HPCS2014 - Building a storage system for genomics

Calcul Québec - Université Laval
Building a Storage System for
Genomics
1
HPCS 2014
Halifax, NS
Florent.Parent@calculquebec.ca
Frederick.Lefebvre@calculquebec.ca

Agenda
Genomics storage project background
Reviewing and optimizing the proposal
Network + politics issues
Writing the RFP
Lessons learned
!
!
2

Genomics storage project: background
FCI Leading Edge Fund (2012 competition)
“Human and Microbial Integrative Genomics”
Project Lead: Dr. Jacques Simard, CRCHUQ, (Université Laval)
16 researchers from Université Laval
Bioinformatics and Computational Infrastructure
Arnaud Droit
Large storage component
3

CRCHUQ
Genomics, proteomics and metabolomics
Data sources: HiSeq 2500, 2000 and MiSeq
Applications: RAY, genomics pipeline …
Some researchers already active HPC users
Jacques Corbeil, Sébastien Boisvert (RAY), Arnaud Droit,
Yohan Bossé
4

Site specifications: Physical
Number of racks in silo: 56 max
Floor loading capacity: 940 lb/pi2
5

Site specifications: Power
6
1 MW generator
Campus Data
Center
CII: Centre des Infrastructure Informationelles
Silo:
1.1 MW available (~33% used)
72 kW UPS (+ generator)
25 kV hydro line
2 MVA transformer

Site specifications: Cooling
Rack cooling: 100% air
No CRAC units! Using campus wide
chilled-water loop for cooling
Cooling capacity: 1.5 MW
Residual heat transferred to campus hot-
water loop
Partial free air cooling (up to 300 kW)
7
Cooling
coils
Air blowers
Free air
cooling

Site specifications: Networking
8
Fibre optic network
to Québec hospital
research networks

Timeline
9
2014
Feb 26
All tests pass
system accepted
Jan 6
Physical
installation
2013
Oct 3
RFP
published
Jan 15
MSSS
meeting
Jan 22
Acceptance
testing starts
Nov 20
RFP winner
announced
number of meetings with vendors/manufacturers
July 9
MSSS
derogation
2012
Feb
First
meeting
number of meetings with vendors/manufacturers
Nov
identify
FW issue
April
FCI
conditions
met
March
finalize
budget

Researcher LEF proposal
Initial contact: Researcher->VPR->CC staﬀ
Initial meetings: Review proposal, discussions
Researchers planned to install storage at CRCHUQ facilities
Based on quote from local supplier
Review and optimize
Discuss possible optimization in proposal
Scheduled meetings with HPC storage suppliers
10

CFI LEF
Discussed option to host storage at CC site
Install some storage and compute at CRCHUQ
Bulk storage at UL/CQ/CC site
High speed connectivity already in place (10G UL-CRCHUQ)
Sounds simple, right? …
11

Concerns raised
Ease of access to CC hosted storage
Security
12

Refining the proposal
Evaluate benefits to hosts at CQ/CC
Power, cooling infrastructure already in place
O&M handled by CQ staﬀ.
Collaborate with CRCHUQ sysadmin
Initial budget planned room renovations and
extra A/C: $$ saved for more infrastructure
13

MOU
MOU sent to CFI (Jan 2013)
CRCHUQ and CQ/CC staﬀ work on RFP and acquisition process
CQ/CC staﬀ manage storage
Storage is for exclusive usage of CRCHUQ
Local storage for CRCHUQ, Parallel FS at CQ/UL
Archival (tapes) will use existing system available at remote
CQ/CC site
14

Genomics Storage Components
15

Interconnect
Université Laval owns fibre optics MAN
Interconnects all QC hospital research networks
16

Test node
Network testing
17
Test node (VM)
4 Gbps
141 Mbps
“IS-QC” Firewall
Limits flows to 1.2 Gbps

“Pile of firewalls”
CRCHUQ already manages it’s security
firewall at it’s periphery
IS-QC under MSSS authority
acts as“safety valve”
Work with CRCHUQ to request derogation to
remove IS-QC
18

MSSS Derogation
Document and prepare meeting in Dec 2012
Jan 2013: meeting with MSSS security staﬀ
Jan 2013: regional security coordinator refusal
Feb 2013: CRCHUQ director writes to deputy minister
of MSSS IT
July 2013: Deputy minister (MSSS IT) visits UL/CQ
Derogation done.
19

Network Measurements
perfSonar for periodic network measurements
20

Archival
Use existing tape archives at CQ
Plenty of network bandwidth (for now…)
21

V1.0Calcul Québec - Université Laval
RFP
22

Building the RFP
An iterative process
Based on multiple meetings with researchers
+ Expertise and market knowledge of local HPC team
23
Vendors
RFP
Researcher HPC team

Premise
2 storage systems with diﬀerent requirements in
very diﬀerent environments
Parallel storage
Large and high-speed in modern datacenter with plenty of
power and cooling
On-site storage
Smaller capacity with slower interconnect in air-conditioned
server room
24

Challenges
Budget is limited. We want to get the most out
of it !
But the most of what ?
Parallel storage capacity/
Parallel storage write speed
On-site storage capacity
etc…
25

Challenges (cont.)
Most of the budget to be allocated to the
parallel storage
To enable computing and mid-term storage
On-site storage must be large enough. No more.
A quality based RFP allows for such distinctions
26

How large is large enough
The sequencing platform could generate 10TB of
data per week
Operating at full capacity
40TB would provide 1 month of buﬀering
27
On-site StorageSequencers Parallel Storage
Buﬀering
Automated Data
Synchronisation

quality based RFP
We chose to publish a quality based RFP
In contrast to a lowest-bidder process
!
Evaluated on cost + « quality criteria »
Vendors are asked to spend at least 95% of budget
28

Challenges (solution)
Define 2 indépendant sets of requirements
!
Use the « quality criteria » to let vendors know
what they should prioritize
More weight will be given to the parallel storage components
!
29

Hardware only or integrated solution ?
A) Hardware only:Write an RFP to buy XTB of raw disk space
+Y servers and the accompanying interconnect. Integrate
everything in-house to deploy a storage system.
B) Integrated solution: Ask for a complete system to meet a
size and performance requirements.
First things first
30

Integrated Solution
Cumbersome question … Lustre, GPFS or
anything
Should we ask for a specific parallel FS ?
Some parallel FS are tied to a specific vendor or a very small
set of vendors
Went with Lustre because it is a multi-vendor
ecosystem
… and our team is already familiar with it
31

Fostering competition
The RFP can be so specific as to open the door
only to a single product
!
Or it can let bidders come up with their own
solution to our problem
32
Specific
product
Surprise…

Fostering competition (cont.)
Vendors know when a RFP is targeted to them
They will price accordingly
Inversely, vendors will not bid if they do not feel
they have a fair chance
Less bid will often equal « higher price »
A less constrained RFP will generally attract
more proposals
!
33

Fostering competition (cont.)
Example of being too specific:
« Storage units with 60 drives in raid5, 8+2 configuration »
!
Such a statement could apply to a single vendor,
while limiting the available technologies
34

Spec'ing a storage system
Power & Cooling capacity
Physical space and room topology
Compatibility with existing infrastructure
Software
Physical
35

Physical infrastructure
36
Document floor/rack plan
Maximum weight per square foot ?
How much space do we actually have ?
Where does the system need to connect?
Both power and interconnect
Cable length

Power & Cooling
37
How much electrical capacity is available
Total?
Per rack ?
UPS ?
Can our room cooling system handle that much
new power ?

Requirements for parallel storage
1 PB usable (or more) Lustre FS
Compatible with Lustre clients 1.8.9 and 2.4.x
20 GB/s aggregate read/write speed (or more)
Drives and Lustre servers redundancy
« how » is purposely left unspecified
Infiniband interconnect
2:1 blocking factor with computing resources
38

Requirements for parallel storage
Vendor to provide all interconnect
Leaf IB switch, ethernet switch for management and cabling
Site provides uplink to core switches
20KW maximum electrical consumption
Vendor to supply PDUs (switched)
Site to connect PDUs to existing electrical infrastructure
39

Requirements for on-site storage
Export network filesystem
Compatible with sequencers,Windows 7, Linux and Mac
10G Ethernet interconnect
50TB usable capacity (or more)
with option to grow up to 300TB
Drives and servers redundancy
40

Requirements for on-site storage
Site to provide all cabling and interconnect for
on-site storage
PDUs and rack space provided by the site
41

Measuring the quality of a proposal
Final evaluation is based on « adjusted price »
calculated from the bid price and the rating of
the « quality criteria » given by the evaluation
committee
!
« adjusted price » can vary from the real price by
up to 30%
42

Quality criteria
43
Parallel Storage 45 %
On-site Storage 20 %
Interconnect & Networking 10 %
Vendor’s Experience & Reputation 25 %

Quality criteria (cont.)
!
In the 1st three categories, meeting the base
requirements gives a passing score of 70%.
Any specs or meaningful features above base
requirements will improve the mark.
!
44

Quality criteria (cont.)
In the « vendor » category, score is based on the
bidder’s experience in deploying similar
systems with a requirement for at least 1 such
system in the past 18 months.
Support structure and resume of the lead
architect for the project are also a factor.
!
45

Benchmarks &
stability tests
46

Acceptance tests
We define stability tests to validate the system
can operate in a real production environment.
!
We run synthetic benchmarks to make sure the
system hits the performance targets set by the
vendor as requested by the quality criteria.
47

Stability tests
To validate normal operation
Homogenous firmware and software versions everywhere
No errors or warning
Verify the systems reboots cleanly
Lustre mounts properly
Simulate drive failures
Verify rebuild process
48

Benchmarks
We set some base rules
No custom tools. Re-use existing software
Let the vendor tune the tests for his system
But test must be large enough to avoid cache eﬀect
What to benchmark
Read/write speed of single target : IOZone
Maximum aggregate read/write speed : IOR
Maximum I/O operations per second (IOPS) : mdtest
49

RFP results
50

Bids
We got 6 valid proposals
Parallel storage capacity varied from more than 60% across bids
Aggregate speed for parallel storage varied by almost 50%
On-site capacity varied by almost 100%
On-site storage went from a NAS on ZFS to full fledges Lustre or
GPFS systems
51

System selected
Parallel storage: Xyratex CS6000
1.4 PB usable Lustre FS
12 OSS and 4 targets per OSS
4TB NL SAS drives +SSD for journals
30 GB/s maximum aggregated R/W speed
On-site storage: Xyratex CS1500
120TB usable Lustre FS (scales to 7 PB)
4 CIFS/NFS exporters
52

Deployment
53

Operation
Both system in production since early february
Parallel storage dedicated to research group
mounted on compute ressources
Data transfers are enabled by Globus endpoints
on dedicated DTNs at both sites.
Todo: Review network topology for transfers
Perfsonar nodes to be deployed at research center
54

Operation (cont.)
Researchers need a CC account to access Parallel
Storage
Access control and allocations are a challenge
Shared spreadsheet filled by research center to allocate space
on parallel FS for their users (Cumbersome!)
Integration with the CCDB would leverage existing system to
manage storage allocations
!
55

Lessons learned
56

Lessons learned
Time consuming (2 year projects)
Mostly thrust and relationship building
Time needed to write an RFP should not be underestimated
Benefit for the research group
Access to a team of specialist to lead their project
Major cost saving on the infrastructure. No investment to
upgrade an existing server room (UPS, Power, Cooling, etc)
57

Cost to integrate CS6000
Installation: 900$ (rack enclosure)
Power: 1457$ (new outlets)
Cooling: 0$
Infiniband: Used existing cables
6 CXP - QSFP cables (18 QDR links)
58

Improving the process
Sharing RFPs between Compute Canada site
could ease the process for new projects
Common benchmarks across Compute Canada
would help when designing acceptance tests
Applies to both storage and computing
59

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