duerrsimon
commented
4 months ago RFAA doesn't run on a windows machine because some dependencies cannot be installed there.
Open EulusMaximus opened 4 months ago
duerrsimon
commented
4 months ago RFAA doesn't run on a windows machine because some dependencies cannot be installed there.
adamrbentham
commented
4 months ago I'm getting the same issue on Apple M3 MacOS Sonoma 14.1 - do we know if we can get a similar work around to the fork for RFdiffusion provided by @YaoYinYing ?
duerrsimon
commented
4 months ago You can try this environment.yml from that is less specific towards a linux environment. It'll probably work but I am not sure if all depenencies will also work on OSX. https://github.com/baker-laboratory/RoseTTAFold-All-Atom/pull/51/files#diff-0ff3348ae0de662ef053d7de057a7a92c091a09fc3d245c8da02bec028ca3d0b
It would probably be a better idea to install it in a docker image.
YaoYinYing
commented
3 months ago I'm getting the same issue on Apple M3 MacOS Sonoma 14.1 - do we know if we can get a similar work around to the fork for RFdiffusion provided by @YaoYinYing ?
Hi @adamrbentham , I didnot test RF2AA on my Mac, since the sequences databases are too huge for local hard drive. I think it might be possible to work around with NVTX contexts like RFdifussion. However, MPS is still experimental so GPU calling might not work. Good luck!
Update: I did some code change against this issue. This now should work to you. Fork of RFdiffusionAA and Fork of RF2AA. Good luck mate!
Hello, when I am trying to create the mamba environment from the "environment.yaml" file, solving the environment fails. This is the error code: PS C:\Dokumente\PhD\Folding\RoseTTAFold-All-Atom> mamba env create -f environment.yaml Retrieving notices: ...working... done Channels:
LibMambaUnsatisfiableError: Encountered problems while solving:
Could not solve for environment specs The following packages are incompatible ├─ _libgcc_mutex ==0.1 conda_forge does not exist (perhaps a typo or a missing channel); ├─ _openmp_mutex ==4.5 2_kmp_llvm does not exist (perhaps a typo or a missing channel); ├─ aiohttp ==3.9.3 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ alsa-lib ==1.2.8 h166bdaf_0 does not exist (perhaps a typo or a missing channel); ├─ attr ==2.5.1 h166bdaf_1 does not exist (perhaps a typo or a missing channel); ├─ blas-devel ==3.9.0 21_linux64_mkl does not exist (perhaps a typo or a missing channel); ├─ blast-legacy ==2.2.26 2 does not exist (perhaps a typo or a missing channel); ├─ brotli-bin ==1.1.0 hd590300_1 does not exist (perhaps a typo or a missing channel); ├─ brotli-python ==1.1.0 py310hc6cd4ac_1 does not exist (perhaps a typo or a missing channel); ├─ brotli ==1.1.0 hd590300_1 does not exist (perhaps a typo or a missing channel); ├─ bzip2 ==1.0.8 hd590300_5 does not exist (perhaps a typo or a missing channel); ├─ c-ares ==1.27.0 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ ca-certificates ==2024.2.2 hbcca054_0 does not exist (perhaps a typo or a missing channel); ├─ cairo ==1.16.0 ha61ee94_1014 does not exist (perhaps a typo or a missing channel); ├─ cffi ==1.16.0 py310h2fee648_0 does not exist (perhaps a typo or a missing channel); ├─ click ==8.1.7 unix_pyh707e725_0 is not installable because it requires │ └─ __unix, which is missing on the system; ├─ contourpy ==1.2.0 py310hd41b1e2_0 does not exist (perhaps a typo or a missing channel); ├─ cryptography ==42.0.2 py310hb8475ec_0 does not exist (perhaps a typo or a missing channel); ├─ cudatoolkit ==11.8.0 h4ba93d1_13 does not exist (perhaps a typo or a missing channel); ├─ cudnn ==8.8.0.121 hcdd5f01_4 does not exist (perhaps a typo or a missing channel); ├─ dbus ==1.13.6 h5008d03_3 does not exist (perhaps a typo or a missing channel); ├─ dgl ==1.1.2 cuda112py310hc641c19_2 does not exist (perhaps a typo or a missing channel); ├─ expat ==2.6.1 h59595ed_0 does not exist (perhaps a typo or a missing channel); ├─ ffmpeg ==4.3 hf484d3e_0 does not exist (perhaps a typo or a missing channel); ├─ fftw ==3.3.10 nompi_hc118613_108 does not exist (perhaps a typo or a missing channel); ├─ flatbuffers ==22.12.06 hcb278e6_2 does not exist (perhaps a typo or a missing channel); ├─ fontconfig ==2.14.2 h14ed4e7_0 does not exist (perhaps a typo or a missing channel); ├─ fonttools ==4.49.0 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ freetype ==2.12.1 h267a509_2 does not exist (perhaps a typo or a missing channel); ├─ frozenlist ==1.4.1 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ gettext ==0.21.1 h27087fc_0 does not exist (perhaps a typo or a missing channel); ├─ giflib ==5.2.1 h0b41bf4_3 does not exist (perhaps a typo or a missing channel); ├─ glib-tools ==2.78.4 hfc55251_4 does not exist (perhaps a typo or a missing channel); ├─ glib ==2.78.4 hfc55251_4 does not exist (perhaps a typo or a missing channel); ├─ gmp ==6.3.0 h59595ed_0 does not exist (perhaps a typo or a missing channel); ├─ gmpy2 ==2.1.2 py310h3ec546c_1 does not exist (perhaps a typo or a missing channel); ├─ gnutls ==3.6.13 h85f3911_1 does not exist (perhaps a typo or a missing channel); ├─ graphite2 ==1.3.13 h58526e2_1001 does not exist (perhaps a typo or a missing channel); ├─ grpcio ==1.51.1 py310h4a5735c_1 does not exist (perhaps a typo or a missing channel); ├─ gst-plugins-base ==1.22.0 h4243ec0_2 does not exist (perhaps a typo or a missing channel); ├─ gstreamer-orc ==0.4.38 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ gstreamer ==1.22.0 h25f0c4b_2 does not exist (perhaps a typo or a missing channel); ├─ gzip ==1.13 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ h5py ==3.9.0 nompi_py310hcca72df_101 does not exist (perhaps a typo or a missing channel); ├─ harfbuzz ==6.0.0 h8e241bc_0 does not exist (perhaps a typo or a missing channel); ├─ hdf5 ==1.14.1 nompi_h4f84152_100 does not exist (perhaps a typo or a missing channel); ├─ hhsuite ==3.3.0 py310pl5321h068649b_10 does not exist (perhaps a typo or a missing channel); ├─ icu ==70.1 h27087fc_0 does not exist (perhaps a typo or a missing channel); ├─ jack ==1.9.22 h11f4161_0 does not exist (perhaps a typo or a missing channel); ├─ jpeg ==9e h0b41bf4_3 does not exist (perhaps a typo or a missing channel); ├─ keyutils ==1.6.1 h166bdaf_0 does not exist (perhaps a typo or a missing channel); ├─ kiwisolver ==1.4.5 py310hd41b1e2_1 does not exist (perhaps a typo or a missing channel); ├─ krb5 ==1.20.1 h81ceb04_0 does not exist (perhaps a typo or a missing channel); ├─ lame ==3.100 h166bdaf_1003 does not exist (perhaps a typo or a missing channel); ├─ lcms2 ==2.15 hfd0df8a_0 does not exist (perhaps a typo or a missing channel); ├─ ld_impl_linux-64 ==2.40 h41732ed_0 does not exist (perhaps a typo or a missing channel); ├─ lerc ==4.0.0 h27087fc_0 does not exist (perhaps a typo or a missing channel); ├─ libabseil ==20220623.0 cxx17_h05df665_6 does not exist (perhaps a typo or a missing channel); ├─ libaec ==1.1.2 h59595ed_1 does not exist (perhaps a typo or a missing channel); ├─ libblas ==3.9.0 21_linux64_mkl does not exist (perhaps a typo or a missing channel); ├─ libbrotlicommon ==1.1.0 hd590300_1 does not exist (perhaps a typo or a missing channel); ├─ libbrotlidec ==1.1.0 hd590300_1 does not exist (perhaps a typo or a missing channel); ├─ libbrotlienc ==1.1.0 hd590300_1 does not exist (perhaps a typo or a missing channel); ├─ libcap ==2.67 he9d0100_0 does not exist (perhaps a typo or a missing channel); ├─ libcblas ==3.9.0 21_linux64_mkl does not exist (perhaps a typo or a missing channel); ├─ libclang13 ==15.0.7 default_ha2b6cf4_4 does not exist (perhaps a typo or a missing channel); ├─ libclang ==15.0.7 default_hb11cfb5_4 does not exist (perhaps a typo or a missing channel); ├─ libcufile ==1.9.0.20 0 does not exist (perhaps a typo or a missing channel); ├─ libcups ==2.3.3 h36d4200_3 does not exist (perhaps a typo or a missing channel); ├─ libcurl ==8.1.2 h409715c_0 does not exist (perhaps a typo or a missing channel); ├─ libdb ==6.2.32 h9c3ff4c_0 does not exist (perhaps a typo or a missing channel); ├─ libdeflate ==1.17 h0b41bf4_0 does not exist (perhaps a typo or a missing channel); ├─ libedit ==3.1.20191231 he28a2e2_2 does not exist (perhaps a typo or a missing channel); ├─ libev ==4.33 hd590300_2 does not exist (perhaps a typo or a missing channel); ├─ libevent ==2.1.10 h28343ad_4 does not exist (perhaps a typo or a missing channel); ├─ libexpat ==2.6.1 h59595ed_0 does not exist (perhaps a typo or a missing channel); ├─ libffi ==3.4.2 h7f98852_5 does not exist (perhaps a typo or a missing channel); ├─ libflac ==1.4.3 h59595ed_0 does not exist (perhaps a typo or a missing channel); ├─ libgcc-ng ==13.2.0 h807b86a_5 does not exist (perhaps a typo or a missing channel); ├─ libgcrypt ==1.10.3 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ libgfortran-ng ==13.2.0 h69a702a_5 does not exist (perhaps a typo or a missing channel); ├─ libgfortran5 ==13.2.0 ha4646dd_5 does not exist (perhaps a typo or a missing channel); ├─ libglib ==2.78.4 hf2295e7_4 does not exist (perhaps a typo or a missing channel); ├─ libgomp ==13.2.0 h807b86a_5 does not exist (perhaps a typo or a missing channel); ├─ libgpg-error ==1.48 h71f35ed_0 does not exist (perhaps a typo or a missing channel); ├─ libgrpc ==1.51.1 h4fad500_1 does not exist (perhaps a typo or a missing channel); ├─ libhwloc ==2.9.1 hd6dc26d_0 does not exist (perhaps a typo or a missing channel); ├─ libiconv ==1.17 hd590300_2 does not exist (perhaps a typo or a missing channel); ├─ liblapack ==3.9.0 21_linux64_mkl does not exist (perhaps a typo or a missing channel); ├─ liblapacke ==3.9.0 21_linux64_mkl does not exist (perhaps a typo or a missing channel); ├─ libllvm15 ==15.0.7 hadd5161_1 does not exist (perhaps a typo or a missing channel); ├─ libnghttp2 ==1.58.0 h47da74e_0 does not exist (perhaps a typo or a missing channel); ├─ libnsl ==2.0.1 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ libogg ==1.3.4 h7f98852_1 does not exist (perhaps a typo or a missing channel); ├─ libopus ==1.3.1 h7f98852_1 does not exist (perhaps a typo or a missing channel); ├─ libpng ==1.6.43 h2797004_0 does not exist (perhaps a typo or a missing channel); ├─ libpq ==15.3 hbcd7760_1 does not exist (perhaps a typo or a missing channel); ├─ libprotobuf ==3.21.12 hfc55251_2 does not exist (perhaps a typo or a missing channel); ├─ libsndfile ==1.2.2 hc60ed4a_1 does not exist (perhaps a typo or a missing channel); ├─ libsqlite ==3.45.1 h2797004_0 does not exist (perhaps a typo or a missing channel); ├─ libssh2 ==1.11.0 h0841786_0 does not exist (perhaps a typo or a missing channel); ├─ libstdcxx-ng ==13.2.0 h7e041cc_5 does not exist (perhaps a typo or a missing channel); ├─ libsystemd0 ==253 h8c4010b_1 does not exist (perhaps a typo or a missing channel); ├─ libtiff ==4.5.0 h6adf6a1_2 does not exist (perhaps a typo or a missing channel); ├─ libtool ==2.4.7 h27087fc_0 does not exist (perhaps a typo or a missing channel); ├─ libudev1 ==253 h0b41bf4_1 does not exist (perhaps a typo or a missing channel); ├─ libuuid ==2.38.1 h0b41bf4_0 does not exist (perhaps a typo or a missing channel); ├─ libuv ==1.48.0 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ libvorbis ==1.3.7 h9c3ff4c_0 does not exist (perhaps a typo or a missing channel); ├─ libwebp-base ==1.3.2 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ libxcb ==1.13 h7f98852_1004 does not exist (perhaps a typo or a missing channel); ├─ libxcrypt ==4.4.36 hd590300_1 does not exist (perhaps a typo or a missing channel); ├─ libxkbcommon ==1.5.0 h79f4944_1 does not exist (perhaps a typo or a missing channel); ├─ libxml2 ==2.10.3 hca2bb57_4 does not exist (perhaps a typo or a missing channel); ├─ libzlib ==1.2.13 hd590300_5 does not exist (perhaps a typo or a missing channel); ├─ llvm-openmp ==17.0.6 h4dfa4b3_0 does not exist (perhaps a typo or a missing channel); ├─ lz4-c ==1.9.4 hcb278e6_0 does not exist (perhaps a typo or a missing channel); ├─ markupsafe ==2.1.5 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ matplotlib-base ==3.8.3 py310h62c0568_0 does not exist (perhaps a typo or a missing channel); ├─ matplotlib ==3.8.3 py310hff52083_0 does not exist (perhaps a typo or a missing channel); ├─ metis ==5.1.1 h59595ed_2 does not exist (perhaps a typo or a missing channel); ├─ mkl-devel ==2024.0.0 ha770c72_49657 does not exist (perhaps a typo or a missing channel); ├─ mkl-include ==2024.0.0 ha957f24_49657 does not exist (perhaps a typo or a missing channel); ├─ mkl ==2024.0.0 ha957f24_49657 does not exist (perhaps a typo or a missing channel); ├─ mpc ==1.3.1 hfe3b2da_0 does not exist (perhaps a typo or a missing channel); ├─ mpfr ==4.2.1 h9458935_0 does not exist (perhaps a typo or a missing channel); ├─ mpg123 ==1.32.4 h59595ed_0 does not exist (perhaps a typo or a missing channel); ├─ multidict ==6.0.5 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ mysql-common ==8.0.33 hf1915f5_6 does not exist (perhaps a typo or a missing channel); ├─ mysql-libs ==8.0.33 hca2cd23_6 does not exist (perhaps a typo or a missing channel); ├─ nccl ==2.20.5.1 h6103f9b_0 does not exist (perhaps a typo or a missing channel); ├─ ncurses ==6.4 h59595ed_2 does not exist (perhaps a typo or a missing channel); ├─ nettle ==3.6 he412f7d_0 does not exist (perhaps a typo or a missing channel); ├─ nspr ==4.35 h27087fc_0 does not exist (perhaps a typo or a missing channel); ├─ nss ==3.98 h1d7d5a4_0 does not exist (perhaps a typo or a missing channel); ├─ numpy ==1.26.4 py310hb13e2d6_0 does not exist (perhaps a typo or a missing channel); ├─ openbabel ==3.1.1 py310heaf86c6_5 does not exist (perhaps a typo or a missing channel); ├─ openh264 ==2.1.1 h780b84a_0 does not exist (perhaps a typo or a missing channel); ├─ openjpeg ==2.5.0 hfec8fc6_2 does not exist (perhaps a typo or a missing channel); ├─ openssl ==3.1.5 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ orjson ==3.9.15 py310hcb5633a_0 does not exist (perhaps a typo or a missing channel); ├─ pandas ==2.2.1 py310hcc13569_0 does not exist (perhaps a typo or a missing channel); ├─ pcre2 ==10.43 hcad00b1_0 does not exist (perhaps a typo or a missing channel); ├─ perl ==5.32.1 7_hd590300_perl5 does not exist (perhaps a typo or a missing channel); ├─ pillow ==9.4.0 py310h023d228_1 does not exist (perhaps a typo or a missing channel); ├─ pixman ==0.43.2 h59595ed_0 does not exist (perhaps a typo or a missing channel); ├─ protobuf ==4.21.12 py310heca2aa9_0 does not exist (perhaps a typo or a missing channel); ├─ psipred ==4.01 1 does not exist (perhaps a typo or a missing channel); ├─ psutil ==5.9.8 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ pthread-stubs ==0.4 h36c2ea0_1001 does not exist (perhaps a typo or a missing channel); ├─ pulseaudio-client ==16.1 h5195f5e_3 does not exist (perhaps a typo or a missing channel); ├─ pulseaudio-daemon ==16.1 ha8d29e2_3 does not exist (perhaps a typo or a missing channel); ├─ pulseaudio ==16.1 hcb278e6_3 does not exist (perhaps a typo or a missing channel); ├─ pyqt5-sip ==12.12.2 py310hc6cd4ac_5 does not exist (perhaps a typo or a missing channel); ├─ pyqt ==5.15.9 py310h04931ad_5 does not exist (perhaps a typo or a missing channel); ├─ pysocks ==1.7.1 pyha2e5f31_6 is not installable because it requires │ └─ unix, which is missing on the system; ├─ python ==3.10.13 hd12c33a_0_cpython does not exist (perhaps a typo or a missing channel); ├─ pytorch-cuda ==11.8 h7e8668a_5 does not exist (perhaps a typo or a missing channel); ├─ pytorch ==2.0.1 py3.10_cuda11.8_cudnn8.7.0_0 does not exist (perhaps a typo or a missing channel); ├─ qt-main ==5.15.8 h5d23da1_6 does not exist (perhaps a typo or a missing channel); ├─ re2 ==2023.02.01 hcb278e6_0 does not exist (perhaps a typo or a missing channel); ├─ readline ==8.2 h8228510_1 does not exist (perhaps a typo or a missing channel); ├─ scikit-learn ==1.4.1.post1 py310h1fdf081_0 does not exist (perhaps a typo or a missing channel); ├─ scipy ==1.12.0 py310hb13e2d6_2 does not exist (perhaps a typo or a missing channel); ├─ signalp6 ==6.0g 1 is not installable because it requires │ └─ gzip, which does not exist (perhaps a missing channel); ├─ sip ==6.7.12 py310hc6cd4ac_0 does not exist (perhaps a typo or a missing channel); ├─ snappy ==1.1.10 h9fff704_0 does not exist (perhaps a typo or a missing channel); ├─ sympy ==1.12 pypyh9d50eac_103 is not installable because it requires │ └─ unix, which is missing on the system; ├─ tbb ==2021.9.0 hf52228f_0 does not exist (perhaps a typo or a missing channel); ├─ tensorboard-data-server ==0.6.1 py310h600f1e7_4 does not exist (perhaps a typo or a missing channel); ├─ tensorflow-base ==2.11.0 cuda112py310h52da4a5_0 does not exist (perhaps a typo or a missing channel); ├─ tensorflow-estimator ==2.11.0 cuda112py310h37add04_0 does not exist (perhaps a typo or a missing channel); ├─ tensorflow ==2.11.0 cuda112py310he87a039_0 does not exist (perhaps a typo or a missing channel); ├─ tk ==8.6.13 noxft_h4845f30_101 does not exist (perhaps a typo or a missing channel); ├─ torchtriton ==2.0.0 py310 does not exist (perhaps a typo or a missing channel); ├─ tornado ==6.4 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ unicodedata2 ==15.1.0 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ unzip ==6.0 h7f98852_3 does not exist (perhaps a typo or a missing channel); ├─ wrapt ==1.16.0 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ xcb-util-image ==0.4.0 h166bdaf_0 does not exist (perhaps a typo or a missing channel); ├─ xcb-util-keysyms ==0.4.0 h516909a_0 does not exist (perhaps a typo or a missing channel); ├─ xcb-util-renderutil ==0.3.9 h166bdaf_0 does not exist (perhaps a typo or a missing channel); ├─ xcb-util-wm ==0.4.1 h516909a_0 does not exist (perhaps a typo or a missing channel); ├─ xcb-util ==0.4.0 h516909a_0 does not exist (perhaps a typo or a missing channel); ├─ xkeyboard-config ==2.38 h0b41bf4_0 does not exist (perhaps a typo or a missing channel); ├─ xorg-kbproto ==1.0.7 h7f98852_1002 does not exist (perhaps a typo or a missing channel); ├─ xorg-libice ==1.1.1 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ xorg-libsm ==1.2.4 h7391055_0 does not exist (perhaps a typo or a missing channel); ├─ xorg-libx11 ==1.8.4 h0b41bf4_0 does not exist (perhaps a typo or a missing channel); ├─ xorg-libxau ==1.0.11 hd590300_0 does not exist (perhaps a typo or a missing channel); ├─ xorg-libxdmcp ==1.1.3 h7f98852_0 does not exist (perhaps a typo or a missing channel); ├─ xorg-libxext ==1.3.4 h0b41bf4_2 does not exist (perhaps a typo or a missing channel); ├─ xorg-libxrender ==0.9.10 h7f98852_1003 does not exist (perhaps a typo or a missing channel); ├─ xorg-renderproto ==0.11.1 h7f98852_1002 does not exist (perhaps a typo or a missing channel); ├─ xorg-xextproto ==7.3.0 h0b41bf4_1003 does not exist (perhaps a typo or a missing channel); ├─ xorg-xproto ==7.0.31 h7f98852_1007 does not exist (perhaps a typo or a missing channel); ├─ xz ==5.2.6 h166bdaf_0 does not exist (perhaps a typo or a missing channel); ├─ yarl ==1.9.4 py310h2372a71_0 does not exist (perhaps a typo or a missing channel); ├─ zip ==3.0 hd590300_3 does not exist (perhaps a typo or a missing channel); ├─ zlib ==1.2.13 hd590300_5 does not exist (perhaps a typo or a missing channel); └─ zstd ==1.5.5 hfc55251_0 does not exist (perhaps a typo or a missing channel).
As I am not that highly trained in programming I would be very happy if someone can help me with that issue.