strategy of the code - ixpug · ofs1 xiamen marine environment forecasting station, ofs1 unesco/ioc...
TRANSCRIPT
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HPC Asia 2019
Guangzhou, Jan 14, 2019
Strategy of the code modernization optimization for ocean numerical model: A case study of MASNUM wave model
Zhenya Song*, +
Xiaodan Yang *, +
* First Institute of Oceanography (FIO), State Oceanic Administrative (SOA), China+ Intel® Parallel Computing Center at FIO
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Outline
❖ Brief Introduction of Intel® PCC at FIO
❖ Background
❖ Optimization strategy
❖ Future work
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Introduction of FIO
❖ MNR Headquarters, Beijing
❖ 4 Research Institute
- FIO, Qingdao
- SIO, Hangzhou
- TIO, Xiamen
- 4IO, Beihai (being built)
❖ 8 Operational Centers
- NMEFC, NMEMC, NMDIS…
❖ 3 Branches
- North Sea, East Sea, South Sea
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Introduction of FIO
Mission
❖ Basic and applied research in oceanography, marine science and
technology.
❖ Technical support and research service to the development of high-
tech industries, marine resources management, marine environment
protection, public service, marine safety, etc.
❖ Major research priorities: Marine Geology/Geophysics, Physical
Oceanography, Sea-Air Interaction, Marine Ecology, Marine
Engineering, Remote Sensing, Marine Policy, etc.
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Introduction of FIO
Structure
MASNUM
HPCC
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Introduction of FIOMASNUM Major Research Fields
❖ Oceanography dynamics in the Chinese offshore area, polar region and global oceans
- Formation and variation mechanisms of major marine phenomena and circulation systems in the Chinese offshore area, polar region and global oceans
- General ocean circulation, mass transport and its ecological effect
- Land-sea-air interaction and climate changes
❖ Ocean survey and experiment techniques
- Sound, light and electricity measurement techniques
- Wave tank and physical model experiments
- Survey technique application and data process in oceanography
❖ Ocean numerical modeling
- Numerical computing scheme and data analysis
- Wind-wave-current interaction mechanism and coupled numerical model
- Application systems including database and data assimilation technique
❖ Marine information system
- Database, visualization and system integration techniques
- Application information systems in climate forecast, disaster prediction, engineering oceanography and military security
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Intel® PCC at FIOLarge-Scale and Highly-Effective Numerical Simulation of
Marine Environment with Global Surface Waves Model
❖ Optimize the MASNUM wave model
- Computing performance——Better Scalability and simulation faster
- Simulation ability——More accuracy by using deep learning
❖ Release the code to the ocean community worldwide
❖ Publish papers in SCI/EI journal
❖ Training course, and workshop of best known method sharing
Fangli Qiao Zhenya Song Xiaomeng Huang
Zhe Wang Haifeng LvYanguo
YangShan Zhou
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Intel® PCC at FIOLarge-Scale and Highly-Effective Numerical Simulation of
Marine Environment with Global Surface Waves Model
❖ Project period
• July 1, 2018——June 30, 2020
❖ Unveiling ceremony on July 28, 2018, Qingdao
❖ First one in Chinese ocean fields
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Outline
❖ Brief Introduction of Intel® PCC at FIO
❖ Background
❖ Optimization strategy
❖ Future work
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Ocean surface wave model
Ocean surface wave
❖ Occur in the ocean surface driven by winds
❖ Wave height range from several centimeters to tens meters
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Ocean surface wave model
Importance of ocean surface wave
❖ Ocean surface wave is important for navigation.
❖ Ocean surface wave is important for ocean engineering
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Ocean surface wave model
❖ Three methods: Theoretical research, Lab experiments and Observation, and Numerical simulation
❖ Model is the key tool for forecasting and prediction
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Ocean surface wave model
History of ocean surface wave model
❖ First ocean surface wave forecasting during World War II (1944)
❖ Ocean surface wave model is the key tool to wave forecasting
❖ Accurately ocean surface wave forecasting is still a challenge
World War II
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Ocean surface wave model
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Ocean surface wave model
Evolution of MASNUM wave model
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Ocean surface wave modelMilestone 1: Irregular quasi-rectangular domain decomposition
(2014)
Problem: In order to keep load balance, we should eliminate the land points.
About 30% land points in global domain
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Ocean surface wave modelMilestone 1: Irregular quasi-rectangular domain decomposition
(2014)
Comparing with the method of space filling curve, we keep the quasi-rectangular shape to simplify the implementation
of communication and maintain good data locality.
An interesting mathematical game : Transforming a 2D plane into an 1D line.
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Ocean surface wave modelMilestone 1: Irregular quasi-rectangular domain decomposition
(2014)
TIANHE-1A (National SuperComputer Center in Tianjin)
CPU 2* Intel Xeon [email protected] + Tesla M2050
Memory 24 GB/node
OS RedHat
Fortran/C Compiler Intel Compiler v12
MPI
Network 40 Gbps
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Ocean surface wave modelMilestone 1: Irregular quasi-rectangular domain decomposition
(2014)
Upper: Computation time (minutes); Lower: Speed-up
Number of processesCo
mp
uta
tio
n t
ime (
s)
Linear speed-up
Sp
eed
-up
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Ocean surface wave modelMilestone 2: Master-slave cooperative computing workflow(2016)
Sunway Taihulight Supercomputer
SW26010 processors
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Ocean surface wave modelMilestone 2: Master-slave cooperative computing workflow(2016)
✤Cooperation: overlapping of communication and computing; data prefetching
✤Synchronization : highly efficient synchronization among CPEs
✤Memory utilization: fully applied the local memory in CPEs (64KB)
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Ocean surface wave modelMilestone 2: Master-slave cooperative computing workflow(2016)
Strong Scalability Weak Scalability
Peak Performance Efficiency
10,649
,600
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Ocean surface wave modelMilestone 2: Master-slave cooperative computing workflow(2016)
EfficiencyPeak Performance
Weak ScalabilityStrong Scalability 2016 Gordon
Bell Finalist
10,649
,600
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Operational forecasting system
OFS for ocean: Global Ocean Environment Forecasting Systems
❖ 1st generation OFS
- POM + MASNUM
- Assimilation: Nudging
- HR with 50 km
๏ 2nd generation OFS
- MOM + SIS + MASNUM
- Assimilation: Ensemble adjust Kalman Filter
- HR with 10 km
National Marine
Environment
Forecasting Center,
OFS2
East China Sea
Marine Environment
Forecasting Center,
OFS1
Xiamen Marine
Environment
Forecasting Station,
OFS1
UNESCO/IOC Ocean
Forecasting
demonstration
System in the
Southeast Asian
Sea, OFS1
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Outline
❖ Brief Introduction of Intel® PCC at FIO
❖ Background
❖ Optimization strategy
❖ Future work
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Optimization strategy
Based on Code Modernization Optimization
Optimization Methodology
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Optimization strategy
Based on Code Modernization Optimization
Optimization Methodology
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Optimization strategy
Optimization of MASNUM surface wave model on Xeon
Testing Environment
Xeon
CPU Intel Xeon E5 2699 v3, 18 cores
amount 2 way in single node
Nodes 7 nodes, 252 cores in total
Frequency 2.3 GHz
Memory 128 GB
OS RHEL 6.5
Compiler Intel Compiler 16.0
MPI Intel MPI 5.1.1
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Optimization strategy
Based on Code Modernization Optimization
Optimization Methodology
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Optimization strategy
Step 1.1: Analysis Load-balance with ITAC
Load-balance is good!
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Optimization strategyStep 1.2: Analysis Hotspots on Single node with Intel Vtune
implsch is the hotspot!
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Optimization strategy
Based on Code Modernization Optimization
Optimization Methodology
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Optimization strategyStep 2.1: Best Compiler Option before optimized on Single Node
Default
-O3 -xHost -align array32byte -no-prec-div
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Optimization strategy
Step 2.2: Serial and Scalar Optimization
Reduce the redundant computations
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Optimization strategy
Step 2.2: Serial and Scalar Optimization
Reduce the redundant computations
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Optimization strategy
Step 2.3: Vectorization Optimization
Analyze by using compiler option “-qopt-report=5”
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Optimization strategy
Step 2.3: Vectorization Optimization
Exchange the Loop sequence
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Optimization strategy
Step 2.3: Vectorization Optimization
Remove the dependence
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Optimization strategy
Step 2.3: Vectorization Optimization
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Optimization strategy
Step 2.4: Fine-Grained Parallelism
use Open MP “!$OMP PARALLELDO” for parallelization
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Optimization strategy
Step 2.4: Fine-Grained Parallism
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Optimization strategy
Step 2.4: Fine-Grained Parallism
Time (s)
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Optimization strategy
Based on Code Modernization Optimization
Optimization Methodology
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Optimization strategy
Step 3: Optimization on multi-nodes
Scalability before and after optimizationExecution times before and after
optimization
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Outline
❖ Brief Introduction of Intel® PCC at FIO
❖ Background
❖ Optimization strategy
❖ Future work
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Future work
❖ Optimize on the new Intel Architecture (wider
vector length)
❖ Optimize the MASNUM surface wave model on
large-scale cluster
❖ Try to apply the optimization strategy to other
ocean and atmosphere models
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Coupled models by incorporated ocean surface wave model
Importance of ocean surface wave
❖ Ocean surface wave is also important in the ocean and climate system.
❖ Coupled with ocean surface wave model is a way to accurate simulating and forecasting for ocean and climate
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Intel® PCC at FIO
State-of-the-art of wave forecasting
✤ 7-days forecasting within 90 minutes✤ Resolution finer, simulation ability better ✤ Fine-resolution is still a challenge
T1: Model computing performance——simulating faster
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Intel® PCC at FIO
✤ Model tuning: a hard work, depending on modeler empirically ✤ Parameter optimization: by using deep learning
T2: Model simulation ability——more accurate
Parameterization: unsolved
physical process due to
resolution