It depends on your workload. RAID5 is good for large sequential writes,
but sucks at small sequential writes because for every write it has to
do a read to compare parity.

well, it's bad at small random writes. small _sequential_ writes would be able to avoid reads for all but the first transaction.

IMO, raid5 is often unappealing because raid10 avoids the write penalty,
and raid6 is a lot more survivable.  ultimately it depends on your taste
in trading off performance, space efficiency, risk.

2) I want to put the /home at the beginning of the disks go get faster
write/seek speeds, if the partitions are the same, software RAID doesn't
care where they are?

I don't think this will buy you much performance. There probably is a
measurable difference, but I don't think it's enough to worry about.

inner tracks are normally about 60% of the speed of outer tracks - that's for a normal density-optimized disk, not a latency-optimized (and therefore inherently small) "enterprise" disk.

3) I'll leave the /boot partition on one of the 3 disks and it will NOT
be included in the RAID array, is this ok?

Sure, but /boot is actually trivial to mirror. Just make sure your boot
loader is on each disk in the mirror and that each disk is partitioned
identically, and all you have to do if a drive dies is change the device
you boot off of if a drive dies.

or better yet, don't bother booting of the local disk. simply make your head/admin/master server reliable and net-boot. it's likley that nodes won't be functional without the master server anyway, and net-booting doesn't mean you can't use the local disk for swap/scratch/...

4) I've read about setting up parallel swaping via priority given to
swap partitions in fstab, but also how it would be ok to create RAID 1
array of swap partitions for the HA of the cluster. What should I choose?

Any swapping at all will kill performance. I would get enough RAM to
make sure you don't swap.

well, using swap space is harmless as long as you're not actually swapping
_in_ any nontrivial amount.

unless you have some very extreme parameters (uncheckpointable long jobs,
flakey hardware or power, banking-level reliability expectations),
I wouldn't bother raiding swap.
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