cctbx draft

[ThomasHoffmann77]

(created using eb --new-pr)

see:

• {bio,lib}[foss/2022a] AlphaPulldown v0.30.7, cctbx-base v2023.5 #18506

[ThomasHoffmann77]

remark: I did not test, whether configopts "--enable_cuda" actually has an effect

[boegel]

My main comment after a quick scroll through this: yikes... 🙈

I guess the only sensible thing to do is to implement a custom easyblock for cctbx, since it's way complexer than I thought it was based on the work I did for #18506 ... Would you agree @ThomasHoffmann77?

Maybe the main difference with my approach in #18506 is that I was focusing on cctbx-base (which is what's necessary for AlphaPulldown), while this seems to be a full-blown cctbx.

@ThomasHoffmann77 Do you know how cctbx-base and cctbx the way you install it here relate?

[ThomasHoffmann77]

My main comment after a quick scroll through this: yikes... 🙈

I guess the only sensible thing to do is to implement a custom easyblock for cctbx, since it's way complexer than I thought it was based on the work I did for #18506 ... Would you agree @ThomasHoffmann77?

Maybe the main difference with my approach in #18506 is that I was focusing on cctbx-base (which is what's necessary for AlphaPulldown), while this seems to be a full-blown cctbx.

@ThomasHoffmann77 Do you know how cctbx-base and cctbx the way you install it here relate?

I fully agree that we would need a custom easyblock - maybe one for the libtbx build system handling the paths set in libtbx_env. This could then be used for any of the cctbx "modules" and for the entire phenix package.
In order to get alphapulldown running, it should be sufficient to only build libtbx, sctbx,and iotbx and their dependencies.
I'll have a closer look on friday.

[ThomasHoffmann77]

@boegel
sources downloaded by bootstrap.py on the fly for "--builder cctbx":

python ./libtbx/auto_build/bootstrap.py --download-only --builder cctbx|grep "git clone":
===== Running in modules: git clone --recursive https://github.com/cctbx/boost.git boost --progress --verbose
===== Running in modules: git clone --recursive https://github.com/yayahjb/cbflib.git cbflib --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/cctbx_project.git cctbx_project --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/dxtbx.git dxtbx --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/gui_resources.git gui_resources --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/ccp4io.git ccp4io --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/ccp4io_adaptbx.git ccp4io_adaptbx --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/annlib.git annlib --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/tntbx.git tntbx --progress --verbose
===== Running in modules: git clone --recursive https://github.com/cctbx/clipper.git clipper --progress --verbose
===== Running in modules: git clone --recursive -b 3.4.0 https://gitlab.com/libeigen/eigen.git eigen --progress --verbose
===== Running in modules: git clone --recursive -b v3.7.2 https://github.com/rlabduke/reduce.git reduce --progress --verbose

In the easyconfig I added the sources for probe and molprobity in order to get libtbx.run_tests_parallel module=mmtbx running as sanity check. I'd assume this can be omitted, if the package is configured without the "module" mmtbx.

If I run configure.py only for cctbx, scitbx, and iotbx required by AlphaPulldown (see: alphapulldown/analysis_pipeline/af2_3dmol.py), I get:

Top-down list of all modules involved:
  iotbx           "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/iotbx"
  cbflib+adaptbx  "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cbflib"
                  "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/cbflib_adaptbx"
  ccp4io+adaptbx  "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/ccp4io"
                  "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/ccp4io_adaptbx"
  smtbx           "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/smtbx"
  ucif            "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/ucif"
  cctbx           "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/cctbx"
  scitbx          "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/scitbx"
  fable           "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/fable"
  cma_es          "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/cma_es"
  omptbx          "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/omptbx"
  boost+adaptbx   "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/boost"
                  "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/boost_adaptbx"
  tbxx            "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/tbxx"
  chiltbx         "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/chiltbx"
  libtbx          "/tmp/th/eb_cctbx/REPO/znver2/software/cctbx/2023.6-foss-2022a-CUDA-11.7.0/modules/cctbx_project/libtbx"

[boegel]

@ThomasHoffmann77 Is it worth pursuing this, since it's no longer a required dependency for AlphaPulldown (see #21179)?

[ThomasHoffmann77]

@ThomasHoffmann77 Is it worth pursuing this, since it's no longer a required dependency for AlphaPulldown (see #21179)?

It's required for phenix

[boegel]

No longer relevant since 2022a toolchains are deprecated since foss/2025b was defined, see also https://docs.easybuild.io/policies/toolchains/, so closing...