introduced rpath to tell executable where libraries are located

DAMASK_env.sh

@@ -25,24 +25,25 @@ if [ ! -z "$PS1" ]; then
   echo Using environment with ...
   echo "DAMASK installation in $DAMASK_ROOT"
   echo "DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
-  echo "F90=$F90"
+  echo "Compiler: F90=$F90"
-  echo "FFTW_ROOT=$FFTW_ROOT"
   if [ "x$LAPACK_ROOT" != "x" ]; then
-      echo "LAPACK_ROOT=$LAPACK_ROOT"
+    echo "LAPACK libaries located in $LAPACK_ROOT"
   fi
   if [ "x$ACML_ROOT" != "x" ]; then
-      echo "ACML_ROOT=$ACML_ROOT"
+    echo "ACML libaries located in $ACML_ROOT"
   fi
   if [ "x$IMKL_ROOT" != "x" ]; then
-      echo "IMKL_ROOT=$IMKL_ROOT"
+    echo "IMKL libaries located in $IMKL_ROOT"
   fi
-  echo "MARC_ROOT=$MARC_ROOT"
+  echo "MSC.Marc root $MARC_ROOT"
-  echo "HDF5_ROOT=$HDF5_ROOT (future use)"
+  echo "FFTW libaries located in $FFTW_ROOT"
+  echo "HDF5 libaries located in $HDF5_ROOT (future use)"
 fi
 ulimit -s unlimited
 ulimit -c 0
 ulimit -v unlimited
 ulimit -m unlimited
 export PYTHONPATH=$PYTHONPATH:$DAMASK_ROOT/lib
-unset DAMASK_ROOT
+unset DAMASK_ROOT LAPACK_ROOT ACML_ROOT IMKL_ROOT MARC_ROOT FFTW_ROOT HDF5_ROOT
+
 

Makefile

@@ -2,6 +2,13 @@ SHELL = /bin/sh
 ########################################################################################
 # Makefile for the installation of DAMASK
 ########################################################################################
+.PHONY: all
+all:
+	spectral
+	marc
+	processing
+	install
+
 .PHONY: spectral
 spectral:
 	@$(MAKE) clean -C code >/dev/null

code/Makefile

@@ -41,12 +41,12 @@ else
 	include /etc/damask.conf
 endif  
 
-
 COMPILERNAME ?= $(F90)
 
 INCLUDE_DIRS :=-I../lib
 LIBRARIES :=-lfftw3
-LIB_DIRS  :=-L$$FFTW_ROOT/lib
+LIB_DIRS  :=-L$(FFTW_ROOT)/lib
+RUN_PATH  :=-Wl,-rpath,$(FFTW_ROOT)/lib
 
 ifeq "$(FASTBUILD)" "YES"
 OPENMP := OFF
@@ -94,29 +94,30 @@ IMKL_ARCH =_sequential
 endif
 
 ifneq  "x$(IMKL_ROOT)" "x"
-LIB_DIRS  :=-L$$IMKL_ROOT/lib/intel64
+LIB_DIRS  :=-L$(IMKL_ROOT)/lib/intel64
+RUN_PATH  +=$(RUNPATH) -Wl,-rpath,$(IMKL_ROOT)/lib/intel64
 INCLUDE_DIRS +=-I$(IMKL_ROOT)/include
 LIBRARIES +=-lmkl_intel_lp64 -lmkl_core -lmkl$(ACML_ARCH) -lm -lpthread -liomp5
 else
 ifneq  "x$(ACML_ROOT)" "x"
-LIB_DIRS  +=-L$$ACML_ROOT/$(F90)64$(ACML_ARCH)/lib
+LIB_DIRS  +=-L$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
+RUN_PATH  +=$(RUNPATH) -Wl,-rpath,$(ACML_ROOT)/$(F90)64$(ACML_ARCH)/lib
 LIBRARIES +=-lacml$(ACML_ARCH)
 else
 ifneq  "x$(LAPACK_ROOT)" "x"
-LIB_DIRS  +=-L$$LAPACK_ROOT/lib64 -L$$LAPACK_ROOT/lib
+LIB_DIRS  +=-L$(LAPACK_ROOT)/lib64 -L$(LAPACK_ROOT)/lib
+RUN_PATH  +=$(RUN_PATH) -Wl,-rpath,$(LAPACK_ROOT)/lib64 -Wl,-rpath,$(LAPACK_ROOT)/lib
 LIBRARIES +=-llapack
 endif
 endif
 endif
 
-
-
-
 #hdf5
 ifeq "$(HDF5)" "ON"
 LIBRARIES +=-lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5
-LIB_DIRS  +=-L$$HDF5ROOT/lib
+LIB_DIRS  +=-L$(HDF5_ROOT)/lib
-INCLUDE_DIRS +=-I$(HDF5ROOT)/include -DHDF
+RUN_PATH  +=$(RUNPATH) -Wl,-rpath,$(HDF5_ROOT)/lib
+INCLUDE_DIRS +=-I$(HDF5_ROOT)/include -DHDF
 endif
 
 ifdef PETSC_DIR
@@ -360,7 +361,7 @@ endif
 DAMASK_spectral.exe: DAMASK_spectral_driver.o 
 	$(PREFIX) $(COMPILERNAME) $(OPENMP_FLAG_$(F90)) $(OPTIMIZATION_$(MAXOPTI)_$(F90)) $(STANDARD_CHECK_$(F90)) \
   -o DAMASK_spectral.exe DAMASK_spectral_driver.o \
-  $(COMPILED_FILES) $(LIB_DIRS) $(LIBRARIES) $(SUFFIX)
+  $(COMPILED_FILES) $(LIB_DIRS) $(LIBRARIES) $(RUN_PATH) $(SUFFIX)
 
 DAMASK_spectral_driver.o: DAMASK_spectral_driver.f90 DAMASK_spectral_solverBasic.o $(PETSC_FILES)
 	$(PREFIX) $(COMPILERNAME) $(COMPILE_MAXOPTI) -c DAMASK_spectral_driver.f90 $(SUFFIX)

configure

@@ -142,7 +142,7 @@ if options.compiler not in ['ifort','gfortran']:
 if not subprocess.call(['which', options.compiler],stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
   print('Compiler Warning: executable %s not found!'%options.compiler)
 
-for lib in ['libfftw3.a','libfftw3.a']:
+for lib in ['libfftw3.so','libfftw3.a']:
   if not os.path.isfile(os.path.join(options.fftwRoot,'lib/%s'%lib)):
     print('FFTW Warning: %s not found in %s!'%(lib,os.path.join(options.fftwRoot,'lib')))
 
@@ -154,16 +154,16 @@ if options.blasType == 'LAPACK':
     blasLocation = os.path.join(options.blasRoot,'lib64')
   else:
     blasLocation=os.path.join(options.blasRoot,'lib')
-  for lib in ['liblapack.a','liblapack.a']:
+  for lib in ['liblapack.so','liblapack.a']:
     if not os.path.isfile(os.path.join(blasLocation,lib)): 
       print('LAPACK Warning: %s not found in %s!'%(lib,blasLocation))
 elif options.blasType == 'ACML':
   blasLocationSerial=os.path.join(options.blasRoot,'%s64/lib'%options.compiler)
-  for lib in ['libacml.a','libacml.a']:
+  for lib in ['libacml.so','libacml.a']:
     if not os.path.isfile(os.path.join(blasLocationSerial,lib)): 
       print('ACML Warning: %s not found in %s!'%(lib,blasLocationSerial))
   blasLocationParallel=os.path.join(options.blasRoot,'%s64_mp/lib'%options.compiler)
-  for lib in ['libacml_mp.a','libacml_mp.a']:
+  for lib in ['libacml_mp.so','libacml_mp.a']:
     if not os.path.isfile(os.path.join(blasLocationParallel,lib)): 
       print('ACML Warning: %s not found in %s!'%(lib,blasLocationParallel))
 elif options.blasType == 'IMKL':
@@ -173,6 +173,7 @@ elif options.blasType == 'IMKL':
   blasLocation=os.path.join(options.blasRoot,'lib/intel64')
   for lib in ['libmkl_core.so','libmkl_core.a',\
               'libmkl_sequential.so','libmkl_sequential.a',\
+              'libmkl_intel_thread.so','libmkl_intel_thread.a',\
               'libmkl_intel_lp64.so','libmkl_intel_lp64.a']:
     if not os.path.isfile(os.path.join(blasLocation,lib)): 
       print('IMKL Warning: %s not found in %s!'%(lib,blasLocation))

installation/compile_CoreModule.py

@@ -23,20 +23,29 @@ compilers = ['ifort','gfortran']
 if options['F90'] not in compilers:
   sys.exit('compiler "F90" (in installation/options or as Shell variable) has to be one out of: %s'%(', '.join(compilers)))
 
-compileCommand = {
+compiler       = {
-                  'gfortran': 'gnu95 --f90flags="-fPIC -fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics'+\
+                  'gfortran': '--fcompiler=gnu95 --f90flags="-fPIC -fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics'+\
-                          ' -DSpectral -fdefault-real-8 -fdefault-double-8 -DFLOAT=8 -DINT=4 -I%s/lib"'%damaskEnv.rootDir(),
+                              ' -fdefault-real-8 -fdefault-double-8"',
-                  'ifort':    'intelem --f90flags="-fPIC -fpp -stand f08 -diag-disable 5268 -assume byterecl'+\
+                  'ifort':    '--fcompiler=intelem --f90flags="-fPIC -fpp -stand f08 -diag-disable 5268 -assume byterecl'+\
-                          ' -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I%s/lib"'%damaskEnv.rootDir(),
+                              ' -real-size 64 -integer-size 32"',
                   }[options['F90']]
 
+# option not depending on compiler
+compileOptions =' -DSpectral -DFLOAT=8 -DINT=4 -I%s/lib'%damaskEnv.rootDir()
+
+# this saves the path of libraries during runtime
+LDFLAGS ='-Wl,-rpath,%s/lib'%(options['FFTW_ROOT'])
+
 # see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
 if   options['IMKL_ROOT'] != '' and options['F90'] != 'gfortran':
-  lib_lapack = '-L$IMKL_ROOT/lib/intel64 -I%s/include -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -liomp5'%options['IMKL_ROOT']
+  lib_lapack = '-L%s/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -liomp5'%options['IMKL_ROOT']
+  LDFLAGS +=' -Wl,-rpath,%s/lib/intel64'%(options['IMKL_ROOT'])
 elif options['ACML_ROOT'] != '':
-  lib_lapack = '-L$ACML/%s64/lib -lacml'%options['F90']
+  lib_lapack = '-L%s/%s64/lib  -lacml'%(options['ACML_ROOT'],options['F90'])
+  LDFLAGS +=' -Wl,-rpath,%s/%s64/lib'%(options['ACML_ROOT'],options['F90'])
 elif options['LAPACK_ROOT'] != '':
-  lib_lapack = '-L$LAPACK_ROOT/lib -L$LAPACK_ROOT/lib64 -llapack'                                                   
+  lib_lapack = '-L%s/lib -L%s/lib64  -llapack'%(options['LAPACK_ROOT'],options['LAPACK_ROOT'])
+  LDFLAGS +=' -Wl,-rpath,%s/lib -Wl,-rpath,%s/lib64'%(options['LAPACK_ROOT'],options['LAPACK_ROOT'])                                     
 
 os.chdir(codeDir)                                                                           # needed for compilation with gfortran and f2py
 try:
@@ -55,7 +64,8 @@ except OSError, e:
 #' --overwrite-signature --no-lower prec.f90 DAMASK_spectral_interface.f90 math.f90 mesh.f90,...'
  ###########################################################################
 cmd = 'f2py damask.core.pyf' +\
-      ' -c --no-lower --fcompiler=%s'%(compileCommand) +\
+      ' -c --no-lower %s'%(compiler) +\
+      compileOptions+\
       ' prec.f90'+\
       ' DAMASK_spectral_interface.f90'+\
       ' IO.f90'+\
@@ -66,12 +76,16 @@ cmd = 'f2py damask.core.pyf' +\
       ' FEsolving.f90'+\
       ' mesh.f90'+\
       ' core_quit.f90'+\
-      ' -L$FFTW_ROOT/lib -lfftw3'+\
+      ' -L%s/lib -lfftw3'%(options['FFTW_ROOT'])+\
       ' %s'%lib_lapack
 
+# f2py does not (yet) support setting of special flags for the linker, hence they must be set via 
+# environment variable
+my_env = os.environ
+my_env["LDFLAGS"] = LDFLAGS
 print('Executing: '+cmd)
 try:
-  subprocess.call(shlex.split(cmd))
+  subprocess.call(shlex.split(cmd),env=my_env)
 except subprocess.CalledProcessError:
   print('build failed')
 except OSError:

installation/mods_MarcMentat/apply_DAMASK_modifications.sh

@@ -60,13 +60,13 @@ BLASDIR=${BLASDIR%/}               # remove trailing slash
 
 case $BLASTYPE in
     IMKL | imkl) 
-    BLAS=" -mkl"
+    BLAS=" -mkl=sequential -lpthread -lm -rpath=$BLASDIR/lib/intel64" #rpoath
     ;;
     ACML | acml) 
-    BLAS=" -L$BLASDIR/ifort64_mp/lib -lacml_mp"
+    BLAS=" -L$BLASDIR/ifort64/lib -lacml -rpath=$BLASDIR/ifort64/lib"
     ;;
     LAPACK | lapack) 
-    BLAS=" -L$BLASDIR/lib64 -L$BLASDIR/lib -llapack"
+    BLAS=" -L$BLASDIR/lib64 -L$BLASDIR/lib -llapack -rpath=$BLASDIR/lib64 -rpath$BLASDIR/lib"
     ;;
     *)
     echo "error, BLAS type must be IMKL, ACML, or LAPACK"