RoseTTAFold-All-Atom

[boegel]

• link to support ticket: #2024041960000818

• website: https://github.com/baker-laboratory/RoseTTAFold-All-Atom

• installation docs: https://github.com/baker-laboratory/RoseTTAFold-All-Atom?tab=readme-ov-file#setupinstallation

• toolchain: foss/2023a or newer

• easyblock to use: ???

• notes:

  • SignalP requirement can be avoided through a patch, we should try and make that optional somehow (see https://github.com/baker-laboratory/RoseTTAFold-All-Atom/issues/44)

• required PRs:

  • [ ] https://github.com/easybuilders/easybuild-easyconfigs/pull/20358
  • [ ] https://github.com/easybuilders/easybuild-easyconfigs/pull/20768
  • [ ] https://github.com/easybuilders/easybuild-easyconfigs/pull/20880

• easyconfigs to create:

  • [x] dgl with CUDA
    • from https://github.com/easybuilders/easybuild-easyconfigs/pull/20092
  • [x] gnutls=3.6.13, no - v3.7.8 for 11.3.0
  • [x] libedit
  • [x] libev
  • [x] libgcrypt
  • [x] libgpg-error
  • [x] LAPACK
  • [x] nghttp2
  • [x] libnsl
  • [x] libuuid
  • [x] libuv
  • [x] libxcb
  • [x] libxkbcommon
  • [x] markdown
  • [x] mpmath
  • [x] PSIPRED
  • [x] psutil
  • [x] libpthread-stubs (pthread-stubs)
  • [x] e3nn

• required dependencies:

  • more details in wip of easyconfig
  • [ ] libgcc_mutex=0.1=conda_forge
  • [ ] openmp_mutex=4.5=2_kmp_llvm
  • [x] absl-py=2.1.0
  • [x] aiohttp=3.9.3
  • [x] aiosignal=1.3.1
  • [x] alsa-lib=1.2.8
  • [x] asttokens=2.4.1
  • [x] astunparse=1.6.3
  • [x] async-timeout=4.0.3
  • [x] attr=2.5.1, yes for 2023a
  • [x] attrs=23.2.0
  • [ ] blas=2.121=mkl
  • [x] blas-devel=3.9.0=21_linux64_mkl
  • [ ] blast-legacy=2.2.26=2
  • [x] blinker=1.7.0
  • [x] brotli=1.1.0
  • [x] brotli-bin=1.1.0
  • [x] brotli-python=1.1.0
  • [x] bzip2=1.0.8
  • [x] c-ares=1.27.0
  • [ ] ca-certificates
  • [x] cached-property=1.5.2
  • [x] cached_property=1.5.2=pyha770c72_1
  • [x] cachetools=5.3.3
  • [x] cairo=1.16.0
  • [x] certifi=2024.2.2
  • [x] cffi=1.16.0
  • [x] charset-normalizer=3.3.2
  • [x] click=8.1.7
  • [x] colorama=0.4.6,
  • [x] contourpy=1.2.0
  • [x] cryptography=42.0.2
  • [ ] cuda-cudart=11.8.89=0
  • [ ] cuda-cupti=11.8.87=0
  • [ ] cuda-libraries=11.8.0=0
  • [ ] cuda-nvrtc=11.8.89=0
  • [ ] cuda-nvtx=11.8.86=0
  • [ ] cuda-runtime=11.8.0=0
  • [ ] cuda-version=11.8=h70ddcb2_3
  • [ ] cudatoolkit=11.8.0
  • [x] cudnn=8.8.0.121,
  • [x] cycler=0.12.1,
  • [x] dbus=1.13.6,
  • [x] deepdiff=6.7.1,
  • [x] dgl=1.1.2,
  • [x] executing=2.0.1,
  • [x] expat=2.6.1,
  • [x] ffmpeg=4.3,
  • [x] fftw=3.3.10,
  • [x] filelock=3.13.1,
  • [x] flatbuffers=22.12.06,
  • [ ] font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  • [ ] font-ttf-inconsolata=3.000=h77eed37_0
  • [ ] font-ttf-source-code-pro=2.038=h77eed37_0
  • [ ] font-ttf-ubuntu=0.83=h77eed37_1
  • [x] fontconfig=2.14.2,
  • [ ] fonts-conda-ecosystem=1=0
  • [ ] fonts-conda-forge=1=0
  • [x] fonttools=4.49.0,
  • [x] freetype=2.12.1,
  • [x] frozenlist=1.4.1,
  • [x] fsspec=2024.2.0,
  • [x] gast=0.4.0,
  • [x] gettext=0.21.1,
  • [x] giflib=5.2.1,
  • [x] glib=2.78.4,
  • [ ] glib-tools=2.78.4=hfc55251_4
  • [x] gmp=6.3.0,
  • [x] gmpy2=2.1.2,
  • [x] gnutls=3.6.13,
  • [x] google-auth=2.28.2,
  • [x] google-auth-oauthlib=0.4.6,
  • [x] google-pasta=0.2.0,
  • [x] graphite2=1.3.13,
  • [x] grpcio=1.51.1,
  • [x] gst-plugins-base=1.22.0,
  • [x] gstreamer=1.22.0,
  • [ ] gstreamer-orc=0.4.38=hd590300_0
  • [x] gzip=1.13,
  • [x] h5py=3.9.0,
  • [x] harfbuzz=6.0.0,
  • [x] hdf5=1.14.1,
  • [x] hhsuite=3.3.0,
  • [x] icecream=2.1.3,
  • [x] icu=70.1,
  • [x] idna=3.6,
  • [x] importlib-metadata=7.0.2,
  • [ ] jack=1.9.22, ? https://jackaudio.org/downloads/
  • [x] jinja2=3.1.3,
  • [x] joblib=1.3.2,
  • [ ] jpeg=9e=h0b41bf4_3
  • [x] keras=2.11.0,
  • [x] keras-preprocessing=1.1.2,
  • [ ] keyutils=1.6.1, ?
  • [x] kiwisolver=1.4.5,
  • [ ] krb5=1.20.1,
  • [x] lame=3.100,
  • [x] lcms2=2.15,
  • [ ] ld_impl_linux-64=2.40 ?
  • [x] lerc=4.0.0,
  • [x] libabseil=20220623.0,
  • [x] libaec=1.1.2,
  • [x] libblas=3.9.0, ?
  • [x] libbrotlicommon=1.1.0,
  • [x] libbrotlidec=1.1.0,
  • [x] libbrotlienc=1.1.0,
  • [x] libcap=2.67,
  • [x] libcblas=3.9.0,
  • [x] libclang=15.0.7,
  • [ ] libclang13=15.0.7=default_ha2b6cf4_4
  • [ ] libcublas=11.11.3.6, ?
  • [ ] libcufft=10.9.0.58,
  • [ ] libcufile=1.9.0.20,
  • [ ] libcups=2.3.3,
  • [ ] libcurand=10.3.5.119, ?
  • [x] libcurl=8.1.2, cURL,
  • [ ] libcusolver=11.4.1.48, ?
  • [ ] libcusparse=11.7.5.86, ?
  • [x] libdb=6.2.32, ?
  • [x] libdeflate=1.17,
  • [x] libedit=3.1.20191231,
  • [x] libev=4.33,
  • [x] libevent=2.1.10,
  • [x] libexpat=2.6.1,
  • [x] libffi=3.4.2,
  • [x] libflac=1.4.3, FLAC
  • [ ] libgcc-ng=13.2.0, ?
  • [x] libgcrypt=1.10.3,
  • [ ] libgfortran-ng=13.2.0, ?
  • [ ] libgfortran5=13.2.0, ?
  • [x] libglib=2.78.4, GLib
  • [ ] libgomp=13.2.0, ?
  • [x] libgpg-error=1.48,
  • [x] libgrpc=1.51.1, gRPC
  • [x] libhwloc=2.9.1, hwloc
  • [x] libiconv=1.17,
  • [x] liblapack=3.9.0,
  • [x] liblapacke=3.9.0=21_linux64_mkl
  • [x] libllvm15=15.0.7,
  • [x] libnghttp2=1.58.0,
  • [ ] libnpp=11.8.0.86,
  • [x] libnsl=2.0.1,
  • [ ] libnvjpeg=11.9.0.86,
  • [x] libogg=1.3.4,
  • [x] libopus=1.3.1,
  • [x] libpng=1.6.43,
  • [ ] libpq=15.3,
  • [x] libprotobuf=3.21.12,
  • [x] libsndfile=1.2.2,
  • [x] libsqlite=3.45.1,
  • [ ] libssh2=1.11.0,
  • [ ] libstdcxx-ng=13.2.0, ?
  • [ ] libsystemd0=253, ?
  • [x] libtiff=4.5.0,
  • [x] libtool=2.4.7,
  • [ ] libudev1=253, ?
  • [x] libuuid=2.38.1,
  • [x] libuv=1.48.0,
  • [x] libvorbis=1.3.7,
  • [x] libwebp-base=1.3.2,
  • [x] libxcb=1.13,
  • [ ] libxcrypt=4.4.36,
  • [x] libxkbcommon=1.5.0,
  • [x] libxml2=2.10.3,
  • [x] libzlib=1.2.13,
  • [ ] llvm-openmp=17.0.6,
  • [x] lz4-c=1.9.4,
  • [x] markdown=3.5.2,
  • [x] markupsafe=2.1.5,
  • [x] matplotlib=3.8.3,
  • [x] matplotlib-base=3.8.3,
  • [x] metis=5.1.1,
  • [ ] mkl=2024.0.0,
  • [ ] mkl-devel=2024.0.0,
  • [ ] mkl-include=2024.0.0,
  • [x] mpc=1.3.1,
  • [x] mpfr=4.2.1,
  • [ ] mpg123=1.32.4,
  • [x] mpmath=1.3.0,
  • [x] multidict=6.0.5,
  • [x] munkres=1.1.4,
  • [ ] mysql-common=8.0.33=hf1915f5_6
  • [ ] mysql-libs=8.0.33=hca2cd23_6
  • [x] nccl=2.20.5.1,
  • [x] ncurses=6.4,
  • [x] nettle=3.6,
  • [x] networkx=3.2.1,
  • [x] nspr=4.35,
  • [x] nss=3.98,
  • [x] *numpy=1.26.4, -> 2023a: v1.25.1
  • [x] oauthlib=3.2.2,
  • [x] openbabel=3.1.1,
  • [ ] openh264=2.1.1,
  • [x] openjpeg=2.5.0,
  • [ ] openssl=3.1.5,
  • [x] opt_einsum=3.3.0,
  • [x] ordered-set=4.1.0,
  • [x] orjson=3.9.15,
  • [x] packaging=23.2,
  • [x] **pandas=2.2.1,
  • [x] pcre2=10.43=hcad00b1_0
  • [x] perl=5.32.1=7_hd590300_perl5
  • [x] pillow=9.4.0=py310h023d228_1
  • [x] pip=24.0=pyhd8ed1ab_0
  • [x] pixman=0.43.2=h59595ed_0
  • [x] ply=3.11=py_1
  • [x] protobuf=4.21.12=py310heca2aa9_0
  • [x] psipred=4.01=1
  • [x] psutil=5.9.8=py310h2372a71_0
  • [x] pthread-stubs=0.4=h36c2ea0_1001
  • [ ] pulseaudio=16.1=hcb278e6_3
  • [ ] pulseaudio-client=16.1=h5195f5e_3
  • [ ] pulseaudio-daemon=16.1=ha8d29e2_3
  • [x] pyasn1=0.5.1=pyhd8ed1ab_0
  • [x] pyasn1-modules=0.3.0=pyhd8ed1ab_0
  • [x] pycparser=2.21=pyhd8ed1ab_0
  • [x] pyg=2.5.0=py310_torch_2.0.0_cu118
  • [x] pygments=2.17.2=pyhd8ed1ab_0
  • [x] pyjwt=2.8.0=pyhd8ed1ab_1
  • [x] pyopenssl=24.0.0=pyhd8ed1ab_0
  • [x] pyparsing=3.1.2=pyhd8ed1ab_0
  • [x] pyqt=5.15.9=py310h04931ad_5
  • [x] pyqt5-sip=12.12.2=py310hc6cd4ac_5
  • [x] pysocks=1.7.1=pyha2e5f31_6
  • [x] python=3.10.13
  • [x] python-dateutil=2.9.0=pyhd8ed1ab_0
  • [x] python-flatbuffers=24.3.6=pyh59ac667_0
  • [x] python-tzdata=2024.1=pyhd8ed1ab_0
  • [ ] python_abi=3.10=4_cp310
  • [x] pytorch=2.0.1, v2.1.2 for 2023a
  • [x] pytorch-cuda=11.8=h7e8668a_5
  • [ ] pytorch-mutex=1.0=cuda
  • [x] pytz=2024.1=pyhd8ed1ab_0
  • [x] pyu2f=0.1.5=pyhd8ed1ab_0
  • [ ] qt-main=5.15.8=h5d23da1_6
  • [x] re2=2023.02.01=hcb278e6_0
  • [x] readline=8.2=h8228510_1
  • [x] requests=2.31.0=pyhd8ed1ab_0
  • [x] requests-oauthlib=1.3.1=pyhd8ed1ab_0
  • [x] rsa=4.9=pyhd8ed1ab_0
  • [x] scikit-learn=1.4.1.post1=py310h1fdf081_0
  • [x] scipy=1.12.0, 2023a: v1.11.1
  • [x] setuptools=69.1.1=pyhd8ed1ab_0
  • [ ] signalp6=6.0g=1
  • [x] sip=6.7.12=py310hc6cd4ac_0
  • [x] six=1.16.0=pyh6c4a22f_0
  • [x] snappy=1.1.10=h9fff704_0
  • [x] sympy=1.12=pypyh9d50eac_103
  • [x] tbb=2021.9.0=hf52228f_0
  • [x] tensorboard=2.11.2=pyhd8ed1ab_0
  • [x] tensorboard-data-server=0.6.1=py310h600f1e7_4
  • [x] tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0
  • [ ] tensorflow=2.11.0=cuda112py310he87a039_0
  • [ ] tensorflow-base=2.11.0=cuda112py310h52da4a5_0
  • [ ] tensorflow-estimator=2.11.0=cuda112py310h37add04_0
  • [x] termcolor=2.4.0=pyhd8ed1ab_0
  • [x] threadpoolctl=3.3.0=pyhc1e730c_0
  • [x] tk=8.6.13=noxft_h4845f30_101
  • [x] toml=0.10.2=pyhd8ed1ab_0
  • [x] tomli=2.0.1=pyhd8ed1ab_0
  • [x] torchaudio=2.0.2=py310_cu118
  • [x] torchtriton=2.0.0=py310
  • [x] torchvision=0.15.2=py310_cu118
  • [x] tornado=6.4=py310h2372a71_0
  • [x] tqdm=4.66.2=pyhd8ed1ab_0
  • [x] typing-extensions=4.10.0=hd8ed1ab_0
  • [x] typing_extensions=4.10.0=pyha770c72_0
  • [x] tzdata=2024a=h0c530f3_0
  • [x] unicodedata2=15.1.0=py310h2372a71_0
  • [x] unzip=6.0=h7f98852_3
  • [x] urllib3=2.2.1=pyhd8ed1ab_0
  • [x] werkzeug=3.0.1=pyhd8ed1ab_0
  • [x] wheel=0.42.0=pyhd8ed1ab_0
  • [x] wrapt=1.16.0=py310h2372a71_0
  • [ ] xcb-util=0.4.0=h516909a_0
  • [ ] xcb-util-image=0.4.0=h166bdaf_0
  • [ ] xcb-util-keysyms=0.4.0=h516909a_0
  • [ ] xcb-util-renderutil=0.3.9=h166bdaf_0
  • [ ] xcb-util-wm=0.4.1=h516909a_0
  • [ ] xkeyboard-config=2.38=h0b41bf4_0
  • [ ] xorg-kbproto=1.0.7=h7f98852_1002
  • [ ] xorg-libice=1.1.1=hd590300_0
  • [ ] xorg-libsm=1.2.4=h7391055_0
  • [ ] xorg-libx11=1.8.4=h0b41bf4_0
  • [ ] xorg-libxau=1.0.11=hd590300_0
  • [ ] xorg-libxdmcp=1.1.3=h7f98852_0
  • [ ] xorg-libxext=1.3.4=h0b41bf4_2
  • [ ] xorg-libxrender=0.9.10=h7f98852_1003
  • [ ] xorg-renderproto=0.11.1=h7f98852_1002
  • [ ] xorg-xextproto=7.3.0=h0b41bf4_1003
  • [ ] xorg-xproto=7.0.31=h7f98852_1007
  • [x] xz=5.2.6=h166bdaf_0
  • [x] yarl=1.9.4=py310h2372a71_0
  • [x] zip=3.0=hd590300_3
  • [x] zipp=3.17.0=pyhd8ed1ab_0
  • [x] zlib=1.2.13=hd590300_5
  • [x] zstd=1.5.5=hfc55251_0
  • pip:
    • [x] antlr4-python3-runtime==4.9.3
    • [x] assertpy==1.1
    • [x] configparser==6.0.1
    • [ ] git+https://github.com/NVIDIA/dllogger.git@0540a43971f4a8a16693a9de9de73c1072020769
    • [x] docker-pycreds==0.4.0
    • [x] e3nn==0.3.3
    • [x] gitdb==4.0.11
    • [x] gitpython==3.1.42
    • [x] hydra-core==1.3.2
    • [x] omegaconf==2.3.0
    • [x] opt-einsum-fx==0.1.4
    • [x] pathtools==0.1.2
    • [x] promise==2.3
    • [x] pynvml==11.0.0
    • [x] pyrsistent==0.20.0
    • [x] pyyaml==6.0.1
    • [x] sentry-sdk==1.41.0
    • [x] shortuuid==1.0.12
    • [x] smmap==5.0.1
    • [x] subprocess32==3.5.4
    • [x] wandb==0.12.0

• effort: (TBD)

• other install methods

  • conda: yes (sort of)
  • container image: no
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: no

[pavelToman]

WIP: https://github.com/vscentrum/vsc-software-stack/blob/wip/327_RoseTTAFold-All-Atom/RoseTTAFold-All-Atom.eb

[pavelToman]

Dependencies PR:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20616

[pavelToman]

PR of DGL and its deps:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20768