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build.py
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build.py
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from build_utils import compile_a_file_collection, Link
import optparse
import collections
import os
from build_config import get_config_options_for
if __name__ == '__main__':
parser = optparse.OptionParser(usage='%prog [--build-conf] [--cuda] [--build] [--clean] [--clean-all]', version='4.0.0')
parser.add_option('--build-conf', dest = "conf_file", help="Determines the file storing build configuration info.")
parser.add_option('--cuda', dest = "cuda_type", help="Use this flag if you want to compile the CUDA calculator.")
parser.add_option('--build', dest = "build", action="store_true", help="Use this flag if you want to compile pyRMSD.")
parser.add_option('--clean', dest = "clear", action="store_true", help="Clear all .o generated files.")
parser.add_option('--clean-all', dest = "clear_all", action="store_true", help="The same as --clear, but it also removes generates libs and exes.")
options, args = parser.parse_args()
# Load configuration
conf = get_config_options_for(os.path.join("build_conf","default.conf"), options.conf_file)
######################################
### SET CUDA FLAGS
######################################
CUDA_PRECISION_FLAG = ""
if not options.cuda_type is None:
if options.cuda_type == "single":
CUDA_PRECISION_FLAG = "CUDA_PRECISION_SINGLE"
elif options.cuda_type =="double":
CUDA_PRECISION_FLAG = "CUDA_PRECISION_DOUBLE"
else:
parser.error("Please, choose precision for CUDA building: 'single' or 'double'")
options.use_cuda = True
conf["CUDA_OPTIONS"] = conf["CUDA_OPTIONS"] +" -D"+CUDA_PRECISION_FLAG
conf["DEFINE_USE_CUDA"] = conf["DEFINE_USE_CUDA"] +" -D"+CUDA_PRECISION_FLAG
else:
options.use_cuda = False
######################################
######################################
### FILE DESCRIPTION
######################################
files_to_compile_with_nvcc = {
"src/calculators/QCP":["QCPCUDAKernel.cu","QCPCUDAMemKernel.cu","kernel_functions_cuda.cu"]
}
files_to_compile_with_gcc = {
"src/calculators":["RMSDCalculator.cpp","RMSDTools.cpp","RMSDCalculationData.cpp","KernelFunctions.cpp"],
"src/calculators/factory":["RMSDCalculatorFactory.cpp"],
"src/calculators/KABSCH":["KABSCHSerialKernel.cpp"],
"src/calculators/QTRFIT":["QTRFITSerialKernel.cpp"],
"src/calculators/QCP":["QCPSerialKernel.cpp","QCPSerialFloatKernel.cpp"],
"src/calculators/NOSUP":["NOSUPSerialKernel.cpp"],
"src/matrix":["Matrix.cpp","Statistics.cpp"],
"src/python":["pyRMSD.cpp"],
"src/pdbreaderlite":["PDBReader.cpp","PDBReaderObject.cpp"],
"src/calculators/test":["main.cpp","test_tools.cpp","tests.cpp"],
}
files_to_compile_with_gcc_and_openmp = {
"src/calculators/KABSCH":["KABSCHOmpKernel.cpp"],
"src/calculators/QTRFIT":["QTRFITOmpKernel.cpp"],
"src/calculators/QCP":["QCPOmpKernel.cpp"],
"src/calculators/NOSUP":["NOSUPOmpKernel.cpp"]
}
######################################
#########################################
###
### BUILDING PROCESS
###
#########################################
if options.build:
files_to_link = collections.defaultdict(str)
if options.use_cuda:
conf["PYTHON_EXTENSION_OPTIONS"] = conf["PYTHON_EXTENSION_OPTIONS"]+" "+conf["DEFINE_USE_CUDA"]
compile_a_file_collection(conf["BASE_DIR"], files_to_compile_with_gcc, "gcc", conf["PYTHON_EXTENSION_OPTIONS"], [conf["PYTHON_INCLUDE_FOLDER"], conf["NUMPY_INCLUDE"]], ".o",files_to_link)
compile_a_file_collection(conf["BASE_DIR"], files_to_compile_with_gcc_and_openmp, "gcc", conf["PYTHON_EXTENSION_OPTIONS"]+" "+conf["OPENMP_OPTION"], [conf["PYTHON_INCLUDE_FOLDER"], conf["NUMPY_INCLUDE"]], ".o",files_to_link)
if options.use_cuda:
compile_a_file_collection(conf["BASE_DIR"], files_to_compile_with_nvcc, "nvcc", conf["CUDA_OPTIONS"], [conf["CUDA_INCLUDE"]], ".o",files_to_link)
linkDSL = Link().\
using("g++").\
with_options([conf["PYTHON_EXTENSION_LINKING_OPTIONS"],conf["OPENMP_OPTION"]]).\
using_libs([conf["PYTHON_LIBRARY"]]).\
using_lib_locations([conf["PYTHON_LIBRARY_FOLDER"]]).\
this_object_files([files_to_link["Matrix"],files_to_link["Statistics"]]).\
to_produce("condensedMatrix.so")
os.system('echo "\033[34m'+ linkDSL.getLinkingCommand()+'\033[0m"')
os.system( linkDSL.getLinkingCommand())
linkDSL = Link().\
using("g++").\
with_options([conf["PYTHON_EXTENSION_LINKING_OPTIONS"],conf["OPENMP_OPTION"]]).\
using_libs([conf["PYTHON_LIBRARY"]]).\
using_lib_locations([conf["PYTHON_LIBRARY_FOLDER"]]).\
this_object_files([files_to_link["PDBReaderObject"],files_to_link["PDBReader"]]).\
to_produce("pdbReader.so")
os.system('echo "\033[34m'+ linkDSL.getLinkingCommand()+'\033[0m"')
os.system( linkDSL.getLinkingCommand())
calculator_obj_files = [
files_to_link["RMSDTools"],
files_to_link["KernelFunctions"],
files_to_link["KABSCHSerialKernel"],
files_to_link["KABSCHOmpKernel"],
files_to_link["QTRFITSerialKernel"],
files_to_link["QTRFITOmpKernel"],
files_to_link["QCPSerialKernel"],
files_to_link["QCPSerialFloatKernel"],
files_to_link["QCPOmpKernel"],
files_to_link["NOSUPSerialKernel"],
files_to_link["NOSUPOmpKernel"],
files_to_link["RMSDCalculatorFactory"],
files_to_link["RMSDCalculationData"],
files_to_link["RMSDCalculator"],
files_to_link["pyRMSD"]
]
if options.use_cuda:
calculator_obj_files.extend([files_to_link["QCPCUDAKernel"],files_to_link["QCPCUDAMemKernel"],files_to_link["kernel_functions_cuda"]])
calculator_libraries = [conf["PYTHON_LIBRARY"],conf["CUDA_LIBRARY"]]
calculator_library_locations = [conf["PYTHON_LIBRARY_FOLDER"], conf["CUDA_LIBRARIES"]]
else:
calculator_libraries = [conf["PYTHON_LIBRARY"]]
calculator_library_locations = [conf["PYTHON_LIBRARY_FOLDER"]]
linkDSL = Link().\
using("g++").\
with_options([conf["PYTHON_EXTENSION_LINKING_OPTIONS"],conf["OPENMP_OPTION"]]).\
using_libs(calculator_libraries).\
using_lib_locations(calculator_library_locations).\
this_object_files(calculator_obj_files).\
to_produce("calculators.so")
os.system('echo "\033[34m'+ linkDSL.getLinkingCommand()+'\033[0m"')
os.system(linkDSL.getLinkingCommand())
test_obj_files = list(calculator_obj_files)
test_obj_files.remove(files_to_link["pyRMSD"])
test_obj_files.extend([files_to_link["main"], files_to_link["test_tools"], files_to_link["tests"]])
linkDSL = Link().\
using("g++").\
with_options([conf["OPENMP_OPTION"]]).\
using_libs(calculator_libraries).\
using_lib_locations(calculator_library_locations).\
this_object_files(test_obj_files).\
to_produce("test_rmsdtools_main")
os.system('echo "\033[34m'+ linkDSL.getLinkingCommand()+'\033[0m"')
os.system(linkDSL.getLinkingCommand())
os.system("mv calculators.so pyRMSD/")
os.system("mv condensedMatrix.so pyRMSD/")
os.system("mv pdbReader.so pyRMSD/")
os.system("mv test_rmsdtools_main src/calculators/test")
##Calculators
if options.use_cuda:
calcs_str = """
def availableCalculators():
return {
"KABSCH_SERIAL_CALCULATOR": 0,
"KABSCH_OMP_CALCULATOR":1,
#"KABSCH_CUDA_CALCULATOR":2,
"QTRFIT_SERIAL_CALCULATOR":3,
"QTRFIT_OMP_CALCULATOR":4,
#"QTRFIT_CUDA_CALCULATOR":5,
"QCP_SERIAL_CALCULATOR":6,
#"QCP_SERIAL_FLOAT_CALCULATOR":7,
"QCP_OMP_CALCULATOR":8,
"QCP_CUDA_CALCULATOR":9,
"QCP_CUDA_MEM_CALCULATOR":10,
"NOSUP_SERIAL_CALCULATOR":11,
"NOSUP_OMP_CALCULATOR":12,
#"NOSUP_CUDA_CALCULATOR":13
}
"""
else:
calcs_str = """
def availableCalculators():
return {
"KABSCH_SERIAL_CALCULATOR": 0,
"KABSCH_OMP_CALCULATOR":1,
#"KABSCH_CUDA_CALCULATOR":2,
"QTRFIT_SERIAL_CALCULATOR":3,
"QTRFIT_OMP_CALCULATOR":4,
#"QTRFIT_CUDA_CALCULATOR":5,
"QCP_SERIAL_CALCULATOR":6,
#"QCP_SERIAL_FLOAT_CALCULATOR":7,
"QCP_OMP_CALCULATOR":8,
#"QCP_CUDA_CALCULATOR":9,
#"QCP_CUDA_MEM_CALCULATOR":10,
"NOSUP_SERIAL_CALCULATOR":11,
"NOSUP_OMP_CALCULATOR":12,
#"NOSUP_CUDA_CALCULATOR":13
}
"""
os.system('echo "\033[33mWriting available calculators...\033[0m"')
open("pyRMSD/availableCalculators.py","w").write(calcs_str)
# Save all produced files
produced_file_handler = open(".products","w")
for produced_file in files_to_link:
if files_to_link[produced_file] != "":
produced_file_handler.write(files_to_link[produced_file] +"\n")
produced_file_handler.close()
######################################
#########################################
###
### REMOVE ALL .o AND TRACKING FILES
###
#########################################
if options.clear or options.clear_all:
os.system('echo "\033[32mCleaning...\033[0m"')
if os.path.exists(".products"):
produced_file = open(".products","r")
for produced_file_line in produced_file:
os.system("rm "+produced_file_line)
print "rm "+produced_file_line[:-1]
produced_file.close()
# Clear the products file itself
os.system("rm .products")
# Remove all trackers
os.system("find src/ -name '.modif*' -exec rm {} \;")
# remove .pyc
os.system("find src/ -name '*.pyc' -exec rm {} \;")
######################################
#########################################
###
### REMOVE ALL LIBS AND EXES
###
#########################################
if options.clear_all:
os.system('echo "\033[32mCleaning exes and libs...\033[0m"')
os.system("rm pyRMSD/calculators.so")
os.system("rm pyRMSD/condensedMatrix.so")
os.system("rm pyRMSD/pdbReader.so")
os.system("rm src/calculators/test/test_rmsdtools_main")
######################################