CHROMSTOGRAPHY SOFTWARE

CLARUS 600 GC IPM

Installation Manual
Clarus 600 GC IPM
Installation Manual
Release History

Part Number Release Publication Date

N5156089 A November 2006

Any comments about the documentation for this product should be addressed to:

User Assistance
PerkinElmer, Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.

Or emailed to: info@perkinelmer.com

Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no
warranty of any kind with regard to this document, including, but not limited to, the implied
warranties of merchantability and fitness for a particular purpose.
PerkinElmer shall not be liable for errors contained herein for incidental consequential damages in
connection with furnishing, performance or use of this material.
NOTE: TotalChrom is the updated version of the software previously marketed as Turbochrom. This
product is compatible with TotalChrom and Turbochrom version 6.1.x. The term TotalChrom has
been used throughout this document to denote either system.

Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form whatsoever or
translated into any language without the prior, written permission of PerkinElmer, Inc.

Copyright © 2006 PerkinElmer, Inc.

Produced in the USA.

Trademarks
Registered names, trademarks, etc. used in this document, even when not specifically marked as such,
are protected by law.

PerkinElmer is a registered trademark of PerkinElmer, Inc.

2

Table of Contents

Instrument Configuration................................................................................3
Cable Requirements.................................................................................3
Uploading Instrument Configuration for TotalChrom.............................3
Supported Instrument Functions .....................................................................4
dotLINK Error Messages ................................................................................8
Clarus GC Specific IPM Errors .............................................................13
Wiring Diagram ............................................................................................16
 Clarus 600 GC IPM
The PerkinElmer dotLINK Interface is used with PerkinElmer software products to
acquire and buffer digital data from laboratory instruments and to control the
operating parameters of such instruments. To perform these functions, firmware
must be down-loaded from the host computer to the dotLINK Interface. This
firmware is called an Instrument Personality Module (IPM); there is a unique IPM
for each instrument that can be controlled by the dotLINK Interface. The dotLINK
may be installed inside the Clarus GC or as a standalone external box.
SoftLINK is a software emulation of the dotLINK hardware. It may be used with
TotalChrom Workstation only, not with Client/Server. Refer to the SoftLINK User’s
Guide for information on this configuration.
In addition to down-loading the IPM to dotLINK, the host software requires
configuration information that describes the features available on the specific
instrument in use. This information is contained in a LIB file that is read by the
Configuration Utility of the host software. The IPM file and the LIB file are provided
on the distribution media.
Prior to using dotLINK for controlling a Clarus GC, you must install the PAK for the
PerkinElmer AutoSystem GC and Clarus GC. This document provides instructions
for the following procedures:
1. Installation of the necessary cables to connect the Clarus 600 GC to a
PerkinElmer dotLINK Interface.
2. Initial configuration of the Clarus 600 GC communication parameters.
Information concerning installation of dotLINK is available in the dotLINK User’s
Guide. Information on the routine use of the software is available in the product
documentation.
The dotLINK Interface is available in two forms. The stand-alone module that
connects to both the host computer and to the controlled Clarus GC. The Integral
dotLINK is a version of dotLINK that is installed inside the Clarus GC. The

Clarus 600 GC IPM 1

 operation of these various models is identical from the user perspective, only the
cabling is different. However, the Integral dotLINK is capable of controlling only
one Clarus 600 GC, while an external dotLINK can control up to three GCs.

2 Clarus 600 GC IPM

Instrument Configuration
The Clarus 600 GC firmware should be Revision 1.8 or later. Also verify that on the
Clarus GC analog terminal strip positions 5 and 6 are jumpered together.

Cable Requirements
Connect the external dotLINK to the RS-232 External Computer port of the Clarus
600 GC using the PerkinElmer cable P/N 0929-0146, 10 foot or P/N 0929-0147, 25
foot.
A wiring diagram of this cable is provided in the Appendix of this manual.
If you are using a Clarus GC with an Integral LINK, connect the captive RS-232
cable to the External Computer port, located under the electronics access panel of the
Clarus 600 GC.
If you are using SoftLINK, connect the Clarus 600 external computer port to the
selected COM port of the PC using cable P/N N650-0143. Check the cable ends to
determine which end connects to the Clarus 600 GC.

Uploading Instrument Configuration for TotalChrom

The Clarus 600 GC IPM supports the [Query Inst for Config] button in
TotalChrom’s CONFIG program. It is strongly recommended that this feature be
used instead of manually setting the instrument configuration in CONFIG.
If any configuration changes need to be made you should first release control,
make the changes at the GC and then use [Query Inst for Config] to
update TotalChrom’s configuration. This prevents illegal configurations from
being specified which will result in a dotLINK error when you attempt to
download a method to the GC.
Furthermore, if you do get a dotLINK error when you try to download a method to
the GC it is helpful to try to manually enter the setpoints at the GC’s keypad. Some
pressure/flow settings have limits that depend upon column dimensions and
temperatures that are not available to TotalChrom at the time the method is created.
For a list of dotLINK Error Messages, refer to the “dotLINK Error Messages”
section.

Clarus 600 GC IPM 3

Table 1
Supported Instrument Functions
The IPM for the Clarus 600 GC supports the instrument functions and configurations
listed in Table 1. The accepted values for configuration options and method
parameters are also tabulated.

FUNCTION PARAMETER VALUES NOTES

Inlet Configuration None, PKD, CAP, GSV, PKD = Packed Column
POCI, POCO, PSSI, PSSO
CAP = Capillary
GSV = Gas Sampling Valve
POCx = Programmable On-
Column
PSSx = Programmable Split
Splitless
Valves Installed (1-6) None, Valve, Split GSV
Valve State (1-6) ON, OFF
Detectors (A, B) None, FID, TCD, ECD, FID = Flame Ionization
NPD, PID, FPD, Extn, Detector
Output
TCD = Thermal
Conductivity Detector
ECD = Electron Capture
Detector
NPD = Nitrogen-
Phosphorus Detector
PID = Photo Ionization
Detector – use FID
FPD = Flame Photometric

Detector Range (A, B) FID, PID, NPD, EXTN,

OUTPUT: 1, 20, TCD: −4
to 4, FPD: 0, 1
Detector Polarity (TCD) +, −

4 Clarus 600 GC IPM

 FUNCTION PARAMETER VALUES NOTES
Detector Autozero ON, OFF
Detector Mode −, NP, NOHEAT, HEAT,
LIN, NONLIN
Data Channel (A, B) Det A, Det B, Det A -
Comp1, Det B - Comp2
Analog Attenuation
Recorder
−6 (Attenuation = 1) to +6
(Attenuation = 4096)
Integrator -6 (Attenuation = 1) to 0
(Attenuation = 64)

Analog Offset Recorder −50 to 100% FS

Integrator −0.5 to 1000 mV
Sampling Rate (Hz) 50, 25, 12.5, 6.25, 3.125,
1.5625
Time Constant 50, 200, 800 mSec
Injection Type Manual, Auto
Injection Site Front, Rear
Vial Number 0 to 82
Injections Per Vial 1-15
Syringe Capacity 0.5 μL, 5 μL
Sample Size 1 to 5 fifths of 0.5μL, 1 to
10 tenths of 5μL
Injection Speed Normal, On-Column, Fast
Pre-Inj Sample Wash 0 to 15

Clarus 600 GC IPM 5

 FUNCTION PARAMETER VALUES NOTES
Sample Pumps 0 to 15
Viscosity Delay 0 to 15 sec
Post-Inj Solvent Wash 0 to 15
Wash/Waste Vial 1, 2
Pre-Sequence Solvent Wash 0, 1, 2
Inlet Temperature (A, B) 0, 50 to 450
Initial Temp Hold Time
Ramps (3)
Detector Temperature 0, 100 to 450, 0 = Off
Oven Max. Temperature 50 to 450
Oven Equilibrium Time 0 to 99.9 min
Cryogenics Off, LN2, CO2
Oven Temp Program Limited to 3 ramps
on TotalChrom
a. Initial Temp −99° C to Oven Max versions prior to v
b. Initial Hold 0 to 999 min 6.3.1. Rate is
dependent of
c. Ramps (9) instrument
(i.) Rate 0 to a max of 20 to 140 °/min configuration, line
(ii.) End Temp −99° C to Oven Max voltage and oven
(iii) Hold Time 0 to 999 min setpoint.
Timed Events
a. Det. Range (1, 2) −4 to 4,20
b. Valve (1, 6) ON, OFF
c. AutoZero (1, 2) ON, OFF
d. Attenuation (1, 2) −6 to 10 (1,2) DET1, DET2
e. Output Event Times −99.9 to 999.9
Real-Time Valve Setpoint ON, OFF
Aux Zone Temp None, AUX, TCD
Aux Aone Temp 0, 100 to 450

6 Clarus 600 GC IPM

 FUNCTION PARAMETER VALUES NOTES
Pneumatics Type None; Pressure - psig; Cflow holds a constant flow
Pressure - kPa; Flow - He; given an initial pressure.
Flow - N2; Flow - H2; Flow
- Ar/CH4; Cflow - He;
Cflow - N2; Cflow - H2;
Cflow - Ar/CH4; Pflow -
He; Pflow - N2; Pflow - H2;
Pflow - Ar/CH4; Pvel - He;
Pvel - N2; Pvel - H2; Pvel -
Ar/CH4; Press - He; Press -
N2; Press - H2; Press -
Ar/CH4
Pressure/Flow Setpoint 0 to 99.9 psi; 0 to 700 kPa;
0 to 500.0 mL/Min

Clarus 600 GC IPM 7

dotLINK Error Messages
The following errors may be reported by the host software. Following each error is a
description of potential problems that may result in the error message. Additional
Clarus GC errors are documented at the end of this section.

0 No error occurred.
ERROR command was given and no error had occurred.
1 File already exists.
A task tried to create a file, but it already exists.
Could be result of corrupted IPM.
2 File does not exist.
A task tried to access a non-existent file.
Could be result of corrupted IPM.
3 PCB is already open.
A task tried to open a Pipe Control Block that was already being used.
Could be result of corrupted IPM.
4 File is already open.
A task tried to open a file that was already open.
Could be result of corrupted IPM.
5 File is protected (read only)!
A task tried to write to a file that is read only.
Could be result of corrupted IPM.
6 PCB has no open file. No file was open.
A task tried to read from or write to a file that had not been opened yet.
Could be result of corrupted IPM.
7 File not open for write.
A task tried to write to a file that had not been opened yet.
Could be result of corrupted IPM.
8 File not open for read.
A task tried to write to a file that had not been opened yet.
Could be result of corrupted IPM.
Could be result of bug in LINK OS EPROM.

8 Clarus 600 GC IPM

 9 Illegal calling parameters.
Probably result of bug in IPM.
Could be result of corrupted IPM.
10 Ran out of memory.
LINK is not supposed to begin a run if there would not be enough space to
hold all the data.
Could be result of corrupted IPM.
11 Ran out of directory entries.
LINK has a limit of 512 files. This error could result from a lot of very short
runs.
Probably result of connecting too many instruments to LINK.
Could be result of corrupted IPM.
12 Ran out of Task Control Blocks.
This is probably the result of a task which creates new tasks but fails to
return Task Control Blocks to system when done. May require that the
rogue task execute several times before error occurs.
Could be result of corrupted IPM.
13 Memory Pool does not exist for this file.
14 Unexpected end of file or device timed-out.
Probably result of communications failure via Serial Port.
Could be result of corrupted IPM.
15 Ran out of Pipe Control Blocks.
This is probably the result of a task which requests Pipe Control Blocks
from System but fails to return them when done. May require that the rogue
task execute several times before error occurs.
Could be result of corrupted IPM.
16 Pipe Control Block not assigned to Task yet.
Could be result of corrupted IPM.
17 Illegal filename.
Illegal characters were given in a filename.
Could be result of corrupted IPM.

Clarus 600 GC IPM 9

 18 File is erased.

19 This is a DEVICE not a file.

20 File is too large.
This error results if you try to download an IPM that is larger than 16K
bytes.
Could be result of a corrupted IPM file at Host computer.
21 BIN failed verification during write operation.
When you download an IPM, LINK always verifies that it was written
correctly. If verification fails, then this error would result.
Could be result of defective SRAM chip(s).
Could be result of bug in Host control program.
22 Syntax error on command line.
Although LINK recognized the command, the parameters on command line
do not make sense.
Could be result of corrupted IPM.
23 Cable not connected.
Probably result of cable not plugged into LINK port.
Could be result of improperly wired RS-232 cable.
24 STOP command was given.
The STOP command does not apply to instrument control and thus should
never be issued to an IPM.
25 Binary data not allowed here.
26 Not allowed in an INVOKE file.
Could be result of corrupted IPM.
27 BIN library is not compatible.
Probably result of using an out-of-date LINK EPROM or an out-of-date
IPM.
Could be result of corrupted IPM.
28 BIN library is corrupted or not available.
Probably result of corrupted IPM.
29 Command line parameter is out of range.
Probably result of an incorrectly configured Clarus GC.
Could be result of bug in IPM or LINK EPROM.

10 Clarus 600 GC IPM

 30 BIN module not found in any of the libraries.
LINK could not find the IPM given in the INSTALL command.
31 Device expected here, not file.
An operation was attempted on a file that is only allowed for a device, such
as setting Baud rate with the MODE command.
32 Illegal character found in string.
33 BIN is in use.
This error results if the Host computer tries to erase (BINERASE) or
download to (BINCOPY) an IPM while it is in use (still INSTALLED).
34 Circular input buffer overflowed.
Probably result of data arriving at port before the IPM was installed.
Release control from the Clarus touch screen.
35 Instrument does not respond.
Probably result of instrument being turned off.
Could be result of disconnected RS-232 cable.
36 Command is out of sequence.
This error results when certain commands are given before prerequisite
commands are given.
37 Interrupt not serviced fast enough.
Too much data arrived at instrument port for the CPU to handle.
38 Handle does not exist.
40 GPIB is not bus controller.
No longer a valid error..
50 Command not recognized.
Probably result of bug in Host software.
51 Record is too long for buffer.
Probably fault of RS-232 communications.
52 Ran out of Handles.
This is probably the result of a task which asks for handles from the LINK
Operating System, but neglects to give them back when done with them.
Probably result of a corrupted IPM.

Clarus 600 GC IPM

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1
 53 Ran out of Chores.
This is probably the result of a task which asks for chores from the LINK
Operating System, but neglects to give them back when done with them.
Probably result of a corrupted IPM.
54 Extra Acknowledgment was received.
Results when LINK receives a packet protocol acknowledgment it was not
expecting.
60 Communications error.
Probably result of incorrect Baud rate.
Could be result of noise on RS-232 line.
61 Instrument reports an error.
Probably result of a problem at the instrument. See tabulation of error
messages later in this section.
Could be result of an improper configuration.
The instrument which LINK is controlling has reported an error.
The error message is instrument specific.
62 IPM was already installed.
An INSTALL command was issued when an IPM had already been
installed at that port.
63 Parameter cannot be changed in this mode.
This error typically occurs when the host system attempts to send a non-
setpoint parameter while the chromatograph is in the midst of a run.
64 This is a read only parameter.
This error typically occurs when the host system attempts to change a
parameter that cannot be edited.
65 LINK has not taken control of the instrument yet.
Many instrument commands require that the instrument be seized.
This error results if SEIZE command was not issued first.
66 Autosampler not installed.
Probably result of improper configuration.
67 Data segment has not been released with OC command.
99 The subroutine that was called is not finished yet.
Probably result of a corrupted IPM.
255 Fatal system error.
This error will result on recovery from a Fatal System Error.

12 Clarus 600 GC IPM

Clarus GC Specific IPM Errors

61 ERROR: 100 GETN MUST BE USED TO GET ENTIRE

STRUCTURE
This occurs if the IPM attempts to get a structure from the GC with the GET
command when the GETN command is required. A syntax error, it would
most likely occur if the communications were somehow garbled and the N
character of GETN were lost.
61 ERROR: 101 TOO MANY PARAMETERS FOR THE ARRAY SIZE
This would occur if a structure, e.g., a method, was sent down with too
many entries in it. The problem should only occur if two SET structures
were somehow garbled into one during communications.
61 ERROR: 103 PARAMETER IS READ ONLY
The IPM is attempting to SET a parameter than cannot be set, e.g., the
amplifier structure. This will most likely occur if the communications have
become garbled.
61 ERROR: 104 AUTOSAMPLER IS NOT INSTALLED
A command has been sent from LINK to the GC that involves the
autosampler. This could happen if the user configures an AutoSystem with
an autosampler when none is installed. If the configuration is not checked
until a method is sent, this error will occur.
61 ERROR: 105 GC IS NOT RUNNING
This error typically occurs when the host sends a command to the IPM to
take the Clarus 600 GC out of run and it was not in a running state. This
may be due to a communications failure, or reset at the Clarus 600 GC
keypad.
61 ERROR: 106 AUTOMATION IS NOT RUNNING
A command has been sent from LINK to the GC to stop the autosampler.
However the autosampler is not currently in automation mode. This could
occur if the GC was reset or in an error state that canceled automation with
the IPM being aware of it.
61 ERROR: 108 DATA PACKET NOT READY
This is normally trapped in the IPM and may be indicative of another
problem.

Clarus 600 GC IPM

1
3
 61 ERROR: 2 UNKNOWN PARAMETER
This would occur if LINK attempted to send a bad command parameter.
The implication is that the command set has an error in the LIB file or the
IPM has been corrupted or the transmission has been garbled. The last is the
most likely case.
61 ERROR: 3 VALUE OUT OF RANGE
This error typically occurs during a method download to the Clarus and the
GC rejects one or more of the values contained in the method. A typical
scenario is an improper configuration.
61 ERROR: 4 END OF MEMORY
The GET MEMORY command was rejected because the end of the
memory address space has been reached. This command is not used by
LINK.
61 ERROR: 50 CHANNEL DOES NOT EXIST
This error typically occurs when a SEIZE command is sent from the IPM
and the sequence of commands that must be sent to the AutoSystem cannot
be completed. This may be due to communications glitch or power failure at
the instrument.
61 ERROR: 51 CHANNEL BUSY
This error occurs when the IPM attempts to set up a data channel that is
already controlled. This is likely to happen in the case where a release was
sent from the host and was garbled in transmission. If the release never
occurred, trying to reuse the channel will cause this error.
61 ERROR: 57 UNSUPPORTED COMMUNICATIONS OPTION
This error would occur if the IPM asked for a communications format, e.g.,
message tags, that are not currently supported in the External
Communications structure. There is no reason for an IPM to do so. This
might be an indication of a larger problem in the communications.
61 ERROR: 7 UNKNOWN COMMAND
This error typically occurs when a SEIZE command is sent from the IPM to
the Clarus 600 GC and is rejected. This is typically due to residual garbage
characters in the GC’S RS-232 buffer being treated as commands after
power-on in the GC. Repeat the Seize process to take control.
Another scenario is attempting to take control while the GC is initializing.
Wait until the GC is finished its startup procedure before asserting external
control.
61 ERROR: 92 GC BUSY
This error typically occurs when a SEIZE command is sent from the host,
and the Clarus is already under external control. This may be due to the
LINK interface being reset and the host sending a Seize command to the

14 Clarus 600 GC IPM

 IPM. The GC must be released manually from external control at its own
touchscreen before it can be seized again.
61 ERROR: 97 GC NOT SEIZED
This error typically occurs when a command is sent by the host to the
AutoSystem when the GC is not under external control. This may be due to
a power failure, communications failure, or reset at the Clarus 600 GC
keypad.
A typical scenario would be to turn off the GC without first releasing it
from the host. LINK will attempt to communicate to the GC until the
release is done, thereby generating the error.
61 ERROR: 98 BAD ARRAY INDICES
This occurs if the IPM attempts to get a member of structure from the GC
and has set the structure index incorrectly. This error is would most likely
occur if the communications were somehow garbled.
61 ERROR: 99 USE GETN TO GET THIS PARAMETER
This occurs if the IPM attempts to get a structure from the GC with the GET
command when the GETN command is required. A syntax error, it would
most likely occur if the communications were somehow garbled and the N
character of GETN were lost.
61 ERROR: PUNIT=x
A flow transducer has been configured when none is present. The incorrect
setting is:
0 = None
1 = Press, psi (ASGC only)
2 = Press, kPa (ASGC only)
6 = Flow, He
7 = Flow, N2
8 = Flow, H2
9 = Flow, Ar/CH4
Reset the configuration to None and rebuild any methods to remove the
faulty information.

Clarus 600 GC IPM

1
5
Wiring Diagram

Cable P/N 0929-0144 dotLINK to Clarus 600 GC

Clarus 600 GC dotLINK
DB 9 Female RJ 45

8 1
4 2
2 3
7 4
5
3 6
5 7
9 8

Cable P/N N650-0143 dotLINK to Clarus 600 GC

SoftLINK Clarus 600
Clarus 600 SoftLINK PC Serial
DB 9 Female DB 9 Female

3 2
2 3
6 5

16 Clarus 600 GC IPM