diff --git a/CMakeLists.txt b/CMakeLists.txt
index 874ef37fbc5ff05792703b722f2e87bd76922c3a..bbf244496dd5c2b5cba43cd19fc2f001e3e9872f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,6 +38,11 @@ endif()
# Top level options
#------------------------------------------------------------------------------#
+# Default to a debug build if not specified
+if(NOT CMAKE_BUILD_TYPE)
+ set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "Choose the type of build." FORCE)
+endif()
+
# Force C++11
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)
@@ -61,6 +66,10 @@ if(ADIOS_ENABLE_PIC)
endif()
option(ADIOS_USE_MPI "Enable the MPI version of ADIOS" ON)
+if(ADIOS_USE_MPI)
+ # Workaround for OpenMPI forcing th elink of C++ bindings
+ add_definitions(-DOMPI_SKIP_MPICXX)
+endif()
option(ADIOS_USE_BZip2 "Enable support for BZip2 transforms" ON)
option(ADIOS_USE_ADIOS1 "Enable support for the ADIOS 1 engine" OFF)
option(ADIOS_USE_DataMan "Enable support for the DataMan engine" OFF)
@@ -68,8 +77,9 @@ option(ADIOS_USE_DataMan "Enable support for the DataMan engine" OFF)
#------------------------------------------------------------------------------#
# Third party libraries
#------------------------------------------------------------------------------#
-option(ADIOS_BUILD_TESTING "Build ADIOS tests" OFF)
-set(BUILD_TESTING ${ADIOS_BUILD_TESTING} CACHE INTERNAL "")
+option(ADIOS_BUILD_TESTING "Build ADIOS tests" ON)
+set(BUILD_TESTING ${ADIOS_BUILD_TESTING})
+mark_as_advanced(BUILD_TESTING)
include(CTest)
add_subdirectory(thirdparty)
@@ -113,10 +123,11 @@ message("")
message(" Installation prefix: ${CMAKE_INSTALL_PREFIX}")
message(" Features:")
if(BUILD_SHARED_LIBS)
- message(" Type: shared")
+ message(" Library Type: shared")
else()
- message(" Type: static")
+ message(" Library Type: static")
endif()
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
message(" Testing: ${BUILD_TESTING}")
message(" MPI: ${ADIOS_USE_MPI}")
message(" BZip2: ${ADIOS_USE_BZip2}")
diff --git a/examples/hello/bpWriter/CMakeLists.txt b/examples/hello/bpWriter/CMakeLists.txt
index 3518b42787191b823fce4f840f9275693867b8f3..67e193342b05fe0c7d99881038a69e5233706fda 100644
--- a/examples/hello/bpWriter/CMakeLists.txt
+++ b/examples/hello/bpWriter/CMakeLists.txt
@@ -8,7 +8,16 @@ if(ADIOS_USE_MPI)
add_executable(hello_bpWriter helloBPWriter.cpp)
target_include_directories(hello_bpWriter PRIVATE ${MPI_C_INCLUDE_PATH})
target_link_libraries(hello_bpWriter adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::bpWriter COMMAND hello_bpWriter)
+ endif()
+else()
+ add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
+ target_link_libraries(hello_bpWriter_nompi adios2)
+
+ if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::bpWriter_nompi COMMAND hello_bpWriter_nompi)
+ endif()
endif()
-add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
-target_link_libraries(hello_bpWriter_nompi adios2)
diff --git a/examples/hello/bpWriter/helloBPWriter.cpp b/examples/hello/bpWriter/helloBPWriter.cpp
index 1be2cececb66a16a6c09d2b5b050bc019f53fe05..abc680ffdcfb93be169f51dc41570122713c2458 100644
--- a/examples/hello/bpWriter/helloBPWriter.cpp
+++ b/examples/hello/bpWriter/helloBPWriter.cpp
@@ -11,9 +11,7 @@
#include <iostream>
#include <vector>
-#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
-#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
diff --git a/examples/hello/bpWriter/helloBPWriter_nompi.cpp b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
index edb09e086fd8a8d9b20c8b3a04ea51070e5135d8..3936d3eab4aa6f06db4188809cc7a32e0a6d6263 100644
--- a/examples/hello/bpWriter/helloBPWriter_nompi.cpp
+++ b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
@@ -8,12 +8,14 @@
* Author: wfg
*/
+#include <ios>
#include <iostream>
+#include <stdexcept>
#include <vector>
#include "ADIOS_CPP.h"
-int main(int argc, char *argv[])
+int main(int /*argc*/, char ** /*argv*/)
{
const bool adiosDebug = true;
adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
@@ -55,7 +57,9 @@ int main(int argc, char *argv[])
adios::IOMode::COLLECTIVE);
if (bpFileWriter == nullptr)
+ {
throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
+ }
bpFileWriter->Write<double>(
ioMyDoubles, myDoubles.data()); // Base class Engine own the Write<T>
diff --git a/examples/hello/datamanReader/CMakeLists.txt b/examples/hello/datamanReader/CMakeLists.txt
index f32a2283869203b1157cdb67dc540fe19b7ef90d..3aa3e264ad829cf697e9cd91a6336d6fcf8b668d 100644
--- a/examples/hello/datamanReader/CMakeLists.txt
+++ b/examples/hello/datamanReader/CMakeLists.txt
@@ -3,8 +3,26 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_datamanReader helloDataManReader.cpp)
-target_link_libraries(hello_datamanReader adios2)
+if(ADIOS_USE_MPI)
+ find_package(MPI COMPONENTS C REQUIRED)
-add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
-target_link_libraries(hello_datamanReader_nompi adios2)
+ add_executable(hello_datamanReader helloDataManReader.cpp)
+ target_link_libraries(hello_datamanReader adios2)
+ target_include_directories(hello_datamanReader PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_datamanReader adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::datamanReader COMMAND hello_datamanReader)
+ endif()
+else()
+ add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
+ target_link_libraries(hello_datamanReader_nompi adios2)
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::datamanReader_nompi
+ COMMAND hello_datamanReader_nompi
+ )
+ endif()
+endif()
+
diff --git a/examples/hello/datamanWriter/CMakeLists.txt b/examples/hello/datamanWriter/CMakeLists.txt
index dee5f38e1823c4a55f22d53954d09c440e1c6ff4..7defd6c40b3bd2eba1802a4e6e99dd41f5de1697 100644
--- a/examples/hello/datamanWriter/CMakeLists.txt
+++ b/examples/hello/datamanWriter/CMakeLists.txt
@@ -3,8 +3,26 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_datamanWriter helloDataManWriter.cpp)
-target_link_libraries(hello_datamanWriter adios2)
+if(ADIOS_USE_MPI)
+ find_package(MPI COMPONENTS C REQUIRED)
+
+ add_executable(hello_datamanWriter helloDataManWriter.cpp)
+ target_link_libraries(hello_datamanWriter adios2)
+ target_include_directories(hello_datamanWriter PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_datamanWriter adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::datamanWriter COMMAND hello_datamanWriter)
+ endif()
+else()
+ add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
+ target_link_libraries(hello_datamanWriter_nompi adios2)
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::datamanWriter_nompi
+ COMMAND hello_datamanWriter_nompi
+ )
+ endif()
+endif()
-add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
-target_link_libraries(hello_datamanWriter_nompi adios2)
diff --git a/examples/hello/timeBP/CMakeLists.txt b/examples/hello/timeBP/CMakeLists.txt
index a0e38282532c2bf6cd2c2c726a809e2dd2ea2cac..d86828c90625a3a4e34952730fcd6ed9631c2949 100644
--- a/examples/hello/timeBP/CMakeLists.txt
+++ b/examples/hello/timeBP/CMakeLists.txt
@@ -9,8 +9,18 @@ if(ADIOS_USE_MPI)
target_link_libraries(hello_timeBPWriter adios2)
target_include_directories(hello_timeBPWriter PRIVATE ${MPI_C_INCLUDE_PATH})
target_link_libraries(hello_timeBPWriter adios2 ${MPI_C_LIBRARIES})
-endif()
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::timeBPWriter COMMAND hello_timeBPWriter)
+ endif()
+else()
+ add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
+ target_link_libraries(hello_timeBPWriter_nompi adios2)
-add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
-target_link_libraries(hello_timeBPWriter_nompi adios2)
+ if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::timeBPWriter_nompi
+ COMMAND hello_timeBPWriter_nompi
+ )
+ endif()
+endif()
diff --git a/examples/hello/timeBP/timeBPWriter.cpp b/examples/hello/timeBP/timeBPWriter.cpp
index 846151357b20798aa26070aa8e6044267558bb30..280e97e1e7eb08761a1b7ce5f0eba11bb4ed66e6 100644
--- a/examples/hello/timeBP/timeBPWriter.cpp
+++ b/examples/hello/timeBP/timeBPWriter.cpp
@@ -11,9 +11,7 @@
#include <iostream>
#include <vector>
-#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
-#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
diff --git a/examples/hello/timeBP/timeBPWriter_nompi.cpp b/examples/hello/timeBP/timeBPWriter_nompi.cpp
index dc4135216764e46c753656f5cac4a3f4a1fdc4d9..48fdd2bbf3111f3c36b550c927d03b475893bf4e 100644
--- a/examples/hello/timeBP/timeBPWriter_nompi.cpp
+++ b/examples/hello/timeBP/timeBPWriter_nompi.cpp
@@ -13,7 +13,7 @@
#include "ADIOS_CPP.h"
-int main(int argc, char *argv[])
+int main(int /*argc*/, char ** /*argv*/)
{
const bool adiosDebug = true;
adios::ADIOS adios(adios::Verbose::ERROR, adiosDebug);
diff --git a/include/core/Method.h b/include/core/Method.h
index 686391f96e01de5dae3cae4d2e7de29e91ce3802..f213022eb7ee26dab41c5ac9bad4e548dd77a4f0 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -58,9 +58,9 @@ public:
* @param name is a label that can be used in the config file to set up the
* method at runtime
*/
- Method(const std::string name, const bool debugMode = false);
+ Method(std::string name, bool debugMode = false);
- ~Method();
+ ~Method() = default;
/** Check if the method was defined by the user in the config file.
* @return true if the method was user-defined, false otherwise when method is
@@ -135,6 +135,6 @@ private:
const std::vector<std::string> ¶meters);
};
-} // end namespace
+} // end namespace adios
#endif /* METHOD_H_ */
diff --git a/include/core/Support.h b/include/core/Support.h
index 481f8fb4185ec57f73c60369a1fc8a019152d1af..bb9b451e842f07afbe38d9d3b36da864594e0c65 100644
--- a/include/core/Support.h
+++ b/include/core/Support.h
@@ -51,6 +51,6 @@ struct Support
};
};
-} // end namespace
+} // end namespace adios
#endif /* SUPPORT_H_ */
diff --git a/include/core/Transform.h b/include/core/Transform.h
index 190541dac62c8c84f93abf05eb20d9a6e65194fd..a6a6dc75ab80f232f8f08e724837d6b83655b7e2 100644
--- a/include/core/Transform.h
+++ b/include/core/Transform.h
@@ -33,9 +33,9 @@ public:
* Initialize parent method
* @param method zlib, bzip2, szip
*/
- Transform(const std::string method);
+ Transform(std::string method);
- virtual ~Transform();
+ virtual ~Transform() = default;
virtual void Compress(const std::vector<char> &bufferIn,
std::vector<char> &bufferOut);
@@ -44,5 +44,5 @@ public:
std::vector<char> &bufferOut);
};
-} // end namespace
+} // end namespace adios
#endif /* TRANSFORM_H_ */
diff --git a/include/core/Transport.h b/include/core/Transport.h
index 8b768825a2a5a28688540a5ed581de4d58b21783..0851a9b745462907db42bfd843fa224fd2471c4a 100644
--- a/include/core/Transport.h
+++ b/include/core/Transport.h
@@ -44,9 +44,9 @@ public:
* @param mpiComm passed to m_MPIComm
* @param debugMode passed to m_DebugMode
*/
- Transport(const std::string type, MPI_Comm mpiComm, const bool debugMode);
+ Transport(std::string type, MPI_Comm mpiComm, bool debugMode);
- virtual ~Transport(); ///< empty destructor, using STL for memory management
+ virtual ~Transport() = default;
/**
* Open Output file accesing a mode
@@ -82,6 +82,6 @@ protected:
const bool m_DebugMode = false; ///< if true: additional checks and exceptions
};
-} // end namespace
+} // end namespace adios
#endif /* TRANSPORT_H_ */
diff --git a/include/engine/bp/BPFileReader.h b/include/engine/bp/BPFileReader.h
index 3613ef2833a3e50d86fa6653f0e86105ae7de874..4f4c451532db4769ed6f296e7b342b93cf36c857 100644
--- a/include/engine/bp/BPFileReader.h
+++ b/include/engine/bp/BPFileReader.h
@@ -35,13 +35,12 @@ public:
* @param debugMode
* @param hostLanguage
*/
- BPFileReader(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode = false,
- const unsigned int nthreads = 1);
+ BPFileReader(ADIOS &adios, std::string name, std::string accessMode,
+ MPI_Comm mpiComm, const Method &method, IOMode iomode,
+ float timeout_sec, bool debugMode = false,
+ unsigned int nthreads = 1);
- ~BPFileReader();
+ virtual ~BPFileReader() = default;
Variable<void> *InquireVariable(const std::string name,
const bool readIn = true);
diff --git a/include/mpidummy.h b/include/mpidummy.h
index 65b380f5cd4a229e87ddffad8bb24c806bf452a6..86122ede8af34481a719166a9df32f9cddacd835 100644
--- a/include/mpidummy.h
+++ b/include/mpidummy.h
@@ -73,34 +73,35 @@ int MPI_Comm_size(MPI_Comm comm, int *size);
int MPI_Comm_free(MPI_Comm *comm);
MPI_Comm MPI_Comm_f2c(MPI_Fint comm);
-int MPI_Gather(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf,
- int recvcnt, MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Gatherv(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
- void *recvbuf, int *recvcnts, int *displs,
+int MPI_Gather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, int recvcount, MPI_Datatype recvtype, int root,
+ MPI_Comm comm);
+int MPI_Gatherv(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, const int *recvcounts, const int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
+int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
MPI_Comm comm);
-int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
- void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
+int MPI_Scatter(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, int recvcount, MPI_Datatype recvtype, int root,
MPI_Comm comm);
-int MPI_Scatterv(void *sendbuf, int *sendcnts, int *displs,
- MPI_Datatype sendtype, void *recvbuf, int recvcnt,
+int MPI_Scatterv(const void *sendbuf, const int *sendcounts, const int *displs,
+ MPI_Datatype sendtype, void *recvbuf, int recvcount,
MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Recv(void *recvbuffer, int count, MPI_Datatype type, int source,
- int tag, MPI_Comm comm, MPI_Status *status);
-int MPI_Irecv(void *recvbuffer, int count, MPI_Datatype type, int source,
- int tag, MPI_Comm comm, MPI_Request *request);
-int MPI_Send(void *sendbuffer, int count, MPI_Datatype type, int destination,
+int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
+ MPI_Comm comm, MPI_Status *status);
+int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
+ MPI_Comm comm, MPI_Request *request);
+int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int dest,
int tag, MPI_Comm comm);
-int MPI_Isend(void *recvbuffer, int count, MPI_Datatype type, int source,
+int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int dest,
int tag, MPI_Comm comm, MPI_Request *request);
int MPI_Wait(MPI_Request *request, MPI_Status *status);
-int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info,
+int MPI_File_open(MPI_Comm comm, const char *filename, int amode, MPI_Info info,
MPI_File *fh);
int MPI_File_close(MPI_File *fh);
int MPI_File_get_size(MPI_File fh, MPI_Offset *size);
@@ -108,7 +109,7 @@ int MPI_File_read(MPI_File fh, void *buf, int count, MPI_Datatype datatype,
MPI_Status *status);
int MPI_File_seek(MPI_File fh, MPI_Offset offset, int whence);
-int MPI_Get_count(MPI_Status *status, MPI_Datatype datatype, int *count);
+int MPI_Get_count(const MPI_Status *status, MPI_Datatype datatype, int *count);
int MPI_Error_string(int errorcode, char *string, int *resultlen);
int MPI_Comm_split(MPI_Comm comm, int color, int key, MPI_Comm *comm_out);
diff --git a/include/transport/file/FStream.h b/include/transport/file/FStream.h
index 163b96478e23334fcf2fc0ab8afe1b824789d9f2..8553c35981ebdb87048631033f293404f3774f88 100644
--- a/include/transport/file/FStream.h
+++ b/include/transport/file/FStream.h
@@ -31,7 +31,7 @@ class FStream : public Transport
public:
FStream(MPI_Comm mpiComm, const bool debugMode);
- ~FStream();
+ virtual ~FStream() = default;
void Open(const std::string name, const std::string accessMode);
@@ -48,6 +48,6 @@ private:
};
} // end namespace transport
-} // end namespace
+} // end namespace adios
#endif /* FSTREAM_H_ */
diff --git a/source/ADIOS.cpp b/source/ADIOS.cpp
index a517acd273f08d25b7b40a0fa9eee56913e5c987..d752a127d699ea3726e0db798976356f1eff62e6 100644
--- a/source/ADIOS.cpp
+++ b/source/ADIOS.cpp
@@ -10,12 +10,14 @@
/// \cond EXCLUDE_FROM_DOXYGEN
#include <fstream>
+#include <ios> //std::ios_base::failure
#include <iostream>
#include <sstream>
#include <utility>
/// \endcond
#include "ADIOS.h"
+
#include "functions/adiosFunctions.h"
// Engines
diff --git a/source/core/Engine.cpp b/source/core/Engine.cpp
index 4f2cb8a44bd1b01054bdb357193cf31c861f1c36..971c29df864270332439466237d7da307315b7d9 100644
--- a/source/core/Engine.cpp
+++ b/source/core/Engine.cpp
@@ -8,6 +8,8 @@
* Author: wfg
*/
+#include <ios> //std::ios_base::failure
+
#include "core/Engine.h"
#include "core/Support.h"
#include "functions/adiosFunctions.h"
diff --git a/source/core/Method.cpp b/source/core/Method.cpp
index a97f101fc86f334a5c94bee6d8cdd07d133a4f1c..905b04f9e4c50d6b172c20cfaee909be7309dcb9 100644
--- a/source/core/Method.cpp
+++ b/source/core/Method.cpp
@@ -8,24 +8,24 @@
* Author: wfg
*/
+#include <utility>
+
#include "core/Method.h"
#include "functions/adiosFunctions.h"
namespace adios
{
-Method::Method(const std::string name, const bool debugMode)
-: m_Name{name}, m_DebugMode{debugMode}
+Method::Method(std::string name, bool debugMode)
+: m_Name{std::move(name)}, m_DebugMode{debugMode}
{
// m_Type can stay empty (forcing the choice of the default engine)
m_nThreads = 1;
}
-Method::~Method() {}
-
bool Method::isUserDefined()
{
- return false; // TODO: check if XML has the method defined
+ return false; // TODO(wfg): check if XML has the method defined
}
void Method::SetEngine(const std::string type) { m_Type = type; }
@@ -33,9 +33,13 @@ void Method::SetEngine(const std::string type) { m_Type = type; }
void Method::AllowThreads(const int nThreads)
{
if (nThreads > 1)
+ {
m_nThreads = nThreads;
+ }
else
+ {
m_nThreads = 1;
+ }
}
// PRIVATE Functions
@@ -45,8 +49,10 @@ void Method::AddTransportParameters(const std::string type,
if (m_DebugMode == true)
{
if (type.empty() || type.find("=") != type.npos)
+ {
throw std::invalid_argument("ERROR: first argument in AddTransport must "
"be a single word for transport\n");
+ }
}
std::map<std::string, std::string> mapParameters =
@@ -54,13 +60,15 @@ void Method::AddTransportParameters(const std::string type,
if (m_DebugMode == true)
{
if (mapParameters.count("transport") == 1)
+ {
std::invalid_argument(
"ERROR: transport can't be redefined with \"transport=type\", "
"type must be the first argument\n");
+ }
}
mapParameters["transport"] = type;
m_TransportParameters.push_back(mapParameters);
}
-} // end namespace
+} // end namespace adios
diff --git a/source/core/Support.cpp b/source/core/Support.cpp
index 02be66d86108af579eeafd5805adad1e5a1537b4..65cac135af7ca6a6b428ba5fb5c3a15aedbf7324 100644
--- a/source/core/Support.cpp
+++ b/source/core/Support.cpp
@@ -19,10 +19,9 @@ const std::string Support::Version{"2.00"};
const std::set<std::string> Support::HostLanguages{{"C++", "C", "Fortran"}};
const std::set<std::string> Support::Transports{
- {"NULL", "POSIX", "FStream",
- "MdtmMan"} // "MPI", "MPI_LUSTRE", "MPI_AGGREGATE", "DATASPACES", "DIMES",
- // "FLEXPATH", "PHDF5", "NC4", "ICEE" }
-};
+ {"NULL", "POSIX", "FStream", "MdtmMan"}};
+// TODO(chuckatkins): Add transports MPI, MPI_LUSTRE, MPI_AGGREGATE,
+// DATASPACES, DIMES, FLEXPATH, PHDF5, NC4, ICEE
const std::set<std::string> Support::Transforms{
{"none", "identity", "bzip2", "isobar", "szip", "zlib"}};
@@ -90,4 +89,4 @@ const std::map<std::string, std::set<std::string>> Support::DatatypesAliases{
const std::set<std::string> Support::FileTransports{
{"POSIX", "File", "FStream", "MPIFile"}};
-} // end namespace
+} // end namespace adios
diff --git a/source/core/Transform.cpp b/source/core/Transform.cpp
index 0b719ccc86bcdf858a93c1417f662982817e45c3..7549342b26640480331644a5bdcc0adaded88a55 100644
--- a/source/core/Transform.cpp
+++ b/source/core/Transform.cpp
@@ -7,24 +7,23 @@
* Created on: Dec 5, 2016
* Author: wfg
*/
+#include <utility>
#include "core/Transform.h"
namespace adios
{
-Transform::Transform(const std::string method) : m_Method(method) {}
+Transform::Transform(std::string method) : m_Method(std::move(method)) {}
-Transform::~Transform() {}
-
-void Transform::Compress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void Transform::Compress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
-void Transform::Decompress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void Transform::Decompress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
-} // end namespace
+} // end namespace adios
diff --git a/source/core/Transport.cpp b/source/core/Transport.cpp
index 3f3fd7728137341166862eaa09b6634d80b89942..29fbc773e19e3ecd398f6d4bd79fcae8fe185cda 100644
--- a/source/core/Transport.cpp
+++ b/source/core/Transport.cpp
@@ -8,22 +8,21 @@
* Author: wfg
*/
+#include <utility>
+
#include "core/Transport.h"
namespace adios
{
-Transport::Transport(const std::string type, MPI_Comm mpiComm,
- const bool debugMode)
-: m_Type{type}, m_MPIComm{mpiComm}, m_DebugMode{debugMode}
+Transport::Transport(std::string type, MPI_Comm mpiComm, bool debugMode)
+: m_Type{std::move(type)}, m_MPIComm{mpiComm}, m_DebugMode{debugMode}
{
MPI_Comm_rank(m_MPIComm, &m_RankMPI);
MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
-Transport::~Transport() {}
-
-void Transport::SetBuffer(char *buffer, size_t size) {}
+void Transport::SetBuffer(char * /*buffer*/, size_t /*size*/) {}
void Transport::Flush() {}
@@ -35,13 +34,19 @@ void Transport::InitProfiler(const std::string accessMode,
m_Profiler.m_Timers.emplace_back("open", Support::Resolutions::mus);
if (accessMode == "w" || accessMode == "write")
+ {
m_Profiler.m_Timers.emplace_back("write", resolution);
+ }
else if (accessMode == "a" || accessMode == "append")
+ {
m_Profiler.m_Timers.emplace_back("append", resolution);
+ }
else if (accessMode == "r" || accessMode == "read")
+ {
m_Profiler.m_Timers.emplace_back("read", resolution);
+ }
m_Profiler.m_Timers.emplace_back("close", Support::Resolutions::mus);
@@ -49,4 +54,4 @@ void Transport::InitProfiler(const std::string accessMode,
m_Profiler.m_IsActive = true;
}
-} // end namespace
+} // end namespace adios
diff --git a/source/engine/bp/BPFileReader.cpp b/source/engine/bp/BPFileReader.cpp
index 406c752d39d2e8357c1a0a008c2d2a975cf80425..e658e5580d3046b6cde1847a09c65f2d71d5de4e 100644
--- a/source/engine/bp/BPFileReader.cpp
+++ b/source/engine/bp/BPFileReader.cpp
@@ -21,24 +21,23 @@
namespace adios
{
-BPFileReader::BPFileReader(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode,
- const unsigned int nthreads)
-: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method, debugMode,
- nthreads, " BPFileReader constructor (or call to ADIOS Open).\n"),
+BPFileReader::BPFileReader(ADIOS &adios, std::string name,
+ std::string accessMode, MPI_Comm mpiComm,
+ const Method &method, IOMode /*iomode*/,
+ float /*timeout_sec*/, bool debugMode,
+ unsigned int nthreads)
+: Engine(adios, "BPFileReader", std::move(name), std::move(accessMode), mpiComm,
+ method, debugMode, nthreads,
+ " BPFileReader constructor (or call to ADIOS Open).\n"),
m_Buffer(accessMode, m_RankMPI, m_DebugMode)
{
Init();
}
-BPFileReader::~BPFileReader() {}
-
-Variable<void> *
-BPFileReader::InquireVariable(const std::string name,
- const bool readIn) // not yet implemented
+Variable<void> *BPFileReader::InquireVariable(const std::string /*name*/,
+ const bool /*readIn*/)
{
+ // not yet implemented
return nullptr;
}
@@ -138,13 +137,14 @@ BPFileReader::InquireVariableCLDouble(const std::string name, const bool readIn)
return InquireVariableCommon<std::complex<long double>>(name, readIn);
}
-VariableCompound *BPFileReader::InquireVariableCompound(const std::string name,
- const bool readIn)
+VariableCompound *
+BPFileReader::InquireVariableCompound(const std::string /*name*/,
+ const bool /*readIn*/)
{
return nullptr;
}
-void BPFileReader::Close(const int transportIndex) {}
+void BPFileReader::Close(const int /*transportIndex*/) {}
// PRIVATE
void BPFileReader::Init()
@@ -152,9 +152,11 @@ void BPFileReader::Init()
if (m_DebugMode == true)
{
if (m_AccessMode != "r" && m_AccessMode != "read")
+ {
throw std::invalid_argument(
"ERROR: BPFileReader doesn't support access mode " + m_AccessMode +
", in call to ADIOS Open or BPFileReader constructor\n");
+ }
}
InitCapsules();
@@ -214,19 +216,23 @@ void BPFileReader::InitTransports() // maybe move this?
else
{
if (m_DebugMode == true)
+ {
throw std::invalid_argument(
"ERROR: file transport library " + itLibrary->second +
" not supported, in " + m_Name + m_EndMessage);
+ }
}
}
else
{
if (m_DebugMode == true)
+ {
throw std::invalid_argument("ERROR: transport " + itTransport->second +
" (you mean File?) not supported, in " +
m_Name + m_EndMessage);
+ }
}
}
}
-} // end namespace
+} // end namespace adios
diff --git a/source/engine/bp/BPFileWriter.cpp b/source/engine/bp/BPFileWriter.cpp
index 2785781f002d0b499a7bbc328173080f435fb2ff..14f0d149bb0c0e80c266337208bff5c00c99d973 100644
--- a/source/engine/bp/BPFileWriter.cpp
+++ b/source/engine/bp/BPFileWriter.cpp
@@ -21,8 +21,8 @@ namespace adios
BPFileWriter::BPFileWriter(ADIOS &adios, const std::string name,
const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode,
+ const Method &method, const IOMode /*iomode*/,
+ const float /*timeout_sec*/, const bool debugMode,
const unsigned int nthreads)
: Engine(adios, "BPFileWriter", name, accessMode, mpiComm, method, debugMode,
nthreads, " BPFileWriter constructor (or call to ADIOS Open).\n"),
@@ -34,7 +34,7 @@ BPFileWriter::BPFileWriter(ADIOS &adios, const std::string name,
Init();
}
-BPFileWriter::~BPFileWriter() {}
+BPFileWriter::~BPFileWriter() = default;
void BPFileWriter::Init()
{
@@ -133,7 +133,10 @@ void BPFileWriter::Write(Variable<std::complex<long double>> &variable,
WriteVariableCommon(variable, values);
}
-void BPFileWriter::Write(VariableCompound &variable, const void *values) {}
+void BPFileWriter::Write(VariableCompound & /*variable*/,
+ const void * /*values*/)
+{
+}
// String version
void BPFileWriter::Write(const std::string variableName, const char *values)
@@ -232,12 +235,12 @@ void BPFileWriter::Write(const std::string variableName,
m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
}
-void BPFileWriter::Write(const std::string variableName,
- const void *values) // Compound type
+void BPFileWriter::Write(const std::string /*variableName*/,
+ const void * /*values*/) // Compound type
{
}
-void BPFileWriter::Advance(float timeout_sec)
+void BPFileWriter::Advance(float /*timeout_sec*/)
{
m_BP1Writer.Advance(m_MetadataSet, m_Buffer);
}
@@ -247,10 +250,11 @@ void BPFileWriter::Close(const int transportIndex)
CheckTransportIndex(transportIndex);
if (transportIndex == -1)
{
- for (auto &transport :
- m_Transports) // by reference or value or it doesn't matter?
+ for (auto &transport : m_Transports)
+ { // by reference or value or it doesn't matter?
m_BP1Writer.Close(m_MetadataSet, m_Buffer, *transport, m_IsFirstClose,
false); // false: not using aggregation for now
+ }
}
else
{
@@ -292,9 +296,11 @@ void BPFileWriter::InitParameters()
if (m_DebugMode == true)
{
if (growthFactor == 1.f)
+ {
throw std::invalid_argument(
"ERROR: buffer_growth argument can't be less of equal than 1, in " +
m_EndMessage + "\n");
+ }
}
m_BP1Writer.m_GrowthFactor = growthFactor;
@@ -307,9 +313,11 @@ void BPFileWriter::InitParameters()
if (m_DebugMode == true)
{
if (m_GrowthFactor <= 1.f)
+ {
throw std::invalid_argument("ERROR: Method buffer_growth argument "
"can't be less of equal than 1, in " +
m_EndMessage + "\n");
+ }
}
m_MaxBufferSize = std::stoul(itMaxBufferSize->second) *
@@ -323,9 +331,11 @@ void BPFileWriter::InitParameters()
if (m_DebugMode == true)
{
if (verbosity < 0 || verbosity > 5)
+ {
throw std::invalid_argument("ERROR: Method verbose argument must be an "
"integer in the range [0,5], in call to "
"Open or Engine constructor\n");
+ }
}
m_BP1Writer.m_Verbosity = verbosity;
}
@@ -336,25 +346,33 @@ void BPFileWriter::InitParameters()
auto &profiler = m_MetadataSet.Log;
if (itProfile->second == "mus" || itProfile->second == "microseconds")
+ {
profiler.m_Timers.emplace_back("buffering", Support::Resolutions::mus);
-
+ }
else if (itProfile->second == "ms" || itProfile->second == "milliseconds")
+ {
profiler.m_Timers.emplace_back("buffering", Support::Resolutions::ms);
-
+ }
else if (itProfile->second == "s" || itProfile->second == "seconds")
+ {
profiler.m_Timers.emplace_back("buffering", Support::Resolutions::s);
-
+ }
else if (itProfile->second == "min" || itProfile->second == "minutes")
+ {
profiler.m_Timers.emplace_back("buffering", Support::Resolutions::m);
-
+ }
else if (itProfile->second == "h" || itProfile->second == "hours")
+ {
profiler.m_Timers.emplace_back("buffering", Support::Resolutions::h);
+ }
else
{
if (m_DebugMode == true)
+ {
throw std::invalid_argument("ERROR: Method profile_buffering_units "
"argument must be mus, ms, s, min or h, in "
"call to Open or Engine constructor\n");
+ }
}
profiler.m_IsActive = true;
@@ -383,26 +401,33 @@ void BPFileWriter::InitTransports()
if (itProfile != parameters.end())
{
if (itProfile->second == "mus" || itProfile->second == "microseconds")
+ {
resolution = Support::Resolutions::mus;
-
+ }
else if (itProfile->second == "ms" || itProfile->second == "milliseconds")
+ {
resolution = Support::Resolutions::ms;
-
+ }
else if (itProfile->second == "s" || itProfile->second == "seconds")
+ {
resolution = Support::Resolutions::s;
-
+ }
else if (itProfile->second == "min" || itProfile->second == "minutes")
+ {
resolution = Support::Resolutions::m;
-
+ }
else if (itProfile->second == "h" || itProfile->second == "hours")
+ {
resolution = Support::Resolutions::h;
-
+ }
else
{
if (m_DebugMode == true)
+ {
throw std::invalid_argument("ERROR: Transport profile_units argument "
"must be mus, ms, s, min or h " +
m_EndMessage);
+ }
}
doProfiling = true;
}
@@ -418,7 +443,9 @@ void BPFileWriter::InitTransports()
auto file =
std::make_shared<transport::FileDescriptor>(m_MPIComm, m_DebugMode);
if (doProfiling == true)
+ {
file->InitProfiler(m_AccessMode, resolution);
+ }
m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
m_Transports.push_back(std::move(file));
@@ -428,7 +455,9 @@ void BPFileWriter::InitTransports()
auto file =
std::make_shared<transport::FilePointer>(m_MPIComm, m_DebugMode);
if (doProfiling == true)
+ {
file->InitProfiler(m_AccessMode, resolution);
+ }
m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
m_Transports.push_back(std::move(file));
@@ -440,7 +469,9 @@ void BPFileWriter::InitTransports()
std::make_shared<transport::FStream>(m_MPIComm, m_DebugMode);
if (doProfiling == true)
+ {
file->InitProfiler(m_AccessMode, resolution);
+ }
m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
m_Transports.push_back(std::move(file));
@@ -451,17 +482,21 @@ void BPFileWriter::InitTransports()
else
{
if (m_DebugMode == true)
+ {
throw std::invalid_argument(
"ERROR: file transport library " + itLibrary->second +
" not supported, in " + m_Name + m_EndMessage);
+ }
}
}
else
{
if (m_DebugMode == true)
+ {
throw std::invalid_argument("ERROR: transport " + itTransport->second +
" (you mean File?) not supported, in " +
m_Name + m_EndMessage);
+ }
}
}
}
@@ -469,7 +504,9 @@ void BPFileWriter::InitTransports()
void BPFileWriter::InitProcessGroup()
{
if (m_MetadataSet.Log.m_IsActive == true)
+ {
m_MetadataSet.Log.m_Timers[0].SetInitialTime();
+ }
if (m_AccessMode == "a")
{
@@ -480,7 +517,9 @@ void BPFileWriter::InitProcessGroup()
WriteProcessGroupIndex();
if (m_MetadataSet.Log.m_IsActive == true)
+ {
m_MetadataSet.Log.m_Timers[0].SetTime();
+ }
}
void BPFileWriter::WriteProcessGroupIndex()
diff --git a/source/format/BP1.cpp b/source/format/BP1.cpp
index c81e7b6fe34fcbb63f5e7e62472051ea99cbd672..e9ec112c5753ab5e7905a016cf17815ad7daa1bc 100644
--- a/source/format/BP1.cpp
+++ b/source/format/BP1.cpp
@@ -21,10 +21,13 @@ std::string BP1::GetDirectoryName(const std::string name) const noexcept
std::string directory;
if (name.find(".bp") == name.size() - 3)
+ {
directory = name;
+ }
else
+ {
directory = name + ".bp";
-
+ }
return directory;
}
@@ -48,15 +51,25 @@ std::vector<std::uint8_t> BP1::GetMethodIDs(
auto lf_GetMethodID = [](const std::string method) -> std::uint8_t {
int id = METHOD_UNKNOWN;
if (method == "NULL")
+ {
id = METHOD_NULL;
+ }
else if (method == "POSIX")
+ {
id = METHOD_POSIX;
+ }
else if (method == "FStream")
+ {
id = METHOD_FSTREAM;
+ }
else if (method == "File")
+ {
id = METHOD_FILE;
+ }
else if (method == "MPI")
+ {
id = METHOD_MPI;
+ }
return id;
};
@@ -65,7 +78,9 @@ std::vector<std::uint8_t> BP1::GetMethodIDs(
methodIDs.reserve(transports.size());
for (const auto &transport : transports)
+ {
methodIDs.push_back(lf_GetMethodID(transport->m_Type));
+ }
return methodIDs;
}
diff --git a/source/format/BP1Aggregator.cpp b/source/format/BP1Aggregator.cpp
index c81a72bbffa7ebc2e25a4b3fb9e8873883264202..f0de393a3ef307ed0b1c4959301ca0b3d0b18677 100644
--- a/source/format/BP1Aggregator.cpp
+++ b/source/format/BP1Aggregator.cpp
@@ -28,7 +28,7 @@ BP1Aggregator::BP1Aggregator(MPI_Comm mpiComm, const bool debugMode)
MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
-BP1Aggregator::~BP1Aggregator() {}
+BP1Aggregator::~BP1Aggregator() = default;
void BP1Aggregator::WriteProfilingLog(const std::string fileName,
const std::string &rankLog)
@@ -44,8 +44,10 @@ void BP1Aggregator::WriteProfilingLog(const std::string fileName,
// first receive sizes
for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
MPI_Irecv(&rankLogsSizes[i - 1], 1, MPI_INT, i, 0, m_MPIComm,
&requests[i]);
+ }
for (unsigned int i = 1; i < sizeMPI; ++i)
{
@@ -53,20 +55,26 @@ void BP1Aggregator::WriteProfilingLog(const std::string fileName,
if (m_DebugMode == true)
{
if (rankLogsSizes[i - 1] == -1)
+ {
throw std::runtime_error("ERROR: couldn't get size from rank " +
std::to_string(i) +
", in ADIOS aggregator for Profiling.log\n");
+ }
}
rankLogs[i - 1].resize(rankLogsSizes[i - 1]); // allocate with zeros
}
// receive rankLog from other ranks
for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
MPI_Irecv(rankLogs[i - 1].data(), rankLogsSizes[i - 1], MPI_CHAR, i, 1,
m_MPIComm, &requests[i]);
+ }
for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
MPI_Wait(&requests[i], &statuses[i]);
+ }
// write file
std::string logFile("log = { \n");
@@ -90,8 +98,8 @@ void BP1Aggregator::WriteProfilingLog(const std::string fileName,
MPI_Isend(&rankLogSize, 1, MPI_INT, 0, 0, m_MPIComm, &requestSize);
MPI_Request requestRankLog;
- MPI_Isend(const_cast<char *>(rankLog.c_str()), rankLogSize, MPI_CHAR, 0, 1,
- m_MPIComm, &requestRankLog);
+ MPI_Isend(rankLog.data(), rankLogSize, MPI_CHAR, 0, 1, m_MPIComm,
+ &requestRankLog);
}
}
diff --git a/source/format/BP1Writer.cpp b/source/format/BP1Writer.cpp
index b5aed5404ca9804d498b9f1220bc997f93643a14..97b717eebf8846f119326761578b14fb988ce6c9 100644
--- a/source/format/BP1Writer.cpp
+++ b/source/format/BP1Writer.cpp
@@ -71,7 +71,7 @@ void BP1Writer::WriteProcessGroupIndex(
// offset to pg in data in metadata which is the current absolute position
CopyToBuffer(metadataBuffer,
- reinterpret_cast<std::uint64_t *>(&heap.m_DataAbsolutePosition));
+ static_cast<uint64_t *>(&heap.m_DataAbsolutePosition));
// Back to writing metadata pg index length (length of group)
const std::uint16_t metadataPGIndexLength =
@@ -121,17 +121,23 @@ void BP1Writer::Close(BP1MetadataSet &metadataSet, capsule::STLVector &heap,
const bool doAggregation) const noexcept
{
if (metadataSet.Log.m_IsActive == true)
+ {
metadataSet.Log.m_Timers[0].SetInitialTime();
+ }
if (isFirstClose == true)
{
if (metadataSet.DataPGIsOpen == true)
+ {
FlattenData(metadataSet, heap);
+ }
FlattenMetadata(metadataSet, heap);
if (metadataSet.Log.m_IsActive == true)
+ {
metadataSet.Log.m_Timers[0].SetInitialTime();
+ }
if (doAggregation == true) // N-to-M where 1 <= M <= N-1, might need a new
// Log metadataSet.Log.m_Timers just for
@@ -177,7 +183,9 @@ std::string BP1Writer::GetRankProfilingLog(
rankLog += "'lib': " + transports[t]->m_Type + ", ";
for (unsigned int i = 0; i < 3; ++i)
+ {
lf_WriterTimer(rankLog, timers[i]);
+ }
rankLog += "}, ";
}
@@ -196,7 +204,7 @@ void BP1Writer::WriteDimensionsRecord(
auto lf_WriteFlaggedDim = [](std::vector<char> &buffer, const char no,
const std::size_t dimension) {
CopyToBuffer(buffer, &no);
- CopyToBuffer(buffer, reinterpret_cast<const std::uint64_t *>(&dimension));
+ CopyToBuffer(buffer, static_cast<const uint64_t *>(&dimension));
};
// BODY Starts here
@@ -216,8 +224,7 @@ void BP1Writer::WriteDimensionsRecord(
{
for (const auto &localDimension : localDimensions)
{
- CopyToBuffer(buffer,
- reinterpret_cast<const std::uint64_t *>(&localDimension));
+ CopyToBuffer(buffer, static_cast<const uint64_t *>(&localDimension));
buffer.insert(buffer.end(), skip, 0);
}
}
@@ -238,12 +245,11 @@ void BP1Writer::WriteDimensionsRecord(
{
for (unsigned int d = 0; d < localDimensions.size(); ++d)
{
- CopyToBuffer(buffer, reinterpret_cast<const std::uint64_t *>(
- &localDimensions[d]));
- CopyToBuffer(buffer, reinterpret_cast<const std::uint64_t *>(
- &globalDimensions[d]));
- CopyToBuffer(
- buffer, reinterpret_cast<const std::uint64_t *>(&globalOffsets[d]));
+ CopyToBuffer(buffer,
+ static_cast<const uint64_t *>(&localDimensions[d]));
+ CopyToBuffer(buffer,
+ static_cast<const uint64_t *>(&globalDimensions[d]));
+ CopyToBuffer(buffer, static_cast<const uint64_t *>(&globalOffsets[d]));
}
}
}
@@ -391,7 +397,9 @@ void BP1Writer::FlattenMetadata(BP1MetadataSet &metadataSet,
heap.m_DataAbsolutePosition += footerSize;
if (metadataSet.Log.m_IsActive == true)
+ {
metadataSet.Log.m_TotalBytes.push_back(heap.m_DataAbsolutePosition);
+ }
}
} // end namespace format
diff --git a/source/functions/adiosFunctions.cpp b/source/functions/adiosFunctions.cpp
index 0886e029ad14a4e6fc4dd8b04b296071175d3678..78393c641f2c502c35728c46e590252ff8580749 100644
--- a/source/functions/adiosFunctions.cpp
+++ b/source/functions/adiosFunctions.cpp
@@ -37,10 +37,12 @@ void DumpFileToString(const std::string fileName, std::string &fileContent)
{
std::ifstream fileStream(fileName);
- if (fileStream.good() == false) // check file
+ if (fileStream.good() == false)
+ { // check file
throw std::ios_base::failure(
"ERROR: file " + fileName +
" could not be opened. Check permissions or file existence\n");
+ }
std::ostringstream fileSS;
fileSS << fileStream.rdbuf();
@@ -48,7 +50,9 @@ void DumpFileToString(const std::string fileName, std::string &fileContent)
fileContent = fileSS.str(); // convert to string and check
if (fileContent.empty())
+ {
throw std::invalid_argument("ERROR: file " + fileName + " is empty\n");
+ }
}
void GetSubString(const std::string initialTag, const std::string finalTag,
@@ -101,25 +105,35 @@ void GetSubString(const std::string initialTag, const std::string finalTag,
(singleQuotePosition == content.npos && end < doubleQuotePosition) ||
(doubleQuotePosition == content.npos && end < singleQuotePosition) ||
(end < singleQuotePosition && end < doubleQuotePosition))
+ {
break;
+ }
// find the closing corresponding quote
std::string::size_type closingQuotePosition;
- if (singleQuotePosition == content.npos) // no ' anywhere
+ if (singleQuotePosition == content.npos)
+ { // no ' anywhere
lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
closingQuotePosition);
- else if (doubleQuotePosition == content.npos) // no " anywhere
+ }
+ else if (doubleQuotePosition == content.npos)
+ { // no " anywhere
lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
closingQuotePosition);
+ }
else
{
if (singleQuotePosition < doubleQuotePosition)
+ {
lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
closingQuotePosition);
- else // find the closing "
+ }
+ else
+ { // find the closing "
lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
closingQuotePosition);
+ }
}
if (closingQuotePosition ==
@@ -132,7 +146,9 @@ void GetSubString(const std::string initialTag, const std::string finalTag,
currentPosition = closingQuotePosition + 1;
if (closingQuotePosition < end)
+ {
continue;
+ }
// if this point is reached it means it's a value inside " " or ' ', move to
// the next end
@@ -151,8 +167,10 @@ void GetQuotedValue(const char quote,
auto nextQuotePosition = currentTag.find(quote);
if (nextQuotePosition == currentTag.npos)
+ {
throw std::invalid_argument("ERROR: Invalid attribute in..." + currentTag +
"...check XML file\n");
+ }
value = currentTag.substr(0, nextQuotePosition);
currentTag = currentTag.substr(nextQuotePosition + 1);
@@ -201,8 +219,10 @@ void GetPairsFromTag(
">"); // check for closing tagName
if (fileContent.find(closingTagName) == fileContent.npos)
+ {
throw std::invalid_argument("ERROR: closing tag " + closingTagName +
" missing, check XML file\n");
+ }
GetPairs(tag, pairs);
}
@@ -411,7 +431,9 @@ std::size_t GetTotalSize(const std::vector<std::size_t> &dimensions)
std::size_t product = 1;
for (const auto dimension : dimensions)
+ {
product *= dimension;
+ }
return product;
}
@@ -420,13 +442,17 @@ void CreateDirectory(const std::string fullPath) noexcept
{
auto lf_Mkdir = [](const std::string directory, struct stat &st) {
if (stat(directory.c_str(), &st) == -1)
+ {
mkdir(directory.c_str(), 0777);
+ }
};
auto directoryPosition = fullPath.find("/");
- if (fullPath[0] == '/' || fullPath[0] == '.') // find the second '/'
+ if (fullPath[0] == '/' || fullPath[0] == '.')
+ { // find the second '/'
directoryPosition = fullPath.find("/", directoryPosition + 1);
+ }
struct stat st = {0};
if (directoryPosition == fullPath.npos) // no subdirectories
@@ -464,9 +490,11 @@ void SetTransformsHelper(const std::vector<std::string> &transformNames,
if (debugMode == true)
{
if (colonPosition == transformName.size() - 1)
+ {
throw std::invalid_argument("ERROR: wrong format for transform " +
transformName +
", in call to SetTransform\n");
+ }
}
transformMethod = transformName.substr(0, colonPosition);
@@ -528,14 +556,18 @@ BuildParametersMap(const std::vector<std::string> ¶meters,
if (debugMode == true)
{
if (equalPosition == parameter.npos)
+ {
throw std::invalid_argument("ERROR: wrong format for parameter " +
parameter +
", format must be field=value \n");
+ }
if (equalPosition == parameter.size() - 1)
+ {
throw std::invalid_argument("ERROR: empty value in parameter " +
parameter +
", format must be field=value \n");
+ }
}
field = parameter.substr(0, equalPosition);
@@ -553,8 +585,10 @@ BuildParametersMap(const std::vector<std::string> ¶meters,
if (debugMode == true)
{
if (parametersOutput.count(field) == 1)
+ {
throw std::invalid_argument("ERROR: parameter " + field +
" already exists, must be unique\n");
+ }
}
parametersOutput[field] = value;
@@ -567,7 +601,9 @@ std::vector<int> CSVToVectorInt(const std::string csv)
{
std::vector<int> numbers;
if (csv.empty())
+ {
return numbers;
+ }
if (csv.find(",") == csv.npos) // check if no commas, one int
{
@@ -600,7 +636,9 @@ bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
bool doTransportsFlush = (requiredDataSize > maxBufferSize) ? true : false;
if (GrowBuffer(requiredDataSize, growthFactor, buffer) == -1)
+ {
doTransportsFlush = true;
+ }
return doTransportsFlush;
}
@@ -639,8 +677,8 @@ int GrowBuffer(const std::size_t incomingDataSize, const float growthFactor,
bool IsLittleEndian() noexcept
{
- std::uint16_t hexa = 0x1234;
- return *reinterpret_cast<std::uint8_t *>(&hexa) != 0x12;
+ uint16_t hexa = 0x1234;
+ return *reinterpret_cast<uint8_t *>(&hexa) != 0x12; // NOLINT
}
-} // end namespace
+} // namespace adios
diff --git a/source/mpidummy.cpp b/source/mpidummy.cpp
index a0675138b3bf50af3f0a9e1108da5734207f9289..f85e40a44a64c84718691452db59a420e1b8f369 100644
--- a/source/mpidummy.cpp
+++ b/source/mpidummy.cpp
@@ -20,9 +20,10 @@
#include <cstring>
//#define _LARGEFILE64_SOURCE
+#include <unistd.h>
+
#include <sys/time.h>
#include <sys/types.h>
-#include <unistd.h>
/// \endcond
#include "mpidummy.h"
@@ -95,8 +96,9 @@ int MPI_Comm_free(MPI_Comm *comm)
MPI_Comm MPI_Comm_f2c(MPI_Fint comm) { return comm; }
-int MPI_Gather(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf,
- int recvcnt, MPI_Datatype recvtype, int root, MPI_Comm comm)
+int MPI_Gather(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
+ void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
+ MPI_Comm comm)
{
int ier = MPI_SUCCESS;
size_t n = 0, nsent = 0, nrecv = 0;
@@ -146,8 +148,8 @@ int MPI_Gather(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf,
return ier;
}
-int MPI_Gatherv(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
- void *recvbuf, int *recvcnts, int *displs,
+int MPI_Gatherv(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
+ void *recvbuf, const int *recvcnts, const int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm)
{
int ier = MPI_SUCCESS;
@@ -165,7 +167,7 @@ int MPI_Gatherv(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
return ier;
}
-int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
+int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
MPI_Comm comm)
{
@@ -173,7 +175,7 @@ int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
0, comm);
}
-int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
+int MPI_Scatter(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
MPI_Comm comm)
{
@@ -216,7 +218,7 @@ int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
if (ier == MPI_SUCCESS)
{
- memcpy(sendbuf, recvbuf, nsent);
+ memcpy(recvbuf, sendbuf, nsent);
}
else
{
@@ -226,7 +228,7 @@ int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
return ier;
}
-int MPI_Scatterv(void *sendbuf, int *sendcnts, int *displs,
+int MPI_Scatterv(const void *sendbuf, const int *sendcnts, const int *displs,
MPI_Datatype sendtype, void *recvbuf, int recvcnt,
MPI_Datatype recvtype, int root, MPI_Comm comm)
{
@@ -260,13 +262,13 @@ int MPI_Irecv(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
return 0;
}
-int MPI_Send(void * /*sendbuffer*/, int /*count*/, MPI_Datatype /*type*/,
+int MPI_Send(const void * /*sendbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*destination*/, int /*tag*/, MPI_Comm /*comm*/)
{
return 0;
}
-int MPI_Isend(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
+int MPI_Isend(const void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*source*/, int /*tag*/, MPI_Comm /*comm*/,
MPI_Request * /*request*/)
{
@@ -275,7 +277,7 @@ int MPI_Isend(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int MPI_Wait(MPI_Request * /*request*/, MPI_Status * /*status*/) { return 0; }
-int MPI_File_open(MPI_Comm /*comm*/, char *filename, int amode,
+int MPI_File_open(MPI_Comm /*comm*/, const char *filename, int amode,
MPI_Info /*info*/, MPI_File *fh)
{
*fh = open64(filename, amode);
@@ -327,7 +329,7 @@ int MPI_File_seek(MPI_File fh, MPI_Offset offset, int whence)
return MPI_SUCCESS;
}
-int MPI_Get_count(MPI_Status *status, MPI_Datatype, int *count)
+int MPI_Get_count(const MPI_Status *status, MPI_Datatype, int *count)
{
*count = static_cast<int>(*status);
return MPI_SUCCESS;
diff --git a/source/transform/BZip2.cpp b/source/transform/BZip2.cpp
index 646b8bc6c75ba201e575cf245c54380eff9e712f..c267af7540249968dd42d9e9bb210b2917661150 100644
--- a/source/transform/BZip2.cpp
+++ b/source/transform/BZip2.cpp
@@ -17,15 +17,15 @@ namespace transform
BZIP2::BZIP2() : Transform("bzip2") {}
-BZIP2::~BZIP2() {}
+BZIP2::~BZIP2() = default;
-void BZIP2::Compress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void BZIP2::Compress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
-void BZIP2::Decompress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void BZIP2::Decompress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
diff --git a/source/transport/file/FStream.cpp b/source/transport/file/FStream.cpp
index 15bf60b58072ae17c4fa5fe171ef65789ea1c395..2a404ae6a96a10471e5ccd97acd547617a73fdb0 100644
--- a/source/transport/file/FStream.cpp
+++ b/source/transport/file/FStream.cpp
@@ -9,6 +9,7 @@
*/
/// \cond EXCLUDED_FROM_DOXYGEN
+#include <ios> // std::ios_base::failure
#include <stdexcept>
/// \endcond
@@ -19,33 +20,37 @@ namespace adios
namespace transport
{
-FStream::FStream(MPI_Comm mpiComm, const bool debugMode)
+FStream::FStream(MPI_Comm mpiComm, bool debugMode)
: Transport("fstream", mpiComm, debugMode)
{
}
-FStream::~FStream() {}
-
void FStream::Open(const std::string name, const std::string accessMode)
{
m_Name = name;
m_AccessMode = accessMode;
if (accessMode == "w" || accessMode == "write")
+ {
m_FStream.open(name, std::fstream::out);
-
+ }
else if (accessMode == "a" || accessMode == "append")
+ {
m_FStream.open(name, std::fstream::out | std::fstream::app);
-
+ }
else if (accessMode == "r" || accessMode == "read")
+ {
m_FStream.open(name, std::fstream::in);
+ }
if (m_DebugMode == true)
{
if (!m_FStream)
+ {
throw std::ios_base::failure(
"ERROR: couldn't open file " + name +
", in call to Open from FStream transport\n");
+ }
}
}
@@ -61,8 +66,10 @@ void FStream::Write(const char *buffer, std::size_t size)
if (m_DebugMode == true)
{
if (!m_FStream)
+ {
throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
", in call to FStream write\n");
+ }
}
}
@@ -71,4 +78,4 @@ void FStream::Flush() { m_FStream.flush(); }
void FStream::Close() { m_FStream.close(); }
} // end namespace transport
-} // end namespace
+} // end namespace adios
diff --git a/source/transport/file/FileDescriptor.cpp b/source/transport/file/FileDescriptor.cpp
index d3433d2e50aa1613ef16aa95daf7d4553c51dc49..0d6a87c96826042d79581ec356b9c96d796a85cf 100644
--- a/source/transport/file/FileDescriptor.cpp
+++ b/source/transport/file/FileDescriptor.cpp
@@ -45,87 +45,115 @@ void FileDescriptor::Open(const std::string name, const std::string accessMode)
if (accessMode == "w" || accessMode == "write")
{
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[0].SetInitialTime();
+ }
m_FileDescriptor = open(m_Name.c_str(), O_WRONLY | O_CREAT, 0777);
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[0].SetTime();
+ }
}
else if (accessMode == "a" || accessMode == "append")
{
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[0].SetInitialTime();
+ }
m_FileDescriptor =
open(m_Name.c_str(), O_WRONLY | O_APPEND); // we need to change this
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[0].SetTime();
+ }
}
else if (accessMode == "r" || accessMode == "read")
{
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[0].SetInitialTime();
+ }
m_FileDescriptor = open(m_Name.c_str(), O_RDONLY);
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[0].SetTime();
+ }
}
if (m_DebugMode == true)
{
if (m_FileDescriptor == -1)
+ {
throw std::ios_base::failure("ERROR: couldn't open file " + m_Name +
", from call to Open in FD transport using "
"POSIX open. Does file exists?\n");
+ }
}
}
void FileDescriptor::Write(const char *buffer, std::size_t size)
{
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[1].SetInitialTime();
+ }
auto writtenSize = write(m_FileDescriptor, buffer, size);
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[1].SetTime();
+ }
if (m_DebugMode == true)
{
if (writtenSize == -1)
+ {
throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
", in call to POSIX write\n");
+ }
if (static_cast<std::size_t>(writtenSize) != size)
+ {
throw std::ios_base::failure(
"ERROR: written size + " + std::to_string(writtenSize) +
" is not equal to intended size " + std::to_string(size) +
" in file " + m_Name + ", in call to POSIX write\n");
+ }
}
}
void FileDescriptor::Close()
{
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[2].SetInitialTime();
+ }
int status = close(m_FileDescriptor);
if (m_Profiler.m_IsActive == true)
+ {
m_Profiler.m_Timers[2].SetTime();
+ }
if (m_DebugMode == true)
{
if (status == -1)
+ {
throw std::ios_base::failure("ERROR: couldn't close file " + m_Name +
", in call to POSIX write\n");
+ }
}
m_IsOpen = false;
}
} // end namespace transport
-} // end namespace
+} // namespace adios
diff --git a/source/transport/file/FilePointer.cpp b/source/transport/file/FilePointer.cpp
index 704b93f08d55ad410d25f9a04a501c73d60d49a7..1ba57204e6a6827c7454c688b37b8e2f1d62e2c9 100644
--- a/source/transport/file/FilePointer.cpp
+++ b/source/transport/file/FilePointer.cpp
@@ -26,8 +26,10 @@ FilePointer::FilePointer(MPI_Comm mpiComm, const bool debugMode)
FilePointer::~FilePointer()
{
- if (m_File != NULL)
+ if (m_File != nullptr)
+ {
fclose(m_File);
+ }
}
void FilePointer::Open(const std::string name, const std::string accessMode)
@@ -36,20 +38,26 @@ void FilePointer::Open(const std::string name, const std::string accessMode)
m_AccessMode = accessMode;
if (accessMode == "w" || accessMode == "write")
+ {
m_File = fopen(name.c_str(), "w");
-
+ }
else if (accessMode == "a" || accessMode == "append")
+ {
m_File = fopen(name.c_str(), "a");
-
+ }
else if (accessMode == "r" || accessMode == "read")
+ {
m_File = fopen(name.c_str(), "r");
+ }
if (m_DebugMode == true)
{
- if (m_File == NULL)
+ if (m_File == nullptr)
+ {
throw std::ios_base::failure("ERROR: couldn't open file " + name +
", "
"in call to Open from File* transport\n");
+ }
}
}
@@ -60,8 +68,10 @@ void FilePointer::SetBuffer(char *buffer, std::size_t size)
if (m_DebugMode == true)
{
if (status == 1)
+ {
throw std::ios_base::failure("ERROR: could not set buffer in rank " +
std::to_string(m_RankMPI) + "\n");
+ }
}
}
@@ -72,8 +82,10 @@ void FilePointer::Write(const char *buffer, std::size_t size)
if (m_DebugMode == true)
{
if (ferror(m_File))
+ {
throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
", in call to File* write\n");
+ }
}
}
@@ -87,4 +99,4 @@ void FilePointer::Close()
}
} // end namespace transport
-} // end namespace
+} // namespace adios
diff --git a/thirdparty/CMakeLists.txt b/thirdparty/CMakeLists.txt
index 0825c4704eca3867613ee2f58fdd5636d2fdee5b..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/thirdparty/CMakeLists.txt
+++ b/thirdparty/CMakeLists.txt
@@ -1,41 +0,0 @@
-#------------------------------------------------------------------------------#
-# Distributed under the OSI-approved Apache License, Version 2.0. See
-# accompanying file Copyright.txt for details.
-#------------------------------------------------------------------------------#
-
-set(ADIOS_THIRDPARTY_DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR}/downloads
- CACHE PATH "Download directory for third party dependencies")
-
-include(ExternalProject)
-
-# Boilerplate settings for a common external project infrastructure
-set(EP_ARGS
- DOWNLOAD_DIR ${ADIOS_THIRDPARTY_DOWNLOAD_DIR}
- PREFIX .
- SOURCE_DIR source
- BINARY_DIR build
- STAMP_DIR stamp
- INSTALL_DIR install)
-
-# Use Google Test for a unit testing framework
-cmake_dependent_option(ADIOS_USE_SYSTEM_GOOGLETEST
- "Use a system-supplied Google Test framework" ON
- "BUILD_TESTING" OFF)
-if(BUILD_TESTING)
- if(ADIOS_USE_SYSTEM_GOOGLETEST)
- find_package(GTest REQUIRED)
- if(NOT GTEST_FOUND)
- message(WARNING
- "Unable to find Google Test framework. "
- "Using an internal version")
- set(ADIOS_USE_SYSTEM_GOOGLETEST OFF
- CACHE BOOL "Use a system-supplied Google Test framework" FORCE)
- endif()
- endif()
- if(NOT ADIOS_USE_SYSTEM_GOOGLETEST)
- add_subdirectory(googletest)
- find_package(GTest REQUIRED)
- add_dependencies(GTest::GTest googletest)
- add_dependencies(GTest::Main googletest)
- endif()
-endif()
diff --git a/thirdparty/googletest/CMakeLists.txt b/thirdparty/googletest/CMakeLists.txt
deleted file mode 100644
index 5fc4fa9ee1dfe938e27473fbc1ae7ea0b9c90aea..0000000000000000000000000000000000000000
--- a/thirdparty/googletest/CMakeLists.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-#------------------------------------------------------------------------------#
-# Distributed under the OSI-approved Apache License, Version 2.0. See
-# accompanying file Copyright.txt for details.
-#------------------------------------------------------------------------------#
-
-ExternalProject_Add(googletest
- URL https://github.com/google/googletest/archive/release-1.8.0.zip
- URL_MD5 adfafc8512ab65fd3cf7955ef0100ff5
- ${EP_ARGS}
- CMAKE_ARGS
- -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/install
- -DCMAKE_POLICY_DEFAULT_CMP0048=OLD
- -DCMAKE_POLICY_DEFAULT_CMP0063=NEW
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
- -DBUILD_GMOCK=OFF
- -DBUILD_GTEST=ON
- -Dgtest_build_samples=OFF
- -Dgtest_build_tests=OFF
- -Dgtest_hide_internal_symbols=ON
- -Dgtest_disable_pthreads=OFF
- -Dgtest_force_shared_crt=OFF)
-
-function(get_libfile var name)
- if(BUILD_SHARED_LIBS)
- set(${var} ${CMAKE_SHARED_LIBRARY_PREFIX}${name}${CMAKE_SHARED_LIBRARY_SUFFIX} PARENT_SCOPE)
- else()
- set(${var} ${CMAKE_STATIC_LIBRARY_PREFIX}${name}${CMAKE_STATIC_LIBRARY_SUFFIX} PARENT_SCOPE)
- endif()
-endfunction()
-
-get_libfile(GTEST_LIBRARY gtest)
-get_libfile(GTEST_MAIN_LIBRARY gtest_main)
-set(GTEST_ROOT ${CMAKE_CURRENT_BINARY_DIR}/install)
-set(GTEST_INCLUDE_DIR ${GTEST_ROOT}/include
- CACHE PATH "")
-set(GTEST_LIBRARY ${GTEST_ROOT}/lib/${GTEST_LIBRARY}
- CACHE FILEPATH "")
-set(GTEST_MAIN_LIBRARY ${GTEST_ROOT}/lib/${GTEST_MAIN_LIBRARY}
- CACHE FILEPATH "")