If you are a trader and wish to use the mark-to-market election, you should have a trading account which is marked-to-market and another investment account for your investment activities. This is the best way to distinguish your trading activities from your investment activities.
The IRS says:
The securities held for investment must be identified as such in the trader's records on the day he or she acquires them (for example, by holding them in a separate brokerage account).
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