Software Release Notice GeneAmp
Contents
1. click on the OK button Remove the programmed Flash PCMCIA card Verify the Flash PCMCIA card as per Section K below K Verify the upgrade PC card SRAM or Flash Turn on a 9700 and press the following keys F4 Util F1 Diag Stop F3 TmpVer Highlight the service function Other Diags Press F1 Run F1 PCcard F1 Run Verify that the boot and applications section checksums that are stored on the PC card are the same as the checksums calculated by the 9700 F5 Exit 4311000 Page 8 of 82. Error occurs see note2 below When Pass is displayed click on the OK button Remove the programmed Flash PCMCIA card Verify the Flash PCMCIA card as per Section K below 4311000 Page 7 of 8 Note1 If a Card Selection Mismatch error occurs Select one of the following other possible cards Click on menu Selections Select Card Alt 4 Default Flash S1 x 16 bit AMD AMCOO1AFLKA 1 MB FLASH AMD AMCO001CFLKA 1 MB FLASH Note2 If a Blank Check Error occurs the card needs to be manually erased before it can be used Click on menu Card Operation Erase Alt E Click on the OK button to continue the erase When Erase Pass is displayed click on the OK button Program the card again Click on menu Card Operation Program Alt P If a Card Selection Mismatch error occurs see note1 above then set the card addressing again by clicking on menu Selections Card Addressing Alt 6 and enter 0 for the start address and 7FFFF for the end address then click on the OK button If a Pre Conditioning Error occurs follow the direction above for a Card Selection Mismatch J Duplicate a 9700 Flash upgrade PC card Click on menu File File amp path Alt 1 Select the TEC9700 directory and select the image file to duplicate Click on menu Selections Card Addressing Alt 6 and enter 0 for the start address and 7FFFF for the end address then click on the OK button Click on menu Card Operation Program Alt P When Pass is displayed
3. rear of the instrument facing you undo the 2 screws on the back panel and gently pull the chassis of the 9700 about an inch away from the molded cover Gently tilt the back panel about an inch away from the instrument e Locate the 10 pin BDM connector J10 at the top of the CPU board and attach the cable from the BDM card Turn the 9700 around so the keypad is facing front Turn on the 9700 e From File Manager locate the file k emul300 emul300 exe and double click on it to invoke the Nohau emulator e Click on menu Config Project name and select the project TEC_LEV2 Click on the OK button 4311000 Page 6 of 8 Create a 9700 SRAM upgrade PC card Click on menu Config Emulator hardware to open the hardware configuration dialog box On the right side of the box disable the Other Presets by clearing the checkmark next to the label Enabled Click on the button labeled Restore previous user defined values Click on the Reset button Click on the OK button Insert a 512KB or greater SRAM PC card into the card slot on the right side of the 9700 Before inserting check that the write protect switch on the card is in the Off position Click on menu Window Open to open a new data window Click on menu Data Fill Enter Pattern 0 Starting address 0 and End address 80000 Click on the OK button This will zero out the first Ox80000 bytes of memory on the SRAM PC card Click on menu File Load code and locate
4. C card or the serial port DO NOT pull out the PC card or disconnect the serial cable while the upgrade is in progress or there is the possibility that the boot sector of the CPU board Flash memory will only be partially written and the instrument will be INOPERABLE until it is re programmed at the factory If the PC card or serial cable is pulled out before the end of the upgrade or there is an error during the programming of the CPU board Flash memory the instrument will start issuing a series of beeps which can be deciphered by reading the error beep descriptions below 4311000 Page 3 of 8 Power up Failures This section describes beep patterns generated to indicate failures These beeps will only be encountered at power on or reset of the instrument and when reprogramming the CPU board Flash memory during a firmware upgrade Microprocessor Standby RAM Failure A read write test is performed on the Microprocessor s standby RAM at power on If it fails a steady on off on off beep is generated as follows Resolution Replace CPU board CPU Board RAM Failure A read write test is performed on the CPU board s RAM at power on If it fails the following beep pattern is generated Resolution Replace CPU board CPU Board Flash Memory Checksum Failure The checksum of the application section of the Flash memory is verified at boot time If it fails 10 quick beeps are generated The following message appears if NO upgrade car
5. F1 Pccard e Stop F3 Update and wait for the instrument to reboot F This key sequence will force an update of the boot and application section of the CPU board Flash memory G Turn off the 9700 H On the CPU board move jumper SP 10 to position 1 2 This is the normal operating position that tells the 9700 to boot off the CPU board Flash memory Turn on the 9700 and verify that the instrument powers up correctly and that the correct firmware version is displayed on the top level screen J Turn off the 9700 and replace the back panel To upgrade a 9700 which has an existing version of software using PC card A Turn on the 9700 B Insert a 9700 upgrade PC card into the card slot on the right hand side of the 9700 C Press the following keys e F4 Util e F1 Diag e F4 Upgrad e F1 PCcard e F3 Update and wait for the instrument to reboot D Verify the correct firmware version is displayed on the top level screen To upgrade a 9700 which has an existing version of software using Serial Port Turn on the 9700 Connect cable from RS485 port on 9700 to serial port on computer Press the following keys e F4 Util e F1 Diag e F4 Upgrad e F1 Serial e F3 Update Begin download of upgrade file from the computer using the Kermit protocol Wait for instrument to reboot Verify the correct firmware version is displayed on the top level screen QW gt mmo NOTE When upgrading the 9700 firmware through a P
6. Software Release Notice GeneAmp PCR System 9700 1 Items List The release package includes e This Software Release Notice e Acopy of the source code on a CD RW for documentation control 2 Supporting Documentation The design of the software is outlined in the document Software Design Document softwdes doc The design of the user interface is outlined in the document User Interface Specification 9700spec doc Both of these documents are archived in the tec doc directory The use of the 9700 is documented in the manuals Manual name AB Part GeneAmp PCR System 9700 Users Manual in CD it contains 4331608 e GeneAmp PCR System 9700 Base Module User s Manual 4303481 RevE e GeneAmp PCR System 9700 Block Quick Reference Guide 4304192 e GeneAmp PCR System 9700 96 Well Sample Block Module 4316011 User s Manual Rev C Gold Silver and Alu GeneAmp PCR System 9700 Block Assembly User Manual in CD it 4331607 contains GeneAmp PCR System 9700 Dual 384 well Block Users 4304215D Manual GeneAmp PCR System 9700 AutoLid Dual 384 well Block 4310838B Users Manual GeneAmp PCR System 9700 0 5 ml 60 well Block Users 4307808B Manual GeneAmp PCR System 9700 Dual 96 well Block Users Manual Manul and AutoLid 4343363B The 9700 Internet web site is http www appliedbiosystems com products productdetail cfm prod_id 33 3 Hardware Configuration The hardware required for running this software is a Appl
7. d is recognized in the PC card slot FIRMWARE UPGRADE IS INCOMPLETE BEGIN DOWNLOAD OF FILE FROM PC OR POWER DOWN 9700 INSERT UPGRADE PC CARD IN SLOT POWER UP 9700 The user can either initiate a serial port upgrade from their PC or follow the instructions for upgrading with a PC card If a 9700 upgrade PC card is in the slot at power up the user will hear the 10 quick beeps and the message FIRMWARE UPGRADE IS INCOMPLETE is displayed on the top line The messages CHECKING FOR UPGRADE PC CARD and UPGRADING FIRMWARE will follow The instrument will reboot when the firmware has been upgraded 4311000 Page 4 of 8 Invalid Checksum on Upgrade PC Card If the CPU board Flash memory checksum failure as described above is encountered and a PC card with incorrect checksums is inserted in the card slot the user will hear the 10 quick beeps and the message FIRMWARE UPGRADE IS INCOMPLETE is displayed on the top line The messages CHECKING FOR UPGRADE PC CARD and NOT A VALID UPGRADE PC CARD will follow The instrument will continually beep until the bad PC card is removed from the slot When it is removed the message is the box above will be displayed Firmware upgrade failure If a firmware upgrade fails because the data verify failed the instrument will beep 20 times and then reset itself Possible causes of this failure include a faulty CPU board a faulty PC card interface or the operator removing the PC card or serial cable b
8. d linker linker ccc68k Ver 2 0F mcc68k Ver 4 5G Ink68k Ver 7 1C BDM300 This is the Nohau emulator debugger software Ver 2 2X HLD Nohau Corp A Setup the computer The PC must be loaded with MS NT or WIN2000 and should have at least 32MB of RAM and at least 15MB of free hard disk space B Modifying autoexec bat and config sys Add the following lines to your PC s autoexec bat file e SET PATH PATH c tec source c mri mcc68k c mri asm68k e Set MRI_68K_INC c tec source include c tec source include sys c tec source rtxc c tec s ource kernel c tec source rtip xnet e set MRI_68K_BIN c mri mcc68k c mri asm68k c mri mcc68k cpu32 Reboot the PC Start MS Windows C Installing Source Files and Directory Structure 1 Create directory c tec 2 Copy the Directory Structure and all files from disk to c tec 3 Copy the MRI folder and all its contents to c This is the compiler D Building the 9700 executable hex file The outcome of this will be a hex file named checksum xeq in Motorola S record format and will contain checksums for both the boot section and the application section of the code This file is the actual executable hex file that will run the instrument Change directory to c tec source and type make DALL DHEX the source files will be recompile and link Setting up the Nohau emulator e Install the Nohau BDM card in an empty slot in the PC e Locate a 9700 thermal cycler With the
9. efore the upgrade is complete Resolution When the instrument is powered on a Flash checksum failure may be detected and the procedure to recover from this failure is outlined above It is also possible that on reset or power on the software will start up correctly so check the firmware version displayed on the main screen If not the same as the version on the PC card repeat the firmware upgrade procedure 8 System Generation This section describes the generation of the GeneAmp PCR System 9700 firmware To regenerate the firmware the following resources are required Hardware Description IBM compatible computer The PC must be running MS NT Win 2000 have at least 15 MB of free hard disk space Nohau software development Nohau s 68332 BDM Background Debug Mode system emulator card must be installed in the PC Applied Biosystems GeneAmp Nohau s BDM emulator cable must attach to the PCR System 9700 thermal BDM connector J10 on the 9700 CPU board cycler 512KB SRAM PCMCIA card The Nohau BDM emulator will download a checksummed version of the 9700 firmware to this PC card 1MB Flash PCMCIA card This PC card will be duplicated from the SRAM PC P N 0940 1054 card and will hold the final version of firmware ELAN PCMICA card drive This is the PCMCIA card reader writer to duplicate the Flash cards Software Description MRI 68332 This is the Microtec Research C C compiler and 4311000 Page 5 of 8 compiler an
10. file k tec source checksum xeq or I source checksum xeq if the subst command is in effect Click on the OK button This will download the checksummed executable file into the PC card Remove the PC card from the slot and move the write protect switch to the On position Create a 9700 Flash upgrade PC card Install the Elan card in an empty slot in the PC From DOS start up the Elan software by typing elan jc_card The version of the software is Elan Digital Systems LTD Ver 2 08 Dec 1994 Click on menu Misc JC_CARD Address Setup and set the address of the card to 0xD0000 Insert the SRAM PCMCIA card into the slot in the Elan card drive Click on menu File File amp path Alt 1 Select the TEC9700 directory and enter a file name Click on the Open button Click on menu Selections Select Card Alt 4 Select AMD then click on the OK button Select AmC001BFLKA 1MB Flash then click on the OK button Click on menu Selections Card Addressing Alt 6 and enter 0 for the start address and 7FFFF for the end address then click on the OK button Click on menu Card Operation Read Alt R If a Card Selection Mismatch error occurs see note1 below When Read Pass is displayed click on the OK button Remove the SRAM PCMCIA card from the Elan card drive Insert the Flash PCMCIA card to be programmed P N 0940 1054 Click on menu Card Operation Program Alt P Click on the OK button to program the card If a Blank Check
11. ied Biosystems GeneAmp PCR System 9700 thermal cycler Hardware AB Part Dual 96 Well Interchangeable Block Module 4335726 AUTOLID Manual Dual 96 Well Interchangeable Block 4342718 Module 4 Ver 3 08 3 5 Disk for Up grades Mac serial cable for serial port upgrades N805 1328 4 Software Configuration Embedded in the firmware is a checksum for the boot section of code address 0 to 0x3FFF and a checksum for the application section of the code address 0x4000 to 0x7FFFF All firmware upgrade PC cards for Ver 3 10 should contain the following checksums which can be verified by the instructions in Section 8 Subsection K of this document Section Checksum OxESE8 Application 0x8063 5 Software Generation See Section 8 System Generation of this document 6 Software Reproduction See the Manufacturing guidelines for reproducing PCMCIA cards 7 Software Installation To install the software on a 9700 which has a raw CPU board and no existing code in the Flash A B moO Remove the back panel of the 9700 as instructed in Part G of Section 8 below On the CPU board move jumper SP10 to position 1 3 This jumper position tells the 9700 to boot off of the PC card instead of the CPU board Flash memory Insert a 9700 upgrade PC card into the card slot on the right hand side of the 9700 Turn on the 9700 Press the following keys 4311000 Page 2 of 8 F4 Util F1 Diag F4 Upgrad
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