Tom Goddard

As I noted in my original description I do not observe the crash on Ubuntu 24.04, only on the Mac.

I tried building mmseqs2 on my Mac following the instructions in the user guide (without ASan) https://mmseqs.com/latest/userguide.pdf brew install cmake libomp zlib bzip2 ./util/build_osx.sh ~/ucsf/MMseqs2 ~/ucsf/mmseqs2_build >& build.txt and it...

Forgot to mention I was building release 18 of mmseqs not the current code when I got the symbol not found error. My plan was to reproduce the crash in...

I built mmseqs2 release 18-8cc5c as you instructed without OpenMP. It needed an additional cmake option -DREQUIRE_OPENMP=0 but then built with no problem. I ran the crashing mmseqs command with...

Your suggested compile with LIBOMP=... did not work, cmake succeeds, make fails with [ 34%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o In file included from /Users/goddard/ucsf/MMseqs2/src/alignment/Alignment.cpp:1: In file included from /Users/goddard/ucsf/MMseqs2/src/alignment/Alignment.h:4: In...

My mistake. Verbose indicated no -I compile option for libomp and I see cmake didn't get LIBOMP being the path to the homebrew openmp. I must have mistyped something. I...

Tried to reproduce the mmseqs prefilter crash with ASan and release 18 code locally compiled, unfortunately it ran successfully, took 36 hours. I will try compiling locally without ASan and...

I compiled release 18 mmseqs2 with openmp but without ASan on the Mac Studio used in all the above tests I describe and ran the crash test two times and...

Unfortunately when I use my locally compiled Mac mmseqs2 release 18 on a colabfold_search run with 476 query sequences it again crashes in prefilter of the env database. I'm afraid...

Ok, I added --no_write_full_pae and --no_write_full_pde to the documentation options table. Even though the default is true I left --write_full_pae and --write_full_pde in the options table since people may have...