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OPAL
src
Commits
10bdd8ed
Commit
10bdd8ed
authored
Dec 20, 2017
by
gsell
Browse files
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Plain Diff
H5hut >= 2 is now required
parent
80c1a9e8
Changes
26
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26 changed files
with
24 additions
and
214 deletions
+24
-214
CMakeLists.txt
CMakeLists.txt
+0
-4
CMakeModules/FindH5Hut.cmake
CMakeModules/FindH5Hut.cmake
+3
-4
ippl/test/AMR/H5Reader.cpp
ippl/test/AMR/H5Reader.cpp
+2
-12
ippl/test/AMR/H5Reader.h
ippl/test/AMR/H5Reader.h
+1
-6
ippl/test/AMR/boxlib-amr/CMakeLists.txt
ippl/test/AMR/boxlib-amr/CMakeLists.txt
+1
-1
ippl/test/AMR/ippl-amr/CMakeLists.txt
ippl/test/AMR/ippl-amr/CMakeLists.txt
+1
-1
ippl/test/AMR/ippl-bunch/CMakeLists.txt
ippl/test/AMR/ippl-bunch/CMakeLists.txt
+1
-1
ippl/test/particle/CMakeLists.txt
ippl/test/particle/CMakeLists.txt
+1
-1
ippl/test/particle/p3m3dHeating.cpp
ippl/test/particle/p3m3dHeating.cpp
+0
-9
src/CMakeLists.txt
src/CMakeLists.txt
+2
-2
src/Classic/Fields/FM3DH5Block.cpp
src/Classic/Fields/FM3DH5Block.cpp
+0
-10
src/Classic/Fields/FM3DH5Block_nonscale.cpp
src/Classic/Fields/FM3DH5Block_nonscale.cpp
+0
-10
src/Classic/Fields/FM3DMagnetoStaticH5Block.cpp
src/Classic/Fields/FM3DMagnetoStaticH5Block.cpp
+0
-10
src/Classic/Fields/Fieldmap.cpp
src/Classic/Fields/Fieldmap.cpp
+1
-6
src/Classic/Structure/LossDataSink.cpp
src/Classic/Structure/LossDataSink.cpp
+0
-9
src/Classic/Structure/LossDataSink.h
src/Classic/Structure/LossDataSink.h
+1
-5
src/Structure/BoundaryGeometry.cpp
src/Structure/BoundaryGeometry.cpp
+1
-5
src/Structure/DataSink.cpp
src/Structure/DataSink.cpp
+1
-9
src/Structure/DataSink.h
src/Structure/DataSink.h
+1
-5
src/Structure/H5PartWrapper.cpp
src/Structure/H5PartWrapper.cpp
+1
-55
src/Structure/H5PartWrapper.h
src/Structure/H5PartWrapper.h
+0
-11
src/Structure/H5PartWrapperForPS.cpp
src/Structure/H5PartWrapperForPS.cpp
+1
-11
src/Structure/H5PartWrapperForPT.cpp
src/Structure/H5PartWrapperForPT.cpp
+1
-11
tests/CMakeLists.txt
tests/CMakeLists.txt
+1
-1
tools/opal2sdds/CMakeLists.txt
tools/opal2sdds/CMakeLists.txt
+2
-2
tools/opal2sdds/main.cpp
tools/opal2sdds/main.cpp
+1
-13
No files found.
CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -133,10 +133,6 @@ IF (BUILD_OPAL_UNIT_TESTS)
SET
(
CMAKE_CXX_FLAGS
"
${
CMAKE_CXX_FLAGS
}
-DWITH_UNIT_TESTS"
)
ENDIF
(
BUILD_OPAL_UNIT_TESTS
)
IF
(
USE_H5HUT2
)
SET
(
CMAKE_CXX_FLAGS
"
${
CMAKE_CXX_FLAGS
}
-DUSE_H5HUT2"
)
ENDIF
(
USE_H5HUT2
)
IF
(
ENABLE_AMR
)
MESSAGE
(
STATUS
"Enable AMR_SOLVER "
${
ENABLE_AMR
}
)
...
...
CMakeModules/FindH5Hut.cmake
View file @
10bdd8ed
...
...
@@ -39,14 +39,13 @@ SET (CMAKE_REQUIRED_INCLUDES ${H5Hut_INCLUDE_DIR})
CHECK_INCLUDE_FILE
(
H5_file_attribs.h HAVE_API2_FUNCTIONS
"-I
${
H5Hut_INCLUDE_DIR
}
-DPARALLEL_IO"
)
IF
(
HAVE_API2_FUNCTIONS
)
MESSAGE
(
STATUS
"H5hut version is >= 2"
)
SET
(
CMAKE_CXX_FLAGS
"
${
CMAKE_CXX_FLAGS
}
-DUSE_H5HUT2"
)
MESSAGE
(
STATUS
"H5hut version is OK"
)
ELSE
(
HAVE_API2_FUNCTIONS
)
MESSAGE
(
STATUS
"H5hut version is 1.x
"
)
MESSAGE
(
ERROR
"H5hut >= 2 required
"
)
ENDIF
(
HAVE_API2_FUNCTIONS
)
# Local Variables:
# mode:cmake
# cmake-tab-width: 4
# indent-tabs-mode:nil
# End:
\ No newline at end of file
# End:
ippl/test/AMR/H5Reader.cpp
View file @
10bdd8ed
...
...
@@ -18,8 +18,6 @@ H5Reader::H5Reader()
void
H5Reader
::
open
(
int
step
)
{
close
();
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5_err_t
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
...
...
@@ -29,10 +27,6 @@ void H5Reader::open(int step) {
assert
(
h5err
!=
H5_ERR
);
file_m
=
H5OpenFile
(
filename_m
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file_m
!=
(
h5_file_t
)
H5_ERR
);
#else
file_m
=
H5OpenFile
(
filename_m
.
c_str
(),
H5_FLUSH_STEP
|
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file_m
!=
(
void
*
)
H5_ERR
);
#endif
H5SetStep
(
file_m
,
step
);
}
...
...
@@ -135,7 +129,7 @@ void H5Reader::writeScalarField(const container_t& scalfield,
h5_file_t
file
=
0
;
std
::
string
fname
=
"test_scalfield.h5"
;
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
// ParallelDescriptor::m_comm_all; //
h5_err_t
h5err
=
H5SetPropFileMPIOIndependent
(
props
,
&
comm
);
...
...
@@ -146,10 +140,6 @@ void H5Reader::writeScalarField(const container_t& scalfield,
assert
(
h5err
!=
H5_ERR
);
file
=
H5OpenFile
(
fname
.
c_str
(),
H5_O_WRONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
file
=
H5OpenFile
(
fname
.
c_str
(),
H5_O_WRONLY
,
Ippl
::
getComm
());
// ParallelDescriptor::m_comm_all);
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
H5SetStep
(
file
,
0
);
...
...
@@ -252,4 +242,4 @@ void H5Reader::writeScalarField(const container_t& scalfield,
void
H5Reader
::
writeVectorField
(
const
container_t
&
vecfield
)
{
}
\ No newline at end of file
}
ippl/test/AMR/H5Reader.h
View file @
10bdd8ed
...
...
@@ -84,12 +84,7 @@ public:
private:
std
::
string
filename_m
;
///< Path and filename
#if defined (USE_H5HUT2)
h5_file_t
file_m
;
///< Opened file
#else
h5_file_t
*
file_m
;
#endif
};
#endif
\ No newline at end of file
#endif
ippl/test/AMR/boxlib-amr/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -11,7 +11,7 @@ message (STATUS "The MPI C++ compiler is: ${MPI_CXX_COMPILER}")
set
(
CMAKE_CXX_FLAGS
"-O3
${
CMAKE_CXX_FLAGS
}
-DBL_USE_FORTRAN_MPI"
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -D
USEH5FEDV2 -D
PARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -DPARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
)
include_directories
(
...
...
ippl/test/AMR/ippl-amr/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -13,7 +13,7 @@ set (CMAKE_CXX_FLAGS
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -D
USEH5FEDV2 -D
PARALLEL_IO -DIPPL_AMR
${
AMREX_DEFINES
}
${
CMAKE_CXX_FLAGS
}
"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -DPARALLEL_IO -DIPPL_AMR
${
AMREX_DEFINES
}
${
CMAKE_CXX_FLAGS
}
"
)
set
(
BOOSTROOT $ENV{BOOST_DIR}
)
...
...
ippl/test/AMR/ippl-bunch/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -13,7 +13,7 @@ set (CMAKE_CXX_FLAGS
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -D
USEH5FEDV2 -D
PARALLEL_IO -DIPPL_AMR
${
AMREX_DEFINES
}
${
CMAKE_CXX_FLAGS
}
"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -DPARALLEL_IO -DIPPL_AMR
${
AMREX_DEFINES
}
${
CMAKE_CXX_FLAGS
}
"
)
include_directories
(
...
...
ippl/test/particle/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -13,7 +13,7 @@ link_directories (
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -D
USEH5FEDV2 -D
PARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-std=c++11 -DPARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
)
SET
(
IPPL_LIBS ippl
)
...
...
ippl/test/particle/p3m3dHeating.cpp
View file @
10bdd8ed
...
...
@@ -473,17 +473,12 @@ public:
}
void
openH5
(
std
::
string
fn
){
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5_err_t
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
H5f_m
=
H5OpenFile
(
fn
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
H5f_m
!=
(
h5_file_t
)
H5_ERR
);
#else
H5f_m
=
H5OpenFile
(
fn
.
c_str
(),
H5_FLUSH_STEP
|
H5_O_WRONLY
,
Ippl
::
getComm
());
assert
(
H5f_m
!=
(
void
*
)
H5_ERR
);
#endif
}
...
...
@@ -537,11 +532,7 @@ public:
//TEMP debug variable
double
RhoSum
=
0
;
#if defined (USE_H5HUT2)
h5_file_t
H5f_m
;
#else
h5_file_t
*
H5f_m
;
#endif
double
temperature
[
Dim
];
double
avg_vel
[
Dim
];
...
...
src/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 2.8.10)
set
(
DKS_VERSION_OPAL \"
${
DKS_VERSION
}
\"
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-D
USEH5FEDV2 -D
PARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-DPARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
)
IF
(
ENABLE_SAAMG_SOLVER
)
...
...
@@ -164,4 +164,4 @@ install (FILES ${HDRS} DESTINATION "${CMAKE_INSTALL_PREFIX}/include/src")
# mode:cmake
# cmake-tab-width: 4
# indent-tabs-mode:nil
# End:
\ No newline at end of file
# End:
src/Classic/Fields/FM3DH5Block.cpp
View file @
10bdd8ed
...
...
@@ -25,17 +25,12 @@ FM3DH5Block::FM3DH5Block(std::string aFilename):Fieldmap(aFilename) {
Type
=
T3DDynamicH5Block
;
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
aFilename
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
aFilename
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
h5_int64_t
last_step
=
H5GetNumSteps
(
file
)
-
1
;
assert
(
last_step
>=
0
);
...
...
@@ -87,17 +82,12 @@ void FM3DH5Block::readMap() {
#if defined (NDEBUG)
(
void
)
h5err
;
#endif
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
Filename_m
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
Filename_m
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
long
field_size
=
0
;
int
Nnodes
=
Ippl
::
getNodes
();
...
...
src/Classic/Fields/FM3DH5Block_nonscale.cpp
View file @
10bdd8ed
...
...
@@ -25,17 +25,12 @@ FM3DH5Block_nonscale::FM3DH5Block_nonscale(std::string aFilename):
Type
=
T3DDynamicH5Block
;
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
aFilename
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
aFilename
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
h5_int64_t
last_step
=
H5GetNumSteps
(
file
)
-
1
;
assert
(
last_step
>=
0
);
...
...
@@ -91,17 +86,12 @@ void FM3DH5Block_nonscale::readMap() {
#if defined (NDEBUG)
(
void
)
h5err
;
#endif
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
Filename_m
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
Filename_m
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
long
field_size
=
0
;
int
Nnodes
=
Ippl
::
getNodes
();
//min(20, Ippl::getNodes());
...
...
src/Classic/Fields/FM3DMagnetoStaticH5Block.cpp
View file @
10bdd8ed
...
...
@@ -25,17 +25,12 @@ FM3DMagnetoStaticH5Block::FM3DMagnetoStaticH5Block(string aFilename):
Type
=
T3DMagnetoStaticH5Block
;
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
aFilename
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
aFilename
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
h5_int64_t
last_step
=
H5GetNumSteps
(
file
)
-
1
;
assert
(
last_step
>=
0
);
...
...
@@ -94,17 +89,12 @@ void FM3DMagnetoStaticH5Block::readMap() {
(
void
)
h5err
;
#endif
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
Filename_m
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
Filename_m
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
long
field_size
=
0
;
int
Nnodes
=
Ippl
::
getNodes
();
//min(20, Ippl::getNodes());
...
...
src/Classic/Fields/Fieldmap.cpp
View file @
10bdd8ed
...
...
@@ -360,17 +360,12 @@ MapType Fieldmap::readHeader(std::string Filename) {
#endif
char
name
[
20
];
h5_size_t
len_name
=
sizeof
(
name
);
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
h5_file_t
file
=
H5OpenFile
(
Filename
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
file
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
file
=
H5OpenFile
(
Filename
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
file
!=
(
void
*
)
H5_ERR
);
#endif
h5err
=
H5SetStep
(
file
,
0
);
assert
(
h5err
!=
H5_ERR
);
...
...
@@ -805,4 +800,4 @@ REGISTER_PARSE_TYPE(std::string);
std
::
string
Fieldmap
::
alpha_numeric
(
"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789.-+
\211
"
);
std
::
map
<
std
::
string
,
Fieldmap
::
FieldmapDescription
>
Fieldmap
::
FieldmapDictionary
=
std
::
map
<
std
::
string
,
Fieldmap
::
FieldmapDescription
>
();
char
Fieldmap
::
buffer_m
[
READ_BUFFER_LENGTH
];
\ No newline at end of file
char
Fieldmap
::
buffer_m
[
READ_BUFFER_LENGTH
];
src/Classic/Structure/LossDataSink.cpp
View file @
10bdd8ed
...
...
@@ -76,7 +76,6 @@ LossDataSink::~LossDataSink() {
}
void
LossDataSink
::
openH5
(
h5_int32_t
mode
)
{
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
...
...
@@ -86,14 +85,6 @@ void LossDataSink::openH5(h5_int32_t mode) {
throw
GeneralClassicException
(
"LossDataSink::openH5"
,
"failed to open h5 file '"
+
fn_m
+
"'"
);
}
#else
H5file_m
=
H5OpenFile
(
fn_m
.
c_str
(),
mode
,
Ippl
::
getComm
());
if
(
H5file_m
==
(
void
*
)
H5_ERR
)
{
throw
GeneralClassicException
(
"LossDataSink::openH5"
,
"failed to open h5 file '"
+
fn_m
+
"'"
);
}
#endif
}
void
LossDataSink
::
writeHeaderH5
()
{
...
...
src/Classic/Structure/LossDataSink.h
View file @
10bdd8ed
...
...
@@ -100,11 +100,7 @@ private:
bool
h5hut_mode_m
;
/// H5 file for particle data.
#if defined (USE_H5HUT2)
h5_file_t
H5file_m
;
#else
h5_file_t
*
H5file_m
;
#endif
/// Current record, or time step, of H5 file.
h5_int64_t
H5call_m
;
...
...
@@ -143,4 +139,4 @@ void LossDataSink::reportOnError(h5_int64_t rc, const char* file, int line) {
ERRORMSG
(
"H5 rc= "
<<
rc
<<
" in "
<<
file
<<
" @ line "
<<
line
<<
endl
);
}
#endif
\ No newline at end of file
#endif
src/Structure/BoundaryGeometry.cpp
View file @
10bdd8ed
...
...
@@ -1730,14 +1730,10 @@ Change orientation if diff is:
assert
(
rc
!=
H5_ERR
);
H5SetVerbosityLevel
(
1
);
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
h5_file_t
f
=
H5OpenFile
(
h5FileName_m
.
c_str
(),
H5_O_RDONLY
,
props
);
#else
h5_file_t
*
f
=
H5OpenFile
(
h5FileName_m
.
c_str
(),
H5_O_RDONLY
,
Ippl
::
getComm
());
#endif
h5t_mesh_t
*
m
=
NULL
;
H5FedOpenTriangleMesh
(
f
,
"0"
,
&
m
);
...
...
@@ -2602,4 +2598,4 @@ void BoundaryGeometry::createPriPart (
// mode:c
// c-basic-offset: 4
// indent-tabs-mode:nil
// End:
\ No newline at end of file
// End:
src/Structure/DataSink.cpp
View file @
10bdd8ed
...
...
@@ -1003,7 +1003,6 @@ void DataSink::writeSurfaceInteraction(PartBunchBase<double, 3> *beam, long long
if
(
firstWriteH5Surface_m
)
{
firstWriteH5Surface_m
=
false
;
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
...
...
@@ -1012,13 +1011,6 @@ void DataSink::writeSurfaceInteraction(PartBunchBase<double, 3> *beam, long long
throw
OpalException
(
"DataSink::writeSurfaceInteraction"
,
"failed to open h5 file '"
+
surfaceLossFileName_m
+
"' for surface loss"
);
}
#else
H5fileS_m
=
H5OpenFile
(
surfaceLossFileName_m
.
c_str
(),
H5_FLUSH_STEP
|
H5_O_WRONLY
,
Ippl
::
getComm
());
if
(
H5fileS_m
==
(
void
*
)
H5_ERR
)
{
throw
OpalException
(
"DataSink::writeSurfaceInteraction"
,
"failed to open h5 file '"
+
surfaceLossFileName_m
+
"' for surface loss"
);
}
#endif
}
int
nTot
=
bg
.
getNumBFaces
();
...
...
@@ -1520,4 +1512,4 @@ void DataSink::writeMemoryData(PartBunchBase<double, 3> *beam,
/***************************************************************************
* $RCSfile: DataSink.cpp,v $ $Author: adelmann $
* $Revision: 1.3 $ $Date: 2004/06/02 19:38:54 $
***************************************************************************/
\ No newline at end of file
***************************************************************************/
src/Structure/DataSink.h
View file @
10bdd8ed
...
...
@@ -264,11 +264,7 @@ private:
std
::
string
surfaceLossFileName_m
;
/// H5 file for surface loss data.
#if defined (USE_H5HUT2)
h5_file_t
H5fileS_m
;
#else
h5_file_t
*
H5fileS_m
;
#endif
/// Current record, or time step, of H5 file.
int
H5call_m
;
...
...
@@ -332,4 +328,4 @@ std::string DataSink::convertToString(int number) {
/***************************************************************************
* $RCSfile: DataSink.h,v $ $Author: adelmann $
* $Revision: 1.1.1.1 $ $Date: 2003/01/23 13:29:44 $
***************************************************************************/
\ No newline at end of file
***************************************************************************/
src/Structure/H5PartWrapper.cpp
View file @
10bdd8ed
...
...
@@ -16,19 +16,11 @@
extern
Inform
*
gmsg
;
namespace
{
#if defined (USE_H5HUT2)
const
h5_int64_t
H5TypesCHAR
=
H5_STRING_T
;
const
h5_int64_t
H5TypesFLOAT
=
H5_FLOAT32_T
;
const
h5_int64_t
H5TypesDOUBLE
=
H5_FLOAT64_T
;
const
h5_int64_t
H5TypesINT32
=
H5_INT32_T
;
const
h5_int64_t
H5TypesINT64
=
H5_INT64_T
;
#else
const
h5_int64_t
H5TypesCHAR
=
H5T_NATIVE_CHAR
;
const
h5_int64_t
H5TypesFLOAT
=
H5T_NATIVE_FLOAT
;
const
h5_int64_t
H5TypesDOUBLE
=
H5T_NATIVE_DOUBLE
;
const
h5_int64_t
H5TypesINT32
=
H5T_NATIVE_INT32
;
const
h5_int64_t
H5TypesINT64
=
H5T_NATIVE_INT64
;
#endif
}
std
::
string
H5PartWrapper
::
copyFilePrefix_m
=
".copy"
;
...
...
@@ -76,7 +68,6 @@ void H5PartWrapper::close() {
void
H5PartWrapper
::
open
(
h5_int32_t
flags
)
{
close
();
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5_err_t
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
...
...
@@ -86,12 +77,6 @@ void H5PartWrapper::open(h5_int32_t flags) {
assert
(
h5err
!=
H5_ERR
);
file_m
=
H5OpenFile
(
fileName_m
.
c_str
(),
flags
,
props
);
assert
(
file_m
!=
(
h5_file_t
)
H5_ERR
);
#else
file_m
=
H5OpenFile
(
fileName_m
.
c_str
(),
H5_FLUSH_STEP
|
flags
,
Ippl
::
getComm
());
assert
(
file_m
!=
(
void
*
)
H5_ERR
);
#endif
}
void
H5PartWrapper
::
storeCavityInformation
()
{
...
...
@@ -99,18 +84,10 @@ void H5PartWrapper::storeCavityInformation() {
h5_int64_t
nAutopPhaseCavities
=
OpalData
::
getInstance
()
->
getNumberOfMaxPhases
();
h5_int64_t
nFormerlySavedAutoPhaseCavities
=
0
;
#ifdef USE_H5HUT2
if
(
!
H5HasFileAttrib
(
file_m
,
"nAutoPhaseCavities"
)
||
H5ReadFileAttribInt64
(
file_m
,
"nAutoPhaseCavities"
,
&
nFormerlySavedAutoPhaseCavities
)
!=
H5_SUCCESS
)
{
nFormerlySavedAutoPhaseCavities
=
0
;
}
#else
H5SetErrorHandler
(
H5ReportErrorhandler
);
if
(
H5ReadFileAttribInt64
(
file_m
,
"nAutoPhaseCavities"
,
&
nFormerlySavedAutoPhaseCavities
)
!=
H5_SUCCESS
)
{
nFormerlySavedAutoPhaseCavities
=
0
;
}
H5SetErrorHandler
(
H5AbortErrorhandler
);
#endif
if
(
nFormerlySavedAutoPhaseCavities
==
nAutopPhaseCavities
)
return
;
WRITEFILEATTRIB
(
Int64
,
file_m
,
"nAutoPhaseCavities"
,
&
nAutopPhaseCavities
,
1
);
...
...
@@ -145,7 +122,6 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
}
if
(
sourceFile
==
fileName_m
)
{
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5_err_t
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
...
...
@@ -155,10 +131,6 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
assert
(
h5err
!=
H5_ERR
);
h5_file_t
source
=
H5OpenFile
(
sourceFile
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
source
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
source
=
H5OpenFile
(
sourceFile
.
c_str
(),
H5_FLUSH_STEP
|
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
source
!=
(
void
*
)
H5_ERR
);
#endif
h5_ssize_t
numStepsInSource
=
H5GetNumSteps
(
source
);
if
(
lastStep
==
-
1
||
lastStep
>=
numStepsInSource
)
{
...
...
@@ -186,17 +158,12 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
Ippl
::
Comm
->
barrier
();
open
(
flags
);
#if defined (USE_H5HUT2)
props
=
H5CreateFileProp
();
comm
=
Ippl
::
getComm
();
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
assert
(
h5err
!=
H5_ERR
);
source
=
H5OpenFile
(
sourceFileName
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
source
!=
(
h5_file_t
)
H5_ERR
);
#else
source
=
H5OpenFile
(
sourceFileName
.
c_str
(),
H5_FLUSH_STEP
|
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
source
!=
(
void
*
)
H5_ERR
);
#endif
copyHeader
(
source
);
if
(
lastStep
<
0
)
{
...
...
@@ -222,7 +189,6 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
open
(
flags
);
#if defined (USE_H5HUT2)
h5_prop_t
props
=
H5CreateFileProp
();
MPI_Comm
comm
=
Ippl
::
getComm
();
h5_err_t
h5err
=
H5SetPropFileMPIOCollective
(
props
,
&
comm
);
...
...
@@ -232,10 +198,6 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
assert
(
h5err
!=
H5_ERR
);
h5_file_t
source
=
H5OpenFile
(
sourceFile
.
c_str
(),
H5_O_RDONLY
,
props
);
assert
(
source
!=
(
h5_file_t
)
H5_ERR
);
#else
h5_file_t
*
source
=
H5OpenFile
(
sourceFile
.
c_str
(),
H5_FLUSH_STEP
|
H5_O_RDONLY
,
Ippl
::
getComm
());
assert
(
source
!=
(
void
*
)
H5_ERR
);
#endif
h5_ssize_t
numStepsInSource
=
H5GetNumSteps
(
source
);
if
(
lastStep
==
-
1
||
lastStep
>=
numStepsInSource
)
{
...
...
@@ -311,11 +273,7 @@ void H5PartWrapper::copyFileSystem(const std::string &sourceFile) {
}
void
H5PartWrapper
::
copyHeader
(
#if defined (USE_H5HUT2)
h5_file_t
source
#else
h5_file_t
*
source
#endif
)
{
h5_int64_t
numFileAttributes
=
H5GetNumFileAttribs
(
source
);
...
...
@@ -385,11 +343,7 @@ void H5PartWrapper::copyHeader(
}
void
H5PartWrapper
::
copyStep
(
#if defined (USE_H5HUT2)
h5_file_t
source
,
#else
h5_file_t
*
source
,
#endif
int
step
)
{
REPORTONERROR
(
H5SetStep
(
file_m
,
numSteps_m
));
...
...
@@ -400,11 +354,7 @@ void H5PartWrapper::copyStep(
}
void
H5PartWrapper
::
copyStepHeader
(
#if defined (USE_H5HUT2)
h5_file_t
source
#else
h5_file_t
*
source
#endif
)
{
h5_int64_t
numStepAttributes
=
H5GetNumStepAttribs
(
source
);
...
...
@@ -478,11 +428,7 @@ void H5PartWrapper::copyStepHeader(
}
void
H5PartWrapper
::
copyStepData
(
#if defined (USE_H5HUT2)
h5_file_t
source
#else
h5_file_t
*
source
#endif
)
{
h5_size_t
lengthSetName
=
256
;
char
setName
[
lengthSetName
];
...
...
@@ -576,4 +522,4 @@ size_t H5PartWrapper::getNumParticles() const {
// mode:c++
// c-basic-offset: 4
// indent-tabs-mode:nil
// End:
\ No newline at end of file
// End:
src/Structure/H5PartWrapper.h
View file @
10bdd8ed
...
...
@@ -53,17 +53,10 @@ protected:
void
copyFile
(
const
std
::
string
&
sourceFile
,
int
lastStep
=
-
1
,
h5_int32_t
flags
=
H5_O_WRONLY
);
void
copyFileSystem
(
const
std
::
string
&
sourceFile
);
#if defined (USE_H5HUT2)
void
copyHeader
(
h5_file_t
source
);
void
copyStep
(
h5_file_t
source
,
int
step
);
void
copyStepHeader
(
h5_file_t
source
);
void
copyStepData
(
h5_file_t
source
);
#else
void
copyHeader
(
h5_file_t
*
source
);
void
copyStep
(
h5_file_t
*
source
,
int
step
);
void
copyStepHeader
(
h5_file_t
*
source
);
void
copyStepData
(
h5_file_t
*
source
);
#endif
void
sendFailureMessage
(
bool
failed
,
const
std
::
string
&
where
,
const
std
::
string
&
what
);
...
...
@@ -73,11 +66,7 @@ protected:
static
void
reportOnError
(
h5_int64_t
rc
,
const
char
*
file
,
int
line
);
#if defined (USE_H5HUT2)
h5_file_t
file_m
;
#else
h5_file_t
*
file_m
;
#endif
std
::
string
fileName_m
;
std
::
string
predecessorOPALFlavour_m
;
h5_int64_t
numSteps_m
;
...
...
src/Structure/H5PartWrapperForPS.cpp
View file @
10bdd8ed
...
...
@@ -70,20 +70,10 @@ void H5PartWrapperForPS::readHeader() {
auto
opal
=
OpalData
::
getInstance
();
h5_float64_t
phase
;
h5_int64_t
numAutoPhaseCavities
;
#ifdef USE_H5HUT2
if
(
!
H5HasFileAttrib
(
file_m
,
"nAutoPhaseCavities"
)
||
H5ReadFileAttribInt64
(
file_m
,
"nAutoPhaseCavities"
,
&
numAutoPhaseCavities
)
!=
H5_SUCCESS
)
{
numAutoPhaseCavities
=
0
;
}
#else
H5SetErrorHandler
(
H5ReportErrorhandler
);
h5_int64_t
rc
=
H5ReadFileAttribInt64
(
file_m
,
"nAutoPhaseCavities"
,
&
numAutoPhaseCavities
);
H5SetErrorHandler
(
H5AbortErrorhandler
);
if
(
rc
!=
H5_SUCCESS
)
{
numAutoPhaseCavities
=
0
;
}
#endif
else
{
}
else
{
for
(
long
i
=
0
;
i
<
numAutoPhaseCavities
;
++
i
)
{
std
::
string
elementName
=
"Cav-"
+
std
::
to_string
(
i
+
1
)
+
"-name"
;
std
::
string
elementPhase
=
"Cav-"
+
std
::
to_string
(
i
+
1
)
+
"-value"
;
...
...
src/Structure/H5PartWrapperForPT.cpp
View file @
10bdd8ed
...
...
@@ -69,20 +69,10 @@ void H5PartWrapperForPT::readHeader() {
auto
opal
=
OpalData
::
getInstance
();
h5_float64_t
phase
;
h5_int64_t
numAutoPhaseCavities
=
0
;
#ifdef USE_H5HUT2
if
(
!
H5HasFileAttrib
(
file_m
,
"nAutoPhaseCavities"
)
||
H5ReadFileAttribInt64
(
file_m
,
"nAutoPhaseCavities"
,
&
numAutoPhaseCavities
)
!=
H5_SUCCESS
)
{
numAutoPhaseCavities
=
0
;
}
#else
H5SetErrorHandler
(
H5ReportErrorhandler
);
h5_int64_t
rc
=
H5ReadFileAttribInt64
(
file_m
,
"nAutoPhaseCavities"
,
&
numAutoPhaseCavities
);
H5SetErrorHandler
(
H5AbortErrorhandler
);
if
(
rc
!=
H5_SUCCESS
)
{
numAutoPhaseCavities
=
0
;
}
#endif
else
{
}
else
{
for
(
long
i
=
0
;
i
<
numAutoPhaseCavities
;
++
i
)
{
std
::
string
elementName
=
"Cav-"
+
std
::
to_string
(
i
+
1
)
+
"-name"
;
std
::
string
elementPhase
=
"Cav-"
+
std
::
to_string
(
i
+
1
)
+
"-value"
;
...
...
tests/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -5,7 +5,7 @@ set (TEST_EXE opal_unit_tests)
set
(
SRC_DIRS classic_src opal_src
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-D
USEH5FEDV2 -D
PARALLEL_IO
${
CMAKE_CXX_FLAGS
}
-DWITH_UNIT_TESTS"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-DPARALLEL_IO
${
CMAKE_CXX_FLAGS
}
-DWITH_UNIT_TESTS"
)
set
(
TEST_SRC_DIR
${
CMAKE_CURRENT_SOURCE_DIR
}
)
...
...
tools/opal2sdds/CMakeLists.txt
View file @
10bdd8ed
...
...
@@ -6,7 +6,7 @@ SET (OPAL2SDDS_VERSION_MINOR 1)
configure_file
(
config.h.in
${
CMAKE_CURRENT_SOURCE_DIR
}
/config.h
)
set
(
CMAKE_CXX_FLAGS
"
${
IPPL_CMAKE_CXX_FLAGS
}
-D
USEH5FEDV2 -D
PARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
"
${
IPPL_CMAKE_CXX_FLAGS
}
-DPARALLEL_IO
${
CMAKE_CXX_FLAGS
}
"
)
INCLUDE_DIRECTORIES
(
...
...
@@ -34,4 +34,4 @@ SET (SDDS_LIBS
ADD_EXECUTABLE
(
opal2sdds main.cpp
)
TARGET_LINK_LIBRARIES
(
opal2sdds
${
SDDS_LIBS
}
)
INSTALL
(
TARGETS opal2sdds RUNTIME DESTINATION
"
${
CMAKE_INSTALL_PREFIX
}
/bin"
)
\ No newline at end of file
INSTALL
(
TARGETS opal2sdds RUNTIME DESTINATION
"
${
CMAKE_INSTALL_PREFIX
}
/bin"
)
tools/opal2sdds/main.cpp
View file @
10bdd8ed
...
...
@@ -35,11 +35,7 @@ enum FORMAT {
ASCII
=
SDDS_ASCII
};