the library, it
now applies to the serial version as well. Its value must lie in the range
\Code{[0.0, 1.0]}. 0.01 is reasonable in the serial case, and 0.3 in the
parallel.

A potential interaction, discovered at release 1.8.3, between the enforcement of
the \ref H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" and the
adaptive cache resize code can severely degrade performance. While this
interaction is easily dealt with in the serial case by setting \ref
H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" to 0.01, the problem
is more difficult in the parallel case. Please see the Interactions section
below for further details.

The \ref H5AC_cache_config_t.max_size "max_size" and \ref
H5AC_cache_config_t.min_size "min_size" fields specify the range of maximum
sizes that may be set for the cache by the automatic resize code. \ref
H5AC_cache_config_t.min_size "min_size" must be less than or equal to
\ref H5AC_cache_config_t.max_size "max_size", and both must lie in the range
\Code{[H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]} -- currently [1 KB,
128 MB]. If you routinely run a cache size in the top half of this range, you
should increase the hash table size. To do this, modify the \c
H5C__HASH_TABLE_LEN \Code{\#define} in \c H5Cpkg.h and re-compile. At present,
\c H5C__HASH_TABLE_LEN must be a power of two.

The \c epoch_length is the number of cache accesses between runs of the adaptive
cache size control algorithms. It is ignored if these algorithms are turned
off. It must lie in the range \Code{[H5C__MIN_AR_EPOCH_LENGTH,
H5C__MAX_AR_EPOCH_LENGTH]} -- currently [100, 1000000]. The above constants are
defined in \c H5Cprivate.h. 50000 is a reasonable value.

\subsection increment Increment Configuration

The \ref H5AC_cache_config_t.incr_mode "incr_mode" field specifies the cache
size increment algorithm used. Its value must be a member of the \ref
H5C_cache_incr_mode enum type -- currently either #H5C_incr__off or
#H5C_incr__threshold (note the double underscores after \c "incr"). This type is
defined in H5Cpublic.h.

If \ref H5AC_cache_config_t.incr_mode "incr_mode" is set to #H5C_incr__off,
regular automatic cache size increases are disabled, and the \ref
H5AC_cache_config_t.lower_hr_threshold "lower_hr_threshold", \ref
H5AC_cache_config_t.increment "increment", \ref
H5AC_cache_config_t.apply_max_increment "apply_max_increment", and \ref
H5AC_cache_config_t.max_increment "max_increment", fields are ignored.

The \ref H5AC_cache_config_t.flash_incr_mode "flash_incr_mode" field specifies
the flash cache size increment algorithm used. Its value must be a member of the
\ref H5C_cache_flash_incr_mode enum type -- currently either
#H5C_flash_incr__off or #H5C_flash_incr__add_space (note the double underscores
after \c "incr"). This type is defined in H5Cpublic.h.

If \ref H5AC_cache_config_t.flash_incr_mode "flash_incr_mode" is set to
#H5C_flash_incr__off, flash cache size increases are disabled, and the \ref
H5AC_cache_config_t.flash_multiple "flash_multiple", and \ref
H5AC_cache_config_t.flash_threshold "flash_threshold", fields are ignored.

\subsubsection hrtcsic Hit Rate Threshold Cache Size Increase Configuration

If \ref H5AC_cache_config_t.incr_mode "incr_mode" is #H5C_incr__threshold, the
cache size is increased via the hit rate threshold algorithm. The remaining
fields in the section are then used as follows:

\ref H5AC_cache_config_t.lower_hr_threshold "lower_hr_threshold" is the
threshold below which the hit rate must fall to trigger an increase. The value
must lie in the range \Code{[0.0 - 1.0]}. In my tests, a relatively high value
seems to work best -- 0.9 for example.

\ref H5AC_cache_config_t.increment "increment" is the factor by which the old
maximum cache size is multiplied to obtain an initial new maximum cache size
when an increment is needed. The actual change in size may be smaller as
required by \ref H5AC_cache_config_t.max_size "max_size" (above) and \c
max_increment (discussed below). increment must be greater than or equal to
1.0. If you set it to 1.0, you will effectively turn off the increment code. 2.0
is a reasonable value.

\ref H5AC_cache_config_t.apply_max_increment "apply_max_increment" and \ref
H5AC_cache_config_t.max_increment "max_increment" allow the user to specify a
maximum increment. If \ref H5AC_cache_config_t.apply_max_increment
"apply_max_increment" is \c TRUE, the cache size will never be increased by more
than the number of bytes specified in \ref H5AC_cache_config_t.max_increment
"max_increment" in any single increase.

\subsubsection fcsic Flash Cache Size Increase Configuration

If \ref H5AC_cache_config_t.flash_incr_mode "flash_incr_mode" is set to
#H5C_flash_incr__add_space, flash cache size increases are enabled. The size of
the cache will be increased under the following circumstances:

Let \c t be the current maximum cache size times the value of the \ref
H5AC_cache_config_t.flash_threshold "flash_threshold" field.

Let \c x be either the size of the newly inserted entry, the size of the newly
loaded entry, or the number of bytes added to the size of the entry under
consideration for triggering a flash cache size increase.

If \Code{t < x}, the basic condition for a flash cache size increase is met, and
we proceed as follows:

Let \c space_needed equal \c x less the amount of free space in the cache.

Further, let \ref H5AC_cache_config_t.increment "increment" equal \c
space_needed times the value of the \ref H5AC_cache_config_t.flash_multiple
"flash_multiple" field. If \ref H5AC_cache_config_t.increment "increment" plus
the current cache size is greater than \ref H5AC_cache_config_t.max_size
"max_size" (discussed above), reduce \ref H5AC_cache_config_t.increment
"increment" so that \ref H5AC_cache_config_t.increment "increment" plus the
current cache size is equal to \ref H5AC_cache_config_t.max_size "max_size".

If the increment is greater than zero, increase the current cache size by \ref
H5AC_cache_config_t.increment "increment". To avoid confusing the other cache
size increment or decrement algorithms, start a new epoch. Note, however, that
we do not cycle the epoch markers if some variant of the age out algorithm is in
use.

The use of the \ref H5AC_cache_config_t.flash_threshold "flash_threshold" field
is discussed above. It must be a floating-point value in the range of
\Code{[0.1, 1.0]}. 0.25 is a reasonable value.

The use of the \ref H5AC_cache_config_t.flash_multiple "flash_multiple" field is
also discussed above. It must be a floating-point value in the range of
\Code{[0.1, 10.0]}. 1.4 is a reasonable value.

\subsection decrement Decrement Configuration

The \ref H5AC_cache_config_t.decr_mode "decr_mode" field specifies the cache
size decrement algorithm used. Its value must be a member of the \ref
H5C_cache_decr_mode enum type -- currently either #H5C_decr__off,
#H5C_decr__threshold, #H5C_decr__age_out, or #H5C_decr__age_out_with_threshold
(note the double underscores after \c "decr"). This type is defined in
H5Cpublic.h.

If \ref H5AC_cache_config_t.decr_mode "decr_mode" is set to #H5C_decr__off,
automatic cache size decreases are disabled, and the remaining fields in the
cache size decrease control section are ignored.

\subsubsection hrtcsdc Hit Rate Threshold Cache Size Decrease Configuration

If \ref H5AC_cache_config_t.decr_mode "decr_mode" is #H5C_decr__threshold, the
cache size is decreased by the threshold algorithm, and the remaining fields of
the decrement section are used as follows:

\ref H5AC_cache_config_t.upper_hr_threshold "upper_hr_threshold" is the
threshold above which the hit rate must rise to trigger cache size reduction. It
must be in the range \Code{[0.0, 1.0]}. In my synthetic tests, very high values
like .9995 or .99995 seemed to work best.

\ref H5AC_cache_config_t.decrement "decrement" is the factor by which the
current maximum cache size is multiplied to obtain a tentative new maximum cache
size. It must lie in the range \Code{[0.0, 1.0]}. Relatively large values like
.9 seem to work best in my synthetic tests. Note that the actual size reduction
may be smaller as required by \ref H5AC_cache_config_t.min_size "min_size" and
\ref H5AC_cache_config_t.max_decrement "max_decrement" (discussed below).  \ref
H5AC_cache_config_t.apply_max_decrement "apply_max_decrement" and \ref
H5AC_cache_config_t.max_decrement "max_decrement" allow the user to specify a
maximum decrement. If \ref H5AC_cache_config_t.apply_max_decrement
"apply_max_decrement" is \c TRUE, the cache size will never be reduced by more
than \ref H5AC_cache_config_t.max_decrement "max_decrement" bytes in any single
reduction.

With the hit rate threshold cache size decrement algorithm, the remaining fields
in the section are ignored.

\subsubsection dacsr Ageout Cache Size Reduction

If \ref H5AC_cache_config_t.decr_mode "decr_mode" is #H5C_decr__age_out the
cache size is decreased by the ageout algorithm, and the remaining fields of the
decrement section are used as follows:

\ref H5AC_cache_config_t.epochs_before_eviction "epochs_before_eviction" is the
number of epochs an entry must reside unaccessed in the cache before it is
evicted. This value must lie in the range \Code{[1, H5C__MAX_EPOCH_MARKERS]}. \c
H5C__MAX_EPOCH_MARKERS is defined in H5Cprivate.h, and is currently set to 10.

\ref H5AC_cache_config_t.apply_max_decrement "apply_max_decrement" and \ref
H5AC_cache_config_t.max_decrement "max_decrement" are used as in section
2.4.3.1.

\ref H5AC_cache_config_t.apply_empty_reserve "apply_emty_reserve" and \ref
H5AC_cache_config_t.empty_reserve "empty_reserve" allow the user to specify a
minimum empty reserve as discussed in section 2.3.2.2. An empty reserve of 0.05
or 0.1 seems to work well.

The \ref H5AC_cache_config_t.decrement "decrement" and \ref
H5AC_cache_config_t.upper_hr_threshold "upper_hr_threshold" fields are ignored
in this case.

\subsubsection dawhrtcsr Ageout With Hit Rate Threshold Cache Size Reduction

If \ref H5AC_cache_config_t.decr_mode "decr_mode" is
#H5C_decr__age_out_with_threshold, the cache size is decreased by the ageout
with hit rate threshold algorithm, and the fields of decrement section are used
as per the Ageout algorithm (see 5.3.2) with the exception of \ref
H5AC_cache_config_t.upper_hr_threshold "upper_hr_threshold".

Here, \ref H5AC_cache_config_t.upper_hr_threshold "upper_hr_threshold" is the
threshold above which the hit rate must rise to trigger cache size reduction. It
must be in the range \Code{[0.0, 1.0]}. In my synthetic tests, high values like
.999 seemed to work well.

\subsection parallel Parallel Configuration

This section is a catch-all for parallel specific configuration data. At
present, it has only one field --
\ref H5AC_cache_config_t.dirty_bytes_threshold "dirty_bytes_threshold".

In PHDF5, all operations that modify metadata must be executed collectively. We
used to think that this was enough to ensure consistency across the metadata
caches, but since we allow processes to read metadata individually, the order of
dirty entries in the LRU list can vary across processes. This, in turn, can
change the order in which dirty metadata cache entries reach the bottom of the
LRU and are flushed to disk -- opening the door to messages from the past and
messages from the future bugs.

To prevent this, only the metadata cache on process 0 of the file communicator
is allowed to write to file, and then only after entering a sync point with the
other caches. After it writes entries to file, it sends the base addresses of
the now clean entries to the other caches, so they can mark these entries clean
as well, and then leaves the sync point. The other caches mark the specified
entries as clean before they leave the sync point as well. (Observe, that since
all caches see the same stream of dirty metadata, they will all have the same
set of dirty entries upon sync point entry and exit.)

The different caches know when to synchronize by counting the number of bytes of
dirty metadata created by the collective operations modifying metadata. Whenever
this count exceeds the value specified in the \ref
H5AC_cache_config_t.dirty_bytes_threshold "dirty_bytes_threshold", they all
enter the sync point, and process 0 flushes down to its minimum clean size and
sends the list of newly cleaned entries to the other caches.

Needless to say, the value of the \ref H5AC_cache_config_t.dirty_bytes_threshold
"dirty_bytes_threshold" field must be consistent across all the caches operating
on a given file.

All dirty metadata can also by flushed under programmatic control via the
H5Fflush() call. This call must be collective and will reset the dirty data
counts on each metadata cache.

Absent calls to H5Fflush(), dirty metadata will only be flushed when the \ref
H5AC_cache_config_t.dirty_bytes_threshold "dirty_bytes_threshold" is exceeded,
and then only down to the H5AC_cache_config_t.min_clean_fraction
"min_clean_fraction". Thus, if a program does all its metadata modifications in
one phase, and then doesn't modify metadata thereafter, a residue of dirty
metadata will be frozen in the metadata caches for the remainder of the
computation -- effectively reducing the sizes of the caches.

In the default configuration, the caches will eventually resize themselves to
maintain an acceptable hit rate. However, this will take time, and it will
increase the application's footprint in memory.

If your application behaves in this manner, you can avoid this by a collective
call to H5Fflush() immediately after the metadata modification phase.

\subsection interactions Interactions

Evictions may not be disabled unless the automatic cache resize code is disabled
as well (by setting \ref H5AC_cache_config_t.decr_mode "decr_mode" to
#H5C_decr__off, \c flash_decr_mode to #H5C_flash_incr__add_space, and \ref
H5AC_cache_config_t.incr_mode "incr_mode" to #H5C_incr__off) -- thus placing the
cache size under the direct control of the user program.

There is no logical necessity for this restriction. It is imposed because it
simplifies testing greatly and because I can't see any reason why one would want
to disable evictions while the automatic cache size adjustment code was
enabled. This restriction can be relaxed if anyone can come up with a good
reason to do so.

At present, there are two interactions between the increment and decrement
sections of the configuration.

If \ref H5AC_cache_config_t.incr_mode "incr_mode" is #H5C_incr__threshold, and
\ref H5AC_cache_config_t.decr_mode "decr_mode" is either #H5C_decr__threshold or
#H5C_decr__age_out_with_threshold, then \ref
H5AC_cache_config_t.lower_hr_threshold "lower_hr_threshold" must be strictly
less than \ref H5AC_cache_config_t.upper_hr_threshold "upper_hr_threshold".

Also, if the flash cache size increment code is enabled and is triggered, it
will restart the current epoch without calling any other cache size increment or
decrement code.

In both the serial and parallel cases, there is the potential for an interaction
between the \ref H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" and
the cache size increment code that can severely degrade
performance. Specifically, if the \ref H5AC_cache_config_t.min_clean_fraction
"min_clean_fraction" is large enough, it is possible that keeping the specified
fraction of the cache clean may generate enough flushes to seriously degrade
performance even though the hit rate is excellent.

In the serial case, this is easily dealt with by selecting a very small \ref
H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" -- 0.01 for example
-- as this still avoids the "metadata blizzard" phenomenon that appears when the
cache fills with dirty metadata and must then flush all of it before evicting an
entry to make space for a new entry.

The problem is more difficult in the parallel case, as the \ref
H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" is used to ensure
that the cache contains clean entries that can be evicted to make space for new
entries when metadata writes are forbidden -- i.e. between sync points.

This issue was discovered shortly before release 1.8.3 and an automated solution
has not been implemented. Should it become an issue for an application, try
manually setting the cache size to ~1.5 times the maximum working set size for
the application, and leave \ref H5AC_cache_config_t.min_clean_fraction
"min_clean_fraction" set to 0.3.

You can approximate the working set size of your application via repeated calls
to H5Fget_mdc_size() and H5Fget_mdc_hit_rate() while running your program with
the cache resize code enabled. The maximum value returned by H5Fget_mdc_size()
should be a reasonable approximation -- particularly if the associated hit rate
is good. In the parallel case, there is also an interaction between \c
min_clean_fraction and \ref H5AC_cache_config_t.dirty_bytes_threshold
"dirty_bytes_threshold". Absent calls to H5Fflush() (discussed above), the upper
bound on the amount of dirty data in the metadata caches will oscillate between
(1 - \ref H5AC_cache_config_t.min_clean_fraction "min_clean_fraction") times
current maximum cache size, and that value plus the \ref
H5AC_cache_config_t.dirty_bytes_threshold "dirty_bytes_threshold". Needless to
say, it will be best if the \ref H5AC_cache_config_t.min_size "min_size", \ref
H5AC_cache_config_t.min_clean_fraction "min_clean_fraction", and the \ref
H5AC_cache_config_t.dirty_bytes_threshold "dirty_bytes_threshold"
are chosen so that the cache can't fill with dirty data.

\subsection defaults Default Metadata Cache Configuration

Starting with release 1.8.3, HDF5 provides different default metadata cache
configurations depending on whether the library is compiled for serial or
parallel.

The default configuration for the serial case is as follows:

\code{.c}
{
  /* int         version                = */ H5C__CURR_AUTO_SIZE_CTL_VER,
  /* hbool_t     rpt_fcn_enabled        = */ FALSE,
  /* hbool_t     open_trace_file        = */ FALSE,
  /* hbool_t     close_trace_file       = */ FALSE,
  /* char        trace_file_name[]      = */ "",
  /* hbool_t     evictions_enabled      = */ TRUE,
  /* hbool_t     set_initial_size       = */ TRUE,
  /* size_t      initial_size           = */ ( 2 * 1024 * 1024),
  /* double      min_clean_fraction     = */ 0.01,
  /* size_t      max_size               = */ (32 * 1024 * 1024),
  /* size_t      min_size               = */ ( 1 * 1024 * 1024),
  /* long int    epoch_length           = */ 50000,
  /* enum H5C_cache_incr_mode incr_mode = */ H5C_incr__threshold,
  /* double      lower_hr_threshold     = */ 0.9,
  /* double      increment              = */ 2.0,
  /* hbool_t     apply_max_increment    = */ TRUE,
  /* size_t      max_increment          = */ (4 * 1024 * 1024),
  /* enum H5C_cache_flash_incr_mode       */
  /*                    flash_incr_mode = */ H5C_flash_incr__add_space,
  /* double      flash_multiple         = */ 1.4,
  /* double      flash_threshold        = */ 0.25,
  /* enum H5C_cache_decr_mode decr_mode = */ H5C_decr__age_out_with_threshold,
  /* double      upper_hr_threshold     = */ 0.999,
  /* double      decrement              = */ 0.9,
  /* hbool_t     apply_max_decrement    = */ TRUE,
  /* size_t      max_decrement          = */ (1 * 1024 * 1024),
  /* int         epochs_before_eviction = */ 3,
  /* hbool_t     apply_empty_reserve    = */ TRUE,
  /* double      empty_reserve          = */ 0.1,
  /* int         dirty_bytes_threshold  = */ (256 * 1024)
}
\endcode

The default configuration for the parallel case is as follows:

\code{.c}
{
  /* int         version                = */ H5C__CURR_AUTO_SIZE_CTL_VER,
  /* hbool_t     rpt_fcn_enabled        = */ FALSE,
  /* hbool_t     open_trace_file        = */ FALSE,
  /* hbool_t     close_trace_file       = */ FALSE,
  /* char        trace_file_name[]      = */ "",
  /* hbool_t     evictions_enabled      = */ TRUE,
  /* hbool_t     set_initial_size       = */ TRUE,
  /* size_t      initial_size           = */ ( 2 * 1024 * 1024),
  /* double      min_clean_fraction     = */ 0.3,
  /* size_t      max_size               = */ (32 * 1024 * 1024),
  /* size_t      min_size               = */ ( 1 * 1024 * 1024),
  /* long int    epoch_length           = */ 50000,
  /* enum H5C_cache_incr_mode incr_mode = */ H5C_incr__threshold,
  /* double      lower_hr_threshold     = */ 0.9,
  /* double      increment              = */ 2.0,
  /* hbool_t     apply_max_increment    = */ TRUE,
  /* size_t      max_increment          = */ (4 * 1024 * 1024),
  /* enum H5C_cache_flash_incr_mode       */
  /*                    flash_incr_mode = */ H5C_flash_incr__add_space,
  /* double      flash_multiple         = */ 1.0,
  /* double      flash_threshold        = */ 0.25,
  /* enum H5C_cache_decr_mode decr_mode = */ H5C_decr__age_out_with_threshold,
  /* double      upper_hr_threshold     = */ 0.999,
  /* double      decrement              = */ 0.9,
  /* hbool_t     apply_max_decrement    = */ TRUE,
  /* size_t      max_decrement          = */ (1 * 1024 * 1024),
  /* int         epochs_before_eviction = */ 3,
  /* hbool_t     apply_empty_reserve    = */ TRUE,
  /* double      empty_reserve          = */ 0.1,
  /* int         dirty_bytes_threshold  = */ (256 * 1024)
}
\endcode

The default serial configuration should be adequate for most serial HDF5 users.

The same may not be true for the default parallel configuration due to the
interaction between the \ref H5AC_cache_config_t.min_clean_fraction "min_clean_fraction" and the cache size increase code. See
the Interactions section for further details.

Should you need to change the default configuration, it can be found in
H5ACprivate.h. Look for the definition of H5AC__DEFAULT_RESIZE_CONFIG.

\section controlling Controlling the New Metadata Cache Size From Your Program

You have already seen how \ref H5AC_cache_config_t has facilities that allow you
to control the metadata cache size directly. Use H5Fget_mdc_config() and
H5Fset_mdc_config() to get and set the metadata cache configuration on an open
file. Use H5Pget_mdc_config() and H5Pset_mdc_config() to get and set the initial
metadata cache configuration in a file access property list. Recall that this
list contains configuration data used when opening a file.

Use H5Fget_mdc_hit_rate() to get the average hit rate since the last time the
hit rate stats were reset. This happens automatically at the beginning of each
epoch if the adaptive cache resize code is enabled. You can also do it manually
with H5Freset_mdc_hit_rate_stats(). Be careful about doing this if the adaptive
cache resize code is enabled, as you may confuse it.

Use H5Fget_mdc_size() to get metadata cache size data on an open file.

Finally, note that cache size and cache footprint are two different things -- in
my tests, the cache footprint (as inferred from the UNIX \c top command) is
typically about three times the maximum cache size. I haven't tracked it down
yet, but I would guess that most of this is due to the very small typical cache
entry size combined with the rather large size of the cache entry header
structure. This should be investigated further, but there are other matters of
higher priority.

\section news New Metadata Cache Debugging Facilities

The new metadata cache has a variety of debugging facilities that may be of
use. I doubt that any other than the report function and the trace file will
ever be accessible via the API, but they are relatively easy to turn on in the
source code.

Note that none of this should be viewed as supported -- it is described here on
the off chance that you want to use it, but you are on your own if you do. Also,
there are no promises as to consistency between versions.

As mentioned above, you can use the \ref H5AC_cache_config_t.rpt_fcn_enabled "rpt_fcn_enabled" field of the
configuration structure to enable the default reporting function
(H5C_def_auto_resize_rpt_fcn() in H5C.c). If this function doesn't work for you,
you will have to write your own. In particular, remember that it uses \c stdout,
so it will probably be unhappy under Windows.

Again, remember that this facility is not supported. Further, it is likely to
change every time I do any serious work on the cache.

There is also an extensive statistics collection code. Use
H5C_COLLECT_CACHE_STATS and H5C_COLLECT_CACHE_ENTRY_STATS in H5Cprivate.h to
turn this on. If you also turn on H5AC_DUMP_STATS_ON_CLOSE in H5ACprivate.h,
stats will be dumped when you close a file. Alternatively you can call
H5C_stats() and H5C_stats__reset() within the library to dump and reset
stats. Both of these functions are defined in H5C.c.

Finally, the cache also contains an extensive sanity checking code. Much of this
is turned on when you compile in debug mode, but to enable the full suite, turn
on H5C_DO_SANITY_CHECKS in H5Cprivate.h.

\section trouble Troubleshooting

Absent major bugs in the cache, the only troubleshooting you should have to do
is diagnosing and fixing problems with your cache configuration.

Assuming it runs on your platform (I've only used it under Linux), the reporting
function is probably the most convenient diagnosis tool. However, since it is
unsupported code, I will not discuss it further beyond directing you to the
source (H5C_def_auto_resize_rpt_fcn() in H5C.c).

Absent the reporting function, regular calls to H5Fget_mdc_hit_rate() should
give you a good idea of the hit rate over time. Remember that the hit rate stats
are reset at the end of each epoch (when adaptive cache resizing is enabled), so
you should expect some jitter.

Similar calls to H5Fget_mdc_size() should allow you to monitor cache size and
the fraction of the current maximum cache size that is actually in use.

If the hit rate is consistently low, and the cache it at its current maximum
size, increasing the maximum size is an obvious fix.

If you see hit rate and cache size oscillations, try disabling adaptive cache
resizing and setting a fixed cache size a bit greater than the high end of the
cache size oscillations you observed.

If the hit rate oscillations don't go away, you are probably looking at a
feature of your application that can't be helped without major changes to the
cache. Please send along a description of the situation.

If the oscillations do go away, you may be able to come up with a configuration
that deals with the situation. If that fails, control the cache size manually,
and write to me, so I can try to develop an adaptive resize algorithm that works
in your case.

Needless to say, you should give the cache a few epochs to adapt to
circumstances. If that is too slow for you, try manual cache size control.

If you find it necessary to disable evictions, you may find it useful to enable
the internal statistics collection code mentioned above in the section on
debugging facilities.

Amongst many other things, the stats code will report the maximum cache size,
and the average successful and unsuccessful search depths in the hash table. If
these latter figures are significantly above 1, you should increase the size of
the hash table.

 */