You will have to find out whether /dev/mem supports what you want, and whether the seek call accepts offsets larger than 2GB on your system.
If either of these fails, you will have to find a different approach than reading from /dev/mem, like using one of the mmap calls.
If the seek function takes and understands a 64bit value, you will have to look at the output of perl -V to find out why it is not using this version of the seek call. For example if -Duselargefiles is missing in the output, that is a sure sign that your Perl was not build properly for your system.
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