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Backofen, Rainer
amdis
Commits
e82f87e3
Commit
e82f87e3
authored
Jul 18, 2010
by
Thomas Witkowski
Browse files
Fixed Sebastians bug no. 1 in parallelization code with periodic boundary conditions.
parent
be58240d
Changes
3
Hide whitespace changes
Inline
Side-by-side
AMDiS/libtool
View file @
e82f87e3
...
...
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
# Libtool was configured on host
deimos102
:
# Libtool was configured on host
linux-dxyz.site
:
# Shell to use when invoking shell scripts.
SHELL
=
"/bin/sh"
...
...
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS
=
"cru"
# A C compiler.
LTCC
=
"/
licsoft/libraries/openmpi/1.2.6/64bit
/bin/mpicc"
LTCC
=
"/
usr/lib64/mpi/gcc/openmpi/
/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS
=
"-g -O2"
# A language-specific compiler.
CC
=
"/
licsoft/libraries/openmpi/1.2.6/64bit
/bin/mpicc"
CC
=
"/
usr/lib64/mpi/gcc/openmpi/
/bin/mpicc"
# Is the compiler the GNU C compiler?
with_gcc
=
yes
...
...
@@ -325,10 +325,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs
=
unknown
# Compile-time system search path for libraries
sys_lib_search_path_spec
=
" /
fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2
/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.
1.2
/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../x86_64-suse-linux/4.
1.2
/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../lib64/ /lib/x86_64-suse-linux/4.
1.2
/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.
1.2
/ /usr/lib/../lib64/
/fastfs/wir/local/lib/
/usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../ /lib/ /usr/lib/"
sys_lib_search_path_spec
=
" /
usr/lib64/gcc/x86_64-suse-linux/4.5
/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.
5
/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../x86_64-suse-linux/4.
5
/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../lib64/ /lib/x86_64-suse-linux/4.
5
/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.
5
/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../ /lib/ /usr/lib/"
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec
=
"/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib
64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso
"
sys_lib_dlsearch_path_spec
=
"/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64
/usr/lib64/Xaw3d
/usr/X11R6/lib/Xaw3d /usr/X11R6/lib
/usr/lib/Xaw3d
/usr/x86_64-suse-linux/lib /usr/local/lib
/opt/kde3/lib /lib64 /lib /usr/lib64 /usr/lib /usr/local/lib64 /opt/kde3/lib64 /usr/lib64/graphviz /usr/lib64/graphviz/sharp /usr/lib64/graphviz/java /usr/lib64/graphviz/perl /usr/lib64/graphviz/php /usr/lib64/graphviz/ocaml /usr/lib64/graphviz/python /usr/lib64/graphviz/lua /usr/lib64/graphviz/tcl /usr/lib64/graphviz/guile /usr/lib64/graphviz/ruby
"
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path
=
""
...
...
@@ -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
deimos102
:
# Libtool was configured on host
linux-dxyz.site
:
# Shell to use when invoking shell scripts.
SHELL
=
"/bin/sh"
...
...
@@ -6798,13 +6798,13 @@ AR="ar"
AR_FLAGS
=
"cru"
# A C compiler.
LTCC
=
"/
licsoft/libraries/openmpi/1.2.6/64bit
/bin/mpicc"
LTCC
=
"/
usr/lib64/mpi/gcc/openmpi/
/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS
=
"-g -O2"
# A language-specific compiler.
CC
=
"/
licsoft/libraries/openmpi/1.2.6/64bit
/bin/mpicxx"
CC
=
"/
usr/lib64/mpi/gcc/openmpi/
/bin/mpicxx"
# Is the compiler the GNU C compiler?
with_gcc
=
yes
...
...
@@ -6942,11 +6942,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
predep_objects
=
"/usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/crtbeginS.o"
predep_objects
=
"/usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.
5
/crtbeginS.o"
# Dependencies to place after the objects being linked to create a
# shared library.
postdep_objects
=
"/usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../lib64/crtn.o"
postdep_objects
=
"/usr/lib64/gcc/x86_64-suse-linux/4.
5
/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../lib64/crtn.o"
# Dependencies to place before the objects being linked to create a
# shared library.
...
...
@@ -6954,11 +6954,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
postdeps
=
"-lmpi_cxx -lmpi -lopen-rte -lopen-pal
-libverbs -lrt -lnuma
-ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
postdeps
=
"-lmpi_cxx -lmpi -lopen-rte -lopen-pal -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
-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/fastfs/wir/local/lib
-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
/mpi/gcc/openmpi
/lib
64
-L/usr/lib64/gcc/x86_64-suse-linux/4.
5
-L/usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../.."
# Method to check whether dependent libraries are shared objects.
deplibs_check_method
=
"pass_all"
...
...
@@ -7038,10 +7038,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs
=
unknown
# Compile-time system search path for libraries
sys_lib_search_path_spec
=
" /
fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2
/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.
1.2
/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../x86_64-suse-linux/4.
1.2
/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../lib64/ /lib/x86_64-suse-linux/4.
1.2
/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.
1.2
/ /usr/lib/../lib64/
/fastfs/wir/local/lib/
/usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.
1.2
/../../../ /lib/ /usr/lib/"
sys_lib_search_path_spec
=
" /
usr/lib64/gcc/x86_64-suse-linux/4.5
/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.
5
/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../x86_64-suse-linux/4.
5
/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../lib64/ /lib/x86_64-suse-linux/4.
5
/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.
5
/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.
5
/../../../ /lib/ /usr/lib/"
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec
=
"/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib
64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso
"
sys_lib_dlsearch_path_spec
=
"/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64
/usr/lib64/Xaw3d
/usr/X11R6/lib/Xaw3d /usr/X11R6/lib
/usr/lib/Xaw3d
/usr/x86_64-suse-linux/lib /usr/local/lib
/opt/kde3/lib /lib64 /lib /usr/lib64 /usr/lib /usr/local/lib64 /opt/kde3/lib64 /usr/lib64/graphviz /usr/lib64/graphviz/sharp /usr/lib64/graphviz/java /usr/lib64/graphviz/perl /usr/lib64/graphviz/php /usr/lib64/graphviz/ocaml /usr/lib64/graphviz/python /usr/lib64/graphviz/lua /usr/lib64/graphviz/tcl /usr/lib64/graphviz/guile /usr/lib64/graphviz/ruby
"
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path
=
""
...
...
@@ -7065,7 +7065,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
# Libtool was configured on host
deimos102
:
# Libtool was configured on host
linux-dxyz.site
:
# Shell to use when invoking shell scripts.
SHELL
=
"/bin/sh"
...
...
@@ -7103,16 +7103,16 @@ AR="ar"
AR_FLAGS
=
"cru"
# A C compiler.
LTCC
=
"/
licsoft/libraries/openmpi/1.2.6/64bit
/bin/mpicc"
LTCC
=
"/
usr/lib64/mpi/gcc/openmpi/
/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS
=
"-g -O2"
# A language-specific compiler.
CC
=
"g
77
"
CC
=
"g
fortran
"
# Is the compiler the GNU C compiler?
with_gcc
=
with_gcc
=
yes
# An ERE matcher.
EGREP
=
"grep -E"
...
...
@@ -7346,10 +7346,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs
=
unknown
# Compile-time system search path for libraries
sys_lib_search_path_spec
=
" /
fastfs/wir/local/lib
/x86_64-suse-linux/
3.3
.5/
/fastfs/wir/local/lib/
/usr/lib64/gcc
-lib
/x86_64-suse-linux/
3.3.5/ /usr/lib/gcc
/x86_64-suse-linux/
3.3
.5/ /usr/lib64/gcc
-lib
/x86_64-suse-linux/
3.3
.5/../../../../x86_64-suse-linux/lib/
x86_64-suse-linux/3.3.5
/ /usr/lib64/gcc
-lib
/x86_64-suse-linux/
3.3.5/..
/../../../x86_64-suse-linux/
lib
/ /usr/lib64/gcc
-lib
/x86_64-suse-linux/
3.3
.5/../../../x86_64-suse-linux/
3.3
.5/ /
usr
/lib64/
gcc-
lib/x86_64-suse-linux/
3.3.5/../../../ /lib/x86_64-suse-linux/3.3.5/
/lib/ /usr/lib/x86_64-suse-linux/
3.3.5
/ /usr/lib/"
sys_lib_search_path_spec
=
" /
usr/lib64/gcc
/x86_64-suse-linux/
4
.5/ /usr/lib64/gcc/x86_64-suse-linux/
4.5/../../../../x86_64-suse-linux/lib
/x86_64-suse-linux/
4
.5/ /usr/lib64/gcc/x86_64-suse-linux/
4
.5/../../../../x86_64-suse-linux/lib/
../lib64
/ /usr/lib64/gcc/x86_64-suse-linux/
4.5
/../../../x86_64-suse-linux/
4.5
/ /usr/lib64/gcc/x86_64-suse-linux/
4
.5/../../../
../lib64/ /lib/
x86_64-suse-linux/
4
.5/ /
lib/..
/lib64/
/usr/
lib/x86_64-suse-linux/
4.5/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux
/lib/ /usr/lib
64/gcc
/x86_64-suse-linux/
4.5/../../../ /lib
/ /usr/lib/"
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec
=
"/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib
64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso
"
sys_lib_dlsearch_path_spec
=
"/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64
/usr/lib64/Xaw3d
/usr/X11R6/lib/Xaw3d /usr/X11R6/lib
/usr/lib/Xaw3d
/usr/x86_64-suse-linux/lib /usr/local/lib
/opt/kde3/lib /lib64 /lib /usr/lib64 /usr/lib /usr/local/lib64 /opt/kde3/lib64 /usr/lib64/graphviz /usr/lib64/graphviz/sharp /usr/lib64/graphviz/java /usr/lib64/graphviz/perl /usr/lib64/graphviz/php /usr/lib64/graphviz/ocaml /usr/lib64/graphviz/python /usr/lib64/graphviz/lua /usr/lib64/graphviz/tcl /usr/lib64/graphviz/guile /usr/lib64/graphviz/ruby
"
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path
=
""
...
...
AMDiS/src/parallel/MeshDistributor.cc
View file @
e82f87e3
...
...
@@ -1992,6 +1992,7 @@ namespace AMDiS {
DofContainer
&
dofs
=
rankPeriodicDofs
[
it
->
first
];
for
(
std
::
vector
<
AtomicBoundary
>::
iterator
boundIt
=
it
->
second
.
begin
();
boundIt
!=
it
->
second
.
end
();
++
boundIt
)
{
int
nDofs
=
dofs
.
size
();
Element
*
el
=
boundIt
->
rankObj
.
el
;
if
(
boundIt
->
rankObj
.
reverseMode
)
{
...
...
@@ -2010,7 +2011,7 @@ namespace AMDiS {
el
->
getVertexDofs
(
feSpace
,
boundIt
->
rankObj
,
dofs
);
el
->
getNonVertexDofs
(
feSpace
,
boundIt
->
rankObj
,
dofs
);
for
(
unsigned
int
i
=
0
;
i
<
dofs
.
size
();
i
++
)
for
(
unsigned
int
i
=
0
;
i
<
(
dofs
.
size
()
-
nDofs
)
;
i
++
)
rankToDofType
[
it
->
first
].
push_back
(
boundIt
->
type
);
}
...
...
@@ -2048,16 +2049,21 @@ namespace AMDiS {
int
mapGlobalDofIndex
=
stdMpi
.
getRecvData
(
it
->
first
)[
i
];
BoundaryType
type
=
types
[
i
];
periodicDof
[
type
][
globalDofIndex
]
=
mapGlobalDofIndex
;
periodicDofAssociations
[
globalDofIndex
].
insert
(
type
);
dofFromRank
[
globalDofIndex
].
insert
(
it
->
first
);
}
// Check if this global dof with the corresponding boundary type was
// not added before by another periodic boundary from other rank.
if
(
periodicDofAssociations
[
globalDofIndex
].
count
(
type
)
==
0
)
{
periodicDof
[
type
][
globalDofIndex
]
=
mapGlobalDofIndex
;
periodicDofAssociations
[
globalDofIndex
].
insert
(
type
);
dofFromRank
[
globalDofIndex
].
insert
(
it
->
first
);
}
}
}
if
(
dofFromRank
.
size
()
>
0
)
if
(
dofFromRank
.
size
()
>
0
)
{
TEST_EXIT_DBG
(
mesh
->
getDim
()
==
2
)
(
"Periodic boundary corner problem must be generalized to 3d!
\n
"
);
}
MPI
::
Request
request
[
min
(
static_cast
<
int
>
(
periodicBoundary
.
boundary
.
size
()
*
2
),
4
)];
int
requestCounter
=
0
;
...
...
@@ -2067,7 +2073,8 @@ namespace AMDiS {
it
!=
dofFromRank
.
end
();
++
it
)
{
if
(
it
->
second
.
size
()
==
2
)
{
TEST_EXIT_DBG
(
periodicDofAssociations
[
it
->
first
].
size
()
==
2
)
(
"Missing periodic dof!
\n
"
);
(
"DOF %d has only %d periodic associations!
\n
"
,
it
->
first
,
periodicDofAssociations
[
it
->
first
].
size
());
int
type0
=
*
(
periodicDofAssociations
[
it
->
first
].
begin
());
int
type1
=
*
(
++
(
periodicDofAssociations
[
it
->
first
].
begin
()));
...
...
AMDiS/src/parallel/MpiHelper.h
View file @
e82f87e3
...
...
@@ -24,6 +24,8 @@
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
#include <time.h>
#include <stdlib.h>
#include <mpi.h>
namespace
AMDiS
{
...
...
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