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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions The F-MPJ Challenge: Solving Complex Problems on Hierachical Architectures with Java Sabela Ramos Garea

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions

The F-MPJ Challenge: Solving Complex Problems on Hierachical Architectures with Java

Sabela Ramos Garea Roberto Rey Expósito

Group of Computer Architecture University of A Coruña sramos@udc.es, rreye@udc.es

ComplexHPC Challenge 2011

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions

Outline

1 Introduction

2 Message Passing in Java with F-MPJ

3 Complex Application in Bioinformatic: ProtTest

4 Performance Evaluation

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Java for HPC

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Java for HPC

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Java for HPC

Java for High Performance Computing (HPC)

Features:

Network communication support. Multithreading support. Portable, platform independent. Object Oriented. Safe, robust, simple and with easy maintenance. Similar performance as native languages (C, Fortran).

Parallel/distributed programming in Java:

Concurrency Framework. Java Sockets. Java RMI. Message-Passing in Java (MPJ).

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

Message Passing in Java

Message-passing is the main HPC programming model.

Implementation approaches RMI. Wrapping a native library via JNI.

(e.g., MPI libraries: OpenMPI, MPICH).

Sockets. APIs implemented: PVM-like. mpiJava. MPJ. Others.

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

Pure Java Impl. Socket impl. High-speed network support API Java IO Java NIO Myrinet InfiniBand SCI mpiJava 1.2 JGF MPJ Other APIs MPJava

Jcluster
Parallel Java
mpiJava
P2P-MPI
MPJ Express
MPJ/Ibis
JMPI
F-MPJ
Sabela Ramos Garea, Roberto Rey Expósito

The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

F-MPJ Communication Devices

JVM native comms device layer

smpdev Java Threads

Shared Memory

MPJ Applications ibvdev TCP/IP JNI IBV

mxdev

Open−MX

InfiniBand Ethernet Myrinet/Ethernet

Java Sockets niodev/iodev F−MPJ Library

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

F-MPJ Communication Devices for Heterogeneity

Different sorts of devices:

Distributed memory.

Native communication layers: ibvdev, omxdev. Java sockets: iodev, niodev.

Shared memory.

Java threads: smpdev.

Hybrid shared-distributed memory.

In development. It combines a distributed memory device with smpdev.

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

Optimizing performance:

No buffering layer for primitive types. Multi-core aware collective operations library. Configurable algorithms depending on the message size and the number of processors.

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Message Passing in Java F-MPJ: Fast MPJ

Multi-core aware algorithms for collective operations:

Operation Algorithms Barrier BT, Gather+Bcast, BTe, Gather+Bcast Optimized Bcast MST, NBFT, BFT Scatter/v MST, NBFT Gather/v MST, NBFT, NB1FT, BFT Allgather/v NBFT, NBBDE, BBKT, NBBKT, BTe, Gather + Bcast Alltoall/v NBFT, NB1FT, NB2FT, BFT Reduce MST, NBFT, BFT Allreduce NBFT, BBDE, NBBDE, BTe, Reduce + Bcast Reduce-scatter BBDE, NBBDE, BBKT, NBBKT, Reduce + Scatter Scan NBFT, OneToOne

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

ProtTest

One of the most popular tools for selecting models of protein evolution. Almost 4,000 registered users. Over 700 citations. Written in Java. Intensive in computational needs. ProtTest 3 designed to take advantage of parallel processing.

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

Shared Memory Implementation

Java concurrence API Implementation of a thread pool. Dynamic task distribution over the pool.

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

Distributed Memory Implementation

Message Passing in Java Allow both distributions (static and dynamic). Includes a distributor process with a negligible workload.

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions ProtTest Parallel Strategies

Hybrid Shared/Distributed Memory Implementation

MPJ + OpenMP Scalability is limited by the task-based high level parallelization. Solution:

Two-level parallelism. Combination of message passing with multithread computation of likelihood. Implementation of a parallel version of PhyML using OpenMP .

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Experimental Configuration:

Pluton: Departmental cluster (16 nodes) 2xIntel Xeon 5520 Quad-core CPU (8 cores with hyper-threading per node) 8 GB RAM InfiniBand Network 16 Gbps (QLogic QLE7240 DDR) Linux, Sun JDK 1.6, F-MPJ, MPJ Express, OpenMPI, MVAPICH DAS-4 VU cluster (74 nodes) 2xIntel Xeon 5620 Quad-core CPU (8 cores with hyper-threading per node) 24 GB RAM InfiniBand Network 32 Gbps (Mellanox MT26428 QDR) Linux, OpenJDK 1.6, F-MPJ, MPJ Express, IntelMPI Special shared memory node (node075): 4xAMD Opteron 6172 12-core (48 cores) and 128 GB RAM

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Point-to-Point Performance

Message size (bytes)

Point-to-point Performance on InfiniBand (Pluton)

10 20 30 40 50 60 70 80 4 16 64 256 1K Latency (µs) 1K 4K 16K 64K 256K 1M 2M 4M 1 2 3 4 5 6 7 8 9 10 11 Bandwidth (Gbps) F-MPJ (ibvdev) - IBV MPJE (niodev) - IPoIB MVAPICH v1.2.0- IBV OpenMPI v1.3.3 - IBV

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Point-to-Point Performance

Message size (bytes)

Point-to-point Performance on InfiniBand (DAS-4)

5 10 15 20 25 30 35 40 45 50 55 60 65 4 16 64 256 1K Latency (µs) 1K 4K 16K 64K 256K 1M 2M 4M 2 4 6 8 10 12 14 16 18 20 22 24 26 28 Bandwidth (Gbps) F-MPJ (ibvdev) - IBV MPJE (niodev) - IPoIB IntelMPI 4 - IBV

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Point-to-Point Performance

Message size (bytes)

Point-to-point Performance on Shared Memory (Pluton)

2 4 6 8 10 12 14 16 18 20 22 24 26 4 16 64 256 1K Latency (µs) 1K 4K 16K 64K 256K 1M 2M 4M 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 Bandwidth (Gbps) F-MPJ (ibvdev) F-MPJ (smpdev) MPJE (smpdev) MVAPICH v1.2.0 OpenMPI v1.3.3

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Point-to-Point Performance

Message size (bytes)

Point-to-point Performance on Shared Memory (DAS-4)

5 10 15 20 25 30 35 40 45 4 16 64 256 1K Latency (µs) 1K 4K 16K 64K 256K 1M 2M 4M 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 Bandwidth (Gbps) F-MPJ (ibvdev) F-MPJ (smpdev) MPJE (smpdev) IntelMPI 4

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Collective Operations Performance

20 40 60 80 100 120 140 160 180 200 220 240 260 1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M

Aggregated Bandwidth (Gbps) Message size (bytes)

Broadcast Performance (128 Processes)

F−MPJ (ibvdev) − IBV MPJE (niodev) − IPoIB MVAPICH − IBV OpenMPI − IBV

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Collective Operations Performance

200 400 600 800 1000 1200 1400 1600 1800 1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M

Aggregated Bandwidth (Gbps) Message size (bytes)

Broadcast Performance on DAS−4 (512 Processes)

F−MPJ (ibvdev) − IBV Intel MPI 4 − IBV

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Collective Operations Performance

20 40 60 80 100 120 140 160 180 200 1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M

Aggregated Bandwidth (Gbps) Message size (bytes)

Broadcast Performance (8 Threads)

F−MPJ (smpdev) MPJE (smpdev) MVAPICH OpenMPI

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

Collective Operations Performance

10 20 30 40 50 60 70 80 1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M

Aggregated Bandwidth (Gbps) Message size (bytes)

Broadcast Performance on DAS−4 (48 Threads)

F−MPJ (smpdev) MPJE (smpdev) IntelMPI 4

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

ProtTest 3 Performance

5 10 15 20 25 30 35 40 45 50 1 2 4 8 16 32 64 128

Speedup Number of Processes

ProtTest 3 Distributed Memory Scalability on Pluton

F−MPJ (ibvdev) F−MPJ (ibvdev) + OpenMP

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

ProtTest 3 Performance

4 8 12 16 20 24 28 32 36 40 1 2 4 8 16 32 64 128

Speedup Number of Processes

ProtTest 3 Distributed Memory Scalability on DAS−4

F−MPJ (ibvdev) − IBV F−MPJ (ibvdev) + OpenMP − IBV

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

ProtTest 3 Performance

1 2 3 4 5 6 7 8 9 10 11 1 2 4 8 16

Speedup Number of Threads

ProtTest 3 Shared Memory Scalability on Pluton

F−MPJ (smpdev) ProtTest 3 (threads)

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Experimental Configuration F-MPJ Performance ProtTest 3 Performance

ProtTest 3 Performance

2 4 6 8 10 12 14 16 18 20 1 2 4 8 16 32 48

Speedup Number of Threads

ProtTest 3 Shared Memory Scalability on DAS−4

F−MPJ (smpdev) ProtTest 3 (threads) F−MPJ (smpdev) + OpenMP

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Summary Questions

1 Introduction Java for HPC

2 Message Passing in Java with F-MPJ Message Passing in Java F-MPJ: Fast MPJ

3 Complex Application in Bioinformatic: ProtTest ProtTest Parallel Strategies

4 Performance Evaluation Experimental Configuration F-MPJ Performance ProtTest 3 Performance

5 Conclusions

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Summary Questions

Summary

This work presents our current research efforts for HPC in Java with F-MPJ. F-MPJ has been applied to a real complex problem with large scale needs for computational resources. Taking advantage of hierarchical architectures: shared memory, distributed memory, hybrid shared/distributed memory. Other applications that benefit from the use of F-MPJ: ESA Gaia project, jGadget, financial applications, petro-seismic JavaSeis, ...

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge

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Introduction Message Passing in Java with F-MPJ Complex Application in Bioinformatic: ProtTest Performance Evaluation Conclusions Summary Questions

THE F-MPJ CHALLENGE: SOLVING COMPLEX PROBLEMS ON HIERACHICAL ARCHITECTURES WITH JAVA Sabela Ramos Garea Roberto Rey Expósito University of A Coruña

Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge