From 12648d7b8ffff5752761943360c3f181f85ea61b Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Mon, 8 Feb 2010 07:16:19 +0000
Subject: [PATCH] Some changes in source directory structure.
---
AMDiS/bin/Makefile.am | 9 +-
AMDiS/bin/Makefile.in | 48 ++--
AMDiS/libtool | 24 +-
AMDiS/src/DOFAdmin.cc | 0
AMDiS/src/Estimator.cc | 0
AMDiS/src/Estimator.h | 0
.../src/{ => parallel}/ParallelDomainBase.cc | 0
AMDiS/src/{ => parallel}/ParallelDomainBase.h | 0
AMDiS/src/{ => parallel}/ParallelDomainVec.cc | 0
AMDiS/src/{ => parallel}/ParallelDomainVec.h | 0
AMDiS/src/parareal/AdaptParaReal.cc | 60 -----
AMDiS/src/parareal/AdaptParaReal.h | 85 -------
AMDiS/src/parareal/ProblemBase.h | 216 ------------------
13 files changed, 33 insertions(+), 409 deletions(-)
mode change 100755 => 100644 AMDiS/src/DOFAdmin.cc
mode change 100755 => 100644 AMDiS/src/Estimator.cc
mode change 100755 => 100644 AMDiS/src/Estimator.h
rename AMDiS/src/{ => parallel}/ParallelDomainBase.cc (100%)
rename AMDiS/src/{ => parallel}/ParallelDomainBase.h (100%)
rename AMDiS/src/{ => parallel}/ParallelDomainVec.cc (100%)
rename AMDiS/src/{ => parallel}/ParallelDomainVec.h (100%)
delete mode 100644 AMDiS/src/parareal/AdaptParaReal.cc
delete mode 100644 AMDiS/src/parareal/AdaptParaReal.h
delete mode 100644 AMDiS/src/parareal/ProblemBase.h
diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index c40b17b2..109860c5 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -28,8 +28,8 @@ endif
if USE_PARALLEL_DOMAIN_AMDIS
PARALLEL_AMDIS_SOURCES += \
- $(PARALLEL_DIR)/ParallelDomainBase.h $(PARALLEL_DIR)/ParallelDomainBase.cc \
- $(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
+ $(SOURCE_DIR)/parallel/ParallelDomainBase.h $(SOURCE_DIR)/parallel/ParallelDomainBase.cc \
+ $(SOURCE_DIR)/parallel/ParallelDomainVec.h $(SOURCE_DIR)/parallel/ParallelDomainVec.cc
libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
AMDIS_INCLUDES += -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
endif
@@ -217,10 +217,7 @@ $(SOURCE_DIR)/SolutionDataStorage.h $(SOURCE_DIR)/SolutionDataStorage.hh \
$(SOURCE_DIR)/InteriorBoundary.h $(SOURCE_DIR)/InteriorBoundary.cc \
$(SOURCE_DIR)/ElementDofIteartor.h $(SOURCE_DIR)/ElementDofIterator.cc \
$(SOURCE_DIR)/Debug.h $(SOURCE_DIR)/Debug.cc \
-$(SOURCE_DIR)/MpiHelper.h $(SOURCE_DIR)/MpiHelper.cc \
-$(SOURCE_DIR)/parareal/ProblemBase.h \
-$(SOURCE_DIR)/parareal/AdaptParaReal.h $(SOURCE_DIR)/parareal/AdaptParaReal.cc
-
+$(SOURCE_DIR)/MpiHelper.h $(SOURCE_DIR)/MpiHelper.cc
COMPOSITE_SOURCE_DIR = ../compositeFEM/src
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index 6144e1a1..d0079e0a 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -38,8 +38,8 @@ build_triplet = @build@
host_triplet = @host@
@USE_PARALLEL_AMDIS_TRUE@am__append_1 = -DHAVE_PARALLEL_AMDIS=1
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_2 = \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelDomainBase.h $(PARALLEL_DIR)/ParallelDomainBase.cc \
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDomainBase.h $(SOURCE_DIR)/parallel/ParallelDomainBase.cc \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ $(SOURCE_DIR)/parallel/ParallelDomainVec.h $(SOURCE_DIR)/parallel/ParallelDomainVec.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
@@ -72,10 +72,11 @@ am__installdirs = "$(DESTDIR)$(libdir)"
libLTLIBRARIES_INSTALL = $(INSTALL)
LTLIBRARIES = $(lib_LTLIBRARIES)
libamdis_la_LIBADD =
-am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ParallelDomainBase.h \
- $(PARALLEL_DIR)/ParallelDomainBase.cc \
- $(PARALLEL_DIR)/ParallelDomainVec.h \
- $(PARALLEL_DIR)/ParallelDomainVec.cc \
+am__libamdis_la_SOURCES_DIST = \
+ $(SOURCE_DIR)/parallel/ParallelDomainBase.h \
+ $(SOURCE_DIR)/parallel/ParallelDomainBase.cc \
+ $(SOURCE_DIR)/parallel/ParallelDomainVec.h \
+ $(SOURCE_DIR)/parallel/ParallelDomainVec.cc \
$(PARALLEL_DIR)/ConditionalEstimator.h \
$(PARALLEL_DIR)/ConditionalEstimator.cc \
$(PARALLEL_DIR)/ConditionalMarker.h \ \
@@ -227,10 +228,7 @@ am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ParallelDomainBase.h \
$(SOURCE_DIR)/ElementDofIteartor.h \
$(SOURCE_DIR)/ElementDofIterator.cc $(SOURCE_DIR)/Debug.h \
$(SOURCE_DIR)/Debug.cc $(SOURCE_DIR)/MpiHelper.h \
- $(SOURCE_DIR)/MpiHelper.cc \
- $(SOURCE_DIR)/parareal/ProblemBase.h \
- $(SOURCE_DIR)/parareal/AdaptParaReal.h \
- $(SOURCE_DIR)/parareal/AdaptParaReal.cc
+ $(SOURCE_DIR)/MpiHelper.cc
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__objects_1 = libamdis_la-ParallelDomainBase.lo \
@USE_PARALLEL_DOMAIN_AMDIS_TRUE@ libamdis_la-ParallelDomainVec.lo
@USE_PARALLEL_AMDIS_FALSE@am__objects_2 = $(am__objects_1)
@@ -293,7 +291,7 @@ am_libamdis_la_OBJECTS = $(am__objects_2) libamdis_la-DOFIndexed.lo \
libamdis_la-DataCollector.lo libamdis_la-ScalableQuadrature.lo \
libamdis_la-SubElInfo.lo libamdis_la-InteriorBoundary.lo \
libamdis_la-ElementDofIterator.lo libamdis_la-Debug.lo \
- libamdis_la-MpiHelper.lo libamdis_la-AdaptParaReal.lo
+ libamdis_la-MpiHelper.lo
libamdis_la_OBJECTS = $(am_libamdis_la_OBJECTS)
libcompositeFEM_la_LIBADD =
am_libcompositeFEM_la_OBJECTS = libcompositeFEM_la-CFE_Integration.lo \
@@ -633,9 +631,7 @@ $(SOURCE_DIR)/SolutionDataStorage.h $(SOURCE_DIR)/SolutionDataStorage.hh \
$(SOURCE_DIR)/InteriorBoundary.h $(SOURCE_DIR)/InteriorBoundary.cc \
$(SOURCE_DIR)/ElementDofIteartor.h $(SOURCE_DIR)/ElementDofIterator.cc \
$(SOURCE_DIR)/Debug.h $(SOURCE_DIR)/Debug.cc \
-$(SOURCE_DIR)/MpiHelper.h $(SOURCE_DIR)/MpiHelper.cc \
-$(SOURCE_DIR)/parareal/ProblemBase.h \
-$(SOURCE_DIR)/parareal/AdaptParaReal.h $(SOURCE_DIR)/parareal/AdaptParaReal.cc
+$(SOURCE_DIR)/MpiHelper.h $(SOURCE_DIR)/MpiHelper.cc
COMPOSITE_SOURCE_DIR = ../compositeFEM/src
libcompositeFEM_la_CXXFLAGS = $(libamdis_la_CXXFLAGS)
@@ -732,7 +728,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptBase.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptInfo.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptInstationary.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptParaReal.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptStationary.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Assembler.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BasisFunction.Plo@am__quote@
@@ -860,19 +855,19 @@ distclean-compile:
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LTCXXCOMPILE) -c -o $@ $<
-libamdis_la-ParallelDomainBase.lo: $(PARALLEL_DIR)/ParallelDomainBase.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainBase.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo" -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(PARALLEL_DIR)/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainBase.cc; \
+libamdis_la-ParallelDomainBase.lo: $(SOURCE_DIR)/parallel/ParallelDomainBase.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainBase.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo" -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainBase.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo" "$(DEPDIR)/libamdis_la-ParallelDomainBase.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDomainBase.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(PARALLEL_DIR)/ParallelDomainBase.cc' object='libamdis_la-ParallelDomainBase.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/ParallelDomainBase.cc' object='libamdis_la-ParallelDomainBase.lo' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(PARALLEL_DIR)/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainBase.cc
+@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainBase.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainBase.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainBase.cc
-libamdis_la-ParallelDomainVec.lo: $(PARALLEL_DIR)/ParallelDomainVec.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainVec.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo" -c -o libamdis_la-ParallelDomainVec.lo `test -f '$(PARALLEL_DIR)/ParallelDomainVec.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainVec.cc; \
+libamdis_la-ParallelDomainVec.lo: $(SOURCE_DIR)/parallel/ParallelDomainVec.cc
+@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ParallelDomainVec.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo" -c -o libamdis_la-ParallelDomainVec.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainVec.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainVec.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo" "$(DEPDIR)/libamdis_la-ParallelDomainVec.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ParallelDomainVec.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(PARALLEL_DIR)/ParallelDomainVec.cc' object='libamdis_la-ParallelDomainVec.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parallel/ParallelDomainVec.cc' object='libamdis_la-ParallelDomainVec.lo' libtool=yes @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainVec.lo `test -f '$(PARALLEL_DIR)/ParallelDomainVec.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ParallelDomainVec.cc
+@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ParallelDomainVec.lo `test -f '$(SOURCE_DIR)/parallel/ParallelDomainVec.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parallel/ParallelDomainVec.cc
libamdis_la-ConditionalEstimator.lo: $(PARALLEL_DIR)/ConditionalEstimator.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ConditionalEstimator.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ConditionalEstimator.Tpo" -c -o libamdis_la-ConditionalEstimator.lo `test -f '$(PARALLEL_DIR)/ConditionalEstimator.cc' || echo '$(srcdir)/'`$(PARALLEL_DIR)/ConditionalEstimator.cc; \
@@ -1553,13 +1548,6 @@ libamdis_la-MpiHelper.lo: $(SOURCE_DIR)/MpiHelper.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-MpiHelper.lo `test -f '$(SOURCE_DIR)/MpiHelper.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/MpiHelper.cc
-libamdis_la-AdaptParaReal.lo: $(SOURCE_DIR)/parareal/AdaptParaReal.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-AdaptParaReal.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-AdaptParaReal.Tpo" -c -o libamdis_la-AdaptParaReal.lo `test -f '$(SOURCE_DIR)/parareal/AdaptParaReal.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parareal/AdaptParaReal.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-AdaptParaReal.Tpo" "$(DEPDIR)/libamdis_la-AdaptParaReal.Plo"; else rm -f "$(DEPDIR)/libamdis_la-AdaptParaReal.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/parareal/AdaptParaReal.cc' object='libamdis_la-AdaptParaReal.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-AdaptParaReal.lo `test -f '$(SOURCE_DIR)/parareal/AdaptParaReal.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parareal/AdaptParaReal.cc
-
libcompositeFEM_la-CFE_Integration.lo: $(COMPOSITE_SOURCE_DIR)/CFE_Integration.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libcompositeFEM_la_CXXFLAGS) $(CXXFLAGS) -MT libcompositeFEM_la-CFE_Integration.lo -MD -MP -MF "$(DEPDIR)/libcompositeFEM_la-CFE_Integration.Tpo" -c -o libcompositeFEM_la-CFE_Integration.lo `test -f '$(COMPOSITE_SOURCE_DIR)/CFE_Integration.cc' || echo '$(srcdir)/'`$(COMPOSITE_SOURCE_DIR)/CFE_Integration.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libcompositeFEM_la-CFE_Integration.Tpo" "$(DEPDIR)/libcompositeFEM_la-CFE_Integration.Plo"; else rm -f "$(DEPDIR)/libcompositeFEM_la-CFE_Integration.Tpo"; exit 1; fi
diff --git a/AMDiS/libtool b/AMDiS/libtool
index b33f6fac..486eabd3 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
-# Libtool was configured on host p1s122:
+# Libtool was configured on host deimos103:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="gcc"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -171,7 +171,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6760,7 +6760,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host p1s122:
+# Libtool was configured on host deimos103:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6798,13 +6798,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="g++"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -6887,7 +6887,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6954,11 +6954,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path="-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
+compiler_lib_search_path="-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7065,7 +7065,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host p1s122:
+# Libtool was configured on host deimos103:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7103,7 +7103,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
diff --git a/AMDiS/src/DOFAdmin.cc b/AMDiS/src/DOFAdmin.cc
old mode 100755
new mode 100644
diff --git a/AMDiS/src/Estimator.cc b/AMDiS/src/Estimator.cc
old mode 100755
new mode 100644
diff --git a/AMDiS/src/Estimator.h b/AMDiS/src/Estimator.h
old mode 100755
new mode 100644
diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/parallel/ParallelDomainBase.cc
similarity index 100%
rename from AMDiS/src/ParallelDomainBase.cc
rename to AMDiS/src/parallel/ParallelDomainBase.cc
diff --git a/AMDiS/src/ParallelDomainBase.h b/AMDiS/src/parallel/ParallelDomainBase.h
similarity index 100%
rename from AMDiS/src/ParallelDomainBase.h
rename to AMDiS/src/parallel/ParallelDomainBase.h
diff --git a/AMDiS/src/ParallelDomainVec.cc b/AMDiS/src/parallel/ParallelDomainVec.cc
similarity index 100%
rename from AMDiS/src/ParallelDomainVec.cc
rename to AMDiS/src/parallel/ParallelDomainVec.cc
diff --git a/AMDiS/src/ParallelDomainVec.h b/AMDiS/src/parallel/ParallelDomainVec.h
similarity index 100%
rename from AMDiS/src/ParallelDomainVec.h
rename to AMDiS/src/parallel/ParallelDomainVec.h
diff --git a/AMDiS/src/parareal/AdaptParaReal.cc b/AMDiS/src/parareal/AdaptParaReal.cc
deleted file mode 100644
index 8ba8d910..00000000
--- a/AMDiS/src/parareal/AdaptParaReal.cc
+++ /dev/null
@@ -1,60 +0,0 @@
-#include "parareal/ProblemBase.h"
-#include "parareal/AdaptParaReal.h"
-
-namespace AMDiS {
- int AdaptParaReal::adapt()
- {
- // Compute number of coarse and fine time stages.
- int coarseStages =
- static_cast<int>(round(adaptInfo->getEndTime() / coarseTimestep));
- int fineStages = static_cast<int>(round(coarseTimestep / fineTimestep));
-
- // First, sequentially calculate first approximation on coarse time grid.
- adaptInfo->setTimestep(coarseTimestep);
- pararealProb->setStoreSolutions(false, true);
- pararealProb->setStoreInitSolution(true);
- pararealProb->setInitSolutionVec(NULL);
- AdaptInstationary::adapt();
-
- // ParaReal iterations
- for (int k = 0; k < pararealIter; k++) {
- // Compute solutions with fine timestep on the coarse grid slides.
- for (int i = 0; i < coarseStages; i++) {
- adaptInfo->resetTimeValues(fineTimestep,
- i * coarseTimestep,
- (i + 1) *coarseTimestep);
- pararealProb->setStoreSolutions(true, false);
- pararealProb->setStoreInitSolution(false);
- pararealProb->setInitSolutionVec((*pararealProb->getCoarseSolutions())[i]);
- pararealProb->cleanUp();
-
- AdaptInstationary::adapt();
- }
-
- // Copy coarse grid solutions to another vector.
- std::vector<DOFVector<double> *> coarseSolutions =
- (*pararealProb->getCoarseSolutions());
- pararealProb->clearCoarseSolutions();
- (*pararealProb->getCoarseSolutions()).push_back(coarseSolutions[0]);
-
- // Again, compute solutions on coarse grid and calculate the corrected solutions.
- for (int i = 1; i <= coarseStages; i++) {
- adaptInfo->resetTimeValues(coarseTimestep,
- (i - 1) * coarseTimestep,
- i * coarseTimestep);
- pararealProb->setStoreSolutions(false, true);
- pararealProb->setStoreInitSolution(false);
- pararealProb->setInitSolutionVec((*pararealProb->getCoarseSolutions())[i - 1]);
-
- AdaptInstationary::adapt();
-
- DOFVector<double>* tmp = (*pararealProb->getCoarseSolutions())[i];
- *tmp += *(*pararealProb->getFineSolutions())[(i * fineStages) - 1];
- *tmp -= *(coarseSolutions[i]);
- }
- }
-
- return 0;
- }
-
-}
diff --git a/AMDiS/src/parareal/AdaptParaReal.h b/AMDiS/src/parareal/AdaptParaReal.h
deleted file mode 100644
index 2f452a97..00000000
--- a/AMDiS/src/parareal/AdaptParaReal.h
+++ /dev/null
@@ -1,85 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == TU Dresden ==
-// == ==
-// == Institut für Wissenschaftliches Rechnen ==
-// == Zellescher Weg 12-14 ==
-// == 01069 Dresden ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == https://gforge.zih.tu-dresden.de/projects/amdis/ ==
-// == ==
-// ============================================================================
-
-/** \file parareal/AdaptInfo.h */
-
-#ifndef AMDIS_PARAREAL_ADAPTINFO_H
-#define AMDIS_PARAREAL_ADAPTINFO_H
-
-#include "AdaptInstationary.h"
-#include "parareal/ProblemBase.h"
-
-namespace AMDiS {
-
- class AdaptParaReal : public AdaptInstationary
- {
- public:
- AdaptParaReal(const char *name,
- ProblemIterationInterface *problemStat,
- AdaptInfo *info,
- ProblemTimeInterface *problemInstat,
- ParaRealProblemBase< DOFVector<double> > *paraProb,
- AdaptInfo *initialInfo,
- time_t initialTimestamp = 0)
- : AdaptInstationary(name, problemStat, info, problemInstat, initialInfo, initialTimestamp),
- coarseTimestep(0.0),
- fineTimestep(0.0),
- pararealIter(1),
- pararealProb(paraProb)
- {
- GET_PARAMETER(0, static_cast<std::string>(name) + "->coarse timestep", "%f", &coarseTimestep);
- GET_PARAMETER(0, static_cast<std::string>(name) + "->timestep", "%f", &fineTimestep);
- GET_PARAMETER(0, static_cast<std::string>(name) + "->parareal iteration", "%d", ¶realIter);
-
- TEST_EXIT(fineTimestep > 0.0)("fineTimestep must be greater than zero!\n");
- TEST_EXIT(coarseTimestep > 0.0)("coarseTimestep must be greater than zero!\n");
- TEST_EXIT(fineTimestep < coarseTimestep)("fineTimestep must be smaller than coarseTimestep!\n");
- TEST_EXIT(pararealIter >= 0)("ParaReal Iterations must be >= 0!\n");
- }
-
- /** \brief
- * Here, the parareal algorithm is executed.
- */
- virtual int adapt();
-
- protected:
- /** \brief
- * Timestep for the coarse time grid.
- */
- double coarseTimestep;
-
- /** \brief
- * Timestep for the fine time grid.
- */
- double fineTimestep;
-
- /** \brief
- * Number of parareal iterations.
- */
- int pararealIter;
-
- /** \brief
- * Pointer to the parareal problem.
- */
- ParaRealProblemBase< DOFVector<double> > *pararealProb;
- };
-
-}
-
-#endif // AMDIS_PARAREAL_ADAPTINFO
diff --git a/AMDiS/src/parareal/ProblemBase.h b/AMDiS/src/parareal/ProblemBase.h
deleted file mode 100644
index 181f0ca1..00000000
--- a/AMDiS/src/parareal/ProblemBase.h
+++ /dev/null
@@ -1,216 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == TU Dresden ==
-// == ==
-// == Institut für Wissenschaftliches Rechnen ==
-// == Zellescher Weg 12-14 ==
-// == 01069 Dresden ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == https://gforge.zih.tu-dresden.de/projects/amdis/ ==
-// == ==
-// ============================================================================
-
-/** \file parareal/ProblemBase.h */
-
-#ifndef AMDIS_PARAREAL_PROBLEMBASE_H
-#define AMDIS_PARAREAL_PROBLEMBASE_H
-
-#include <vector>
-#include "CreatorInterface.h"
-#include "DOFVector.h"
-#include "SystemVector.h"
-#include "ProblemInstat.h"
-
-namespace AMDiS {
-
- template<typename T>
- class ParaRealProblemBase
- {
- public:
- ParaRealProblemBase(CreatorInterface<T> *creator)
- : storeFineSolutions(false),
- storeCoarseSolutions(false),
- vectorCreator(creator)
- {
- fineSolutions.clear();
- coarseSolutions.clear();
- }
-
- virtual ~ParaRealProblemBase() {};
-
- void storeSolution(T *vec)
- {
- if (storeFineSolutions) {
- storeFineSolution(vec);
- }
- if (storeCoarseSolutions) {
- storeCoarseSolution(vec);
- }
- }
-
- void storeFineSolution(T *vec)
- {
- T *tmp = vectorCreator->create();
- *tmp = *vec;
- fineSolutions.push_back(tmp);
- }
-
- void storeCoarseSolution(T *vec)
- {
- T *tmp = vectorCreator->create();
- *tmp = *vec;
- coarseSolutions.push_back(tmp);
- }
-
- void setStoreSolutions(bool fine, bool coarse) {
- storeFineSolutions = fine;
- storeCoarseSolutions = coarse;
- }
-
- void setInitSolutionVec(T *vec) {
- initSolutionVec = vec;
- }
-
- void setStoreInitSolution(bool store) {
- storeInitSolution = store;
- }
-
- std::vector<T*> *getFineSolutions() {
- return &fineSolutions;
- }
-
- std::vector<T*> *getCoarseSolutions() {
- return &coarseSolutions;
- }
-
- void clearFineSolutions() {
- fineSolutions.clear();
- }
-
- void clearCoarseSolutions() {
- coarseSolutions.clear();
- }
-
- /** \brief
- * This functions is called between switching from coarse
- * time grid to fine time grid, or vice versa. Can be overwritten
- * to clean up some data.
- */
- virtual void cleanUp() {};
-
- protected:
- /** \brief
- * Stores all solutions on the fine time grid.
- */
- std::vector<T*> fineSolutions;
-
- /** \brief
- * Stores all solutions on the coarse time grid.
- */
- std::vector<T*> coarseSolutions;
-
- /** \brief
- * If true, after closeTimestep() the solution is stored
- * in vector \ref fineSolutions .
- */
- bool storeFineSolutions;
-
- /** \brief
- * If true, after closeTimestep() the solution is stored
- * in vector \ref coarseSolution .
- */
- bool storeCoarseSolutions;
-
- /** \brief
- * If true, the initial solution is also stored in either
- * \ref fineSolutions or in \ref coarseSolutions .
- */
- bool storeInitSolution;
-
- /** \brief
- * Creator interface to create new vectors (either DOFVector or
- * SystemVector).
- */
- CreatorInterface<T> *vectorCreator;
-
- /** \brief
- * The initial solution for the problem can be set to this
- * vector.
- */
- T* initSolutionVec;
- };
-
-
-
- class ParaRealScal : public ProblemInstatScal,
- public ParaRealProblemBase< DOFVector<double> >
- {
- public:
- ParaRealScal(char* name,
- ProblemScal *prob,
- ProblemStatBase *initialProb = NULL)
- : ProblemInstatScal(name, prob, initialProb),
- ParaRealProblemBase< DOFVector<double> >(new DOFVector<double>::Creator(prob->getFESpace()))
- {}
-
- virtual void closeTimestep(AdaptInfo *adaptInfo) {
- ProblemInstatScal::closeTimestep(adaptInfo);
-
- storeSolution(problemStat->getSolution());
- }
-
- virtual void solveInitialProblem(AdaptInfo *adaptInfo) {
- if (initSolutionVec == NULL) {
- ProblemInstatScal::solveInitialProblem(adaptInfo);
- } else {
- *(problemStat->getSolution()) = *initSolutionVec;
- }
-
- if (storeInitSolution) {
- storeSolution(problemStat->getSolution());
- }
- }
- };
-
-
- class ParaRealVec : public ProblemInstatVec,
- public ParaRealProblemBase< SystemVector >
- {
- public:
- ParaRealVec(char *name,
- ProblemVec *prob,
- ProblemStatBase *initialProb = NULL)
- : ProblemInstatVec(name, prob, initialProb),
- ParaRealProblemBase< SystemVector >(new SystemVector::Creator(name,
- prob->getFESpaces(),
- prob->getNumComponents()))
- {}
-
- virtual void closeTimestep(AdaptInfo *adaptInfo) {
- ProblemInstatVec::closeTimestep(adaptInfo);
-
- storeSolution(problemStat->getSolution());
- }
-
- virtual void solveInitialProblem(AdaptInfo *adaptInfo) {
- if (initSolutionVec == NULL) {
- ProblemInstatVec::solveInitialProblem(adaptInfo);
- } else {
- *(problemStat->getSolution()) = *initSolutionVec;
- }
-
- if (storeInitSolution) {
- storeSolution(problemStat->getSolution());
- }
- }
- };
-}
-
-#endif
--
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