I have a suggestion but I am going to make some assumptions as I don't know your system but I have an idea how it might work.
If you had these things
1. NI Internet Toolkit
2. Telnet server on your unix box
3. FTP server on your unix box.
4. Command line version of your unix_app.exe
you should be able to do this
1. Generate your data from you pc labview application and save the results to file.
2. Get your labview application to ftp (put) your data file to the directory as unix_app.exe on your unix box.
3. In your labview app telnet to the unix box and change directory to where your unix_app.exe
4. In your telnet session run you unix_app.exe to read the labview result file and return the result to unix console or save unix_app_result file.
5. Parse the results in you Labview application. If the unix_app produces a results file you would ftp (get) to transfer the file back to your PC.
Does this help at all?
David