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PowerMVDescriptorsV01

PowerMV will compute a number of molecular descriptors.

For a description of PowerMV and many of the descriptors that PowerVM can compute, see

Eight molecular descriptor sets can be computed using PowerMV. Four are bit string, one is continuous, one is a collection useful for judging the drug-like nature of a molecule and one gives simple counts of 90 atom types.

For the bit string descriptors, each bit is set to “1” when a certain feature is presented and “0” when it is not. For Atom Pair and Atom Pair(Carhart) we adopt the Carhart strategy where a feature refers to two chemical groups or atoms

separated by a certain 2D path length, the bond count of the shortest path between the two atom types. The atoms are typed in the following way: The atom symbol is give, e.g. C for carbon, O for oxygen, N for nitrogen, etc.; next is given the number of non-hydrogen connections of the atom; finally the number of pi electrons. So C(1,0) refers to a carbon, connected to one non-hydrogen, having no pi electrons. C(1,0) stands for -CH3. Halogen atoms only have one possibility, (1,0), in organic molecules, so their extended notation is ignored. All undefined atom features are assigned to feature Y. If longer paths are counted then we go from 546 (paths up to seven bonds) features to 4662 features (paths up to xx bonds). For Atom Pair and Atom Pair(Carhart), Atom Pair, we simply note the absence or presence, 0/1, of the feature. Note that we deviate from the original Carhart in noting presence/absence rather than using counts of features. For Atom Pair (count) we give the counts of the features in a molecule. For Fragment Fingerprints we replace atom types with groups of atoms, Table 2,

and again count the shortest through-bond distance between the pharmacophores. For fragment-based descriptors, 14 classes are defined. For example, two phenyl rings, which are separated by two bonds, are expressed as AR_02_AR.

Pharmacophore Fingerprint descriptors were built based on bioisosteric principles (Two atoms or groups that are expected to have roughly the same biological effect are called bioisosteres.). For example, the disulfide (-S-) is often used to replace ester group (-O-), so we assign these two groups to the same type. This type of thinking leads to our pharmacophore-based descriptors, giving six classes; see Table 3.

The continuous descriptors we implemented are a variation on the Burden number.
We place one of three properties on the diagonal of the Burden connectivity matrix: electro negativity, Gasteiger partial charge or atomic lipophilicity, XLogP. It is common to scale the off diagonal elements of the connectivity matrix before computing eigen values. The off-diagonal elements were weighted by one of the following values: 2.5, 5.0, 7.5 or 10.0. We use the largest and smallest eigen values. This procedure gives us a total of 24 numerical descriptors. Our procedure is similar to the method used by Dr. Pearlman calculating his BCUT descriptors. Dragon software also has Burden Number inspired eigen value descriptors. All three methods are computed somewhat differently, but all are inspired by Burden.

The Properties set of descriptors include eight descriptors useful for judging the drug-like nature of a molecule, XlogP (a measure of the propensity of a molecule to partition into water or oil), polar surface area, PSA, number of rotatable bonds, H-bond donors, H-bond acceptors, molecular weight, blood-brain indicator (0 does not go into the brain, 1, goes into the brain) and bad group indicator (the molecule contains a chemically reactive or toxic group). These properties are useful for judging the drug-like nature of a molecule.

The Fragment Count gives the counts of 90 different typed atoms. These counts were very useful for a regression model for water solubility and are expected to be useful for other molecular physical properties.

Volker Haug Power Systems Architekt Mitglied des IBM Technical Expert Council (TEC) IBM Deutschland GmbH Systems & Technology Group IBM Power Systems – Technical Sales volker.haug@de.ibm.com
Agenda

POWER8 Namenskonvention
Systems Software Familie

POWER8 Technologie
Scale Out Systems – DCMs und POWER8 Chips
POWER8 Memory Buffer Chip

POWER8 integriert PCIe Gen3
POWER Prozessor Design
I/O Roadmap*
Power System S822 2U Server
Power S822 – POWER8 2S2U Scale-Out System
Power S822 Architektur Layout
Power S822 – Vorderansicht
Power S822 – R?ºckansicht

AIX RAID Manager -Anlegen eines Arrays
AIX RAID Manager -Anzeigen der Tiered Arrays

Power System S814 und S824 4U Server
Power S814 – POWER8 1S4U Scale-Out System
Power S824 – POWER8 2S4U Scale-Out System
Power S824 Architektur Layout
Power S814 und S824 – Vorderansicht
Power S814 und S824 – R?ºckansicht
Power S824 -Ansicht von oben
Weitere Bilder zur Power S824
Weitere Bilder zur Power S824
Weitere Bilder zur Power S824

Power System S812L und S822L 2U Linux Server
Power S812L – POWER8 Linux 1S2U Scale-Out System
Power S822L – POWER8 Linux 2S2U Scale-Out System
Power S812L und S822L – Vorderansicht
Hardware – Virtualization – Betriebssystem Strategie
Performance 740 vs. S824
Performance 740 vs. S824
Performance 750 vs. S824
Performance 760 vs. S824

AIX Betriebssystem Support
IBM AIX Version 6.1
AIX Version 6.1 Technologie Level 9 und Service Pack3 , mit APAR IV56366 oder h??her
Diese AIX Level werden in LPARs und virtualisiertem I/O unterst?ºtzt:
AIX Version 6.1 Technologie Level 9 und Service Pack 1, oder h??her
AIX Version 6.1 Technologie Level 8 und Service Pack 1, oder h??her
AIX Version 6.1 Technologie Level 7 und Service Pack 6, oder h??her
IBM AIX Version 7.1
AIX Version 7.1 Technologie Level 3 und Service Pack 3, mit APAR IV56367 oder h??her
Diese AIX Level werden LPARs und virtualisiertem I/O unterst?ºtzt:
AIX Version 7.1 Technologie Level 3 und Service Pack 1, oder h??her
AIX Version 7.1 Technologie Level 2 und Service Pack 1, oder h??her
AIX Version 7.1 Technologie Level 1 und Service Pack 6, oder h??her
Bemerkung zur Unterst?ºtzung von AIX
Der POWER8 Compatibility Modus wird mit AIX Version 7.1 Technologie Level 3 und Service Pack 3 oder h??her unterst?ºtzt.
Alle fr?ºheren AIX 7.1 und AIX 6.1 Level k??nnen im POWER6, POWER6+ und POWER7 Compatibility Modus betrieben werden.
Die Easy Tier Funktionalit?§t der high function Backplane wird mit folgenden AIX Leveln unterst?ºtzt:
AIX Version 7.1 Technologie Level 3 und Service Pack 3 mit APAR IV56367 oder h??her
AIX Version 6.1 Technologie Level 8 und Service Pack 3 mit APAR IV56366 oder h??her
Unterst?ºtzung f?ºr IBM i, Linux und VIOS
IBM i Betriebssystem
IBM i 7.1 mit Technologie Refresh 8, oder h??her
IBM i 7.2, oder h??her

Linux Betriebssystem
Red Hat Enterprise Linux 6.5, oder h??her
SUSE Linux Enterprise Server 11 Service Pack 3, oder h??her
Ubuntu 14.04 (nur f?ºr Power S812L und Power S822L und ben??tigt PowerKVM)

Virtual I/O Server
VIOS 2.2.3.3
Die Easy Tier Funktionalit?§t der high function Backplane ben??tigt VIOS 2.2.3.3 mit dem Interim Fix IV56366 oder h??her
POWER8 Redbook Landing Page
Weitere Informationen
Agenda
… und Sonstiges
Neue Rack-Mount HMC 7042-CR8
Neuer HMC Code V8R8.1.0
PowerVM 2.2.3.3
IBM i 7.2
Verl?§ngerung Service f?ºr PowerHA 6.1
WDFM PowerVM Express Edition
Update zu PowerVC
Update zu PowerVP
HMC Performance Monitoring
HMC Performance Monitoring -Processor Utilization
SR-IOV
IBM Knowledge Center (KC)

CalCloud Government End-User Group
November 4, 2015
Introducing
Chris Cruz
Chief Deputy Director, Operations
Department of Technology
Agenda
Welcome
Introduction (Chris or myself)
CDFA migration of 70 apps (Hence)
Security (Dave)
Technical Architecture (Scott And Kyle)
Q/A
What is CalCloud?
CalCloud is a suite of cloud services offered by the Department of Technology, which includes:
IaaS – A private cloud infrastructure service:
O/S Licenses with Security updates
O/S Licenses (customer managed patching)
Customer Provided O/S (customer managed patching)
SaaS – Vendor Hosted Subscription Services (VHSS):
SalesForce
Clarity
Remedy on Demand
Lines of Business:
Disaster Recovery
Storage
Email
HR

CalCloud Strategy

Introducing

Robert Schmidt
Office of Technology (OTech) Chief
California Department of Technology
Introduction of User Group
User Group was implemented to:
Align IT Tactical efforts with IT Strategy;
Ensure that the CalCloud achieves its implementation roadmap;
Recommend CalCloud requirements;
Enhance CalCloud visibility while managing implementation risk;
Communicate the organization’ s cloud strategy to government business and IT leaders.

Introduction of User Group
Members are responsible for:
Serve as change champion within their agency;
Aligning tactical IT implementation with IT strategy;
Assess business impact of moving IT services to the hybrid cloud.

New User Group Lead
Hence Phillips – CDFA
CDFA has 70 applications running on CalCloud.
Time to deploy applications
Performance standards of applications
Ease of use for customers
Security
Lessons Learned/Tips

User Group Lead
Answer as a developer using CalCloud:
How does CalCloud help me do my job?
How does CalCloud solve my technical problem?
What do developers most appreciate about CalCloud?
What technical benefit do I receive from using CalCloud?

CDFA CalCloud Architecture
Introducing
Scott MacDonald
CalCloud Chief
California Department of Technology
Kyle E Pribilski
IBM

Introducing
David Langston
Branch Chief
Security Management
California Department of Technology
CalCloud Security General
Provide services that meet the operational and compliance requirements of the State.
SAM/SIMM
NIST
FedRAMP where applicable
Other regulatory if/where applicable
Ensure that vendors are conforming to best security practice.
CalCloud IaaS Security Goals
Provide a service that is equally or more secure to that which can be provided with a physical, dedicated infrastructure.
Support both mission-critical and non-mission-critical systems.
Provide an infrastructure that can meet the operational and compliance requirements of the State and supported agencies.

CalCloud IaaS Security Stack
CalCloud IaaS Security Controls
CalCloud IaaS Security Key Elements
CalCloud IaaS – Security Compliance Status
CDT Authorization to Operate based on FedRAMP v2 signed in Sept 2015.
Major documents and processes in place.
System Security Plan
Security Assessment Report
POAM tracking process
Privacy Threshold and Impact Report
Annual revue process.

CalCloud IaaS Security Then and Now
CalCloud IaaS – Security Dialog – Tenant Space
Questions & Answers

For more information, visit

????????????????????????????????????????????????????????????????????Chris Churchey – Principal ATS Group, LLC churchey@TheATSgroup.com (610-574-0207) October 2013
Exploit PowerVM Features to Maximize Performance & Efficiencies
© 2013 IBM Corporation
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© 2013 IBM Corporation
Exploit PowerVM Features to Maximize
Performance & Efficiencies
Multiple Shared Processor Pools (MSPP)
??????Exploit PowerVM Features to Maximize Performance & Efficiencies
What is MSPP?
? Group of physical processors
? Shared among multiple logical partitions
? The sum of the assigned capacity for each LPAR cannot exceed the total capacity of the processor group
? Applies to Power6 and above
3 © 2013 IBM Corporation
??????Exploit PowerVM Features to Maximize Performance & Efficiencies
Why use MSPPs?
? Reduce software license (e.g. # of cores) costs by placing LPAR(s) in their own pool – Customers have reported saving $100K to >$8M a year
? Share the software license across LPAR(s) by placing them in the same pool (e.g. Float across Prod & Dev)
? Limit a group of LPAR(s) to a combined MAX CPU consumption to protect others
– Example: Power 770 with 32 cores
• Dev LPAR(s) pool Max CPU=5
• Prod LPAR(s) pool Max CPU=32 (All)
4 © 2013 IBM Corporation
???????Exploit PowerVM Features to Maximize Performance & Efficiencies
MSPP Analysis
1. Identify candidate LPAR(s)
– Software licensed by # of cores currently Dedicated or Capped, or license ALL cores on
the server
2. Collect physical CPU usage for candidate LPAR(s)
3. View the candidate LPAR(s) over a period of time
4. Determine usage mix and observed Peaks
– The pool’s Maximum Processing Units = “peak observed + projected growth + buffer”
? NOTE: Galileo Performance Explorer makes this easy using Virtual Groups to view candidate LPAR(s)!
5 © 2013 IBM Corporation
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MSPP Analysis
6 © 2013 IBM Corporation
p795 with 23 LPARs, peaking 23 cores
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MSPP Analysis
7 © 2013 IBM Corporation
Selected 7 Oracle LPARs, peaking 12 Cores
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MSPP Analysis
8 © 2013 IBM Corporation
“What If” Shared Pool Analysis
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MSPP Analysis
9 © 2013 IBM Corporation
Performance View of Pool 0 and Pool 1
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MSPP Analysis
10 © 2013 IBM Corporation
Detailed Performance View of Pool 1 (Oracle Pool)
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MSPP Resources
? IBM PowerVM Virtualization Introduction and Configuration www.redbooks.ibm.com/abstracts/sg247940.html
? Exploiting IBM PowerVM Virtualization Features with IBM Cognos 8 Business Intelligence www.redbooks.ibm.com/abstracts/sg247842.html?Open
? Try it! MSPP Pools can be dynamically created, move LPAR(s) in & out, and increase/decrease MAX
? ATS can help analyze and implement MSPP
11 © 2013 IBM Corporation
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Exploit PowerVM Features to Maximize
Performance & Efficiencies
Shared Ethernet Adapters (SEA)
12 © 2013 IBM Corporation
??????Exploit PowerVM Features to Maximize Performance & Efficiencies
What is a SEA?
? Group Virtual I/O Server component that bridges a physical Ethernet adapter and Ethernet adapters
? LPAR(s) on the virtual network can share access to the physical network
? LPAR(s) on the virtual network can communicate with stand-alone servers and logical
partitions on other systems
? Eliminates the need for each client logical partition to a dedicated physical adapter
13 © 2013 IBM Corporation
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Why use SEAs?
? Required for Live Partition Mobility (LPM)
? Eliminate dedicated adapters to LPARs
? Reduce network switches, ports and cabling
? Reduce # of adapters, thus reduce slots/IO-drawers
? Share network bandwidth across LPARs
? Balance CPU load across VIO’s (1 often 100% Busy)
? Maximize network throughput using ALL adapters
14 © 2013 IBM Corporation
?????????Exploit PowerVM Features to Maximize Performance & Efficiencies
SEA Options
? SEA-NIB (Network Interface Backup) + vSwitches
– (2) Virtual Ethernet adapters per LPAR
– EtherChannel used on Client LPAR to designate Primary VIO – Script to balance Even/Odd LPAR to primary Even/Odd VIO – Preferred for Max Network Throughput and Availability
– Multiple VLANs NOT required
? SEA-HA (High Availability)
– (1) Virtual Ethernet adapter per LPAR
– All LPAR(s) network goes through 1 VIO w/failover to 2nd VIO – 2nd VIO Ethernet ports idle, unused performance
? SEA-HA Load Sharing (aka Load Balancing)
– Requires multiple VLANs which are balanced between VIO’s – It chooses which VLANs go to which VIO’s
– Requires manual ‘chdev’ to restart if failover
15 © 2013 IBM Corporation
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SEA Architecture – NIB w/vSwitches
16 © 2013 IBM Corporation
1Gb (80-100MB/s) + 1Gb (80-100MB/s) Load Balance=200MB/s
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SEA Architecture – HA
17 © 2013 IBM Corporation
1Gb (80-100MB/s) 1Gb (80-100MB/s) Backup-Wasted
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SEA Architecture – HA Load Sharing
18 © 2013 IBM Corporation
1Gb (80-100MB/s) + 1Gb (80-100MB/s) Load Sharing=200MB/s
??????Exploit PowerVM Features to Maximize Performance & Efficiencies
SEA Analysis
1.
Collect physical CPU and SEA usage for VIO LPARs
2.
Look for:
3. 4.
If using SEA-NIB today, balance script on all LPARs
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© 2013 IBM Corporation
– View VIO LPARs over a period of time
– 1 VIO with high/max CPU and other minimal
– 1 VIO SEA at max throughput (flat line) and other minimal
If using SEA-HA today, use Load Sharing feature
– NOTE: Galileo Performance Explorer can display this performance information quickly
and easily!
??????????????????Exploit PowerVM Features to Maximize Performance & Efficiencies
SEA Analysis – NIB
? Host SEA Network Packet Send & Receive ? Host Physical CPU Utilization Summary Throughput
20 © 2013 IBM Corporation
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SEA Analysis – HA
? Host SEA Network Packet Send & Receive ? Host Physical CPU Utilization Summary Throughput
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Exploit PowerVM Features to Maximize
Performance & Efficiencies
NPIV vs. vSCSI Performance
22 © 2013 IBM Corporation
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What is NPIV and vSCSI?
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NPIV
vSCSI
? Allows a single HBA to register multiple WWPNs
? A SCSI disk, or a volume or file in a VIO Server that is exported to a virtual IO client
? Each virtual server presents a different WWPN to the SAN
? LUNs implement a sub-set of the SCSI protocol
? Each virtual server will see its own unique storage
??????Exploit PowerVM Features to Maximize Performance & Efficiencies
Why NPIV over vSCSI?
? Higher throughput from client LPAR
? Higher IOps from client LPAR
? Better hdisk Service Time from client LPAR
? Less CPU usage by the VIO LPAR
? Load Balance IO across HBAs from client LPAR
24 © 2013 IBM Corporation
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NPIV vs. vSCSI Architecture
25 © 2013 IBM Corporation
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NPIV/vSCSI Test configuration
? AIX LPAR (gvicaix71-10) on a p700 blade and IVM – (2) 8Gb HBA to V7000
• (4) 100GB vdisks (LUNs) created…same mdisk/array group
– (vSCSI) =?(2) 100GB LUNs mapped to VIO, mkvdev to AIX LPAR
• hdisk3 and hdisk4 on gvicaix71-10
– (vfc) =?(2) 100GB LUNs mapped to (2) wwpn’s on AIX LPAR
• hdisk1 and hdisk2 on gvicaix71-10
? ndisk64 Seq./Random Read/Write 4K/256K tests
26 © 2013 IBM Corporation
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NPIV/vSCSI Test configuration
27 © 2013 IBM Corporation
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NPIV vs. vSCSI IOps
28 © 2013 IBM Corporation
NPIV vSCSI
NPIV: Over 500 more IOps!
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NPIV vs. vSCSI Read Service-Times
29 © 2013 IBM Corporation
NPIV
vSCSI
NPIV: 0.75ms faster!
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NPIV vs. vSCSI Write Service-Times
30 © 2013 IBM Corporation
NPIV
vSCSI
NPIV: 0.50ms faster!
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31 © 2013 IBM Corporation
Questions and Answers
???????Exploit PowerVM Features to Maximize Performance & Efficiencies
? We can help analyze and implement. Contact us! ? Check-out Galileo Performance ExplorerTM
– Visit our booth for a hands-on demo
– Complimentary* no-strings attached 6 months use for Conference attendees – Budget-friendly subscription pricing request
* First time Galileo user
32 © 2013 IBM Corporation
www.GalileoSuite.com
??????????????????Exploit PowerVM Features to Maximize Performance & Efficiencies
Referenced Material
?IBM PowerVM Virtualization Introduction and Configuration www.redbooks.ibm.com/abstracts/sg247940.html
www.redbooks.ibm.com/abstracts/sg247842.html (Managing and Monitoring) ?SEA?NIB vs. SEA?HA vs. SEA?HA?Load Sharing
www.ibm.com/developerworks/mydeveloperworks/blogs/aixpert/entry/shared_ethernet_adapter_sea_failover_with_l oad_balancing198?lang=en
www.ibm.com/developerworks/mydeveloperworks/blogs/AIXDownUnder/entry/shared_ethernet_adapter_load_sharin g_and_virtual_switches133?lang=en
? SEA?NIB?vSwitches
www? 03.ibm.com/support/techdocs/atsmastr.nsf/fe582a1e48331b5585256de50062ae1c/81c729a840b213b98625779e000722f4/$FI LE/PowerVM?VirtualSwitches?091010.pdf
ibmsystemsmag.blogs.com/aixchange/2011/09/higher?availability?for?vio?clients?an?alternative.html
? NPIV www.ibm.com/developerworks/aix/library/au?NPIV/index.html
?Galileo Performance Explorer www.galileosuite.com
* First time Galileo user
33 © 2013 IBM Corporation