polishing compile_CoreModule, bug fix for Makefile
This commit is contained in:
Martin Diehl
parent
4648da1f32
commit
ee99216edc
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@ -46,7 +46,7 @@ COMPILERNAME ?= $(F90)
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INCLUDE_DIRS :=-I../lib
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LIBRARIES :=-lfftw3
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LIB_DIRS :=-L$(FFTW_ROOT)/lib
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RUN_PATH :=-Wl,-rpath,$(FFTW_ROOT)/lib
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RUN_PATH :=-Wl,-rpath=$(FFTW_ROOT)/lib
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ifeq "$(FASTBUILD)" "YES"
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OPENMP := OFF
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@ -95,18 +95,18 @@ endif
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ifneq "x$(IMKL_ROOT)" "x"
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LIB_DIRS :=-L$(IMKL_ROOT)/lib/intel64
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RUN_PATH +=$(RUNPATH) -Wl,-rpath,$(IMKL_ROOT)/lib/intel64
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RUN_PATH +=$(RUNPATH) -Wl,-rpath=$(IMKL_ROOT)/lib/intel64
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INCLUDE_DIRS +=-I$(IMKL_ROOT)/include
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LIBRARIES +=-lmkl_intel_lp64 -lmkl_core -lmkl$(ACML_ARCH) -lm -lpthread -liomp5
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LIBRARIES +=-lmkl_intel_lp64 -lmkl_core -lmkl$(IMKL_ARCH) -lm -lpthread -liomp5
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else
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ifneq "x$(ACML_ROOT)" "x"
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LIB_DIRS +=-L$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
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RUN_PATH +=$(RUNPATH) -Wl,-rpath,$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
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RUN_PATH +=$(RUNPATH) -Wl,-rpath=$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
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LIBRARIES +=-lacml$(ACML_ARCH)
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else
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ifneq "x$(LAPACK_ROOT)" "x"
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LIB_DIRS +=-L$(LAPACK_ROOT)/lib64 -L$(LAPACK_ROOT)/lib
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RUN_PATH +=$(RUN_PATH) -Wl,-rpath,$(LAPACK_ROOT)/lib64 -Wl,-rpath,$(LAPACK_ROOT)/lib
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RUN_PATH +=$(RUN_PATH) -Wl,-rpath=$(LAPACK_ROOT)/lib64 -Wl,-rpath=$(LAPACK_ROOT)/lib
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LIBRARIES +=-llapack
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endif
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endif
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@ -116,7 +116,7 @@ endif
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ifeq "$(HDF5)" "ON"
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LIBRARIES +=-lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5
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LIB_DIRS +=-L$(HDF5_ROOT)/lib
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RUN_PATH +=$(RUNPATH) -Wl,-rpath,$(HDF5_ROOT)/lib
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RUN_PATH +=$(RUNPATH) -Wl,-rpath=$(HDF5_ROOT)/lib
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INCLUDE_DIRS +=-I$(HDF5_ROOT)/include -DHDF
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endif
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@ -142,7 +142,7 @@ OPTIMIZATION_OFF_ifort :=-O0 -no-ip
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OPTIMIZATION_OFF_gfortran :=-O0
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OPTIMIZATION_DEFENSIVE_ifort :=-O2
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OPTIMIZATION_DEFENSIVE_gfortran :=-O2
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OPTIMIZATION_AGGRESSIVE_ifort :=-O3 $(PORTABLE_SWITCH) -no-prec-div -fp-model fast=2 -ipo #-static causes trouble at the moment
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OPTIMIZATION_AGGRESSIVE_ifort :=-O3 $(PORTABLE_SWITCH) -no-prec-div -fp-model fast=2 -ipo
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OPTIMIZATION_AGGRESSIVE_gfortran :=-O3 $(PORTABLE_SWITCH) -ffast-math -funroll-loops -ftree-vectorize
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@ -1,18 +1,20 @@
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#!/usr/bin/env python
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# compiles fortran code for Python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,glob,string,subprocess,shlex
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from damask import Environment
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# compiles fortran code for Python
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scriptID = '$Id$'
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damaskEnv = Environment()
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baseDir = damaskEnv.relPath('installation/')
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codeDir = damaskEnv.relPath('code/')
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options={}
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keywords=['IMKL_ROOT','ACML_ROOT','LAPACK_ROOT','FFTW_ROOT','F90']
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options={}
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# getting options from damask.conf or, if not present, from envinronment
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#--- getting options from damask.conf or, if not present, from envinronment -----------------------
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for option in keywords:
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try:
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value = damaskEnv.options[option]
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@ -21,12 +23,13 @@ for option in keywords:
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if value is None: value = '' # env not set
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options[option]=value
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# overwrite default options with keyword=value pair from argument list to mimic make behavior
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#--- overwrite default options with keyword=value pair from argument list to mimic make behavior --
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for i, arg in enumerate(sys.argv):
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for option in keywords:
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if arg.startswith(option):
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options[option] = sys.argv[i][len(option)+1:]
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#--- check for valid compiler and set options -----------------------------------------------------
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compilers = ['ifort','gfortran']
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if options['F90'] not in compilers:
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sys.exit('compiler "F90" (in installation/options or as Shell variable) has to be one out of: %s'%(', '.join(compilers)))
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@ -38,11 +41,11 @@ compiler = {
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' -real-size 64 -integer-size 32"',
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}[options['F90']]
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# option not depending on compiler
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#--- option not depending on compiler -------------------------------------------------------------
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compileOptions =' -DSpectral -DFLOAT=8 -DINT=4 -I%s/lib'%damaskEnv.rootDir()
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# this saves the path of libraries during runtime
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LDFLAGS ='-shared -Wl,-rpath=/lib -Wl,-rpath=/usr/lib -Wl,-rpath=%s/lib'%(options['FFTW_ROOT'])
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#--- this saves the path of libraries to core.so, hence it is known during runtime ----------------
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LDFLAGS ='-shared -Wl,-rpath=%s/lib'%(options['FFTW_ROOT'])
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# see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
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if options['IMKL_ROOT'] != '' and options['F90'] != 'gfortran':
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@ -55,15 +58,16 @@ elif options['LAPACK_ROOT'] != '':
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lib_lapack = '-L%s/lib -L%s/lib64 -llapack'%(options['LAPACK_ROOT'],options['LAPACK_ROOT'])
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LDFLAGS +=' -Wl,-rpath=%s/lib -Wl,-rpath=%s/lib64'%(options['LAPACK_ROOT'],options['LAPACK_ROOT'])
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#--------------------------------------------------------------------------------------------------
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# f2py does not (yet) support setting of special flags for the linker, hence they must be set via
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# environment variable
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# environment variable ----------------------------------------------------------------------------
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my_env = os.environ
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my_env["LDFLAGS"] = LDFLAGS
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os.chdir(codeDir) # needed for compilation with gfortran and f2py
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#--- delete old file ------------------------------------------------------------------------------
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try:
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os.remove(os.path.join(damaskEnv.relPath('lib/damask'),'core.so'))
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except OSError, e: ## if failed, report it back to the user ##
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except OSError, e:
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print ("Error when deleting: %s - %s." % (e.filename,e.strerror))
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@ -76,6 +80,7 @@ except OSError, e:
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#'f2py -h damask.core.pyf' +\
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#' --overwrite-signature --no-lower prec.f90 DAMASK_spectral_interface.f90 math.f90 mesh.f90,...'
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###########################################################################
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os.chdir(codeDir)
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cmd = 'f2py damask.core.pyf' +\
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' -c --no-lower %s'%(compiler) +\
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compileOptions+\
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@ -111,7 +116,7 @@ for module in modules:
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print 'removing', module
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os.remove(module)
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#check if compilation of core module was successful
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#--- check if compilation of core module was successful -------------------------------------------
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try:
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with open(damaskEnv.relPath('lib/damask/core.so')) as f: pass
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except IOError as e:
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@ -544,6 +544,8 @@ for filename in args:
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'quadruple': 4,\
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}
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structure = vtk.vtkIntArray()
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structure.SetName('Microstructures')
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for datatype in fields.keys():
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print '\n%s:'%datatype,
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fields[datatype]['_order_'] = []
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@ -68,15 +68,15 @@ for myFile in files:
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# ------------------------------------------ loop over increments -------------------------------------
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for inc in myFile['file']['increments'].keys():
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print("Current Increment: "+inc)
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for instance in myFile['file']['increments/'+inc].keys():
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dsets = myFile['file']['increments/'+inc].keys()
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for instance in myFile['file']['increments/'+inc+'/'+options.output].keys():
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dsets = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].keys()
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if (options.defgrad in dsets and options.stress in dsets):
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defgrad = myFile['file']['increments/'+inc+'/'+options.defgrad]
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stress = myFile['file']['increments/'+inc+'/'+options.stress]
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defgrad = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.defgrad]
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stress = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.stress]
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cauchy=np.zeros(np.shape(stress),'f')
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for p in range(stress.shape[0]):
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cauchy[p,...] = 1.0/np.linalg.det(defgrad[p,...])*np.dot(stress[p,...],defgrad[p,...].T) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
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cauchyFile = myFile['file']['increments/'+inc].create_dataset('cauchy', data=cauchy)
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cauchyFile = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].create_dataset('cauchy', data=cauchy)
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cauchyFile.attrs['units'] = 'Pa'
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