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Deep Learning Pipelines for High Energy Physics using Apache Spark with Distributed Keras on AZ
You will learn how CERN has implemented an Apache Spark-based data pipeline to support deep learning research work in High Energy Physics (HEP). HEP is a data-intensive domain. For example, the amount of data flowing through the online systems at LHC experiments is currently of the order of 1 PB/s, with particle collision events happening every 25 ns. Filtering is applied before storing data for later processing.
Improvements in the accuracy of the online event filtering system are key to optimize usage and cost of compute and storage resources. A novel prototype of event filtering system based on a classifier trained using deep neural networks has recently been proposed. This presentation covers how we implemented the data pipeline to train the neural network classifier using solutions from the Apache Spark and Big Data ecosystem, integrated with tools, software, and platforms familiar to scientists and data engineers at CERN. Data preparation and feature engineering make use of PySpark, Spark SQL and Python code run via Jupyter notebooks.
We will discuss key integrations and libraries that make Apache Spark able to ingest data stored using HEP data format (ROOT) and the integration with CERN storage and compute systems. You will learn about the neural network models used, defined using the Keras API, and how the models have been trained in a distributed fashion on Spark clusters using BigDL and Analytics Zoo. We will discuss the implementation and results of the distributed training, as well as the lessons learned.
1 .WIFI SSID:Spark+AISummit | Password: UnifiedDataAnalytics
2 .Deep Learning Pipelines for High Energy Physics using Apache Spark with Distributed Keras and Analytics Zoo Luca Canali, CERN #UnifiedDataAnalytics #SparkAISummit
3 .About Luca • Data Engineer at CERN – Hadoop and Spark service, database services – 19+ years of experience with data engineering • Sharing and community – Blog, notes, tools, contributions to Apache Spark @LucaCanaliDB – http://cern.ch/canali #UnifiedDataAnalytics #SparkAISummit 3
4 . CMS CERN: Particle Accelerators (LHC) High Energy Physics Experiments ALICE LHCb ATLAS
5 .Experimental High Energy Physics is Data Intensive Particle Collisions Physics Discoveries Large Scale Computing https://twiki.cern.ch/twiki/pub/CMSPublic/Hig13002TWiki/HZZ4l_animated.gif5 And https://iopscience.iop.org/article/10.1088/1742-6596/455/1/012027
6 .Key Data Processing Challenge • Proton-proton collisions at LHC experiments happen at 40MHz. • Hundreds of TB/s of electrical signals that allow physicists to investigate particle collision events. • Storage, limited by bandwidth • Currently, only 1 every ~40K events stored to disk (~10 GB/s). 2018: 5 collisions/beam cross 2026: 400 collisions/beam cross Current LHC Future: High-Luminosity LHC upgrade
7 .Data Flow at LHC Experiments 40 million 100,000 1,000 collisions selections selections per PB/s per TB/s per GB/s second second second (Raw) (L1) (L2) This can generate up to a petabyte of raw data per second Reduced to GB/s by filtering in real time Key is how to select potentially interesting events (trigger systems).
8 .R&D – Data Pipelines • Improve the quality of filtering systems • Reduce false positive rate • From rule-based algorithms to classifiers based on Deep Learning • Advanced analytics at the edge • Avoid wasting resources in offline computing • Reduction of operational costs
9 .Particle Classifiers Using Neural Networks • R&D to improve the quality of filtering systems • Develop a “Deep Learning classifier” to be used by the filtering system • Goal: Identify events of interest for physics and reduce false positives • False positives have a cost, as wasted storage bandwidth and computing • “Topology classification with deep learning to improve real-time event selection at the LHC”, Nguyen et al. Comput.Softw.Big Sci. 3 (2019) no.1, 12 3 W+j 2 1% 36% Particle Classifier QCD 1 63% t-t̅
10 .Deep Learning Pipeline for Physics Data Data Feature Model Training Ingestion Preparation Development Read physics Prepare 1. Specify model Train the best data and input for topology model feature Deep 2. Tune model engineering Learning topology on network small dataset Technology: the pipeline uses Apache Spark + Analytics Zoo and TensorFlow/Keras. Code on Python Notebooks.
11 .Analytics Platform at CERN Integrating new “Big Data” components with existing infrastructure: • Software distribution • Data platforms Experiments storage HDFS HEP software Personal storage
12 . Text Code Monitoring Visualizations
13 .Hadoop and Spark Clusters at CERN • Clusters: • YARN/Hadoop • Spark on Kubernetes • Hardware: Intel based servers, continuous refresh and capacity expansion Accelerator logging Hadoop - YARN - 30 nodes (part of LHC (Cores - 1200, Mem - 13 TB, Storage – 7.5 PB) infrastructure) General Purpose Hadoop - YARN, 65 nodes (Cores – 2.2k, Mem – 20 TB, Storage – 12.5 PB) Cloud containers Kubernetes on Openstack VMs, Cores - 250, Mem – 2 TB Storage: remote HDFS or EOS (for physics data)
14 . Extending Spark to Read Physics Data • Physics data • Currently: >300 PBs of Physics data, increasing ~90 PB/year • Stored in the CERN EOS storage system in ROOT Format and accessible via XRootD protocol • Integration with Spark ecosystem • Hadoop-XRootD connector, HDFS compatible filesystem • Spark Datasource for ROOT format C++ Java https://github.com/cerndb/hadoop-xrootd EOS Hadoop https://github.com/diana-hep/spark-root Storage HDFS Service XRootD Hadoop- API JNI XRootD Client Connector
15 .Labeled Data for Training and Test ● Simulated events ● Software simulators are used to generate events and calculate the detector response ● Raw data contains arrays of simulated particles and their properties, stored in ROOT format ● 54 million events
16 .Step 1: Data Ingestion • Read input files: 4.5 TB from custom (ROOT) format • Feature engineering • Python and PySpark code, using Jupyter notebooks • Write output in Parquet format Input: • 54 M events ~4.5 TB • Physics data storage (EOS) • Physics data Output: format (ROOT) • 25 M events • 950 GB in Parquet format • Target storage (HDFS)
17 .Feature Engineering ● Filtering ● Multiple filters, keep only events of interest ● Example: “events with one electrons or muon with Pt > 23 Gev” • Prepare “Low Level Features” • Every event is associated to a matrix of particles and features (801x19) • High Level Features (HLF) • Additional 14 features are computed from low level particle features • Calculated based on domain-specific knowledge
18 . Step 2: Feature Preparation Features are converted to formats suitable for training • One Hot Encoding of categories • MinMax scaler for High Level Features • Sorting Low Level Features: prepare input for the sequence classifier, using a metric based on physics. This use a Python UDF. • Undersampling: use the same number of events for each of the three categories Result • 3.6 Million events, 317 GB • Shuffled and split into training and test datasets • Code: in a Jupyter notebook using PySpark with Spark SQL and ML
19 .Performance and Lessons Learned • Data preparation is CPU bound • Heavy serialization-deserialization due to Python UDF • Ran using 400 cores: data ingestion took ~3 hours, • It can be optimized, but is it worth it ? • Use Spark SQL, Scala instead of Python UDF • Optimization: replacing parts of Python UDF code with Spark SQL and higher order functions: run time from 3 hours to 2 hours
20 .Neural Network Models and 1. Fully connected feed-forward deep neural network • Trained using High Level Features (~1 GB of data) 2. Neural network based on Gated Recurrent Unit (GRU) • Trained using Low Level Features (~ 300 GB of Complexity + data) Classifier Performance 3. Inclusive classifier model • Combination of (1) + (2)
21 .Hyper-Parameter Tuning– DNN • Hyper-parameter tuning of the DNN model • Trained with a subset of the data (cached in memory) • Parallelized with Spark, using spark_sklearn.grid_search • And scikit-learn + keras: tensorflow.keras.wrappers.scikit_learn
22 .Deep Learning at Scale with Spark • Investigations and constraints for our exercise • How to run deep learning in a Spark data pipeline? • Neural network models written using Keras API • Deploy on Hadoop and/or Kubernetes clusters (CPU clusters) • Distributed deep learning • GRU-based model is complex • Slow to train on a single commodity (CPU) server
23 .Spark, Analytics Zoo and BigDL • Apache Spark • Leading tool and API for data processing at scale • Analytics Zoo is a platform for unified analytics and AI • Runs on Apache Spark leveraging BigDL / Tensorflow • For service developers: integration with infrastructure (hardware, data access, operations) • For users: Keras APIs to run user models, integration with Spark data structures and pipelines • BigDL is an open source distributed deep learning framework for Apache Spark
24 .BigDL Run as Standard Spark Programs Standard Spark jobs • No changes to the Spark or Hadoop clusters needed Iterative • Each iteration of the training runs as a Spark job Data parallel • Each Spark task runs the same model on a subset of the data (batch) BigDL Program Worker Worker Worker Spark Spark BigDL lib DL App on Driver Executor Task Intel MKL (JVM) Spark BigDL Spark Standard Program library jobs Spark jobs Worker Worker Worker Spark Spark BigDL lib Intel MKL Executor Task (JVM) Source: Intel BigDL Team
25 . BigDL Parameter Synchronization Source: https://github.com/intel-analytics/BigDL/blob/master/docs/docs/whitepaper.md
26 .Model Development – DNN for HLF • Model is instantiated using the Keras- compatible API provided by Analytics Zoo
27 .Model Development – GRU + HLF A more complex network topology, combining a GRU of Low Level Feature + a DNN of High Level Features
28 .Distributed Training Instantiate the estimator using Analytics Zoo / BigDL The actual training is distributed to Spark executors Storing the model for later use
29 .Performance and Scalability of Analytics Zoo/BigDL Analytics Zoo/BigDL on Spark scales up in the ranges tested Inclusive classifier model DNN model, HLF features