This repository has been forked and obsoleted by https://github.com/bio-guoda/idigbio-spark. Please continue development there.
Links iDigBio records to GenBank, Global Names and possibly other open bioinformatics resources. The purpose of this project is to link specimen records to external systems like GenBank and Global Names at scale by using Apache's Spark a distributed data processing tool.
- Apache Spark v1.3.1 installed at
$SPARK_HOME - iDigBio Archive - Download iDigBio DarwinCore Archive unpack
$SPARK_DATA - Java SDK 1.7+
- Scala Build Tool (Sbt) v0.13.8
- git
Clone this repository using git clone [email protected]:idigbio-api-hackathon/idigbio-spark.git
cd [idigbio-spark directory]
# build the idigbio-spark job jar
sbt assembly
# link w/ genbank
./submit-job genbank
# link w/ global names
./submit-job globalnames$ ls $SPARK_HOME
CHANGES.txt README.md conf examples sbin
LICENSE RELEASE data lib
NOTICE bin ec2 python
$ ls $SPARK_DATA/idigbio
meta.xml
multimedia.txt
occurrence.txt
$ sh submit-job.sh genbank
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
15/06/06 10:51:26 INFO SparkContext: Running Spark version 1.3.1
15/06/06 10:51:41 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
...
$ cd $SPARK_DATA/idigbio/occurrence.txt.links
$ ls | head
_SUCCESS
part-00000
part-00001
part-00002
part-00003
part-00004
part-00005
part-00006
part-00007
part-00008
the resulting link table looks something like:
00f8efa0-75ee-45c1-a88d-8a853705c6dd,gn:813583ad-c364-5c15-b01a-43eaa1446fee
004ba454-7cce-4f6d-8a22-bf4aa34981df,gn:dc74c890-d31c-5fb4-aaad-466bf14bb215
00350756-ba40-4fda-8db3-ade4b470160c,gn:e3992c38-df0c-5be6-839c-d84c8edabfd1
where the first column is the idigbio record UUID and the second column is the global name hash associated with the taxonomic name of the specimen.
two systems where used:
Macbook Model 13-inch, Aluminum, Late 2008 Processor 2.4 GHz Intel Core 2 Duo Memory 8 GB 1067 MHz DDR3 Software OS X 10.9.5 (13F1077)
an iDigBio Server Model ? Processor 32 Core (?) Memory 128 GB (?) Software Ubuntu
| #records | mac duration | server duration |
|---|---|---|
| 100k | 10s | 4s |
| 1M | 83s | 11s |
| 15M | 21m | 2m |
For all runs CPU utilization was at ~80% for both mac and server systems. This means that the spark job kept 2 CPUs busy on the mac system and about 32 CPUs busy on the server system.
The spark job created to process large amounts of iDigBio was able to scale from a laptop to a powerful 32 core server without any modifications to the job. This shows the benefits of Apache's Spark - after "sparkizing" the processing algorithms, large amounts of data can be processed on small (laptop) and large (server) servers, where spark figures out how to optimially use the available resources.
Spark jobs can be implemented in Scala, Java and Python. An early attempt to implement the job in Python caused the process to crash due to an out of memory issue. A later implementation in Scala was stable on both small (macbook) and large (32 core server) system. This seems to suggest that Python support might require some more configuration tweaking to get the jobs to complete reliably, while the Scala implementation work without any configuration changes.
These preliminary results seem to suggest that Apache Spark is suitable for stable and performant processing of large (~GB) datasets like iDigBio. Our implementation algorithms that link iDigBio to Global Names and GenBank will hopefully help make it easier to discover iDigBio specimen records and their associations with other web-connected resources.