G. Paciucci - Understanding I/O performance of data intensive

Report
Understanding I/O performance of data
intensive astronomy applications
with Lustre monitoring tools
Gabriele Paciucci, High Performance Data Division
Intel Corporation
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Agenda
• Lustre* metrics and tools
• Analytics and presentation
• Conclusion
3
Why Monitor Lustre*?
• With the exponential growth of high-fidelity sensor and
simulated data, the scientific community is increasingly reliant
on Exascale HPC resources to handle their data analysis
requirements.
• Lustre is the leading parallel file system in the Exascale Era.
• However, to utilize all the Lustre power effectively, the I/O
components must be designed in a proper way, as any
architectural bottleneck will quickly render the platform
inefficient.
4
The challenge of monitoring Lustre
• Understanding the Lustre metrics in the proc filesystem, gives
the opportunity to Administrators to design a Lustre cluster and
maintain the performance requested.
• But there are thousand of metrics in a mid-size Lustre file
system for each components that include clients, servers and
Lustre networks
 These components are distributed: a problem on one node
can affect multiple nodes and finding the initial source of a
problem can be difficult without an integrated monitor tool.
Metrics and Tools
• What you monitor will depend on what you want to know and
on what you think the problems are.
• What you want to measure will also guide your choice of tools
for collecting, analyzing, and presenting the data.
Tools
python/matplotlib

Matplotlib.org

matplotlib is a python 2D plotting library which produces
plt.xlabel('time')
plt.ylabel(r'$MiB/sec$')
plt.setp( ax.get_xticklabels(), rotation=30, horizontalalignment='right')
plt.title("%s on AWS %s Aggregate OST data rates" % (self.application,
dayStr))
plt.legend()
plt.savefig(plot)
plt.cla()
publication quality figures in a variety of hardcopy formats and
interactive environments across platforms. matplotlib can be
used in python scripts, the python and ipython shell
collectl

collectl.sourceforge.net

CollectL is a tool that can be used to monitor Lustre. You can
run CollectL on a Lustre system that has any combination of
MDSs, OSTs and clients. The collected data can be written to a
file for continuous logging and played back at a later time. It
can also be converted to a format suitable for plotting.
LMT

github.com/chaos/lmt/wiki

The Lustre Monitoring Tool (LMT) monitors Lustre File System
servers (MDT, OST, and LNET routers). It collects data using
the Cerebro monitoring system and stores it in a MySQL
database. Graphical and text clients are provided which display
historical and real time data pulled from the database.
[oss]# collectl –scdl –i 3
#<--------CPU--------><----------Disks-----------><---------Lustre OST--------->
#cpu sys inter ctxsw KBRead Reads KBWrit Writes KBRead Reads KBWrit
Writes
19 19 1930 563
0
0 27211 251
0
0 28701 28
9 8 1346 239
0
0 17269 165
0
0 9225
9
[client]# collectl -sl --lustopts R –oTm
#
<---------------Lustre Client--------------->
#Time
KBRead Reads KBWrite Writes Hits Misses
12:20:50.003 17138
8 12854 13 4100
0
12:20:51.002 18450
9 20500 20 4349
0
12:20:52.003 32735 16 20460 20 8447
0
Intel Manager for Lustre
• Bundled with Intel Enterprise Edition for Lustre
• Simplified installation, configuration, monitoring and
management of Lustre
• Provides plugin interface for integration with storage and
other software tools
• Storage hardware neutral
• Intuitive GUI
• Fully featured CLI
IML details
Monitors
• Read and write throughput to the
file system
• Metadata operations to the file
system
• CPU and RAM usage on MDS and
OSS
• Delve down to individual server and
individual Lustre targets
• Aggregate system log of all of
Lustre servers
• The health of Lustre targets and
servers
• LNET status
• The number of clients connected to
the Lustre file system
• The usage of Lustre file system
Manages
• Install Lustre and IML related
packages
• Automatically setup High
Availability
• Power control Lustre servers
• power down, on, cycle
• Manual failover and failback
option
• Create & Setup new Lustre file
systems
• Manage multiple Lustre file
systems
• Rescan network configuration
changes
• Re-configure Lustre file systems
• Support via GUI or CLI
IML dashboard
Agenda
• Lustre* metrics and tools
• Analytics and presentation
• Conclusion
11
Analytics
http://crd-legacy.lbl.gov/~borrill/cmb/madcap/
http://crd-legacy.lbl.gov/~borrill/MADbench2/
• In the MADbench2 application the problem is to generate
simulations of the cosmic microwave background radiation sky
map.
• Each of those simulations involves a very large matrix inversion
that is solved with an out-of-core algorithm (thus the I/O)
•
That phase of the application can be I/O intensive and scales as n2
for a problem of size n (n is the number of pixels in the map). It also
has a communication phase that scales as n3.
Intel Cloud Edition for Lustre*
• We have used Intel Cloud Edition for Lustre to understand how
the application scales, what its workload looks like and how we
can size the environment to maximize the results
• Intel Cloud Edition for Lustre* or ICEL is a scalable, shared
filesystem for HPC applications in the cloud
• AWS allows you to run Lustre on an Amazon Machine Image
(AMI).
• The Intel Lustre AMI is designed to be used with a
CloudFormation template that defines all the resources needed
by the Lustre file system.
13
ICEL for MADBench2 – Scenario 1
We used 256 cores distributed on
32 compute nodes each with 8 cores
Intel Xeon E5-2670.
The total available memory was 960
GB.
MGS
M1.medium
RAID0
8x 40GB
Standard
32x Clients
M3.2xlarge
The RAW space for the Lustre file
system is 5TB.
The max sequential performance is
limited by the OSS’s network to 16
Gbps (16x1Gbps)
MDS
EBS Optimized
Compute
8x 40GB
Standard
OSS
EBS Optimized
M3.2xlarge
M3.2xlarge
16x OSS
8x 40GB
Standard
OSS
EBS Optimized
1Gbps
M3.2xlarge
14
Analytics – Scenario 1
519.51 sec
• The smaller instances ran
quickly (not shown)
• The 32k and 64k pixel
instances became
communication bound
• The MADbench2 application
reads just as much as it
writes
• Even at this larger scale the
I/O fits entirely in client cache,
so the reads do not generate
any traffic to the servers
(where ltop is listening)
3860.67 sec
Changing the compute nodes –
Scenario 2
The decision was to improve
the inter-process
communication using
instances with 10GbE.
The instances with such
networks have 32 cores, so
we could cut the number of
compute nodes from 32 to 16.
We did not modify the size or
the performance of the Lustre
file system.
MGS
M1.medium
RAID0
8x 40GB
Standard
MDS
EBS Optimized
16x Clients
M3.2xlarge
Compute
8x 40GB
Standard
OSS
EBS Optimized
M3.2xlarge
16x OSS
8x 40GB
Standard
Cc2.8xlarge
10GbE
OSS
EBS Optimized
M3.2xlarge
1Gbps
16
Analytics – Scenario 2
• The analysis allowed us
to decrease the Time To
Run the application by
40% increasing the
network bandwidth (1Gb
to 10GbE)
•
Reduce the cost to run
the application by 50%
by lowering the amount
of the servers (32 to 16)
310.44 sec
2427.64 sec
Conclusion
• There is a wealth of information about the health and
performance of Lustre* available in the Proc filesystem
• Proactively tracking the changes in that information will
allow system staff to anticipate and repair problems or
make a better design of the cluster and save money
• Knowing the tools for gathering, analyzing, and presenting
the information will help with system issues and with the
impacts of user codes.
• In the event that a fault is reported, the monitoring
telemetry can help quickly isolate a specific root cause.
18
Risk Factors
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“estimates,” “may,” “will,” “should” and their variations identify forward-looking statements. Statements that refer to or are based on projections,
uncertain events or assumptions also identify forward-looking statements. Many factors could affect Intel’s actual results, and variances from Intel’s
current expectations regarding such factors could cause actual results to differ materially from those expressed in these forward-looking statements.
Intel presently considers the following to be the important factors that could cause actual results to differ materially from the company’s expectations.
Demand could be different from Intel's expectations due to factors including changes in business and economic conditions; customer acceptance of
Intel’s and competitors’ products; supply constraints and other disruptions affecting customers; changes in customer order patterns including order
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matters. Intel operates in intensely competitive industries that are characterized by a high percentage of costs that are fixed or difficult to reduce in
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timing of Intel product introductions and the demand for and market acceptance of Intel's products; actions taken by Intel's competitors, including
product offerings and introductions, marketing programs and pricing pressures and Intel’s response to such actions; and Intel’s ability to respond
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Rev. 7/17/13
Virtual hardware available in ICEL
VMs size
vCP
U
Intel CPU
M3.2xlarge
8
Intel Xeon E5-2670 30
Yes
32
Intel Xeon E5-2670 60
N/A
Amazon EC2 instances:
• Spot Instances
• EBS optimized
•
CC2.8xlarg
High network capabilitiese
vRAM
(GB)
EBS
Network performance
**
M3.2xlarge
CC2.8xlarge
Amazon EBS storage:
M3.2xlarge
1.01 Gbps 1.87 Gbps
• Networked storage
CC2.8xlarge
1.87 Gbps 6.18 Gbps
• Max size 1TB per EBS
volume
EBS Storage
IOPS
Size Performance
(WRITE) **
• Not magic
Standard
N/A
100
24+ MB/sec
• Standard, not Provisioned
in ICEL
Provisioned
2000
200
35+ MB/sec
Provisioned
4000
400
50+ MB/sec
** not intended to be authoritative numbers
21
Analytics – Scenario 1
•
•
•
The MADbench application does
appear to scale as n3 for larger
instances, though not necessarily for
the smaller ones.
This is what we expected.
But the scaling study doesn’t illuminate why.
Linear scale
Log scale
Analytics – Scenario 1
•
The ltop utility in the LMT package records
OST stat file contents much like llstat.
•
An ad hoc python script (with numpy and
matplotlib) that parses the output recorded by
ltop can present a variety of special-case
views of the data.

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