Can i use a separate file to list all the files during compilation.

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Is there a Tcl script so can automate the running of two projects one after the other

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Yes, you just use a loop in Tcl.

For example, I have a board that has four FPGAs. Each one has an ID register and slight differences in functionality. When the design is compiled, I create a timestamp, and then run a loop where each is synthesized.

Here's the basics of the code ...

#  -----------------------------------------------------------------#  Build the design#  -----------------------------------------------------------------
puts " - Building the design for the 4 FPGAs"
#  Build timestamp#    Use the same timestamp for each of the four FPGAs.#    Timestamp is in UTC seconds.
set timestamp 
puts " - Build timestamp $timestamp (0x)"
#  Time the build
set start_build 
#  Create configurations for each FPGA
for {set fpga_num 0} {$fpga_num < 4} {incr fpga_num} {
   #  Time the per FPGA build
    set start_fpga 
   #  Create a working folder
    set dwork $qwork/data$fpga_num
    if {!} {
        puts " - Creating the FPGA#$fpga_num work folder; $dwork"
        file mkdir $dwork
    }
    cd $dwork
   #  Create a new project
    project_new -overwrite "data"
   #  Add the files
    data_files
   #  Setup the pinout and default constraints
    set device_type  0
    set tx_enable    1
    set rx_terminate 1
    data_pinout $device_type $fpga_num $tx_enable $rx_terminate
    
   #  Timing constraints
    data_timing_constraints
   #  Setup the generics
    set_parameter -name FPGA_NUM $fpga_num
    set_parameter -name TIMESTAMP $timestamp
   #  Process the design
    puts " - Processing the design for FPGA#$fpga_num"
    execute_flow -compile
    
   #  Use one of the following to save the settings
    project_close#     export_assignments
   #  Copy the RBF file
    puts " - Renaming the RBF file data$fpga_num.rbf"
    file copy -force "data.rbf" "$qwork/data$fpga_num.rbf"
    set end_fpga 
    set str ]
    puts " - FPGA$fpga_num build time: $str minutes"
}
set end_build 
set str ]
puts " - *** Total build time: $str minutes ***"
#  Create the single DATA-FPGA configuration file
cd $qwork
puts " - Creating the configuration file data_basic.bin"
exec cat data0.rbf data1.rbf data2.rbf data3.rbf > data_basic.bin

You should be able to implement something like this.

Cheers,

Dave