environment.yaml

[yokomaz]

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.