By Brian Whitney on Sep 20, 2010
Oracle's Sun Storage 7410 system, attached via QDR InfiniBand to a cluster of eight of Oracle's Sun Fire X2270 servers, was used to evaluate multiple job throughput of Schlumberger's Linux-64 ECLIPSE 300 compositional reservoir simulator processing their standard 2 Million Cell benchmark model with 8 rank parallelism (MM8 job).
The Sun Storage 7410 system showed little difference in performance (2%) compared to running the MM8 job with dedicated local disk.
When running 8 concurrent jobs on 8 different nodes all to the Sun Storage 7140 system, the performance saw little degradation (5%) compared to a single MM8 job running on dedicated local disk.
Experiments were run changing how the cluster was utilized in scheduling jobs. Rather than running with the default compact mode, tests were run distributing the single job among the various nodes. Performance improvements were measured when changing from the default compact scheduling scheme (1 job to 1 node) to a distributed scheduling scheme (1 job to multiple nodes).
When running at 75% of the cluster capacity, distributed scheduling outperformed the compact scheduling by up to 34%. Even when running at 100% of the cluster capacity, the distributed scheduling is still slightly faster than compact scheduling.
When combining workloads, using the distributed scheduling allowed two MM8 jobs to finish 19% faster than the reference time and a concurrent PSTM workload to find 2% faster.
The Oracle Solaris Studio Performance Analyzer and Sun Storage 7410 system analytics were used to identify a 3D Prestack Kirchhoff Time Migration (PSTM) as a potential candidate for consolidating with ECLIPSE. Both scheduling schemes are compared while running various job mixes of these two applications using the Sun Storage 7410 system for I/O.
These experiments showed a potential opportunity for consolidating applications using Oracle Grid Engine resource scheduling and Oracle Virtual Machine templates.
Results are presented below on a variety of experiments run using the 2009.2 ECLIPSE 300 2 Million Cell Performance Benchmark (MM8). The compute nodes are a cluster of Sun Fire X2270 servers connected with QDR InfiniBand. First, some definitions used in the tables below:
NFSoIB: One node hosts its local disk for NFS mounting to other nodes over InfiniBand.
IB 7410: Sun Storage 7410 system over QDR InfiniBand.
Compact Scheduling: All 8 MM8 MPI processes run on a single node.
Distributed Scheduling: Allocate the 8 MM8 MPI processes across all available nodes.
First TestThe first test compares the performance of a single MM8 test on a single node using local storage to running a number of jobs across the cluster and showing the effect of different storage solutions.
|Cluster Load||Number of MM8 Jobs||Local HDD Relative Throughput||NFSoIB Relative Throughput||IB 7410 Relative Throughput|
\* Performance measured on node hosting its local disk to other nodes in the cluster.
Second TestThis next test uses the Sun Storage 7410 system and compares the performance of running the MM8 job on 1 node using the compact scheduling to running multiple jobs with compact scheduling and to running multiple jobs with the distributed schedule. The tests are run on a 8 node cluster, so each distributed job has only 1 MPI process per node.
Comparing Compact and Distributed Scheduling
|Cluster Load||Number of MM8 Jobs||Compact Scheduling
\* Each distributed job has 1 MPI process per node.
Third TestThis next test uses the Sun Storage 7410 system and compares the performance of running the MM8 job on 1 node using the compact scheduling to running multiple jobs with compact scheduling and to running multiple jobs with the distributed schedule. This test only uses 4 nodes, so each distributed job has two MPI processes per node.
Comparing Compact and Distributed Scheduling on 4 Nodes
|Cluster Load||Number of MM8 Jobs||Compact Scheduling
\* Each distributed job it has two MPI processes per node.
Fourth TestThe last test involves running two different applications on the 4 node cluster. It compares the performance of running the cluster fully loaded and changing how the applications are run, either compact or distributed. The comparisons are made against the individual application running the compact strategy (as few nodes as possible). It shows that appropriately mixing jobs can give better job performance than running just one kind of application on a single cluster.
Multiple Job, Multiple Application Throughput Results
|Number of PSTM Jobs||Number of MM8 Jobs||Compact Scheduling
(1 node x 8 processes
(4 nodes x 2 processes
(4 nodes x 4 processes
(2 nodes x 8 processes per job)
Results and Configuration Summary
24 GB memory (6 x 4 GB memory at 1333 MHz)
1 x 500 GB SATA
128 GB memory
2 Internal 233GB SAS drives (466 GB total)
2 Internal 93 GB read optimized SSD (186 GB total)
1 Sun Storage J4400 with 22 1 TB SATA drives and 2 18 GB write optimized SSD
11 TB mirrored data and mirrored write optimized SSD
Scali MPI Connect 5.6.6
GNU C 4.1.2 compiler
2009.2 ECLIPSE 300
ECLIPSE license daemon flexlm v126.96.36.199
3D Kirchoff Time Migration
The benchmark is a home-grown study in resource usage options when running the Schlumberger ECLIPSE 300 Compositional reservoir simulator with 8 rank parallelism (MM8) to process Schlumberger's standard 2 Million Cell benchmark model. Schlumberger pre-built executables were used to process a 260x327x73 (2 Million Cell) sub-grid with 6,206,460 total grid cells and model 7 different compositional components within a reservoir. No source code modifications or executable rebuilds were conducted.
The ECLIPSE 300 MM8 job uses 8 MPI processes. It can run within a single node (compact) or across multiple nodes of a cluster (distributed). By using the MM8 job, it is possible to compare the performance between running each job on a separate node using local disk to using a shared network attached storage solution. The benchmark tests study the affect of increasing the number of MM8 jobs in a throughput model.
The first test compares the performance of running 1, 2, 4, 6 and 8 jobs on a cluster of 8 nodes using local disk, NFSoIB disk, and the Sun Storage 7410 system connected via InfiniBand. Results are compared against the time it takes to run 1 job with local disk. This test shows what performance impact there is when loading down a cluster.
The second test compares different methods of scheduling jobs on a cluster. The compact method involves putting all 8 MPI processes for a job on the same node. The distributed method involves using 1 MPI processes per node. The results compare the performance against 1 job on one node.
The third test is similar to the second test, but uses only 4 nodes in the cluster, so when running distributed, there are 2 MPI processes per node.
The fourth test compares the compact and distributed scheduling methods on 4 nodes while running a 2 MM8 jobs and one 16-way parallel 3D Prestack Kirchhoff Time Migration (PSTM).
Key Points and Best Practices
ECLIPSE is very sensitive to memory bandwidth and needs to be run on 1333 MHz or greater memory speeds. In order to maintain 1333 MHz memory, the maximum memory configuration for the processors used in this benchmark is 24 GB. Bios upgrades now allow 1333 MHz memory for up to 48 GB of memory. Additional nodes can be used to handle data sets that require more memory than available per node. Allocating at least 20% of memory per node for I/O caching helps application performance.
If allocating an 8-way parallel job (MM8) to a single node, it is best to use an ECLIPSE license for that particular node to avoid the any additional network overhead of sharing a global license with all the nodes in a cluster.
Understanding the ECLIPSE MM8 I/O access patterns is essential to optimizing a shared storage solution. The analytics available on the Oracle Unified Storage 7410 provide valuable I/O characterization information even without source code access. A single MM8 job run shows an initial read and write load related to reading the input grid, parsing Petrel ascii input parameter files and creating an initial solution grid and runtime specifications. This is followed by a very long running simulation that writes data, restart files, and generates reports to the 7410. Due to the nature of the small block I/O, the mirrored configuration for the 7410 outperformed the RAID-Z2 configuration.
A single MM8 job reads, processes, and writes approximately 240 MB of grid and property data in the first 36 seconds of execution. The actual read and write of the grid data, that is intermixed with this first stage of processing, is done at a rate of 240 MB/sec to the 7410 for each of the two operations.
Then, it calculates and reports the well connections at an average 260 KB writes/second with 32 operations/second = 32 x 8 KB writes/second. However, the actual size of each I/O operation varies between 2 to 100 KB and there are peaks every 20 seconds. The write cache is on average operating at 8 accesses/second at approximately 61 KB/second (8 x 8 KB writes/sec). As the number of concurrent jobs increases, the interconnect traffic and random I/O operations per second to the 7410 increases.
MM8 multiple job startup time is reduced on shared file systems, if each job uses separate input files.
- ECLIPSE Performance Presentation
- Schlumberger Reservoir Simulation Software
- Schlumberger Petrel Seismic to Simulation Software
- HPC Advisory Council paper
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