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Merge pull request #98 from rseng/update/analysis-2023-11-29
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Update from update/analysis-2023-11-29
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vsoch authored Nov 29, 2023
2 parents 06b8f7d + 69779e1 commit 1522902
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Showing 39 changed files with 34,166 additions and 32,026 deletions.
16 changes: 8 additions & 8 deletions _data/language_counts.json
Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
{
"unknown": 171,
"Python": 2095,
"Jupyter Notebook": 423,
"unknown": 172,
"Python": 2101,
"Jupyter Notebook": 425,
"Modelica": 1,
"Shell": 31,
"HTML": 85,
"HTML": 87,
"Perl": 47,
"R": 646,
"R": 647,
"C++": 550,
"Java": 102,
"C": 317,
"C": 318,
"Rust": 30,
"JavaScript": 83,
"AMPL": 1,
"MATLAB": 38,
"Haskell": 2,
"Fortran": 142,
"Fortran": 143,
"Clojure": 4,
"Groovy": 6,
"E": 1,
Expand Down Expand Up @@ -60,7 +60,7 @@
"Cython": 9,
"Groff": 1,
"PureBasic": 1,
"Prolog": 6,
"Prolog": 7,
"Forth": 1,
"PLSQL": 3,
"sed": 4,
Expand Down
132 changes: 128 additions & 4 deletions _data/repos.json
Original file line number Diff line number Diff line change
Expand Up @@ -18886,7 +18886,86 @@
"chromatin",
"chromatin-interaction"
],
"github/ericsteinbring/Special-Blurring": []
"github/ericsteinbring/Special-Blurring": [],
"gitlab/habermann_lab/phasik": [],
"github/hdeeg/KvW": [],
"github/2decomp-fft/2decomp-fft": [
"fast-fourier-transform",
"finite-difference-method",
"pencil-decomposition"
],
"github/sbi-dev/sbi": [
"simulation-based-inference",
"likelihood-free-inference",
"bayesian-inference",
"parameter-estimation",
"pytorch",
"machine-learning"
],
"github/ChenfuShi/HiChIP_peaks": [
"bioinformatics",
"bioinformatics-tool",
"hichip"
],
"github/institut-de-genomique/HAPO-G": [
"genomics",
"polishing",
"bioinformatics",
"genome"
],
"github/Xomics/ACTIONdemonstrator_workflow": [],
"github/espnet/espnet": [
"deep-learning",
"end-to-end",
"chainer",
"pytorch",
"kaldi",
"speech-recognition",
"speech-synthesis",
"speech-translation",
"machine-translation",
"voice-conversion",
"speech-enhancement",
"speech-separation",
"singing-voice-synthesis",
"speaker-diarization",
"spoken-language-understanding"
],
"github/DEIB-GECO/CombSAFE": [
"epigenetics",
"semantic-annotation",
"big-data-analysis",
"chromatin-state"
],
"github/DEIB-GECO/CRIS_single-sample": [
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],
"github/DEIB-GECO/ReRa": [],
"github/introlab/opentera": [
"python",
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"iot",
"telerehabilitation",
"telepresence",
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"webrtc",
"redis",
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"twisted",
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],
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"github/pedronachtigall/ToxCodAn-Genome": [],
"github/r3w0p/bobocep": [
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"complex-event-processing",
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"fault-tolerance",
"distributed-systems"
]
},
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Expand Down Expand Up @@ -24082,7 +24161,22 @@
"github/DEIB-GECO/OpenGDC": "Java",
"github/spiketools/spiketools": "Python",
"github/younglab/origami": "Shell",
"github/ericsteinbring/Special-Blurring": "IDL"
"github/ericsteinbring/Special-Blurring": "IDL",
"gitlab/habermann_lab/phasik": "unknown",
"github/hdeeg/KvW": "Prolog",
"github/2decomp-fft/2decomp-fft": "Fortran",
"github/sbi-dev/sbi": "Python",
"github/ChenfuShi/HiChIP_peaks": "HTML",
"github/institut-de-genomique/HAPO-G": "C",
"github/Xomics/ACTIONdemonstrator_workflow": "Jupyter Notebook",
"github/espnet/espnet": "Python",
"github/DEIB-GECO/CombSAFE": "Python",
"github/DEIB-GECO/CRIS_single-sample": "R",
"github/DEIB-GECO/ReRa": "Jupyter Notebook",
"github/introlab/opentera": "Python",
"github/FunctionalUrology/MLcps": "HTML",
"github/pedronachtigall/ToxCodAn-Genome": "Python",
"github/r3w0p/bobocep": "Python"
},
"url": {
"gitlab/chiemotono/mdcontactcom": "https://gitlab.com/chiemotono/mdcontactcom",
Expand Down Expand Up @@ -29278,7 +29372,22 @@
"github/DEIB-GECO/OpenGDC": "https://github.com/DEIB-GECO/OpenGDC",
"github/spiketools/spiketools": "https://github.com/spiketools/spiketools",
"github/younglab/origami": "https://github.com/younglab/origami",
"github/ericsteinbring/Special-Blurring": "https://github.com/ericsteinbring/Special-Blurring"
"github/ericsteinbring/Special-Blurring": "https://github.com/ericsteinbring/Special-Blurring",
"gitlab/habermann_lab/phasik": "https://gitlab.com/habermann_lab/phasik",
"github/hdeeg/KvW": "https://github.com/hdeeg/KvW",
"github/2decomp-fft/2decomp-fft": "https://github.com/2decomp-fft/2decomp-fft",
"github/sbi-dev/sbi": "https://github.com/sbi-dev/sbi",
"github/ChenfuShi/HiChIP_peaks": "https://github.com/ChenfuShi/HiChIP_peaks",
"github/institut-de-genomique/HAPO-G": "https://github.com/institut-de-genomique/HAPO-G",
"github/Xomics/ACTIONdemonstrator_workflow": "https://github.com/Xomics/ACTIONdemonstrator_workflow",
"github/espnet/espnet": "https://github.com/espnet/espnet",
"github/DEIB-GECO/CombSAFE": "https://github.com/DEIB-GECO/CombSAFE",
"github/DEIB-GECO/CRIS_single-sample": "https://github.com/DEIB-GECO/CRIS_single-sample",
"github/DEIB-GECO/ReRa": "https://github.com/DEIB-GECO/ReRa",
"github/introlab/opentera": "https://github.com/introlab/opentera",
"github/FunctionalUrology/MLcps": "https://github.com/FunctionalUrology/MLcps",
"github/pedronachtigall/ToxCodAn-Genome": "https://github.com/pedronachtigall/ToxCodAn-Genome",
"github/r3w0p/bobocep": "https://github.com/r3w0p/bobocep"
},
"description": {
"gitlab/chiemotono/mdcontactcom": "",
Expand Down Expand Up @@ -34474,6 +34583,21 @@
"github/DEIB-GECO/OpenGDC": "An open-source Java tool to automatically extract and convert all clinical and genomic data from the Genomic Data Commons to BED, GTF, CSV, and JSON format",
"github/spiketools/spiketools": "Tools for analyzing spiking data.",
"github/younglab/origami": "Statistical Modeling of ChIA-PET interactions",
"github/ericsteinbring/Special-Blurring": "Calculates the effect of quantum-foam blurring, appropriate for the special gamma-ray burst GRB221009A."
"github/ericsteinbring/Special-Blurring": "Calculates the effect of quantum-foam blurring, appropriate for the special gamma-ray burst GRB221009A.",
"gitlab/habermann_lab/phasik": "Scientific tools for extracting cyclic data via hierarchical clustering",
"github/hdeeg/KvW": "Kwee Van Woerden algorithm for eclipse or transit minimum timing, with improved error calculation",
"github/2decomp-fft/2decomp-fft": "The 2DECOMP&FFT library provides access to a slabs and pencil decompositions as well as FFTs. ",
"github/sbi-dev/sbi": "Simulation-based inference toolkit",
"github/ChenfuShi/HiChIP_peaks": "A tool to analyse HiChIP data",
"github/institut-de-genomique/HAPO-G": "Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.",
"github/Xomics/ACTIONdemonstrator_workflow": "X-omics ACTION demonstrator multi-omics analysis workflow",
"github/espnet/espnet": "End-to-End Speech Processing Toolkit",
"github/DEIB-GECO/CombSAFE": "Combinatorial and Semantic Analysis of Functional Elements",
"github/DEIB-GECO/CRIS_single-sample": "Single-sample classifiers for CRIS on colorectal cancer data",
"github/DEIB-GECO/ReRa": "Supervised Relevance-Redundancy assessments for feature selection in omics-based classification",
"github/introlab/opentera": "OpenTera - Open TeleRehabilitation Server and Micro-Services",
"github/FunctionalUrology/MLcps": null,
"github/pedronachtigall/ToxCodAn-Genome": "Toxin genes annotation in genome assembly",
"github/r3w0p/bobocep": "A fault-tolerant Complex Event Processing engine designed for edge computing in Internet of Things systems."
}
}
2 changes: 1 addition & 1 deletion _data/repos_counts_languages.json
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"Python": 5678,
"Python": 5695,
"R": 2209,
"Cpp": 441,
"Js": 1690,
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6 changes: 3 additions & 3 deletions _data/stats.json
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
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"total_parsed": 2665
}
115 changes: 115 additions & 0 deletions _repos/github/2decomp-fft/2decomp-fft/CMakeLists.txt
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@@ -0,0 +1,115 @@
cmake_minimum_required(VERSION 3.21)
cmake_policy(SET CMP0074 NEW)

project(decomp2d
LANGUAGES Fortran)
set(version 2.0.0)
enable_testing()
if (IO_BACKEND MATCHES "adios2")
# Can be useful to also activate CXX, sometimes is needed by packages
enable_language(C CXX)
endif (IO_BACKEND MATCHES "adios2")


set(BUILD_TARGET "mpi" CACHE STRING "Target for acceleration (mpi (default) or gpu)")
set_property(CACHE BUILD_TARGET PROPERTY STRINGS mpi gpu)

if (BUILD_TARGET MATCHES "gpu")
option(ENABLE_OPENACC "Allow user to activate/deactivate OpenACC support" ON)
option(ENABLE_CUDA "Allow user to activate/deactivate CUDA support" ON)
option(ENABLE_MANAGED "Allow user to activate/deactivate automatic memory managment from NVHPC" OFF)
option(ENABLE_NCCL "Allow user to activate/deactivate Collective Comunication NCCL" OFF)

if (ENABLE_CUDA)
message(STATUS "Before enable CUDA")
enable_language(CUDA)
message(STATUS "After enable CUDA")
endif()

endif(BUILD_TARGET MATCHES "gpu")

set (ENABLE_PROFILER "OFF" CACHE STRING "Activate/select the profiler")
set_property(CACHE ENABLE_PROFILER PROPERTY STRINGS OFF caliper)
option(ENABLE_INPLACE "Enable in-place operation of FFT" OFF)
option(HALO_DEBUG "Enable halo debugging options" OFF)
option(EVEN "Padded alltoall transpose operations" OFF)
option(BUILD_SHARED_LIBS "Set ON to build a shared library" OFF)
set (IO_BACKEND "mpi" CACHE STRING "Default IO backend (mpi (default) or adios2)")
set_property(CACHE IO_BACKEND PROPERTY STRINGS mpi adios2)

set(AUTHOR "Stefano Rolfo;Charles Moulinec;Paul Bartholomew")
set(AUTHOR_DETAILS "[email protected];[email protected];[email protected]")
set(DESCRIPTION "Building 2decomp&fft using cmake")

message(STATUS "building ${PROJECT_NAME}")

include(GNUInstallDirs)
set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_INCLUDEDIR})
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "${PROJECT_BINARY_DIR}/opt" CACHE PATH "..." FORCE)
endif()

# Add support for CMAKE_DEPENDENT_OPTION
INCLUDE(CMakeDependentOption)
INCLUDE(CMakeParseArguments)

# make sure that the default is a RELEASE
if (NOT CMAKE_BUILD_TYPE)
set (CMAKE_BUILD_TYPE RELEASE CACHE STRING
"Choose the type of build, options are: None Dev Debug Release."
FORCE)
endif (NOT CMAKE_BUILD_TYPE)

set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake" "${CMAKE_SOURCE_DIR}/cmake/compilers" "${CMAKE_SOURCE_DIR}/cmake/fft")

if (BUILD_TARGET MATCHES "gpu")
include(D2D_GPU)
endif (BUILD_TARGET MATCHES "gpu")

include(D2D_MPI)

# FFT options
if (BUILD_TARGET MATCHES "gpu")
set(FFT_Choice "cufft" CACHE STRING "FFT for XCompact3d project (with GPU cufft is the default)")
else ()
set(FFT_Choice "generic" CACHE STRING "FFT for XCompact3d project (generic is the default)")
endif (BUILD_TARGET MATCHES "gpu")
set_property(CACHE FFT_Choice PROPERTY STRINGS generic fftw fftw_f03 mkl cufft)

# Set now compilers flags
include(D2D_Compilers)
include(D2D_Profilers)
include(fft)

# Create a static library for the fft
add_subdirectory(src)

# Add tests
option(BUILD_TESTING "Build with tests" OFF)
if (${BUILD_TESTING})
add_subdirectory(examples)
endif (${BUILD_TESTING})

# Add a prettify target
add_custom_target(format sh ${CMAKE_SOURCE_DIR}/scripts/format.sh
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})

# # Create an example dir with all input.i3d example files
# option(BUILD_TESTING "Build with tests" ON)
# set(test_dir "${PROJECT_BINARY_DIR}/Test")
# message(STATUS "Before test main ${test_dir}")
# if (${BUILD_TESTING})
# file(MAKE_DIRECTORY ${test_dir})
# include(CTest)
# message(STATUS "MPI INCL ALSO FOUND: ${MPI_INCLUDE_PATH}")
# message(STATUS "MPI EXEC: ${MPIEXEC_EXECUTABLE}")
# file(MAKE_DIRECTORY ${test_dir}/App)
# add_test(NAME TestAPP COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/xcompact3d WORKING_DIRECTORY ${test_dir}/App)
# #if (PFUNIT_FOUND)
# # file(MAKE_DIRECTORY ${test_dir}/Verif_x_00)
# # add_test(NAME Test_dx_00 COMMAND ${MPIEXEC_EXECUTABLE} -n ${MPIEXEC_MAX_NUMPROCS} ${CMAKE_INSTALL_PREFIX}/bin/verif_x_00 WORKING_DIRECTORY ${test_dir}/Verif_x_00)
# #endif (PFUNIT_FOUND)
# endif()

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