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I am having problems uploading a large file to a web site.

When the file is subsequently downloaded it is corrupt.

How can I do a checksum of the file while it is on the web site so I don't have to keep downloading it everytime just to check that it has uploaded properly?

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The easiest way would be to log into the webserver (e.g. using ssh) and do a compare the MD5 sum.

Unless you are using something truly ancient called FTP and transfer binary files in ASCII mode. In that case just type 'bin' in your FTP client to upload them correctly.

(Granted, this is a wild guess. Your question does not mention which software you use to upload).

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What would you suggest other than FTP to transfer files? –  CJ7 Jun 6 '12 at 7:43
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You would have to get your client side to also run the checksum algorithm, and that means Javascript. Take a look at this SO question. Once there you'd have to use server-side code to run the checksum there (here's a PHP implementation). The question is a bit open-ended so I'm not really sure if this is what you were looking for. But I don't know that this is possible without programming, so I'm not sure if this question would be more appropriate for SO.

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