IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
The F-MPJ Challenge: Solving ComplexProblems on Hierachical Architectures with
Java
Sabela Ramos GareaRoberto Rey Expósito
Group of Computer ArchitectureUniversity of A Coruña
[email protected], [email protected]
ComplexHPC Challenge 2011Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance 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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Java for HPC
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Java for HPC
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance 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 witheasy maintenance.
Similar performance as nativelanguages (C, Fortran).
Parallel/distributed programming inJava:
Concurrency Framework.
Java Sockets.
Java RMI.
Message-Passing in Java (MPJ).
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-MPJ: Fast MPJ
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-MPJ: Fast MPJ
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-MPJ: Fast MPJ
Pur
eJa
vaIm
pl. Socket
impl.High-speednetworksupport
API
Java
IO
Java
NIO
Myr
inet
Infin
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I
mpi
Java
1.2
JGF
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MPJava X X X
Jcluster X X X
Parallel Java X X X
mpiJava X X X X
P2P-MPI X X X X
MPJ Express X X X X
MPJ/Ibis X X X X
JMPI X X X
F-MPJ X X X X X X X
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-MPJ: Fast MPJ
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-MPJ: Fast MPJ
F-MPJ Communication Devices
JVM
native comms
device layer smpdev
Java Threads
Shared Memory
MPJ Applications
ibvdev
TCP/IP
JNI
IBV
omxdev
Open−MX
InfiniBand EthernetMyrinet/Ethernet
Java Sockets
niodev/iodev
F−MPJ Library
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-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 devicewith smpdev.
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-MPJ: Fast MPJ
Optimizing performance:
No buffering layer for primitive types.
Multi-core aware collective operations library.
Configurable algorithms depending on the message sizeand the number of processors.
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Message Passing in JavaF-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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel Strategies
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel Strategies
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel Strategies
ProtTest
One of the most popular tools for selectingmodels of protein evolution.
Almost 4,000 registered users.Over 700 citations.
Written in Java.
Intensive in computational needs.
ProtTest 3 designed to take advantage ofparallel processing.
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel Strategies
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel 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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel 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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
ProtTestParallel 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 oflikelihood.Implementation of a parallel version of PhyML using OpenMP.
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Point-to-Point Performance
Message size (bytes)
Point-to-point Performance on InfiniBand (Pluton)
0
10
20
30
40
50
60
70
80
4 16 64 256 1K
Late
ncy
(µs
)
1K 4K 16K 64K 256K 1M 2M 4M 0
1
2
3
4
5
6
7
8
9
10
11
Ban
dwid
th (
Gbp
s)
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Point-to-Point Performance
Message size (bytes)
Point-to-point Performance on InfiniBand (DAS-4)
0
5
10
15
20
25
30
35
40
45
50
55
60
65
4 16 64 256 1K
Late
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(µs
)
1K 4K 16K 64K 256K 1M 2M 4M 0
2
4
6
8
10
12
14
16
18
20
22
24
26
28
Ban
dwid
th (
Gbp
s)
F-MPJ (ibvdev) - IBV MPJE (niodev) - IPoIB IntelMPI 4 - IBV
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Point-to-Point Performance
Message size (bytes)
Point-to-point Performance on Shared Memory (Pluton)
0
2
4
6
8
10
12
14
16
18
20
22
24
26
4 16 64 256 1K
Late
ncy
(µs
)
1K 4K 16K 64K 256K 1M 2M 4M 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
Ban
dwid
th (
Gbp
s)
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Point-to-Point Performance
Message size (bytes)
Point-to-point Performance on Shared Memory (DAS-4)
0
5
10
15
20
25
30
35
40
45
4 16 64 256 1K
Late
ncy
(µs
)
1K 4K 16K 64K 256K 1M 2M 4M 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30
Ban
dwid
th (
Gbp
s)
F-MPJ (ibvdev) F-MPJ (smpdev) MPJE (smpdev) IntelMPI 4
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Collective Operations Performance
0
20
40
60
80
100
120
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240
260
1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M
Agg
rega
ted
Ban
dwid
th (
Gbp
s)
Message size (bytes)
Broadcast Performance (128 Processes)
F−MPJ (ibvdev) − IBVMPJE (niodev) − IPoIBMVAPICH − IBVOpenMPI − IBV
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Collective Operations Performance
0
200
400
600
800
1000
1200
1400
1600
1800
1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M
Agg
rega
ted
Ban
dwid
th (
Gbp
s)
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Collective Operations Performance
0
20
40
60
80
100
120
140
160
180
200
1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M
Agg
rega
ted
Ban
dwid
th (
Gbp
s)
Message size (bytes)
Broadcast Performance (8 Threads)
F−MPJ (smpdev) MPJE (smpdev) MVAPICHOpenMPI
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
Collective Operations Performance
0
10
20
30
40
50
60
70
80
1K 2K 4K 8K 16K 32K 64K 128K 256K 512K 1M 2M 4M
Agg
rega
ted
Ban
dwid
th (
Gbp
s)
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
ProtTest 3 Performance
0
5
10
15
20
25
30
35
40
45
50
1 2 4 8 16 32 64 128
Spe
edup
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
ProtTest 3 Performance
0
4
8
12
16
20
24
28
32
36
40
1 2 4 8 16 32 64 128
Spe
edup
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
ProtTest 3 Performance
0
1
2
3
4
5
6
7
8
9
10
11
1 2 4 8 16
Spe
edup
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
Experimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
ProtTest 3 Performance
0
2
4
6
8
10
12
14
16
18
20
1 2 4 8 16 32 48
Spe
edup
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
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
SummaryQuestions
1 IntroductionJava for HPC
2 Message Passing in Java with F-MPJMessage Passing in JavaF-MPJ: Fast MPJ
3 Complex Application in Bioinformatic: ProtTestProtTestParallel Strategies
4 Performance EvaluationExperimental ConfigurationF-MPJ PerformanceProtTest 3 Performance
5 Conclusions
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
SummaryQuestions
Summary
This work presents our current research efforts for HPC inJava with F-MPJ.
F-MPJ has been applied to a real complex problem withlarge scale needs for computational resources.
Taking advantage of hierarchical architectures: sharedmemory, distributed memory, hybrid shared/distributedmemory.
Other applications that benefit from the use of F-MPJ: ESAGaia project, jGadget, financial applications, petro-seismicJavaSeis, ...
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge
IntroductionMessage Passing in Java with F-MPJ
Complex Application in Bioinformatic: ProtTestPerformance Evaluation
Conclusions
SummaryQuestions
THE F-MPJ CHALLENGE: SOLVING COMPLEX PROBLEMS ON HIERACHICAL
ARCHITECTURES WITH JAVA
Sabela Ramos GareaRoberto Rey Expósito
University of A Coruña
Sabela Ramos Garea, Roberto Rey Expósito The F-MPJ Challenge