environment.yaml #72
Description
Dear Developer,
Thank you for developing such a great software.
While using PytomGUI, I encountered an issue related to the environment file pytom_full.yaml. I would suggest specifying the versions of UCX and OpenMPI explicitly in this file.
On my machine, the system-wide UCX version is 1.8.0 (checked via ucx_info -v), while OpenMPI 5.0.5 is installed inside the conda environment. This mismatch caused a conflict and led to an initialization error when I attempted to perform template matching using multiple GPUs (e.g., GpuId 0,1,2,3).
I was able to resolve this issue by installing UCX within the conda environment using conda install -c conda-forge ucx, which provided UCX version 1.18.0 and solved the conflict.
on my side the final version of pytom_full.yaml is
name: pytom_env
channels:
- conda-forge
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- defaults
dependencies: - _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- alsa-lib=1.2.12=h4ab18f5_0
- aom=3.9.1=hac33072_0
- asttokens=2.4.1=pyhd8ed1ab_0
- attr=2.5.1=h166bdaf_1
- binutils_impl_linux-64=2.40=ha1999f0_7
- binutils_linux-64=2.40=hb3c18ed_4
- blosc=1.21.6=hef167b5_0
- boost=1.85.0=h9cebb41_4
- brotli=1.1.0=hb9d3cd8_2
- brotli-bin=1.1.0=hb9d3cd8_2
- brunsli=0.1=h9c3ff4c_0
- bzip2=1.0.8=h4bc722e_7
- c-blosc2=2.15.1=hc57e6cf_0
- ca-certificates=2025.4.26=hbd8a1cb_0
- cairo=1.18.0=hebfffa5_3
- certifi=2025.1.31=pyhd8ed1ab_0
- charls=2.4.2=h59595ed_0
- colorama=0.4.6=pyhd8ed1ab_0
- contourpy=1.3.1=py312h68727a3_0
- cuda-cccl_linux-64=12.6.77=ha770c72_0
- cuda-cudart-dev_linux-64=12.6.77=h3f2d84a_0
- cuda-cudart-static_linux-64=12.6.77=h3f2d84a_0
- cuda-cudart_linux-64=12.6.77=h3f2d84a_0
- cuda-nvrtc=12.6.77=hbd13f7d_0
- cuda-version=12.6=h7480c83_3
- cupy=13.3.0=py312h7d319b9_2
- cupy-core=13.3.0=py312h1acd1a8_2
- cycler=0.12.1=pyhd8ed1ab_0
- dav1d=1.2.1=hd590300_0
- dbus=1.13.6=h5008d03_3
- decorator=5.1.1=pyhd8ed1ab_0
- double-conversion=3.3.0=h59595ed_0
- exceptiongroup=1.2.2=pyhd8ed1ab_0
- executing=2.1.0=pyhd8ed1ab_0
- expat=2.6.4=h5888daf_0
- fastrlock=0.8.2=py312h30efb56_2
- fftw=3.3.10=mpi_openmpi_h4a81ba8_9
- 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_3
- fontconfig=2.15.0=h7e30c49_1
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.54.1=py312h178313f_1
- freetype=2.12.1=h267a509_2
- gcc=12.4.0=h236703b_2
- gcc_impl_linux-64=12.4.0=h26ba24d_2
- gcc_linux-64=12.4.0=h6b7512a_10
- gettext=0.22.5=he02047a_3
- gettext-tools=0.22.5=he02047a_3
- gfortran_impl_linux-64=12.4.0=h61783b2_2
- gfortran_linux-64=12.4.0=hd748a6a_10
- giflib=5.2.2=hd590300_0
- glib=2.82.2=h44428e9_0
- glib-tools=2.82.2=h4833e2c_0
- graphite2=1.3.13=h59595ed_1003
- gst-plugins-base=1.24.7=h0a52356_0
- gstreamer=1.24.7=hf3bb09a_0
- gxx_impl_linux-64=12.4.0=h3ff227c_2
- gxx_linux-64=12.4.0=h8489865_10
- harfbuzz=9.0.0=hda332d3_1
- icu=75.1=he02047a_0
- imagecodecs=2024.9.22=py312hf6703b6_0
- imageio=2.36.0=pyh12aca89_1
- importlib-metadata=8.5.0=pyha770c72_0
- ipython=8.29.0=pyh707e725_0
- jedi=0.19.2=pyhff2d567_0
- joblib=1.4.2=pyhd8ed1ab_0
- jxrlib=1.1=hd590300_3
- kernel-headers_linux-64=3.10.0=he073ed8_18
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.7=py312h68727a3_0
- krb5=1.21.3=h659f571_0
- lame=3.100=h166bdaf_1003
- lazy-loader=0.4=pyhd8ed1ab_1
- lazy_loader=0.4=pyhd8ed1ab_1
- lcms2=2.16=hb7c19ff_0
- ld_impl_linux-64=2.40=hf3520f5_7
- lerc=4.0.0=h27087fc_0
- libaec=1.1.3=h59595ed_0
- libasprintf=0.22.5=he8f35ee_3
- libasprintf-devel=0.22.5=he8f35ee_3
- libavif16=1.1.1=h1909e37_2
- libblas=3.9.0=25_linux64_openblas
- libboost=1.85.0=h0ccab89_4
- libboost-devel=1.85.0=h00ab1b0_4
- libboost-headers=1.85.0=ha770c72_4
- libboost-python=1.85.0=py312hf74af30_4
- libboost-python-devel=1.85.0=py312h9cebb41_4
- libbrotlicommon=1.1.0=hb9d3cd8_2
- libbrotlidec=1.1.0=hb9d3cd8_2
- libbrotlienc=1.1.0=hb9d3cd8_2
- libcap=2.71=h39aace5_0
- libcblas=3.9.0=25_linux64_openblas
- libclang-cpp19.1=19.1.3=default_hb5137d0_0
- libclang13=19.1.3=default_h9c6a7e4_0
- libcublas=12.6.3.3=hbd13f7d_1
- libcufft=11.3.0.4=hbd13f7d_0
- libcups=2.3.3=h4637d8d_4
- libcurand=10.3.7.77=hbd13f7d_0
- libcusolver=11.7.1.2=hbd13f7d_0
- libcusparse=12.5.4.2=hbd13f7d_0
- libdeflate=1.22=hb9d3cd8_0
- libdrm=2.4.123=hb9d3cd8_0
- libedit=3.1.20191231=he28a2e2_2
- libegl=1.7.0=ha4b6fd6_2
- libevent=2.1.12=hf998b51_1
- libexpat=2.6.4=h5888daf_0
- libffi=3.4.2=h7f98852_5
- libflac=1.4.3=h59595ed_0
- libgcc=14.2.0=h77fa898_1
- libgcc-devel_linux-64=12.4.0=h1762d19_102
- libgcc-ng=14.2.0=h69a702a_1
- libgcrypt=1.11.0=h4ab18f5_1
- libgcrypt-lib=1.11.0=hb9d3cd8_2
- libgettextpo=0.22.5=he02047a_3
- libgettextpo-devel=0.22.5=he02047a_3
- libgfortran=14.2.0=h69a702a_1
- libgfortran-ng=14.2.0=h69a702a_1
- libgfortran5=14.2.0=hd5240d6_1
- libgl=1.7.0=ha4b6fd6_2
- libglib=2.82.2=h2ff4ddf_0
- libglvnd=1.7.0=ha4b6fd6_2
- libglx=1.7.0=ha4b6fd6_2
- libgomp=14.2.0=h77fa898_1
- libgpg-error=1.55=h3f2d84a_0
- libhwloc=2.11.2=default_h0d58e46_1001
- libhwy=1.1.0=h00ab1b0_0
- libiconv=1.17=hd590300_2
- libjpeg-turbo=3.0.0=hd590300_1
- libjxl=0.11.0=hdb8da77_2
- liblapack=3.9.0=25_linux64_openblas
- libllvm14=14.0.6=hcd5def8_4
- libllvm19=19.1.3=ha7bfdaf_0
- libnl=3.11.0=hb9d3cd8_0
- libnsl=2.0.1=hd590300_0
- libnvjitlink=12.6.77=hbd13f7d_1
- libogg=1.3.5=h4ab18f5_0
- libopenblas=0.3.28=pthreads_h94d23a6_1
- libopengl=1.7.0=ha4b6fd6_2
- libopus=1.3.1=h7f98852_1
- libpciaccess=0.18=hd590300_0
- libpng=1.6.44=hadc24fc_0
- libpq=16.4=h2d7952a_3
- libsanitizer=12.4.0=ha732cd4_2
- libsndfile=1.2.2=hc60ed4a_1
- libsqlite=3.47.0=hadc24fc_1
- libstdcxx=14.2.0=hc0a3c3a_1
- libstdcxx-devel_linux-64=12.4.0=h1762d19_102
- libstdcxx-ng=14.2.0=h4852527_1
- libsystemd0=256.9=h2774228_0
- libtiff=4.7.0=he137b08_1
- libudev1=257.4=h9a4d06a_0
- libuuid=2.38.1=h0b41bf4_0
- libvorbis=1.3.7=h9c3ff4c_0
- libwebp-base=1.4.0=hd590300_0
- libxcb=1.17.0=h8a09558_0
- libxcrypt=4.4.36=hd590300_1
- libxkbcommon=1.7.0=h2c5496b_1
- libxml2=2.13.4=hb346dea_2
- libxslt=1.1.39=h76b75d6_0
- libzlib=1.3.1=hb9d3cd8_2
- libzopfli=1.0.3=h9c3ff4c_0
- llvmlite=0.43.0=py312h374181b_1
- lxml=5.3.0=py312he28fd5a_2
- lz4-c=1.9.4=hcb278e6_0
- make=4.4.1=hb9d3cd8_2
- matplotlib=3.9.2=py312h7900ff3_2
- matplotlib-base=3.9.2=py312hd3ec401_2
- matplotlib-inline=0.1.7=pyhd8ed1ab_0
- mpg123=1.32.9=hc50e24c_0
- mpi=1.0=openmpi
- mpi4py=3.1.6=py312h67a4414_0
- mrcfile=1.5.3=pyhd8ed1ab_0
- munkres=1.1.4=pyh9f0ad1d_0
- mysql-common=9.0.1=h266115a_2
- mysql-libs=9.0.1=he0572af_2
- ncurses=6.5=he02047a_1
- networkx=3.4.2=pyhd8ed1ab_1
- nspr=4.36=h5888daf_0
- nss=3.106=hdf54f9c_0
- numba=0.60.0=py312h83e6fd3_0
- numpy=1.26.4=py312heda63a1_0
- openjpeg=2.5.2=h488ebb8_0
- openmpi=4.1.6=hc5af2df_101---------------------------------------------------------openmpi
- openmpi-mpicc=4.1.6=hd590300_101
- openmpi-mpicxx=4.1.6=h00ab1b0_101
- openmpi-mpifort=4.1.6=heb67821_101
- openssl=3.5.0=h7b32b05_0
- packaging=24.2=pyhd8ed1ab_0
- parso=0.8.4=pyhd8ed1ab_0
- pcre2=10.44=hba22ea6_2
- pexpect=4.9.0=pyhd8ed1ab_0
- pickleshare=0.7.5=py_1003
- pillow=11.0.0=py312h7b63e92_0
- pip=24.3.1=pyh8b19718_0
- pixman=0.43.2=h59595ed_0
- ply=3.11=pyhd8ed1ab_2
- prompt-toolkit=3.0.48=pyha770c72_0
- pthread-stubs=0.4=hb9d3cd8_1002
- ptyprocess=0.7.0=pyhd3deb0d_0
- pulseaudio-client=17.0=hb77b528_0
- pure_eval=0.2.3=pyhd8ed1ab_0
- pygments=2.18.0=pyhd8ed1ab_0
- pyparsing=3.2.0=pyhd8ed1ab_1
- pyqt=5.15.9=py312h949fe66_5
- pyqt5-sip=12.12.2=py312h30efb56_5
- pyqtgraph=0.13.7=pyhd8ed1ab_0
- pyside6=6.7.3=py312h91f0f75_1
- python=3.12.7=hc5c86c4_0_cpython
- python-dateutil=2.9.0=pyhd8ed1ab_0
- python_abi=3.12=5_cp312
- pywavelets=1.7.0=py312hc0a28a1_2
- qhull=2020.2=h434a139_5
- qt-main=5.15.15=h374914d_0
- qt6-main=6.7.3=h20baabe_0
- rav1e=0.6.6=he8a937b_2
- rdma-core=55.0=h5888daf_0
- readline=8.2=h8228510_1
- scikit-image=0.24.0=py312hf9745cd_3
- scipy=1.14.1=py312h62794b6_1
- setuptools=75.3.0=pyhd8ed1ab_0
- sip=6.7.12=py312h30efb56_0
- six=1.16.0=pyh6c4a22f_0
- snappy=1.2.1=ha2e4443_0
- stack_data=0.6.2=pyhd8ed1ab_0
- svt-av1=2.3.0=h5888daf_0
- swig=4.3.0=heed6a68_0
- sysroot_linux-64=2.17=h4a8ded7_18
- tifffile=2024.9.20=pyhd8ed1ab_0
- tk=8.6.13=noxft_h4845f30_101
- toml=0.10.2=pyhd8ed1ab_0
- tomli=2.1.0=pyhff2d567_0
- tornado=6.4.1=py312h66e93f0_1
- tqdm=4.67.0=pyhd8ed1ab_0
- traitlets=5.14.3=pyhd8ed1ab_0
- typing_extensions=4.12.2=pyha770c72_0
- tzdata=2024b=hc8b5060_0
- ucx=1.18.0=h8887438_3 -----------------------------------------------------------------ucx
- unicodedata2=15.1.0=py312h66e93f0_1
- wayland=1.23.1=h3e06ad9_0
- wcwidth=0.2.13=pyhd8ed1ab_0
- wheel=0.45.0=pyhd8ed1ab_0
- xcb-util=0.4.1=hb711507_2
- xcb-util-cursor=0.1.5=hb9d3cd8_0
- xcb-util-image=0.4.0=hb711507_2
- xcb-util-keysyms=0.4.1=hb711507_0
- xcb-util-renderutil=0.3.10=hb711507_0
- xcb-util-wm=0.4.2=hb711507_0
- xkeyboard-config=2.43=hb9d3cd8_0
- xorg-libice=1.1.1=hb9d3cd8_1
- xorg-libsm=1.2.4=he73a12e_1
- xorg-libx11=1.8.10=h4f16b4b_0
- xorg-libxau=1.0.11=hb9d3cd8_1
- xorg-libxdamage=1.1.6=hb9d3cd8_0
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
- xorg-libxext=1.3.6=hb9d3cd8_0
- xorg-libxfixes=6.0.1=hb9d3cd8_0
- xorg-libxi=1.8.2=hb9d3cd8_0
- xorg-libxrender=0.9.11=hb9d3cd8_1
- xorg-libxtst=1.2.5=hb9d3cd8_3
- xorg-libxxf86vm=1.1.5=hb9d3cd8_4
- xorg-xf86vidmodeproto=2.3.1=hb9d3cd8_1005
- xorg-xorgproto=2024.1=hb9d3cd8_1
- xz=5.2.6=h166bdaf_0
- zfp=1.0.1=h5888daf_2
- zipp=3.21.0=pyhd8ed1ab_0
- zlib=1.3.1=hb9d3cd8_2
- zlib-ng=2.2.2=h5888daf_0
- zstd=1.5.6=ha6fb4c9_0
- pip:
- pytom==1.0
I hope this will help improving pytom usage.