Altair OptiStruct 13.0 Performance Benchmark and Profiling. May 2015
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1 Altair OptiStruct 13.0 Performance Benchmark and Profiling May 2015
2 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 OptiStruct performance overview Understanding OptiStruct communication patterns Ways to increase OptiStruct productivity MPI libraries comparisons For more info please refer to
3 Objectives The following was done to provide best practices OptiStruct performance benchmarking Interconnect performance comparisons MPI performance comparison Understanding OptiStruct communication patterns The presented results will demonstrate The scalability of the compute environment to provide nearly linear application scalability The capability of OptiStruct to achieve scalable productivity 3
4 OptiStruct by Altair Altair OptiStruct OptiStruct is an industry proven, modern structural analysis solver Solve for linear and non-linear structural problems under static and dynamic loadings Market-leading solution for structural design and optimization Helps designers and engineers to analyze and optimize structures Optimize for strength, durability and NVH (Noise, Vibration, Harshness) characteristics Help to rapidly develop innovative, lightweight and structurally efficient designs Based on finite-element and multi-body dynamics technology 4
5 Test Cluster Configuration Dell PowerEdge R node (896-core) Thor cluster Dual-Socket 14-core Intel 2.60 GHz CPUs (Turbo on, Early Snoop, Max Perf in BIOS) OS: RHEL 6.5, OFED MLNX_OFED_LINUX InfiniBand SW stack Memory: 64GB memory, DDR MHz Hard Drives: 1TB 7.2 RPM SATA 2.5 Mellanox Switch-IB SB Gb/s InfiniBand VPI switch Mellanox SwitchX SX Gb/s FDR InfiniBand VPI switch Mellanox ConnectX-4 EDR 100Gb/s InfiniBand VPI adapters Mellanox ConnectX-3 40/56Gb/s QDR/FDR InfiniBand VPI adapters MPI: Intel MPI 5.0.2, Mellanox HPC-X v1.2.0 Application: Altair OptiStruct 13.0 Benchmark datasets: Engine Assembly 5
6 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 GbE 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 or - 24 x x 2.5 HDDs in rear of server Up to 26 HDDs with 2 hot plug drives in rear of server for boot or scratch 6
7 OptiStruct Performance CPU Cores Running more cores per node generally improves overall performance The -nproc parameter specified the number of threads spawned per MPI process Guideline: 6 threads per MPI process yields the best performance Ideal threads to be spawned appears to be 6 threads per MPI process (either 2/4 PPN) Having 6 threads spawned by each MPI process performs best among all other tested Higher is better 7
8 OptiStruct Performance Interconnect EDR InfiniBand provides superior scalability performance over Ethernet 11 times better performance than 1GbE at 24 nodes 90% better performance than 10GbE at 24 nodes Ethernet solutions does not scale beyond 4 nodes 11x 90% Higher is better 2 PPN / 6 Threads 8
9 OptiStruct Profiling Number of MPI Calls For 1GbE, communication time is mostly spent on point-to-point transfer MPI_Iprobe and MPI_Test are the tests for non-blocking transfers Overall runtime is significantly longer compared to faster interconnects For 10GbE, communication time is consumed by data transfer Amount of time for non-blocking transfers still significant Overall runtime reduces compared to 1GbE While time for data transfer reduces, collective operations has higher ratio as in overall For InfiniBand, overall runtime reduces Time consumed by MPI_Allreduce is more significant compared to data transfer Overall runtime reduces significantly compared to Ethernet 1GbE 10GbE EDR IB 9
10 OptiStruct Profiling Number of MPI Calls For 1GbE, communication time is mostly spent on point-to-point transfer MPI_Iprobe and MPI_Test are the tests for non-blocking transfers Overall runtime is significantly longer compared to faster interconnects For 10GbE, communication time is consumed by data transfer Amount of time for non-blocking transfers still significant Overall runtime reduces compared to 1GbE While time for data transfer reduces, collective operations has higher ratio as in overall For InfiniBand, overall runtime reduces Time consumed by MPI_Allreduce is more significant compared to data transfer Overall runtime reduces significantly compared to Ethernet 1GbE 10GbE EDR IB 10
11 OptiStruct Profiling MPI Message Sizes The most time consuming MPI communications are: MPI_Allreduce: Messages concentrated at 8B MPI_Iprobe and MPI_Test have volume of calls that test for completion of messages 2 PPN / 6 Threads 11
12 OptiStruct Performance Interconnect EDR IB delivers superior scalability performance over previous InfiniBand EDR InfiniBand improves over FDR IB by 40% at 24 nodes EDR InfiniBand outperforms FDR InfiniBand by 9% at 16 nodes New EDR IB architecture supersedes previous FDR IB generation of in scalability 9% 40% Higher is better 4 PPN / 6 Threads 12
13 OptiStruct Performance Processes Per Node OptiStruct reduces communication by deploying hybrid MPI mode Hybrid MPI process can spawn threads; helps reducing communications on network By enabling more MPI processes per node, it helps to unlock additional performance The following environment setting and tuned flags are used : I_MPI_PIN_DOMAIN auto, I_MPI_ADJUST_ALLREDUCE 2, I_MPI_ADJUST_BCAST 1, I_MPI_ADJUST_REDUCE 2, ulimit -s unlimited 10% 4% Higher is Better 13
14 OptiStruct Performance IMPI Tuning Tuning Intel MPI collective algorithm can improve performance MPI profile shows ~30% of runtime spent on MPI_Allreduce IB communications Default algorithm in Intel MPI is Recursive Doubling (I_MPI_ADJUST_ALLREDUCE=1) Rabenseifner's algorithm for Allreduce appears to the be the best on 24 nodes Higher is better Intel MPI 4 PPN / 6 Threads 14
15 OptiStruct Performance CPU Frequency Increase in CPU clock speed allows higher job efficiency Up to 11% of high productivity by increasing clock speed from 2300MHz to 2600MHz Turbo Mode boosts job efficiency higher than increase in clock speed Up to 31% of performance jump by enabling Turbo Mode at 2600MHz Performance gain by turbo mode depends on environment factors, e.g. temperature 11% 4% 8% 10% 17% 31% Higher is better 4 PPN / 6 Threads 15
16 OptiStruct Profiling Disk I/O OptiStruct makes use of distributed I/O of local scratch of compute nodes Heavy disk IO appears to take place throughout the run on each compute node The high I/O usage causes system memory to also to be utilized for I/O caching Disk I/O is distributed on all compute nodes; thus provides higher I/O performance Workload would complete faster as more nodes take part on the distributed I/O Higher is better 4 PPN / 6 Threads 16
17 OptiStruct Profiling MPI Message Sizes Majority of data transfer takes place from rank 0 to the rest It appears that most data transfer takes place between rank 0 to the rest Those non-blocking communication appears data transfers to hide latency in network The collective operations appear to be much less in size 16 Nodes 32 Nodes 2 PPN / 6 Threads 17
18 OptiStruct Summary OptiStruct is designed to perform structural analysis at large scale OptiStruct designed hybrid MPI mode to perform at scale EDR InfiniBand shows to outperform Ethernet in scalability performance ~70 times better performance than 1GbE at 24 nodes 4.8x better performance than 10GbE at 24 nodes EDR InfiniBand improves over FDR IB by 40% at 24 nodes Hybrid MPI process can spawn threads; helps reducing communications on network By enabling more MPI processes per node, it helps to unlock additional performance Hybrid MPP version enhanced OptiStruct scalability Profiling and Tuning: CPU, I/O, Network MPI_Allreduce accounts for ~30% of runtime at scale Tuning for MPI_Allreduce should allow better performance at high core counts Guideline: 6 threads per MPI process yields the best performance Turbo Mode boosts job efficiency higher than increase in clock speed OptiStruct makes use of distributed I/O of local scratch of compute nodes Heavy disk IO appears to take place throughout the run on each compute node 18
19 Thank You HPC Advisory Council All trademarks are property of their respective owners. All information is provided As-Is without any kind of warranty. The HPC Advisory Council makes no representation to the accuracy and completeness of the information contained herein. HPC Advisory Council undertakes no duty and assumes no obligation to update or correct any information presented herein 19 19
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