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We currently (2017-06-21) have a constant large load of pending txs (over 10k on Etherscan). Many of these transactions seem to have 50GWei gas price. Despite that, the f2pool which ethgasstation http://ethgasstation.info/ reports to accept down to 1GWei gas prices, mines blocks with only very few transactions.

Examples:

What could be a motivation for that? They seem to constantly forgo about 0.2 ETH that other miners make more by filling up the blocks.

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I didn't fully understand your question (specifically, the last part), but hopefully this gives you an answer:

The more transactions included in a block, the more likely it is to be an uncle due to propagation delays. More precisely, the more gas consumed, the more likely the block is to be uncled (resulting in a reduced reward for the miner). Therefore, it is not always in the best interests of a miner to include transactions. Certain EVM instructions may also take longer for a particular node to process (for example, maybe the computer has a particularly poor implementation of Keccak but very fast disk I/O); an algorithm could make use of that information and change the transactions to be incorporated into a block on-the-fly to minimize the time required to find and propagate a block. Mis-pricing of instructions relative to one another led to a denial of service attack on Ethereum in 2016.

Thus, it is possible that a miner's node may believe a transaction to be unfairly (or at least not advantageously) priced and thus not include it. Even though the maximum reward for mining a block with a transaction is higher than mining a block without it, the expected value might be lower. The node could also just be very conservative and avoid adding many transactions just in case they might lead to uncles.

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Miners can choose what transactions get included in their blocks using whatever logic they care to. A miner can implement logic to mine only specific types of transactions regardless of gas price, or as they are trying many different transaction and nonce values to find one that meets the proof-of-work difficulty target, they may publish the block even if it has lower-transaction-fee transactions since getting any reward at all is better than getting no reward (which is what would happen if they didn't publish that block with only low-gas-price transactions, and some other miner published a block before they found a combination that was worth more).

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