Torrent Suite SoftwareAdministration Guide

Torrent Suite Software space on Ion Community

Axeda Remote System Monitoring (RSM)

Overview

The Axeda RSM (Remote System Monitoring) agent is a software component installed automatically on the Torrent Server and Ion sequencers via the software update process.

Approximately every sixty seconds, t his agent sends a heartbeat message to Thermo Fisher. This information is used to track the deployment and software configuration of machines in the field.

Data is collected in the Axeda monitoring database, where Thermo Fisher technical support personnel can review the information collected by the agents. Since the heartbeat message is sent many times an hour, Tech Support can quickly seeif a machine is online, the software versions, and some technical details about the instrument such as temperature and hard drive status.

The agent also allows Ion Torrent to remotely log into the Ion PGM and Ion Proton s ystems and the Torrent Server, whichis required for system support. Without remote access, Ion Torrent Field Application Scientists cannot access,view, and troubleshoot issues regarding machine performance.

Data automatically collected by the RSM Agents

Field names, data types, and examples of the data being collected are described in the following tables. This information is being sent automatically from the Torrent Servers and Ion s equencer s back to Thermo Fisher.

Torrent Server

Event Name	Type	Sample Value
TS.Config.biosversion	String	A07
TS.Config.configuration	String	standalone
TS.Config.hostname	String	Ion-torrent-server
TS.Config.hwname	String	Precision WorkStation T7500
TS.Config.ipaddress	String	10.1.3.234
TS.Config.mode	String	Master
TS.Config.serialnumber	String	1SMJFP1 (Dell service tag)
TS.Contact.IT Contact	String	ionuser@iontorrent.com
TS.Contact.Lab Contact	String	ionuser@iontorrent.com
TS.host	String	Ion-torrent-server
TS.HW.HD./results	Analog	97.220102
TS.TYPE	String	TS1
TS.Version.alignment	String	3.2.1-1
TS.Version.analysis	String	3.2.3-1
TS.Version.dbreports	String	3.2.4-1
TS.Version.docs	String	3.2.1-1
TS.Version.referenceLibrary	String	2.2.0
TS.Version.tmap	String	3.2.0-1
TS.Version.tsconfig	String	3.2.3-1
TS.Location.City	String	Rockville
TS.Location.Org-Name	String	Acme, Inc.
TS.Location.Postal-Code	String	20847
TS.Location.State	String	MD
TS.Location.Street-Address	String	1313 Mockingbird Lane
TS.PGM.1	String	11c111222
TS.PGM.Default	String	11c111222
TS.Server.Crawler	String	ok/offline/error
TS.Server.Archive	String	ok/offline/error
TS.Server.Job	String	ok/offline/error
TS.Server.Plugin	String	ok/offline/error
TS.Experiment	String	serial_number:sn09c121501 run_number:22 chipbarcode:BA0000531 chiptype:316C flows:260 cycles:8 gain:0.63300000000000001 noise:6.24 cal_chip_high_low_inrange:[19052, 9272, 6309130] sysSNR:12.18 aveKeyCounts:40.0 total_mapped_target_bases:1213471703 totalNumReads:5708499 q17_mean_read_length:200.0 q20_mean_read_length:190 RunType:WGNM targetRegionBedFile:/results/uploads/BED/37/hg19/unmerged/detail/TRfilename.bed hotSpotRegionBedFile:/results/uploads/BED/25/hg19/unmerged/detail/HSRfilename.bed isBarcoded:True numBarcodes:1

Ion PGM data

Event Name	Type	Sample Value
Instrument.Alarm.XXX	string	All alarms withoutcustomer sensitive informationare sent, e.g. PressureTooLow, BadBootDriveDetected, etc.
Instrument.Event.XXX	string	All events withoutcustomer sensitive informationare sent, e.g. CompletedRunInfo Pressure RunAborted
Instrument.Event.Pressure	analog	0 (chart)
Instrument.Event.ValveBoard	string	Valve Board not accessible Valve Board Down Stream Errors Valve Board Up Stream Errors
Instrument.Event.RunAborted	String	Run aborted
Instrument.Event.LostChipCon	String	Lost chip connection, run aborted
Instrument.Event.UBoot	String	U-boots dont match
Instrument.Event.Kernel	String	Kernels dont match
Instrument.Event.ResultsDrive	String	Results drive not accessible
Instrument.Event.BootDrive	String	Bad boot drive detected
Instrument.Event.DataDrive	String	Bad data drive detected
Instrument.HW.HD1	analog	34.001 (chart)
Instrument.InstrumentName	String	Stork
Instrument.Pressure	Analog	10.2 (chart)
Instrument.Temperature	Analog	27.06 (chart)
Instrument.TYPE	String	PGM1
Instrument.Version.Board	String	4 A.1
Instrument.Version.Board_Serial	String	012123
Instrument.Version.Datacollect	String	180
Instrument.Version.driver	String	31
Instrument.Version.fpga	String	70
Instrument.Version.Graphics	String	15
Instrument.Version.LiveView	String	268
Instrument.Version.OS	String	12
Instrument.Version.RSMAgent	String	2.01
Instrument.Version.Scripts	String	16.3.58

Ion Proton data

Ion Proton data is divided into these categories:

BIOS These items provide the version numbers for the various BIOS software images installed on the instrument.
DataCollect These items come from the instrument configuration file.
RunData These items reflect parameters from the last Auto pH or sequencing run.
Status These items reflect the current instrument parameters.
System These items provide parameters related to the operating system supporting the instrument.
Version These items provide the version numbers for the various software packages installed on the instrument.

In addition, some items (CleaningTime, InstrumentState, Type) are not placed in any category.

The number and names of these entries are subject to change across software releases.

Data Item Name	Type	Sample value
BIOS.BIOS	String	SE5C600.86B.01.08.0003
BIOS.BMC	String	1.17.4151
BIOS.FRU	String	1.09
BIOS.ME	String	02.01.07.112
CleaningTime	String	2013/06/05
DataCollect.AdvAvgr	Analog	0
DataCollect.AdvScriptFeatures	String	2048
DataCollect.aNucTime	Analog	1.1
DataCollect.AutoAnalyze	String	yes
DataCollect.AutoDelete	String	yes
DataCollect.AutopHMaxStepVol	Analog	0
DataCollect.AutopHTarget	String	0
DataCollect.AutopHW1Diluted	Analog	1
DataCollect.AutopHW1ToSave	Analog	0
DataCollect.CheckSum	String	0001bc02
DataCollect.ChipBayLogFile	String	/software/chipBayTempLog.txt
DataCollect.ChipBayLogLevel	String	0
DataCollect.ChipBayTemperature	String	30
DataCollect.ChipCoolerIntegralTerm	String	0.004
DataCollect.ChipCoolerLogFile	String	/software/chipCoolerTempLog.txt
DataCollect.ChipCoolerLogLevel	String	3
DataCollect.ChipCoolerProportionalTerm	String	0.15
DataCollect.ChipCoolerTecDutyMax	String	23039
DataCollect.ChipCoolerTemperature	String	0
DataCollect.ChipModeOverride	Analog	0
DataCollect.cNucTime	Analog	1.1
DataCollect.DacMax	String	3.3
DataCollect.DacMin	String	0
DataCollect.DefaultPressure	String	8
DataCollect.DHCP	String	yes
DataCollect.ECC_enabled	String	no
DataCollect.Emulate	String	no
DataCollect.EmulateDataDir	String	0
DataCollect.EmulateP1.0	String	no
DataCollect.EmulateP1.1	String	no
DataCollect.EmulateP1.2	String	no
DataCollect.EmulateSpeedUp	String	no
DataCollect.EmulateWholeChip	String	no
DataCollect.EnableVarNucFlowTimes	String	no
DataCollect.ExpertFeatures	String	yes
DataCollectFlowsSinceClean	Analog	0
DataCollect.ftppassword	String	ionguest
DataCollect.ftprootdir	String	results
DataCollect.ftpserver	String	gs1-ftp.ite
DataCollect.ftpusername	String	ionguest
DataCollect.fullChipFtp	String	no
DataCollect.Gateway	String	0
DataCollect.gNucTime	Analog	1.1
DataCollect.hwvfc	String	no
DataCollect.IonHome	String	updates.ite/BB
DataCollect.IP Address	String	127.0.0.1
DataCollect.LocalHome	String	0
DataCollect.MaxTemp	String	38
DataCollect.MinTemp	String	36
DataCollect.name	String	d1
DataCollect.Netmask	String	0
DataCollect.nfsDirectory	String	0
DataCollect.nfsEnabled	String	no
DataCollect.OnInstrAnalysis	String	yes
DataCollect.OPHigh	String	10.5
DataCollect.OPHighTol	String	0.5
DataCollect.OPLow	String	9
DataCollect.OPLowTol	String	0.5
DataCollect.OPZero	String	0
DataCollect.OPZeroTol	String	3
DataCollect.OverSample	String	1
DataCollect.pcigen3	String	no
DataCollect.PGMStatus	String	0
DataCollect.RollTempPres	String	no
DataCollect.RollTempPresLogLevel	Analog	0
DataCollect.RollTempPresLogMax	Analog	60
DataCollect.RollTempPresTzero	Analog	26.5
DataCollectRunsSinceClean	Analog	1
DataCollect.SdatColSize	String	216
DataCollect.SdatRowSize	String	224
DataCollect.Serial	String	2456156-5-0008
DataCollect.streamThumbnail	String	yes
DataCollect.SynchDatCompression	String	9
DataCollect.TimeMode	String	0
DataCollect.TimeServerName	String	192.168.1.1
DataCollect.TimeZone	String	-1
DataCollect.tNucTime	Analog	1.1
DataCollect.TSPasswd	String	ionadmin
DataCollect.TSUrl	String	blackbird
DataCollect.TSUserName	String	ionadmin
DataCollect.UID	String	160
DataCollect.useHwThumbnail	String	no
DataCollect.UseOnlyHDD	String	no
DataCollect.UserName	String	user
DataCollect.UseSynchDats	String	no
DataCollect.UseT0Compression	String	no
DataCollect.use_fps	Analog	0
DataCollect.VarReg_ChipP_init	Analog	0
DataCollect.VarReg_ChipP_run	Analog	0
DataCollect.VarReg_MainP_init	Analog	0
DataCollect.VarReg_MainP_run	Analog	0
DataCollect.VFC	Analog	0
DataCollect.WarnPressHigh	String	11
DataCollect.WarnPressLow	String	10
DataCollect.WarnTempHigh	String	35
DataCollect.WarnTempLow	String	10
DataCollect.WriteRowSum	String	no
DataCollect.WriteRowSumEnd	Analog	100
DataCollect.WriteRowSumPixel	Analog	200
DataCollect.WriteRowSumStart	Analog	1
DataCollect.WriteRowSumTile	Analog	50
DataCollect.WriteSwRowSumSum	String	no
DataCollect.xfrDiagBlks1	Analog	10
DataCollect.xfrDiagBlks2	Analog	50
InstrumentState	String	Idle
RunData.a1a2	String	R_2012_12_17_13_01_08_user_F4--145 W1.dat dffffe cntArry 9 0 0 9
RunData.AutoPhFinal	Analog	7.660635
RunData.AutoPhInitial	Analog	6.321023
RunData.AutoPhIterations	Analog	4
RunData.AutoPhResult	String	Pass
RunData.AutoPhTotalW1Volume	Analog	12.5
RunData.ChipGain	Analog	1.066389
RunData.ChipPixelAverage	Analog	8241
RunData.ChipPixelsInRange	Analog	164698460
RunData.ChipPixelsPinnedHigh	Analog	0
RunData.ChipPixelsPinnedLow	Analog	676
RunData.ChipTemp	Analog	81.826172
RunData.CpuTemp0	Analog	53
RunData.CpuTemp1	Analog	74
RunData.efuse	String	********L:Q6C841,W:4,J:WC2012C00086-C00272,P:16,C:PT4,F:F6,Y:4,X:0,B:3,SB:31,B:1P,N:343***********************************
RunData.FpgaMasterTemp	Analog	113
RunData.FpgaSlaveTemp	Analog	118.4
RunData.GpuTempC	Analog	82
RunData.LastAutoPhRealPh	Analog	766
RunData.LastAutoPhRef	Analog	745
RunData.LastAutoPhTarget	Analog	770
RunData.W1pH	Analog	8762
RunData.W2pH	Analog	7619
RunData.W3RefpH	Analog	7.45
Status.HDPctFull	Analog	0.823612
Status.Pressure0	Analog	7.98
Status.Pressure1	Analog	10.45
Status.SsdPctFull	Analog	6.220454
Status.Thermistor0	Analog	-13.24
Status.Thermistor1	Analog	30.07
Status.Thermistor2	Analog	27.56
Status.Thermistor3	Analog	30.04
Status.Thermistor4	Analog	26.16
System.CpuUsagePct	Analog	7
System.Date	String	2013-01-0
System.FreeMemoryKB	Analog	129951948
System.Hostname	String	d1.ite
System.IpAddress	String	10.25.3.150
System.PhysMemTotalGB	Analog	128
System.Time	String	03:42:58 PM GMT
TYPE	String	Proton1
Version.Datacollect	String	206
Version.DiskImage	String	2012_09_24
Version.Graphics	String	27
Version.KernelRelease	String	3.2.1-ionrt3
Version.LiveView	String	129
Version.OIA	String	18
Version.OS	String	11
Version.Reader FPGA	String	1b000076
Version.Reader FPGA1	Analog	13000076
Version.Reader Woddr FPGA	String	b000027
Version.Reader Woddr FPGA1	String	3000027
Version.RSM	String	4
Version.Scripts	String	2.0.63
Version.Valve FPGA	String	200a

Remote access for troubleshooting

In the event that there is a problem with the Ion sequencer or Torrent Server, this agent will allow Thermo Fisher support personnel to remotely:

Collect log files from the systems for review
Restart the device
Upgrade software
Provide a remote login connection to the device for further diagnostic work

These types of activities would only be initiated at the request of the administrative contact, to ensure compliance with site security policies.

When a issue with the Ion PGM system, Ion Proton system, Ion S5 system, or Torrent Suite Software is reported, we make every effortto solve the issue by telephone or email. If remote access is required for additional troubleshooting, a member of Thermo Fisher support staff requires authorization from the technical contact to initial remote connection. Only after getting authorizationdoes anyone from Thermo Fisher proceed with remote troubleshooting. Once the issue is resolved you are benotified. Additional authorization is required before initiatinganyfurther remoteassistance.

FAQ

What is Axeda?

Axeda is a software provider that Thermo Fisher has partnered with to develop this Remote Monitoring solution. Thermo Fisher has used Axeda successfully with other products (see http://www.axeda.com/community/customers/applied-biosystems ).

What is the benefit of these agents?

The Remote System Monitoring agents facilitate Thermo Fisher's ability to help our customers maintain their systems in running order. The agent provides system metrics many times a hour and if a problem with a sequencer or Torrent Server is detected, the RSM agent provides real time warnings to help proactively diagnose issues before they cause any failures and downtime.

Thermo Fisher has invested significantly in the development of this tool in order to best serve our customers. Without access to the RSM agent, issues may not be detected until the system goes down. Furthermorewithout the remote access capabilitiesdiagnosingand implementing a solution can take much longer and will require significant back and forth over telephone and email with your onsite personal.

By using the agent, downtime can be reduced to hours instead of days and requireminimalonsite resources.

Can the agent be disabled?

Thermo Fisher has invested significantly in the development of this tool in order to best serve our customers. By using the agent, potential issues can be detected before the issues cause downtime. And in case troubleshooting is required, remote access through the agent can reduce resolution time to hours instead of days and require minimal onsite resources. Also keep in mind that no remote troubleshooting can be provided without this agent.Therefore, disabling this agent is not recommended.

If despitethese advantages the agent needs to be disabled, the site firewall can block outbound port 22 and 443.

Contents

Torrent Suite™ Software Administration Guide