You may have two separate issues.
0. Installing from ports fails because you have some cruft in tmp directories. Clean it up, just in case.
1. You have a hardware problem. Compiling is as good as stress test on hardware. Out-of-specs PSU, faulty RAM, dusty CPU cooler, dying HDD, etc.
BTW, what exactly are you trying to achieve running portsdb? You don't need to run it during routine updating/upgrading.
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