Optimization Methods for Iceberg Tables

Posted in Technical |
February 14, 2024 9 min learn

Introduction

Apache Iceberg has not too long ago grown in reputation as a result of it provides information warehouse-like capabilities to your information lake making it simpler to research all of your information—structured and unstructured. It provides a number of advantages resembling schema evolution, hidden partitioning,  time journey, and extra that enhance the productiveness of information engineers and information analysts. Nonetheless, you must commonly keep Iceberg tables to maintain them in a wholesome state in order that learn queries can carry out  sooner. This weblog discusses a couple of issues that you simply would possibly encounter with Iceberg tables and provides methods on learn how to optimize them in every of these situations. You possibly can benefit from a mixture of the methods supplied and adapt them to your explicit use circumstances. 

Drawback with too many snapshots

Everytime a write operation happens on an Iceberg desk, a brand new snapshot is created. Over a time frame this could trigger the desk’s metadata.json file to get bloated and the variety of outdated and doubtlessly pointless information/delete information current within the information retailer to develop, growing storage prices. A bloated metadata.json file might enhance each learn/write instances as a result of a big metadata file must be learn/written each time. Repeatedly expiring snapshots is beneficial to delete information information which are not wanted, and to maintain the scale of desk metadata small. Expiring snapshots is a comparatively low-cost operation and makes use of metadata to find out newly unreachable information.

Resolution: expire snapshots

We will expire outdated snapshots utilizing expire_snapshots 

Drawback with suboptimal manifests

Over time the snapshots would possibly reference many manifest information. This might trigger a slowdown in question planning and enhance the runtime of metadata queries. Moreover, when first created the manifests could not lend themselves properly to partition pruning, which will increase the general runtime of the question. However, if the manifests are properly organized into discrete bounds of partitions, then partition pruning can prune away complete subtrees of information information.

Resolution: rewrite manifests

We will remedy the too many manifest information drawback with rewrite_manifests and doubtlessly get a well-balanced hierarchical tree of information information. 

Drawback with delete information

Background

merge-on-read vs copy-on-write

Since Iceberg V2, each time current information must be up to date (by way of delete, replace, or merge statements), there are two choices obtainable: copy-on-write and merge-on-read. With the copy-on-write choice, the corresponding information information of a delete, replace, or merge operation shall be learn and completely new information information shall be written with the mandatory write modifications. Iceberg doesn’t delete the outdated information information. So if you wish to question the desk earlier than the modifications have been utilized you should utilize the time journey characteristic of Iceberg. In a later weblog, we’ll go into particulars about learn how to benefit from the time journey characteristic. Should you determined that the outdated information information usually are not wanted any extra then you’ll be able to do away with them by expiring the older snapshot as mentioned above. 

With the merge-on-read choice, as a substitute of rewriting your complete information information through the write time, merely a delete file is written. This may be an equality delete file or a positional delete file. As of this writing, Spark doesn’t write equality deletes, however it’s able to studying them. The benefit of utilizing this selection is that your writes may be a lot faster as you aren’t rewriting a whole information file. Suppose you wish to delete a particular person’s information in a desk due to GDPR necessities, Iceberg will merely write a delete file specifying the places of the person information within the corresponding information information the place the person’s information exist. So each time you might be studying the tables, Iceberg will dynamically apply these deletes and current a logical desk the place the person’s information is deleted though the corresponding data are nonetheless current within the bodily information information.

We allow the merge-on-read choice for our prospects by default. You possibly can allow or disable them by setting the next properties primarily based in your necessities. See Write properties.

Serializable vs snapshot isolation

The default isolation assure supplied for the delete, replace, and merge operations is serializable isolation. You might additionally change the isolation degree to snapshot isolation. Each serializable and snapshot isolation ensures present a read-consistent view of your information.  Serializable Isolation is a stronger assure. For example, you could have an worker desk that maintains worker salaries. Now, you wish to delete all data equivalent to workers with wage higher than $100,000. Let’s say this wage desk has 5 information information and three of these have data of workers with wage higher than $100,000. While you provoke the delete operation, the three information containing worker salaries higher than $100,000 are chosen, then in case your “delete_mode” is merge-on-read a delete file is written that factors to the positions to delete in these three information information. In case your  “delete_mode” is copy-on-write, then all three information information are merely rewritten. 

No matter the delete_mode, whereas the delete operation is going on, assume a brand new information file is written by one other person with a wage higher than $100,000. If the isolation assure you selected is snapshot, then the delete operation will succeed and solely the wage data equivalent to the unique three information information are eliminated out of your desk. The data within the newly written information file whereas your delete operation was in progress, will stay intact. However, in case your isolation assure was serializable, then your delete operation will fail and you’ll have to retry the delete from scratch. Relying in your use case you would possibly wish to scale back your isolation degree to “snapshot.”

The issue

The presence of too many delete information will ultimately scale back the learn efficiency, as a result of in Iceberg V2 spec, everytime an information file is learn, all of the corresponding delete information additionally must be learn (the Iceberg neighborhood is at the moment contemplating introducing an idea referred to as “delete vector” sooner or later and that may work otherwise from the present spec). This may very well be very expensive. The place delete information would possibly comprise dangling deletes, as in it may need references to information which are not current in any of the present snapshots.

Resolution: rewrite place deletes

For place delete information, compacting the place delete information mitigates the issue somewhat bit by lowering the variety of delete information that must be learn and providing sooner efficiency by higher compressing the delete information. As well as the process additionally deletes the dangling deletes.

Rewrite place delete information

Iceberg offers a rewrite place delete information process in Spark SQL.

However the presence of delete information nonetheless pose a efficiency drawback. Additionally, regulatory necessities would possibly drive you to ultimately bodily delete the information reasonably than do a logical deletion. This may be addressed by doing a significant compaction and eradicating the delete information fully, which is addressed later within the weblog.

Drawback with small information

We usually wish to reduce the variety of information we’re touching throughout a learn. Opening information is dear. File codecs like Parquet work higher if the underlying file measurement is giant. Studying extra of the identical file is cheaper than opening a brand new file. In Parquet, usually you need your information to be round 512 MB and row-group sizes to be round 128 MB. In the course of the write part these are managed by “write.target-file-size-bytes” and “write.parquet.row-group-size-bytes” respectively. You would possibly wish to go away the Iceberg defaults alone until what you might be doing.

In Spark for instance, the scale of a Spark process in reminiscence will must be a lot increased to succeed in these defaults, as a result of when information is written to disk, it will likely be compressed in Parquet/ORC. So getting your information to be of the fascinating measurement isn’t simple until your Spark process measurement is large enough.

One other drawback arises with partitions. Except aligned correctly, a Spark process would possibly contact a number of partitions. Let’s say you could have 100 Spark duties and every of them wants to put in writing to 100 partitions, collectively they are going to write 10,000 small information. Let’s name this drawback partition amplification.

Resolution: use distribution-mode in write

The amplification drawback may very well be addressed at write time by setting the suitable write distribution mode in write properties. Insert distribution is managed by  “write.distribution-mode”  and is defaulted to none by default. Delete distribution is managed by “write.delete.distribution-mode” and is defaulted to hash, Replace distribution is managed by “write.replace.distribution-mode” and is defaulted to hash and merge distribution is managed by “write.merge.distribution-mode” and is defaulted to none.

The three write distribution modes which are obtainable in Iceberg as of this writing are none, hash, and vary. When your mode is none, no information shuffle happens. You need to use this mode solely once you don’t care in regards to the partition amplification drawback or when that every process in your job solely writes to a particular partition. 

When your mode is about to hash, your information is shuffled by utilizing the partition key to generate the hashcode so that every resultant process will solely write to a particular partition. When your distribution mode is vary, your information is distributed such that your information is ordered by the partition key or type key if the desk has a SortOrder.

Utilizing the hash or vary can get difficult as you are actually repartitioning the information primarily based on the variety of partitions your desk may need. This will trigger your Spark duties after the shuffle to be both too small or too giant. This drawback may be mitigated by enabling adaptive question execution in spark by setting “spark.sql.adaptive.enabled=true” (that is enabled by default from Spark 3.2). A number of configs are made obtainable in Spark to regulate the habits of adaptive question execution. Leaving the defaults as is until precisely what you might be doing might be the most suitable choice. 

Regardless that the partition amplification drawback may very well be mitigated by setting right write distribution mode applicable to your job, the resultant information might nonetheless be small simply because the Spark duties writing them may very well be small. Your job can’t write extra information than it has.

Resolution: rewrite information information

To handle the small information drawback and delete information drawback, Iceberg offers a characteristic to rewrite information information. This characteristic is at the moment obtainable solely with Spark. The remainder of the weblog will go into this in additional element. This characteristic can be utilized to compact and even broaden your information information, incorporate deletes from delete information equivalent to the information information which are being rewritten, present higher information ordering in order that extra information may very well be filtered immediately at learn time, and extra. It is without doubt one of the strongest instruments in your toolbox that Iceberg offers. 

RewriteDataFiles

Iceberg offers a rewrite information information process in Spark SQL.

See RewriteDatafiles JavaDoc to see all of the supported choices. 

Now let’s focus on what the technique choice means as a result of it is very important perceive to get extra out of the rewrite information information process. There are three technique choices obtainable. They’re Bin Pack, Type, and Z Order. Observe that when utilizing the Spark process the Z Order technique is invoked by merely setting the sort_order to “zorder(columns…).”

Technique choice

• Bin Pack
  • It’s the least expensive and quickest.
  • It combines information which are too small and combines them utilizing the bin packing strategy to scale back the variety of output information.
  • No information ordering is modified.
  • No information is shuffled.
• Type
  • Far more costly than Bin Pack.
  • Offers complete hierarchical ordering.
  • Learn queries solely profit if the columns used within the question are ordered. 
  • Requires information to be shuffled utilizing vary partitioning earlier than writing.
• Z Order
  • Most costly of the three choices.
  • The columns which are getting used ought to have some sort of intrinsic clusterability and nonetheless must have a ample quantity of information in every partition as a result of it solely helps in eliminating information from a learn scan, not from eliminating row teams. In the event that they do, then queries can prune a number of information throughout learn time.
  • It solely is sensible if multiple column is used within the Z order. If just one column is required then common type is the higher choice. 
  • See https://weblog.cloudera.com/speeding-up-queries-with-z-order/ to study extra about Z ordering. 

Commit conflicts

Iceberg makes use of optimistic concurrency management when committing new snapshots. So, after we use rewrite information information to replace our information a brand new snapshot is created. However earlier than that snapshot is dedicated, a verify is completed to see if there are any conflicts. If a battle happens all of the work achieved might doubtlessly be discarded. You will need to plan upkeep operations to reduce potential conflicts. Allow us to focus on a few of the sources of conflicts.

1. If solely inserts occurred between the beginning of rewrite and the commit try, then there aren’t any conflicts. It is because inserts end in new information information and the brand new information information may be added to the snapshot for the rewrite and the commit reattempted.
2. Each delete file is related to a number of information information. If a brand new delete file corresponding to an information file that’s being rewritten is added in future snapshot (B), then a battle happens as a result of the delete file is referencing an information file that’s already being rewritten. 

Battle mitigation

1. Should you can, strive pausing jobs that may write to your tables through the upkeep operations. Or at the least deletes shouldn’t be written to information which are being rewritten. 
2. Partition your desk in such a approach that every one new writes and deletes are written to a brand new partition. For example, in case your incoming information is partitioned by date, all of your new information can go right into a partition by date. You possibly can run rewrite operations on partitions with older dates.
3. Benefit from the filter choice within the rewrite information information spark motion to finest choose the information to be rewritten primarily based in your use case in order that no delete conflicts happen.
4. Enabling partial progress will assist save your work by committing teams of information previous to your complete rewrite finishing. Even when one of many file teams fails, different file teams might succeed.

Extra notes and references

Conclusion

Iceberg offers a number of options {that a} trendy information lake wants. With somewhat care, planning and understanding a little bit of Iceberg’s structure one can take most benefit of all of the superior options it offers. 

To strive a few of these Iceberg options your self you’ll be able to sign up for considered one of our subsequent dwell hands-on labs. 

You may also watch the webinar to study extra about Apache Iceberg and see the demo to study the newest capabilities.