Skip/avoid alignment padding bytes when calculating struct checksum

Is there a generic way to skip/avoid alignment padding bytes when calculating the checksum of a C struct?

There is no such mechanism on which a strictly conforming program can rely. This follows from

1. the fact that C implementations are permitted to lay out structures with arbitrary padding following any member or members, for any reason or none, and

2. the fact that

   When a value is stored in an object of structure or union type, including in a member object, the bytes of the object representation that correspond to any padding bytes take unspecified values.

   (C2011, 6.2.6.1/6)

The former means that the standard provides no conforming way to guarantee that a structure layout contains no padding, and the latter means that in principle, there is nothing you can do to control the values of the padding bytes -- even if you initially zero-fill a structure instance, any padding takes indeterminate values as soon as you assign to that object or to any of its members.

In practice, it is likely that any of the approaches you mention in the question will do the job where the C implementation and the nature of the data permit. But only (2), computing the checksum member by member, can be used by a strictly-conforming program, and that one is not "generic" as I take you to mean that term. This is what I would choose. If you have many distinct structures that require checksumming, then it might be worthwhile to deploy a code generator or macro magic to help you with maintaining things.

On the other hand, your most reliable way to provide for generic checksumming is to exercise an implementation-specific extension that enables you to avoid structures containing any padding (your (1)). Note that this will tie you to a specific C implementation or implementations that implement such an extension compatibly, that it may not work at all on some systems (such as those where misaligned access is a hard error), and that it may reduce performance on other systems.

Your (4) is an alternative way to avoid padding, but it would be a portability and maintenance nightmare. Nevertheless, it could provide for generic checksumming, in the sense that the checksum algorithm wouldn't need to pay attention to individual members. But note also that this also places a requirement for initialization behavior analogous to (3). That would come cheaper, but it would not be altogether automatic.

In practice, C implementations do not wantonly modify padding bytes, but they don't necessarily go out of their way to preserve them, either. In particular, even if you zero-filled rigorously, per your (3), padding is not guaranteed to be copied by whole-structure assignment or when you pass or return a structure by value. If you want to do any of those things then you need to take measures on the receiving side to ensure zero-filling, and requires member-by-member attention.