Hello all!
I compiled the most recent hh-suite from source and am using the pdb database from the RosettaFold-All Atom (RFAA) install (https://github.com/baker-laboratory/RoseTTAFold-All-Atom) which looks like a custom database they built that does include the *_a3m.ffindex and *_a3m.ffdata. RFAA also has version 3.3 of hhsearch from what I can tell, but wanted to redownload just in case. When I was running RFAA, I was getting this seg fault, so I popped out the command to run it on the new install of hh-suite.

My command is this:
../hh-suite/build/bin/hhsearch -b 50 -B 500 -z 50 -Z 500 -mact 0.05 -cpu 12 -maxmem 64 -aliw 100000 -e 100 -p
5.0 -d pdb100_2021Mar03/pdb100_2021Mar03 -i 7qxr/A/t000_.msa0.ss2.a3m -o 7qxr/A/t000_.hhr -atab 7qxr/A/t000_.atab -v 2

And my full output is this:

• 10:23:06.172 INFO: 7qxr/A/t000_.msa0.ss2.a3m is in A2M, A3M or FASTA format
• 10:23:07.056 INFO: Searching 153500 database HHMs without prefiltering
• 10:23:07.121 INFO: Iteration 1
• 10:23:07.221 INFO: Scoring 153500 HMMs using HMM-HMM Viterbi alignment
• 10:23:07.853 INFO: Alternative alignment: 0

Segmentation fault (core dumped)

I'm on a server with the following compute specs:
Dell PowerEdge R750XA
dual 24-core/48-thread CPUs
512 GB RAM
2 NVIDIA Ampere A100 GPUs w/80GB onboard RAM each

Thank you so much for your help!!