RFD tNavigator

Performance Benchmarking and Profiling

May 2016
Note
• The following research was performed under the HPC Advisory Council activities
– Participating vendors: Intel, Dell, Mellanox
– Compute resource - HPC Advisory Council Cluster Center
• The following was done to provide best practices
– tNavigator performance overview
– Understanding tNavigator communication patterns
– Ways to increase tNavigator productivity
– MPI libraries comparisons
• For more info please refer to
– http://www.dell.com
– http://www.intel.com
– http://www.mellanox.com
– http://www.rfdyn.com/technology/

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RFD tNavigator
• tNavigator
– Developed by the research and product development teams of Rock Flow Dynamics
– Designed for running dynamic reservoir simulations on engineers’ laptops, servers, and HPC clusters.
– Written in C++ and designed from the ground up to run parallel acceleration algorithms on multicore and manycore
shared and distributed memory computing systems.
– Employs Qt graphical libraries, which makes the system true multiplatform.
– By taking advantage of the latest computing technologies like NUMA, Hyperthreading, MPI/SMP hybrids, the
performance of tNavigator by far exceeds the performance of any industry standard dynamic simulation tools.
– license pricing doesn’t depend on the number of cores employed in the shared memory computing systems
• One of the distinctive features includes the interactive user control of the simulation run
– Users can not only monitor every step of the reservoir simulation at runtime
– but also directly interrupt and change the simulation's configurations with just a mouse click.

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Objectives

• The presented research was done to provide best practices

– tNavigator performance benchmarking
• CPU performance comparison

• MPI library performance comparison

• Interconnect performance comparison

• System generations comparison

• The presented results will demonstrate

– The scalability of the compute environment/application
– Considerations for higher productivity and efficiency

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Test Cluster Configuration
• Dell PowerEdge R730 32-node (1024-core) “Thor” cluster

– Dual-Socket 16-Core Intel E5-2697A v4 @ 2.60 GHz CPUs (Power Management in BIOS sets to Maximum Performance)

– Memory: 64GB memory, DDR4 2133 MHz, Memory Snoop Mode in BIOS sets to Home Snoop, Turbo Enabled

– OS: RHEL 6.5, MLNX_OFED_LINUX-3.0-1.0.1 InfiniBand SW stack

– Hard Drives: 2x 1TB 7.2 RPM SATA 2.5” on RAID 1

• Mellanox ConnectX-4 EDR 100Gbps EDR InfiniBand Adapters

• Mellanox Switch-IB SB7700 36-port 100Gb/s EDR InfiniBand Switch

• Mellanox ConnectX-3 FDR InfiniBand, 10/40GbE Ethernet VPI Adapters

• Mellanox SwitchX-2 SX6036 36-port 56Gb/s FDR InfiniBand / VPI Ethernet Switch

• MPI: Intel MPI 5.1.3

• Application: RFD tNavigator v4.2.3-1177-g638ceab

• Benchmark datasets: SpeedTestModel

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PowerEdge R730
Massive flexibility for data intensive operations
• Performance and efficiency
– Intelligent hardware-driven systems management
with extensive power management features
– Innovative tools including automation for
parts replacement and lifecycle manageability
– Broad choice of networking technologies from GigE to IB
– Built in redundancy with hot plug and swappable PSU, HDDs and fans
• Benefits
– Designed for performance workloads
• from big data analytics, distributed storage or distributed computing
where local storage is key to classic HPC and large scale hosting environments
• High performance scale-out compute and low cost dense storage in one package
• Hardware Capabilities
– Flexible compute platform with dense storage capacity
• 2S/2U server, 6 PCIe slots
– Large memory footprint (Up to 768GB / 24 DIMMs)
– High I/O performance and optional storage configurations
• HDD options: 12 x 3.5” - or - 24 x 2.5 + 2x 2.5 HDDs in rear of server
• Up to 26 HDDs with 2 hot plug drives in rear of server for boot or scratch

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RFD tNavigator Performance – Ethernet vs InfiniBand

• InfiniBand delivers superior scalability performance compared to Ethernet

– EDR InfiniBand provides higher performance and more scalable than Ethernet
– EDR InfiniBand delivers up over 35-72% of higher performance than 10/40 GbE
– InfiniBand continues to scalable to higher nodes or processes

63% 35%
72%

Higher is better 32 MPI Processes / Node

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RFD tNavigator Performance – Processes Per Node

• tNavigator process spawns multiple OpenMP worker threads onto CPU cores
– Typical case: launch 1 process per node (PPN=1), then spawn threads to utilize all cores
– We compare a case with 2PPN, where each process would spawn threads to its CPU socket
– Seen up to 20% gain in performance

13%
20%

Higher is better

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RFD tNavigator Performance – CPU Processor

• “Broadwell” CPU provides more CPU cores per socket than “Haswell” family CPU
– The additional 14% of CPU cores translate to an additional 14% increase in performance
– Haswell: E5-2697 v3 is equipped with 14 cores per CPU which typically runs at 2.6GHz
– Broadwell: E5-2697A v4 is equipped with 16 cores per CPU which typically runs at 2.6GHz

14%

Higher is better

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RFD tNavigator Performance – File system

• tNavigator demonstrates a need of a decent parallel file system

– Parallel file system like Lustre which supports RDMA transport, can be a good alternative to NFS
– Performance of NFS would cause performance degradation at scale
– Performance degradation appears at 4+ nodes, and would impact on scalability around 8+ nodes
– RamFS option is not recommended; it is to demonstrate the ideal situation whne I/O not bottlenecked

29%
195%

Higher is better 16 MPI Processes / Socket

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RFD tNavigator Performance – I/O

• The effect of writing results can have an impact on performance

– Both cases have the results written on shared memory locally on each node
– 8% of performance difference is seen

8%

Higher is better 16 MPI Processes / Socket

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RFD tNavigator Profiling – % MPI Communications

• Majority of the MPI time is spent on MPI_Allreduce

– imbalance is seen for some MPI processes for MPI_Allreduce
– MPI_allreduce accounts for 70% of MPI time (14% of wall time)

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RFD tNavigator Profiling – % MPI Communications

• Majority of data transfer messages are medium sizes for both data, except for:
– MPI_Allreduce has a large concentration (70% MPI, 16% wall) in small sizes (8,4,128 bytes)
– MPI_Bcast is concentrated at 4-byte (13% MPI, 3% wall)
– MPI_Waitall calls are 0-byte call (8% MPI, 2% wall)

Higher is better

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RFD tNavigator Summary
• tNavigator integrates the latest technologies which enables higher performance
– tNavigator uses NUMA, Hyper-Threading, MPI/SMP hybrid to achieve higher scaling
• tNavigator demonstrates to perform with the right set of hardware components
– Network: InfiniBand delivers 72% higher performance compared to Ethernet
– CPU: 14% increase in CPU cores translate directly to a 14% increase in performance
– Running additional MPI process per node could improve performance by up to 20%
– File system: tNavigator demonstrates a need of a decent parallel file system
• Parallel file system, such as Lustre, supports RDMA transport, can be a good alternative to NFS
• Performance of NFS would cause performance degradation at scale
• The effect of writing results can have an impact on performance

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 Thank You
HPC Advisory Council

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completeness of the information contained herein. HPC Advisory Council undertakes no duty and assumes no obligation to update or correct any information presented herein

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