Upgrade 2025 for new AMD

2024/install_elic_python_ext.py

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+#pip install Flask --user --dry-run --upgrade-strategy only-if-needed
+
+pip install Flask Werkzeug absl-py acccmip6 access affine altair antlr4-python3-runtime args asciitree astunparse attrdict aws-requests-auth blinker boto3==1.39.8 brotli cachetools cdo cdsapi cf-units clang clint configobj coverage dash dash-core-components dash-html-components ecmwf-datastores-client itsdangerous multiurl retrying s3transfer tqdm Flask-Compress backports.zstd dash-table deepmerge descartes dill entrypoints eofs esda et_xmlfile fasteners flatbuffers giddy libpysal quantecon seaborn sympy ImageIO google-auth google-auth-oauthlib google-pasta grpcio gsw inequality ipympl jsonlines pyasn1_modules requests-oauthlib rsa keras keras-nightly Keras-Preprocessing mamba Markdown MetPy mgwr momepy nose olefile opencv-contrib-python==4.11.0.86 opencv-python==4.11.0.86 openpyxl opt-einsum pointpats Polygon3 protobuf PuLP pyasn1-modules PyWavelets click jsonlines lazy_loader mapclassify pyresample pysal quilt3 radian rasterio rasterstats rchitect requests-futures rtree rvlib scikit-image segregation spaghetti spint splot spopt tifffile tobler seawater snuggs spvcm tensorboard tensorboard-data-server tensorboard-plugin-wit tensorflow tensorflow-estimator termcolor testpath salem PyQt5 --user --upgrade-strategy only-if-needed
+
+#pygeos pywct
+

2025/Julia-1.12.4.eb

@@ -0,0 +1,36 @@
+easyblock = 'Tarball'
+
+name = 'Julia'
+version = '1.12.4'
+
+homepage = 'https://julialang.org'
+description = "Julia is a high-level, high-performance dynamic programming language for numerical computing"
+
+toolchain = SYSTEM
+
+source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/',
+               'https://julialang-s3.julialang.org/bin/linux/%(arch)s/%(version_major_minor)s/']
+sources = ['%(namelower)s-%(version)s-linux-%(arch)s.tar.gz']
+checksums = [
+    {
+        'julia-1.12.4-linux-x86_64.tar.gz':
+            'c57baf178fe140926acb1a25396d482f325af9d7908d9b066d2fbc0d6639985d',
+        'julia-1.12.4-linux-aarch64.tar.gz':
+            'a602a2dfee931224fd68e47567dc672743e2fd9e80f39d84cf3c99afc9663ddd',
+    }
+]
+sanity_check_paths = {
+    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+}
+
+sanity_check_commands = ['julia --help']
+
+modextravars = {
+    # Use default DEPOT_PATH where first entry is user's depot
+    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
+    # those installations appended to DEPOT_PATH without disabling any of the default paths
+    'JULIA_DEPOT_PATH': ':',
+}
+
+moduleclass = 'lang'

2025/Miniforge3-25.11.0-1.eb

@@ -0,0 +1,26 @@
+easyblock = 'EB_Mamba'
+
+name = 'Miniforge3'
+version = '25.11.0-1'
+
+homepage = 'https://github.com/conda-forge/miniforge'
+description = """Miniforge is a free minimal installer for conda and Mamba specific
+ to conda-forge."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s']
+local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH)
+sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch]
+checksums = [
+    {
+        '%(name)s-%(version)s-Linux-x86_64.sh':
+            'be1bad9d4e67a8753eb76fb4940e9a08036786675c7adf060627e55791bf110d',
+        '%(name)s-%(version)s-Linux-ppc64le.sh':
+            '8fb7a41bd2682381c48c7820608918e7d56f5390bc3be5705a0c1c536f607963',
+        '%(name)s-%(version)s-Linux-aarch64.sh':
+            '43a3783f9e121088f1c92b131b4305b9ebf159424ad2543dfcfc0f1952b5e127',
+    }
+]
+
+moduleclass = 'lang'

2025/README.md

@@ -3,21 +3,19 @@
 ```bash
 eb_noarch Java-21.0.8.eb
 eb_noarch Java-21.eb
-eb_noarch Julia-1.12.2.eb
+eb_noarch Julia-1.12.4.eb
 
-eb_2025b OpenSSL-3.eb --hide-deps=pkgconf,Bison,flex,zlib,binutils,M4,help2man,Perl -r
-```
+eb_noarch Miniforge3-25.11.0-1.eb
 
-```bash
-eb_2025b CDO-2.5.3-gompi-2025b.eb --hide-deps=Bison,flex,zlib,binutils,M4,zlib,Bison,help2man,flex,binutils,Perl,libtool,pkgconf,Szip,bzip2,Autoconf,Automake,ncurses,Autotools,libiconv,UnZip,numactl,UCX,libreadline,gzip,pkgconf,libfabric,lz4,libffi,Tcl,ncurses,SQLite,gettext,XZ,zstd,libxml2,zlib,binutils,Perl,cURL,libarchive,libevent,Ninja,CMake,Doxygen,Meson,UCC,xorg-macros,libpciaccess,hwloc,PMIx,PRRTE,OpenMPI,libidn2,libunistring,libtommath,libpsl,libaec,ecBuild,FFTW,libpng,NASM,jbigkit,expat,libjpeg-turbo,googletest,nlohmann_json,libde265,libdeflate,LibTIFF,util-linux,Yasm,x265,PCRE2,pixman,Brotli,GLib,freetype,gperf,groff,fontconfig,intltool,X11,cairo,GObject-Introspection,Gdk-Pixbuf,libheif,JasPer,ecCodes -r
+eb_2025b OpenSSL-3.eb --hide-deps=pkgconf,Bison,flex,zlib,binutils,M4,help2man,Perl -r
 ```
 
 ```bash
-eb_2025b Python-bundle-PyPI-2025.07-GCCcore-14.3.0.eb --hide-deps=help2man,M4,zlib,Bison,flex,binutils,pkgconf,bzip2,expat,Perl,UnZip,Autoconf,Automake,libtool,ncurses,libidn2,Autotools,libreadline,libiconv,patchelf,Tcl,SQLite,libunistring,libffi,zlib,XZ,libxml2,libarchive,libpsl,gettext,setuptools-rust,Ninja,cffi,hatchling,cURL,scikit-build,flit,CMake,scikit-build-core,Rust,maturin,cryptography,poetry,libtommath,lz4,zstd -r
+eb_2025b CDO-2.5.3-gompi-2025b.eb --hide-deps=Bison,flex,zlib,binutils,M4,zlib,Bison,help2man,flex,binutils,Perl,libtool,pkgconf,Szip,bzip2,Autoconf,Automake,ncurses,Autotools,libiconv,UnZip,numactl,UCX,libreadline,gzip,pkgconf,libfabric,lz4,libffi,Tcl,ncurses,SQLite,gettext,XZ,zstd,libxml2,zlib,binutils,Perl,cURL,libarchive,libevent,Ninja,CMake,Doxygen,Meson,UCC,xorg-macros,libpciaccess,hwloc,PMIx,PRRTE,OpenMPI,libidn2,libunistring,libtommath,libpsl,libaec,ecBuild,FFTW,libpng,NASM,jbigkit,expat,libjpeg-turbo,googletest,nlohmann_json,libde265,libdeflate,LibTIFF,util-linux,Yasm,x265,PCRE2,pixman,Brotli,GLib,freetype,gperf,groff,fontconfig,intltool,X11,cairo,GObject-Introspection,Gdk-Pixbuf,libheif,JasPer,ecCodes,Mako,UDUNITS,PROJ,glslang-SPIRV,Cython,libyaml,Wayland,psutil,elfutils,lit,hatchling,libdrm,libunwind,scikit-build-core,GMP,scikit-build,Z3,LLVM,libclc,nettle,flit,setuptools-rust,patchelf,Rust,maturin,virtualenv,cffi,cryptography,build,poetry,PyYAML,OpenGL,freeglut -r
 ```
 
 ```bash
-eb_2025b ELIC_Python-1-foss-2025b.eb --hide-deps=Bison,flex,zlib,binutils,M4,zlib,Bison,help2man,flex,binutils,Perl,libtool,pkgconf,Szip,bzip2,Autoconf,Automake,ncurses,Autotools,libiconv,UnZip,numactl,UCX,libreadline,gzip,pkgconf,libfabric,lz4,libffi,Tcl,ncurses,SQLite,gettext,XZ,zstd,libxml2,zlib,binutils,Perl,cURL,libarchive,libevent,Ninja,CMake,Doxygen,Meson,UCC,xorg-macros,libpciaccess,hwloc,PMIx,PRRTE,OpenMPI,libidn2,libunistring,libtommath,libpsl,libaec,ecBuild,FFTW,libpng,NASM,jbigkit,expat,libjpeg-turbo,googletest,nlohmann_json,libde265,libdeflate,LibTIFF,util-linux,Yasm,x265,PCRE2,pixman,Brotli,GLib,freetype,gperf,groff,fontconfig,intltool,X11,cairo,GObject-Introspection,Gdk-Pixbuf,libheif,JasPer,ecCodes,patchelf,PCRE,Zip,hatchling,cppy,Cython,scikit-build,flit,setuptools-rust,BLIS,ICU,AOCL-BLAS,cffi,scikit-build-core,Rust,Eigen,Catch2,maturin,Boost,cryptography,Qhull,poetry,hypothesis,meson-python,pybind11,spin,fonttools,giflib,libwebp,OpenJPEG,libgeotiff,LittleCMS,make,Pillow,libtirpc,HDF,CFITSIO,FFTW.MPI,arpack-ng,Armadillo,json-c,Xerces-C++,Brunsli,Imath,OpenEXR,LERC,SWIG,Tk,Tkinter,GSL,ANTLR,hatch-jupyter-builder,Mako,bcrypt,libdap,build,OpenPGM,pyproj,plotly.py,tornado,glslang-SPIRV,jedi,libsodium,py-cpuinfo,nodejs,libyaml,libxslt,ZeroMQ,configurable-http-proxy,PyYAML,lxml,PyZMQ,IPython,Shapely,PycURL,BeautifulSoup,aiohttp,jupyter-server,jupyter-server-proxy,JupyterLab,JupyterNotebook,nbclassic,jupyterlmod,bokeh,jupyter-resource-usage,wrapt,Wayland,Greenlet,psutil,elfutils,lit,typing-extensions,pydantic,libdrm,psycopg,mpi4py,SQLAlchemy,JupyterHub,netcdf4-python,libunwind,GMP,Z3,LLVM,libclc,nettle,OpenGL,freeglut,Fiona,ESMF,PROJ,Deprecated,ESMPy,virtualenv,geopandas,h5netcdf,statsmodels,basemap,networkx,scikit-learn,h5py,numba -r
+eb_2025b ELIC_Python-1-foss-2025b.eb --hide-deps=Bison,flex,zlib,binutils,M4,zlib,Bison,help2man,flex,binutils,Perl,libtool,pkgconf,Szip,bzip2,Autoconf,Automake,ncurses,Autotools,libiconv,UnZip,numactl,UCX,libreadline,gzip,pkgconf,libfabric,lz4,libffi,Tcl,ncurses,SQLite,gettext,XZ,zstd,libxml2,zlib,binutils,Perl,cURL,libarchive,libevent,Ninja,CMake,Doxygen,Meson,UCC,xorg-macros,libpciaccess,hwloc,PMIx,PRRTE,OpenMPI,libidn2,libunistring,libtommath,libpsl,libaec,ecBuild,FFTW,libpng,NASM,jbigkit,expat,libjpeg-turbo,googletest,nlohmann_json,libde265,libdeflate,LibTIFF,util-linux,Yasm,x265,PCRE2,pixman,Brotli,GLib,freetype,gperf,groff,fontconfig,intltool,X11,cairo,GObject-Introspection,Gdk-Pixbuf,libheif,JasPer,ecCodes,patchelf,PCRE,Zip,hatchling,cppy,Cython,scikit-build,flit,setuptools-rust,BLIS,ICU,AOCL-BLAS,cffi,scikit-build-core,Rust,Eigen,Catch2,maturin,Boost,cryptography,Qhull,poetry,hypothesis,meson-python,pybind11,spin,fonttools,giflib,libwebp,OpenJPEG,libgeotiff,LittleCMS,make,Pillow,libtirpc,HDF,CFITSIO,FFTW.MPI,arpack-ng,Armadillo,json-c,Xerces-C++,Brunsli,Imath,OpenEXR,LERC,SWIG,Tk,Tkinter,GSL,ANTLR,hatch-jupyter-builder,Mako,bcrypt,libdap,build,OpenPGM,pyproj,plotly.py,tornado,glslang-SPIRV,jedi,libsodium,py-cpuinfo,nodejs,libyaml,libxslt,ZeroMQ,configurable-http-proxy,PyYAML,lxml,PyZMQ,IPython,Shapely,PycURL,BeautifulSoup,aiohttp,jupyter-server,jupyter-server-proxy,JupyterLab,JupyterNotebook,nbclassic,jupyterlmod,bokeh,jupyter-resource-usage,wrapt,Wayland,Greenlet,psutil,elfutils,lit,typing-extensions,pydantic,libdrm,psycopg,mpi4py,SQLAlchemy,JupyterHub,netcdf4-python,libunwind,GMP,Z3,LLVM,libclc,nettle,OpenGL,freeglut,Fiona,ESMF,PROJ,Deprecated,ESMPy,virtualenv,geopandas,h5netcdf,statsmodels,basemap,networkx,scikit-learn,h5py,numba,UDUNITS,GEOS,GDAL -r
 ```
 
 ```bash
@@ -29,5 +27,5 @@ eb_2025b netCDF-Fortran-4.6.2-iimpi-2025b.eb --hide-deps=M4,imkl,Bison,flex,zlib
 ```
 
 ```bash
-eb_2025b ELIC_R-1-foss-2025b.eb --hide-deps=M4,Bison,flex,zlib,binutils,help2man,M4,zlib,Bison,flex,binutils,bzip2,libtool,Perl,libiconv,pkgconf,Autoconf,UnZip,Automake,ncurses,libreadline,Autotools,GMP,libffi,expat,Tcl,pkgconf,ncurses,SQLite,gettext,XZ,libxml2,libxslt,gettext,nettle,PCRE2,libpng,groff,FFTW,libunwind,gperf,gzip,xorg-macros,util-linux,lz4,zlib,NASM,libogg,zstd,FLAC,binutils,libvorbis,Perl,Ninja,cURL,libarchive,intltool,Mako,ICU,CMake,Meson,NLopt,pixman,Doxygen,libjpeg-turbo,GLib,Brotli,freetype,fontconfig,libpciaccess,Wayland,libopus,Szip,jbigkit,lit,X11,libdrm,cairo,libglvnd,GSL,libgit2,LAME,libdeflate,libsndfile,LibTIFF,LLVM,Mesa,libGLU,Xvfb,Tk,GLPK,Ghostscript,nodejs,FriBidi,JasPer,libevent,GObject-Introspection,numactl,hwloc,LittleCMS,UCX,fonttools,HarfBuzz,MPFR,Pango,libfabric,PMIx,BLIS,PRRTE,PCRE,UCC,make,OpenMPI,FFTW.MPI,gfbf,googletest,nlohmann_json,PROJ,libgeotiff,libtirpc,HDF,CFITSIO,Cython,Boost,hatchling,giflib,json-c,scikit-build,Eigen,arpack-ng,Armadillo,Xerces-C++,flit,Catch2,setuptools-rust,patchelf,Rust,Brunsli,maturin,Imath,OpenEXR,Qhull,LERC,cffi,cryptography,poetry,pybind11,hypothesis,meson-python,OpenJPEG,SWIG,libde265,psutil,Z3,Gdk-Pixbuf,Yasm,x265,libheif,gfbf,libidn2,libunistring,libtommath,libyaml,libpsl,scikit-build-core,libclc,AOCL-BLAS,build,PyYAML,OpenGL,freeglut,spin,glslang-SPIRV,libaec,libwebp,elfutils,Zip,virtualenv,R-bundle-CRAN -r
+eb_2025b ELIC_R-1-foss-2025b.eb --hide-deps=M4,Bison,flex,zlib,binutils,help2man,M4,zlib,Bison,flex,binutils,bzip2,libtool,Perl,libiconv,pkgconf,Autoconf,UnZip,Automake,ncurses,libreadline,Autotools,GMP,libffi,expat,Tcl,pkgconf,ncurses,SQLite,gettext,XZ,libxml2,libxslt,gettext,nettle,PCRE2,libpng,groff,FFTW,libunwind,gperf,gzip,xorg-macros,util-linux,lz4,zlib,NASM,libogg,zstd,FLAC,binutils,libvorbis,Perl,Ninja,cURL,libarchive,intltool,Mako,ICU,CMake,Meson,NLopt,pixman,Doxygen,libjpeg-turbo,GLib,Brotli,freetype,fontconfig,libpciaccess,Wayland,libopus,Szip,jbigkit,lit,X11,libdrm,cairo,libglvnd,GSL,libgit2,LAME,libdeflate,libsndfile,LibTIFF,LLVM,Mesa,libGLU,Xvfb,Tk,GLPK,Ghostscript,nodejs,FriBidi,JasPer,libevent,GObject-Introspection,numactl,hwloc,LittleCMS,UCX,fonttools,HarfBuzz,MPFR,Pango,libfabric,PMIx,BLIS,PRRTE,PCRE,UCC,make,OpenMPI,FFTW.MPI,gfbf,googletest,nlohmann_json,PROJ,libgeotiff,libtirpc,HDF,CFITSIO,Cython,Boost,hatchling,giflib,json-c,scikit-build,Eigen,arpack-ng,Armadillo,Xerces-C++,flit,Catch2,setuptools-rust,patchelf,Rust,Brunsli,maturin,Imath,OpenEXR,Qhull,LERC,cffi,cryptography,poetry,pybind11,hypothesis,meson-python,OpenJPEG,SWIG,libde265,psutil,Z3,Gdk-Pixbuf,Yasm,x265,libheif,gfbf,libidn2,libunistring,libtommath,libyaml,libpsl,scikit-build-core,libclc,AOCL-BLAS,build,PyYAML,OpenGL,freeglut,spin,glslang-SPIRV,libaec,libwebp,elfutils,Zip,virtualenv,R-bundle-CRAN,UDUNITS,GEOS,GDAL -r
 ```

2025/install_elic_R_ext.R

@@ -11,7 +11,7 @@ install_archived <- function(pkg, version) {
   install.packages(url, repos = NULL, type = "source", lib=EBROOTELIC_R)
 }
 
-packages = c('leaflet', 'satellite', 'intervals', 'spacetime', 'gstat', 'automap', 'reporttools', 'rworldmap', 'colorRamps', 'mapdata', 'mapproj', 'RPostgreSQL', 'getPass', 'stringdist', 'here', 'svMisc', 'networkD3', 'wordcloud', 'ngram', 'xgboost', 'rts', 'RgoogleMaps', 'packrat', 'rsconnect', 'rpostgis', 'aws.signature', 'aws.s3', 'geosphere', 'fuzzyjoin', 'refinr', 'x13binary', 'seasonal', 'mitools', 'survey', 'sysfonts', 'showtextdb', 'showtext', 'BiocManager', 'rvcheck', 'scatterpie', 'rlist', 'measurements', 'qpdf', 'fda', 'fda.usc', 'gstat', 'countrycode', 'itcSegment', 'rwunderground', 'corrplot', 'prettymapr', 'prospectr', 'rpart.plot', 'varhandle', 'expint', 'actuar', 'psych', 'plotly', 'spatstat', 'raster', 'treemap', 'ggmap', 'hts', 'thief', 'forecastHybrid', 'colourpicker', 'profvis', 'jsonlite', 'readxl', 'tidyverse', 'data.table', 'lubridate', 'stringi', 'snakecase', 'Matrix', 'RSelenium', 'devtools', 'ggplot2', 'metR', 'raster', 'sp' , 'rmapshaper' ,'adehabitatMA', 'plyr' , 'dplyr' , 'tmap', 'reshape', 'ggplot2', 'png', 'MuMIn', 'tmaptools')
+packages = c('leaflet', 'satellite', 'intervals', 'spacetime', 'gstat', 'automap', 'reporttools', 'rworldmap', 'colorRamps', 'mapdata', 'mapproj', 'RPostgreSQL', 'getPass', 'stringdist', 'here', 'svMisc', 'networkD3', 'wordcloud', 'ngram', 'xgboost', 'rts', 'RgoogleMaps', 'packrat', 'rsconnect', 'rpostgis', 'aws.signature', 'aws.s3', 'geosphere', 'fuzzyjoin', 'refinr', 'x13binary', 'seasonal', 'mitools', 'survey', 'sysfonts', 'showtextdb', 'showtext', 'BiocManager', 'rvcheck', 'scatterpie', 'rlist', 'measurements', 'qpdf', 'fda', 'fda.usc', 'gstat', 'countrycode', 'itcSegment', 'rwunderground', 'corrplot', 'prettymapr', 'prospectr', 'rpart.plot', 'varhandle', 'expint', 'actuar', 'psych', 'plotly', 'spatstat', 'raster', 'treemap', 'ggmap', 'hts', 'thief', 'forecastHybrid', 'colourpicker', 'profvis', 'jsonlite', 'readxl', 'tidyverse', 'data.table', 'lubridate', 'stringi', 'snakecase', 'Matrix', 'RSelenium', 'devtools', 'ggplot2', 'metR', 'raster', 'sp' , 'rmapshaper' ,'adehabitatMA', 'plyr' , 'dplyr' , 'tmap', 'reshape', 'ggplot2', 'png', 'MuMIn', 'tmaptools', 'config', 'huxtable', 'rhino', 'rtables', 'teal', 'tippy', 'Tplyr')
 
 ## Now load or install&load all
 package.check <- lapply(
@@ -41,6 +41,10 @@ install_archived("owmr", "0.8.2")
 install_archived("rgeoboundaries", "1.3")
 install_archived("waffle", "1.0.2")
 install_archived("httpgd", "2.0.4")
+install_archived("tidycmprsk", "1.1.0")
+install_archived("visR", "0.4.1")
+install_archived("collections", "0.3.9")
+install_archived("languageserver", "0.3.15")
 
 # 2. Install the specific archived versions
 #install_archived("rgeos", "0.6-4")

2025/netCDF-4.9.3-iimpi-2025b.eb

@@ -43,11 +43,9 @@ preconfigopts = (
     " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&"
 )
 
-# make sure both static and shared libs are built
-# and disable "remote" tests that access a unreliable external test server over internet
 configopts = [
-    "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF",
-    "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON",
+    "-DENABLE_DAP=OFF -DENABLE_DAP4=OFF -DENABLE_BYTERANGE=OFF -DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF",
+    "-DENABLE_DAP=OFF -DENABLE_DAP4=OFF -DENABLE_BYTERANGE=OFF -DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON",
 ]
 
 # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests