diff --git a/science/Makefile b/science/Makefile index 7c4802f84815..8a9535da9c1f 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,528 +1,529 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += ChipmunkPhysics SUBDIR += InsightToolkit SUBDIR += InsightToolkit501 SUBDIR += PETSc SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-FAdist SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-ks SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += acados SUBDIR += afni SUBDIR += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += apbs SUBDIR += arbor SUBDIR += ascent SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += bout++ SUBDIR += bout++-merging-filaments SUBDIR += buddy SUBDIR += cantera SUBDIR += cardioid SUBDIR += cdf SUBDIR += cdk SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemicalfun SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chimes-calculator SUBDIR += chrono SUBDIR += cif-tools SUBDIR += clhep SUBDIR += clipper SUBDIR += code_saturne SUBDIR += colt SUBDIR += conduit SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += csvtk SUBDIR += dakota SUBDIR += dalton SUBDIR += dd_package SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dftd3 SUBDIR += dftd4 SUBDIR += dimod SUBDIR += dirac SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dssp SUBDIR += dvc SUBDIR += dwave-preprocessing SUBDIR += dynare SUBDIR += eccodes SUBDIR += elk SUBDIR += elmerfem SUBDIR += epte SUBDIR += erd SUBDIR += ergo SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fastjet SUBDIR += feff10 SUBDIR += fleur SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gbtolib SUBDIR += gchemutils SUBDIR += gcp SUBDIR += gdma SUBDIR += geant4 SUBDIR += gemmi SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-110 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += helfem SUBDIR += hepmc3 SUBDIR += highfive SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kim-api SUBDIR += kplib SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcifpp SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgetar SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libint2-psi4 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmbd SUBDIR += libmsym SUBDIR += libnegf SUBDIR += liboglappth SUBDIR += libpsml SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += linearelasticity SUBDIR += linux-zotero SUBDIR += luscus SUBDIR += m-aneos SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcpl SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mctc-lib SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmg SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mopac SUBDIR += mp2d SUBDIR += mpb SUBDIR += mpqc SUBDIR += mrchem SUBDIR += mrcpp SUBDIR += msms SUBDIR += mstore SUBDIR += multicharge SUBDIR += multiwfn SUBDIR += mutationpp SUBDIR += namd SUBDIR += ncrystal SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nlcglib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += ocean SUBDIR += octopus SUBDIR += openbabel SUBDIR += openems SUBDIR += openkim-models SUBDIR += openmc SUBDIR += openmodelica SUBDIR += openmolcas SUBDIR += openmx SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin SUBDIR += optench SUBDIR += orthanc SUBDIR += orthanc-dicomweb SUBDIR += orthanc-mysql SUBDIR += orthanc-postgresql SUBDIR += orthanc-webviewer SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Calc SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-Coordinates-Transform SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += packmol SUBDIR += pagmo2 SUBDIR += paje SUBDIR += paraview SUBDIR += parthenon SUBDIR += pastix SUBDIR += pcmsolver SUBDIR += phonopy SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += polytope SUBDIR += precice SUBDIR += psi4 SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-HepMC3 SUBDIR += py-HofstadterTools SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-OpenFermion-Dirac SUBDIR += py-OpenFermion-PySCF SUBDIR += py-OpenMC SUBDIR += py-PubChemPy SUBDIR += py-PyFR SUBDIR += py-PyNE SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-access SUBDIR += py-arbor SUBDIR += py-arch SUBDIR += py-asap3 SUBDIR += py-asdf SUBDIR += py-asdf-standard SUBDIR += py-asdf-transform-schemas SUBDIR += py-ase SUBDIR += py-atomium SUBDIR += py-avogadrolibs SUBDIR += py-boutdata SUBDIR += py-boututils SUBDIR += py-cdo SUBDIR += py-cfgrib SUBDIR += py-chainer SUBDIR += py-chainer-chemistry SUBDIR += py-chempy SUBDIR += py-cirq-aqt SUBDIR += py-cirq-core SUBDIR += py-cirq-google SUBDIR += py-cirq-ionq SUBDIR += py-cirq-pasqal SUBDIR += py-cirq-rigetti SUBDIR += py-coards SUBDIR += py-dftbplus SUBDIR += py-dftd4 SUBDIR += py-dimod SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-dwave-cloud-client SUBDIR += py-dwave-greedy SUBDIR += py-dwave-hybrid SUBDIR += py-dwave-inspector SUBDIR += py-dwave-neal SUBDIR += py-dwave-networkx SUBDIR += py-dwave-ocean-sdk SUBDIR += py-dwave-optimization SUBDIR += py-dwave-preprocessing SUBDIR += py-dwave-samplers SUBDIR += py-dwave-system SUBDIR += py-dwave-tabu SUBDIR += py-dwavebinarycsp SUBDIR += py-earthpy SUBDIR += py-eccodes SUBDIR += py-emmet-core SUBDIR += py-esda SUBDIR += py-fresnel SUBDIR += py-gemmi SUBDIR += py-geolinks SUBDIR += py-geomet SUBDIR += py-geometer SUBDIR += py-geometric SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5json SUBDIR += py-h5py SUBDIR += py-h5pyd SUBDIR += py-hiphive SUBDIR += py-hoomd-blue SUBDIR += py-icet SUBDIR += py-inequality SUBDIR += py-ipygany SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kimpy SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-kpLib SUBDIR += py-liac-arff SUBDIR += py-libgetar SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mercantile SUBDIR += py-meshio SUBDIR += py-mmcif SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate SUBDIR += py-mp-api SUBDIR += py-mpcontribs-client SUBDIR += py-mplhep SUBDIR += py-mplhep-data SUBDIR += py-mrchem SUBDIR += py-ncrystal SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nglview SUBDIR += py-nibabel SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openEMS SUBDIR += py-openbabel SUBDIR += py-openpiv SUBDIR += py-optking SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-penaltymodel SUBDIR += py-periodictable SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pnetcdf SUBDIR += py-pupynere SUBDIR += py-py3Dmol SUBDIR += py-pyaixi SUBDIR += py-pyberny SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pyked SUBDIR += py-pymatgen SUBDIR += py-pymatgen-analysis-alloys SUBDIR += py-pymbd SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pyphot SUBDIR += py-pyprecice SUBDIR += py-pyqubo SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-rmsd SUBDIR += py-ruffus SUBDIR += py-sarpy SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-optimize SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-sdf SUBDIR += py-seekpath SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-signac SUBDIR += py-sklearn-pandas SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-symfc SUBDIR += py-tensorflow SUBDIR += py-thewalrus SUBDIR += py-tobler SUBDIR += py-trainstation SUBDIR += py-trx-python SUBDIR += py-tweedledum SUBDIR += py-vedo SUBDIR += py-veusz SUBDIR += py-xbout SUBDIR += pybrain SUBDIR += pynn SUBDIR += q SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += qt6-quick3dphysics SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += quantum-jet SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-netcdf SUBDIR += salome-configuration SUBDIR += salome-kernel SUBDIR += scidavis SUBDIR += sciplot SUBDIR += seacas SUBDIR += segyio SUBDIR += serac SUBDIR += shelxle SUBDIR += siconos SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simbody SUBDIR += simgrid SUBDIR += simint SUBDIR += simlib SUBDIR += simple-dftd3 SUBDIR += simsmith SUBDIR += sirius SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += spheral SUBDIR += step + SUBDIR += sz3 SUBDIR += tblite SUBDIR += teem SUBDIR += tfel SUBDIR += tfel-edf SUBDIR += thermofun SUBDIR += tinker SUBDIR += trilinos SUBDIR += ttk SUBDIR += tweedledum SUBDIR += udunits SUBDIR += ukrmol+ SUBDIR += v_sim SUBDIR += vipster SUBDIR += vmd SUBDIR += voro++ SUBDIR += votca SUBDIR += wannier90 SUBDIR += wwplot SUBDIR += wxmacmolplt SUBDIR += xcfun SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xtb SUBDIR += yoda SUBDIR += zotero SUBDIR += zx .include diff --git a/science/sz3/Makefile b/science/sz3/Makefile new file mode 100644 index 000000000000..e65b8ad06873 --- /dev/null +++ b/science/sz3/Makefile @@ -0,0 +1,39 @@ +PORTNAME= sz3 +PORTVERSION= 3.2.1 +DISTVERSIONPREFIX= v +CATEGORIES= science + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Modular Error-bounded Lossy Compression Framework for Scientific Datasets +WWW= https://szcompressor.org/ \ + https://github.com/szcompressor/SZ3 + +LICENSE= BSD4CLAUSE +LICENSE_FILE= ${WRKSRC}/copyright-and-BSD-license.txt + +LIB_DEPENDS= libgsl.so:math/gsl \ + libzstd.so:archivers/zstd + +USES= cmake pkgconfig + +CMAKE_OFF= BUILD_H5Z_FILTER \ + BUILD_MDZ \ + SZ3_DEBUG_TIMINGS \ + SZ3_USE_BUNDLED_ZSTD +CMAKE_ON= BUILD_SHARED_LIBS \ + BUILD_STATIC_LIBS + +DATADIR= ${PREFIX}/share/SZ3 + +USE_GITHUB= yes +GH_ACCOUNT= szcompressor +GH_PROJECT= SZ3 + +post-patch: +# Clean up bundled libraries + @${RM} -r ${WRKSRC}/tools/zstd/ + +post-install: + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/sz3* + +.include diff --git a/science/sz3/distinfo b/science/sz3/distinfo new file mode 100644 index 000000000000..638b3b67e6a1 --- /dev/null +++ b/science/sz3/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1738088812 +SHA256 (szcompressor-SZ3-v3.2.1_GH0.tar.gz) = 24ed1c8159832734a241df66b857eca64d18a2e8e949ef583a2d0bfe01c6b7e1 +SIZE (szcompressor-SZ3-v3.2.1_GH0.tar.gz) = 4474033 diff --git a/science/sz3/pkg-descr b/science/sz3/pkg-descr new file mode 100644 index 000000000000..8cba5dafde49 --- /dev/null +++ b/science/sz3/pkg-descr @@ -0,0 +1,16 @@ +SZ is a modular parametrizable lossy compressor framework for scientific data +(floating point and integers). It has applications in simulations, AI and +instruments. It is a production quality software and a research platform for +lossy compression. SZ is open and transparent. Open because all interested +researchers and students can study or contribute to it. Transparent because all +performance improvements are detailed in publications. + +SZ can be used for classic use-cases: visualization, accelerating I/O, reducing +memory and storage footprint and more advanced use-cases like compression of DNN +models and training sets, acceleration of computation, checkpoint/restart, +reducing streaming intensity and running efficiently large problems that cannot +fit in memory. Other use-cases will augment this list as users find new +opportunities to benefit from lossy compression of scientific data. + +SZ has implementations on CPU, GPU, and FPGA and is integrated in the main I/O +libraries: HFD5, ADIOS, PnetCDF. diff --git a/science/sz3/pkg-plist b/science/sz3/pkg-plist new file mode 100644 index 000000000000..cbe94507605e --- /dev/null +++ b/science/sz3/pkg-plist @@ -0,0 +1,70 @@ +bin/sz3 +bin/sz3_smoke_test +include/SZ3/api/impl/SZAlgoInterp.hpp +include/SZ3/api/impl/SZAlgoLorenzoReg.hpp +include/SZ3/api/impl/SZAlgoNopred.hpp +include/SZ3/api/impl/SZDispatcher.hpp +include/SZ3/api/impl/SZImpl.hpp +include/SZ3/api/impl/SZImplOMP.hpp +include/SZ3/api/sz.hpp +include/SZ3/compressor/Compressor.hpp +include/SZ3/compressor/SZGenericCompressor.hpp +include/SZ3/compressor/SZIterateCompressor.hpp +include/SZ3/compressor/specialized/SZBlockInterpolationCompressor.hpp +include/SZ3/compressor/specialized/SZExaaltCompressor.hpp +include/SZ3/compressor/specialized/SZTruncateCompressor.hpp +include/SZ3/decomposition/Decomposition.hpp +include/SZ3/decomposition/InterpolationDecomposition.hpp +include/SZ3/decomposition/LorenzoRegressionDecomposition.hpp +include/SZ3/decomposition/NoPredictionDecomposition.hpp +include/SZ3/decomposition/TimeSeriesDecomposition.hpp +include/SZ3/def.hpp +include/SZ3/encoder/ArithmeticEncoder.hpp +include/SZ3/encoder/BypassEncoder.hpp +include/SZ3/encoder/Encoder.hpp +include/SZ3/encoder/HuffmanEncoder.hpp +include/SZ3/encoder/RunlengthEncoder.hpp +include/SZ3/lossless/Lossless.hpp +include/SZ3/lossless/Lossless_bypass.hpp +include/SZ3/lossless/Lossless_zstd.hpp +include/SZ3/predictor/ComposedPredictor.hpp +include/SZ3/predictor/LorenzoPredictor.hpp +include/SZ3/predictor/MetaLorenzoPredictor.hpp +include/SZ3/predictor/MetaRegressionPredictor.hpp +include/SZ3/predictor/PolyRegressionCoeffAux.hpp +include/SZ3/predictor/PolyRegressionCoeffAux.m +include/SZ3/predictor/PolyRegressionPredictor.hpp +include/SZ3/predictor/Predictor.hpp +include/SZ3/predictor/RegressionPredictor.hpp +include/SZ3/preprocessor/PreFilter.hpp +include/SZ3/preprocessor/PreProcessor.hpp +include/SZ3/preprocessor/Transpose.hpp +include/SZ3/preprocessor/Wavelet.hpp +include/SZ3/quantizer/LinearQuantizer.hpp +include/SZ3/quantizer/Quantizer.hpp +include/SZ3/utils/ByteUtil.hpp +include/SZ3/utils/Config.hpp +include/SZ3/utils/Extraction.hpp +include/SZ3/utils/FileUtil.hpp +include/SZ3/utils/Interpolators.hpp +include/SZ3/utils/Iterator.hpp +include/SZ3/utils/KmeansUtil.hpp +include/SZ3/utils/MemoryUtil.hpp +include/SZ3/utils/MetaDef.hpp +include/SZ3/utils/QuantOptimizatioin.hpp +include/SZ3/utils/Statistic.hpp +include/SZ3/utils/Timer.hpp +include/SZ3/utils/inih/INIReader.h +include/SZ3/utils/inih/LICENSE.txt +include/SZ3/utils/ska_hash/LICENSE.txt +include/SZ3/utils/ska_hash/bytell_hash_map.hpp +include/SZ3/utils/ska_hash/flat_hash_map.hpp +include/SZ3/utils/ska_hash/unordered_map.hpp +include/SZ3/version.hpp +include/SZ3/version.hpp.in +include/SZ3c/sz3c.h +lib/cmake/SZ3/SZ3Config.cmake +lib/cmake/SZ3/SZ3ConfigVersion.cmake +lib/cmake/SZ3/SZ3Targets.cmake +lib/libSZ3c.so +%%DATADIR%%/testfloat_8_8_128.dat