diff --git a/INSTALL b/INSTALL index 007e939..8865734 100644 --- a/INSTALL +++ b/INSTALL @@ -1,8 +1,8 @@ Installation Instructions ************************* -Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation, -Inc. + Copyright (C) 1994-1996, 1999-2002, 2004-2016 Free Software +Foundation, Inc. Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright @@ -12,97 +12,96 @@ without warranty of any kind. Basic Installation ================== - Briefly, the shell commands `./configure; make; make install' should -configure, build, and install this package. The following -more-detailed instructions are generic; see the `README' file for + Briefly, the shell command './configure && make && make install' +should configure, build, and install this package. The following +more-detailed instructions are generic; see the 'README' file for instructions specific to this package. Some packages provide this -`INSTALL' file but do not implement all of the features documented +'INSTALL' file but do not implement all of the features documented below. The lack of an optional feature in a given package is not necessarily a bug. More recommendations for GNU packages can be found in *note Makefile Conventions: (standards)Makefile Conventions. - The `configure' shell script attempts to guess correct values for + The 'configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses -those values to create a `Makefile' in each directory of the package. -It may also create one or more `.h' files containing system-dependent -definitions. Finally, it creates a shell script `config.status' that +those values to create a 'Makefile' in each directory of the package. +It may also create one or more '.h' files containing system-dependent +definitions. Finally, it creates a shell script 'config.status' that you can run in the future to recreate the current configuration, and a -file `config.log' containing compiler output (useful mainly for -debugging `configure'). +file 'config.log' containing compiler output (useful mainly for +debugging 'configure'). - It can also use an optional file (typically called `config.cache' -and enabled with `--cache-file=config.cache' or simply `-C') that saves -the results of its tests to speed up reconfiguring. Caching is -disabled by default to prevent problems with accidental use of stale -cache files. + It can also use an optional file (typically called 'config.cache' and +enabled with '--cache-file=config.cache' or simply '-C') that saves the +results of its tests to speed up reconfiguring. Caching is disabled by +default to prevent problems with accidental use of stale cache files. If you need to do unusual things to compile the package, please try -to figure out how `configure' could check whether to do them, and mail -diffs or instructions to the address given in the `README' so they can +to figure out how 'configure' could check whether to do them, and mail +diffs or instructions to the address given in the 'README' so they can be considered for the next release. If you are using the cache, and at -some point `config.cache' contains results you don't want to keep, you +some point 'config.cache' contains results you don't want to keep, you may remove or edit it. - The file `configure.ac' (or `configure.in') is used to create -`configure' by a program called `autoconf'. You need `configure.ac' if -you want to change it or regenerate `configure' using a newer version -of `autoconf'. + The file 'configure.ac' (or 'configure.in') is used to create +'configure' by a program called 'autoconf'. You need 'configure.ac' if +you want to change it or regenerate 'configure' using a newer version of +'autoconf'. The simplest way to compile this package is: - 1. `cd' to the directory containing the package's source code and type - `./configure' to configure the package for your system. + 1. 'cd' to the directory containing the package's source code and type + './configure' to configure the package for your system. - Running `configure' might take a while. While running, it prints + Running 'configure' might take a while. While running, it prints some messages telling which features it is checking for. - 2. Type `make' to compile the package. + 2. Type 'make' to compile the package. - 3. Optionally, type `make check' to run any self-tests that come with + 3. Optionally, type 'make check' to run any self-tests that come with the package, generally using the just-built uninstalled binaries. - 4. Type `make install' to install the programs and any data files and + 4. Type 'make install' to install the programs and any data files and documentation. When installing into a prefix owned by root, it is recommended that the package be configured and built as a regular - user, and only the `make install' phase executed with root + user, and only the 'make install' phase executed with root privileges. - 5. Optionally, type `make installcheck' to repeat any self-tests, but + 5. Optionally, type 'make installcheck' to repeat any self-tests, but this time using the binaries in their final installed location. This target does not install anything. Running this target as a - regular user, particularly if the prior `make install' required + regular user, particularly if the prior 'make install' required root privileges, verifies that the installation completed correctly. 6. You can remove the program binaries and object files from the - source code directory by typing `make clean'. To also remove the - files that `configure' created (so you can compile the package for - a different kind of computer), type `make distclean'. There is - also a `make maintainer-clean' target, but that is intended mainly + source code directory by typing 'make clean'. To also remove the + files that 'configure' created (so you can compile the package for + a different kind of computer), type 'make distclean'. There is + also a 'make maintainer-clean' target, but that is intended mainly for the package's developers. If you use it, you may have to get all sorts of other programs in order to regenerate files that came with the distribution. - 7. Often, you can also type `make uninstall' to remove the installed + 7. Often, you can also type 'make uninstall' to remove the installed files again. In practice, not all packages have tested that uninstallation works correctly, even though it is required by the GNU Coding Standards. - 8. Some packages, particularly those that use Automake, provide `make + 8. Some packages, particularly those that use Automake, provide 'make distcheck', which can by used by developers to test that all other - targets like `make install' and `make uninstall' work correctly. + targets like 'make install' and 'make uninstall' work correctly. This target is generally not run by end users. Compilers and Options ===================== Some systems require unusual options for compilation or linking that -the `configure' script does not know about. Run `./configure --help' +the 'configure' script does not know about. Run './configure --help' for details on some of the pertinent environment variables. - You can give `configure' initial values for configuration parameters -by setting variables in the command line or in the environment. Here -is an example: + You can give 'configure' initial values for configuration parameters +by setting variables in the command line or in the environment. Here is +an example: ./configure CC=c99 CFLAGS=-g LIBS=-lposix @@ -113,21 +112,21 @@ Compiling For Multiple Architectures You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their -own directory. To do this, you can use GNU `make'. `cd' to the +own directory. To do this, you can use GNU 'make'. 'cd' to the directory where you want the object files and executables to go and run -the `configure' script. `configure' automatically checks for the -source code in the directory that `configure' is in and in `..'. This -is known as a "VPATH" build. +the 'configure' script. 'configure' automatically checks for the source +code in the directory that 'configure' is in and in '..'. This is known +as a "VPATH" build. - With a non-GNU `make', it is safer to compile the package for one + With a non-GNU 'make', it is safer to compile the package for one architecture at a time in the source code directory. After you have -installed the package for one architecture, use `make distclean' before +installed the package for one architecture, use 'make distclean' before reconfiguring for another architecture. On MacOS X 10.5 and later systems, you can create libraries and executables that work on multiple system types--known as "fat" or -"universal" binaries--by specifying multiple `-arch' options to the -compiler but only a single `-arch' option to the preprocessor. Like +"universal" binaries--by specifying multiple '-arch' options to the +compiler but only a single '-arch' option to the preprocessor. Like this: ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ @@ -136,105 +135,104 @@ this: This is not guaranteed to produce working output in all cases, you may have to build one architecture at a time and combine the results -using the `lipo' tool if you have problems. +using the 'lipo' tool if you have problems. Installation Names ================== - By default, `make install' installs the package's commands under -`/usr/local/bin', include files under `/usr/local/include', etc. You -can specify an installation prefix other than `/usr/local' by giving -`configure' the option `--prefix=PREFIX', where PREFIX must be an + By default, 'make install' installs the package's commands under +'/usr/local/bin', include files under '/usr/local/include', etc. You +can specify an installation prefix other than '/usr/local' by giving +'configure' the option '--prefix=PREFIX', where PREFIX must be an absolute file name. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you -pass the option `--exec-prefix=PREFIX' to `configure', the package uses +pass the option '--exec-prefix=PREFIX' to 'configure', the package uses PREFIX as the prefix for installing programs and libraries. Documentation and other data files still use the regular prefix. In addition, if you use an unusual directory layout you can give -options like `--bindir=DIR' to specify different values for particular -kinds of files. Run `configure --help' for a list of the directories -you can set and what kinds of files go in them. In general, the -default for these options is expressed in terms of `${prefix}', so that -specifying just `--prefix' will affect all of the other directory +options like '--bindir=DIR' to specify different values for particular +kinds of files. Run 'configure --help' for a list of the directories +you can set and what kinds of files go in them. In general, the default +for these options is expressed in terms of '${prefix}', so that +specifying just '--prefix' will affect all of the other directory specifications that were not explicitly provided. The most portable way to affect installation locations is to pass the -correct locations to `configure'; however, many packages provide one or +correct locations to 'configure'; however, many packages provide one or both of the following shortcuts of passing variable assignments to the -`make install' command line to change installation locations without +'make install' command line to change installation locations without having to reconfigure or recompile. The first method involves providing an override variable for each -affected directory. For example, `make install +affected directory. For example, 'make install prefix=/alternate/directory' will choose an alternate location for all directory configuration variables that were expressed in terms of -`${prefix}'. Any directories that were specified during `configure', -but not in terms of `${prefix}', must each be overridden at install -time for the entire installation to be relocated. The approach of -makefile variable overrides for each directory variable is required by -the GNU Coding Standards, and ideally causes no recompilation. -However, some platforms have known limitations with the semantics of -shared libraries that end up requiring recompilation when using this -method, particularly noticeable in packages that use GNU Libtool. - - The second method involves providing the `DESTDIR' variable. For -example, `make install DESTDIR=/alternate/directory' will prepend -`/alternate/directory' before all installation names. The approach of -`DESTDIR' overrides is not required by the GNU Coding Standards, and +'${prefix}'. Any directories that were specified during 'configure', +but not in terms of '${prefix}', must each be overridden at install time +for the entire installation to be relocated. The approach of makefile +variable overrides for each directory variable is required by the GNU +Coding Standards, and ideally causes no recompilation. However, some +platforms have known limitations with the semantics of shared libraries +that end up requiring recompilation when using this method, particularly +noticeable in packages that use GNU Libtool. + + The second method involves providing the 'DESTDIR' variable. For +example, 'make install DESTDIR=/alternate/directory' will prepend +'/alternate/directory' before all installation names. The approach of +'DESTDIR' overrides is not required by the GNU Coding Standards, and does not work on platforms that have drive letters. On the other hand, it does better at avoiding recompilation issues, and works well even -when some directory options were not specified in terms of `${prefix}' -at `configure' time. +when some directory options were not specified in terms of '${prefix}' +at 'configure' time. Optional Features ================= If the package supports it, you can cause programs to be installed -with an extra prefix or suffix on their names by giving `configure' the -option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. - - Some packages pay attention to `--enable-FEATURE' options to -`configure', where FEATURE indicates an optional part of the package. -They may also pay attention to `--with-PACKAGE' options, where PACKAGE -is something like `gnu-as' or `x' (for the X Window System). The -`README' should mention any `--enable-' and `--with-' options that the +with an extra prefix or suffix on their names by giving 'configure' the +option '--program-prefix=PREFIX' or '--program-suffix=SUFFIX'. + + Some packages pay attention to '--enable-FEATURE' options to +'configure', where FEATURE indicates an optional part of the package. +They may also pay attention to '--with-PACKAGE' options, where PACKAGE +is something like 'gnu-as' or 'x' (for the X Window System). The +'README' should mention any '--enable-' and '--with-' options that the package recognizes. - For packages that use the X Window System, `configure' can usually + For packages that use the X Window System, 'configure' can usually find the X include and library files automatically, but if it doesn't, -you can use the `configure' options `--x-includes=DIR' and -`--x-libraries=DIR' to specify their locations. +you can use the 'configure' options '--x-includes=DIR' and +'--x-libraries=DIR' to specify their locations. Some packages offer the ability to configure how verbose the -execution of `make' will be. For these packages, running `./configure +execution of 'make' will be. For these packages, running './configure --enable-silent-rules' sets the default to minimal output, which can be -overridden with `make V=1'; while running `./configure +overridden with 'make V=1'; while running './configure --disable-silent-rules' sets the default to verbose, which can be -overridden with `make V=0'. +overridden with 'make V=0'. Particular systems ================== - On HP-UX, the default C compiler is not ANSI C compatible. If GNU -CC is not installed, it is recommended to use the following options in + On HP-UX, the default C compiler is not ANSI C compatible. If GNU CC +is not installed, it is recommended to use the following options in order to use an ANSI C compiler: ./configure CC="cc -Ae -D_XOPEN_SOURCE=500" and if that doesn't work, install pre-built binaries of GCC for HP-UX. - HP-UX `make' updates targets which have the same time stamps as -their prerequisites, which makes it generally unusable when shipped -generated files such as `configure' are involved. Use GNU `make' -instead. + HP-UX 'make' updates targets which have the same time stamps as their +prerequisites, which makes it generally unusable when shipped generated +files such as 'configure' are involved. Use GNU 'make' instead. On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot -parse its `' header file. The option `-nodtk' can be used as -a workaround. If GNU CC is not installed, it is therefore recommended -to try +parse its '' header file. The option '-nodtk' can be used as a +workaround. If GNU CC is not installed, it is therefore recommended to +try ./configure CC="cc" @@ -242,26 +240,26 @@ and if that doesn't work, try ./configure CC="cc -nodtk" - On Solaris, don't put `/usr/ucb' early in your `PATH'. This + On Solaris, don't put '/usr/ucb' early in your 'PATH'. This directory contains several dysfunctional programs; working variants of -these programs are available in `/usr/bin'. So, if you need `/usr/ucb' -in your `PATH', put it _after_ `/usr/bin'. +these programs are available in '/usr/bin'. So, if you need '/usr/ucb' +in your 'PATH', put it _after_ '/usr/bin'. - On Haiku, software installed for all users goes in `/boot/common', -not `/usr/local'. It is recommended to use the following options: + On Haiku, software installed for all users goes in '/boot/common', +not '/usr/local'. It is recommended to use the following options: ./configure --prefix=/boot/common Specifying the System Type ========================== - There may be some features `configure' cannot figure out + There may be some features 'configure' cannot figure out automatically, but needs to determine by the type of machine the package will run on. Usually, assuming the package is built to be run on the -_same_ architectures, `configure' can figure that out, but if it prints +_same_ architectures, 'configure' can figure that out, but if it prints a message saying it cannot guess the machine type, give it the -`--build=TYPE' option. TYPE can either be a short name for the system -type, such as `sun4', or a canonical name which has the form: +'--build=TYPE' option. TYPE can either be a short name for the system +type, such as 'sun4', or a canonical name which has the form: CPU-COMPANY-SYSTEM @@ -270,101 +268,101 @@ where SYSTEM can have one of these forms: OS KERNEL-OS - See the file `config.sub' for the possible values of each field. If -`config.sub' isn't included in this package, then this package doesn't + See the file 'config.sub' for the possible values of each field. If +'config.sub' isn't included in this package, then this package doesn't need to know the machine type. If you are _building_ compiler tools for cross-compiling, you should -use the option `--target=TYPE' to select the type of system they will +use the option '--target=TYPE' to select the type of system they will produce code for. If you want to _use_ a cross compiler, that generates code for a platform different from the build platform, you should specify the "host" platform (i.e., that on which the generated programs will -eventually be run) with `--host=TYPE'. +eventually be run) with '--host=TYPE'. Sharing Defaults ================ - If you want to set default values for `configure' scripts to share, -you can create a site shell script called `config.site' that gives -default values for variables like `CC', `cache_file', and `prefix'. -`configure' looks for `PREFIX/share/config.site' if it exists, then -`PREFIX/etc/config.site' if it exists. Or, you can set the -`CONFIG_SITE' environment variable to the location of the site script. -A warning: not all `configure' scripts look for a site script. + If you want to set default values for 'configure' scripts to share, +you can create a site shell script called 'config.site' that gives +default values for variables like 'CC', 'cache_file', and 'prefix'. +'configure' looks for 'PREFIX/share/config.site' if it exists, then +'PREFIX/etc/config.site' if it exists. Or, you can set the +'CONFIG_SITE' environment variable to the location of the site script. +A warning: not all 'configure' scripts look for a site script. Defining Variables ================== Variables not defined in a site shell script can be set in the -environment passed to `configure'. However, some packages may run +environment passed to 'configure'. However, some packages may run configure again during the build, and the customized values of these variables may be lost. In order to avoid this problem, you should set -them in the `configure' command line, using `VAR=value'. For example: +them in the 'configure' command line, using 'VAR=value'. For example: ./configure CC=/usr/local2/bin/gcc -causes the specified `gcc' to be used as the C compiler (unless it is +causes the specified 'gcc' to be used as the C compiler (unless it is overridden in the site shell script). -Unfortunately, this technique does not work for `CONFIG_SHELL' due to -an Autoconf limitation. Until the limitation is lifted, you can use -this workaround: +Unfortunately, this technique does not work for 'CONFIG_SHELL' due to an +Autoconf limitation. Until the limitation is lifted, you can use this +workaround: CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash -`configure' Invocation +'configure' Invocation ====================== - `configure' recognizes the following options to control how it + 'configure' recognizes the following options to control how it operates. -`--help' -`-h' - Print a summary of all of the options to `configure', and exit. +'--help' +'-h' + Print a summary of all of the options to 'configure', and exit. -`--help=short' -`--help=recursive' +'--help=short' +'--help=recursive' Print a summary of the options unique to this package's - `configure', and exit. The `short' variant lists options used - only in the top level, while the `recursive' variant lists options - also present in any nested packages. + 'configure', and exit. The 'short' variant lists options used only + in the top level, while the 'recursive' variant lists options also + present in any nested packages. -`--version' -`-V' - Print the version of Autoconf used to generate the `configure' +'--version' +'-V' + Print the version of Autoconf used to generate the 'configure' script, and exit. -`--cache-file=FILE' +'--cache-file=FILE' Enable the cache: use and save the results of the tests in FILE, - traditionally `config.cache'. FILE defaults to `/dev/null' to + traditionally 'config.cache'. FILE defaults to '/dev/null' to disable caching. -`--config-cache' -`-C' - Alias for `--cache-file=config.cache'. +'--config-cache' +'-C' + Alias for '--cache-file=config.cache'. -`--quiet' -`--silent' -`-q' +'--quiet' +'--silent' +'-q' Do not print messages saying which checks are being made. To - suppress all normal output, redirect it to `/dev/null' (any error + suppress all normal output, redirect it to '/dev/null' (any error messages will still be shown). -`--srcdir=DIR' +'--srcdir=DIR' Look for the package's source code in directory DIR. Usually - `configure' can determine that directory automatically. + 'configure' can determine that directory automatically. -`--prefix=DIR' - Use DIR as the installation prefix. *note Installation Names:: - for more details, including other options available for fine-tuning - the installation locations. +'--prefix=DIR' + Use DIR as the installation prefix. *note Installation Names:: for + more details, including other options available for fine-tuning the + installation locations. -`--no-create' -`-n' +'--no-create' +'-n' Run the configure checks, but stop before creating any output files. -`configure' also accepts some other, not widely useful, options. Run -`configure --help' for more details. +'configure' also accepts some other, not widely useful, options. Run +'configure --help' for more details. diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index f9e8deb..d3b5d23 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -6,7 +6,7 @@ if (CUDA_FOUND) set(CUDA_SOURCES ../../openfpm_devices/src/memory/CudaMemory.cu VCluster/cuda/VCluster_semantic_unit_cuda_tests.cu VCluster/cuda/VCluster_unit_tests.cu ) endif() -add_executable(vcluster_test main.cpp VCluster/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp VCluster/VCluster_unit_tests.cpp VCluster/VCluster_semantic_unit_tests.cpp ${CUDA_SOURCES}) +add_executable(vcluster_test main.cpp VCluster/VCluster.cpp VCluster/InVis.cpp VCluster/InVisVolume.cpp ../../openfpm_devices/src/memory/ShmAllocator_manager.cpp ../../openfpm_devices/src/memory/SemManager.cpp ../../openfpm_devices/src/memory/ShmAllocator.cpp ../../openfpm_devices/src/memory/ShmBuffer.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp VCluster/VCluster_unit_tests.cpp VCluster/VCluster_semantic_unit_tests.cpp ${CUDA_SOURCES}) if ( CMAKE_COMPILER_IS_GNUCC ) target_compile_options(vcluster_test PRIVATE "-Wno-deprecated-declarations") @@ -15,7 +15,7 @@ if ( CMAKE_COMPILER_IS_GNUCC ) endif() endif() -add_library(vcluster STATIC VCluster/VCluster.cpp) +add_library(vcluster STATIC VCluster/VCluster.cpp VCluster/InVis.cpp VCluster/InVisVolume.cpp) ########################### @@ -27,6 +27,8 @@ if(CUDA_FOUND) endif() endif() +set(JAVA_HOME /usr/lib/jvm/adoptopenjdk-11-hotspot-amd64) + target_include_directories (vcluster_test PUBLIC ${CUDA_INCLUDE_DIRS}) target_include_directories (vcluster_test PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) target_include_directories (vcluster_test PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_devices/src/) @@ -35,6 +37,8 @@ target_include_directories (vcluster_test PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../ target_include_directories (vcluster_test PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/config) target_include_directories (vcluster_test PUBLIC ${Boost_INCLUDE_DIRS}) target_include_directories (vcluster_test PUBLIC ${PETSC_INCLUDES}) +target_include_directories (vcluster_test PUBLIC ${JAVA_HOME}/include ${JAVA_HOME}/include/linux) + target_include_directories (vcluster PUBLIC ${CUDA_INCLUDE_DIRS}) target_include_directories (vcluster PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) @@ -43,7 +47,11 @@ target_include_directories (vcluster PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/config) target_include_directories (vcluster PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/) target_include_directories (vcluster PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_devices/src/) target_include_directories (vcluster PUBLIC ${Boost_INCLUDE_DIRS}) +target_include_directories (vcluster PUBLIC ${JAVA_HOME}/include ${JAVA_HOME}/include/linux) + +#target_link_libraries(vcluster ${JAVA_HOME}/lib/server/libjvm.so) +target_link_libraries(vcluster_test ${JAVA_HOME}/lib/server/libjvm.so) target_link_libraries(vcluster_test ${Boost_LIBRARIES}) target_link_libraries(vcluster_test ${PETSC_LIBRARIES}) @@ -69,6 +77,8 @@ install(FILES MPI_wrapper/MPI_IallreduceW.hpp install(FILES VCluster/VCluster_base.hpp VCluster/VCluster.hpp VCluster/VCluster_meta_function.hpp + VCluster/InVis.hpp + VCluster/InVisVolume.hpp DESTINATION openfpm_vcluster/include/VCluster ) install (FILES util/Vcluster_log.hpp diff --git a/src/MPI_wrapper/MPI_IAllGather.hpp b/src/MPI_wrapper/MPI_IAllGather.hpp index ce04943..c25b243 100644 --- a/src/MPI_wrapper/MPI_IAllGather.hpp +++ b/src/MPI_wrapper/MPI_IAllGather.hpp @@ -28,9 +28,9 @@ class MPI_IAllGatherWB { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_BYTE, rbuf, sz_r, MPI_BYTE, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_BYTE, rbuf, sz_r, MPI_BYTE, ext_comm,&req)); } }; @@ -44,9 +44,9 @@ template class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sizeof(T) * sz_s,MPI_BYTE, rbuf, sz_r * sizeof(T), MPI_BYTE, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sizeof(T) * sz_s,MPI_BYTE, rbuf, sz_r * sizeof(T), MPI_BYTE, ext_comm,&req)); } }; @@ -57,9 +57,9 @@ template class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_INT, rbuf, sz_r, MPI_INT, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_INT, rbuf, sz_r, MPI_INT, ext_comm,&req)); } }; @@ -69,9 +69,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED, rbuf, sz_r, MPI_UNSIGNED, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED, rbuf, sz_r, MPI_UNSIGNED, ext_comm,&req)); } }; @@ -81,9 +81,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_SHORT, rbuf, sz_r, MPI_SHORT, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_SHORT, rbuf, sz_r, MPI_SHORT, ext_comm,&req)); } }; @@ -94,9 +94,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED_SHORT, rbuf, sz_r, MPI_UNSIGNED_SHORT, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED_SHORT, rbuf, sz_r, MPI_UNSIGNED_SHORT, ext_comm,&req)); } }; @@ -107,9 +107,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_CHAR, rbuf, sz_r, MPI_CHAR, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_CHAR, rbuf, sz_r, MPI_CHAR, ext_comm,&req)); } }; @@ -120,9 +120,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED_CHAR, rbuf, sz_r, MPI_UNSIGNED_CHAR, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED_CHAR, rbuf, sz_r, MPI_UNSIGNED_CHAR, ext_comm,&req)); } }; @@ -132,9 +132,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED_LONG, rbuf, sz_r, MPI_UNSIGNED_LONG, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_UNSIGNED_LONG, rbuf, sz_r, MPI_UNSIGNED_LONG, ext_comm,&req)); } }; @@ -144,9 +144,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_LONG, rbuf, sz_r, MPI_LONG, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_LONG, rbuf, sz_r, MPI_LONG, ext_comm,&req)); } }; @@ -156,9 +156,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_FLOAT, rbuf, sz_r, MPI_FLOAT, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_FLOAT, rbuf, sz_r, MPI_FLOAT, ext_comm,&req)); } }; @@ -168,9 +168,9 @@ template<> class MPI_IAllGatherW template<> class MPI_IAllGatherW { public: - static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req) + static inline void gather(void * sbuf, size_t sz_s ,void * rbuf, size_t sz_r, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_DOUBLE, rbuf, sz_r, MPI_DOUBLE, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallgather(sbuf,sz_s,MPI_DOUBLE, rbuf, sz_r, MPI_DOUBLE, ext_comm,&req)); } }; diff --git a/src/MPI_wrapper/MPI_IBcastW.hpp b/src/MPI_wrapper/MPI_IBcastW.hpp index 6fe9990..97e175e 100644 --- a/src/MPI_wrapper/MPI_IBcastW.hpp +++ b/src/MPI_wrapper/MPI_IBcastW.hpp @@ -33,9 +33,9 @@ class MPI_IBcastWB { public: - static inline void bcast(size_t proc ,void * buf, size_t sz, MPI_Request & req) + static inline void bcast(size_t proc ,void * buf, size_t sz, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(buf,sz,MPI_BYTE, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(buf,sz,MPI_BYTE, proc , ext_comm,&req)); } }; @@ -48,9 +48,9 @@ class MPI_IBcastWB template class MPI_IBcastW { public: - template static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + template static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc , ext_comm,&req)); } }; @@ -61,9 +61,9 @@ template class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_INT, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_INT, proc , ext_comm,&req)); } }; @@ -73,9 +73,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED, proc , ext_comm,&req)); } }; @@ -85,9 +85,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_SHORT, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_SHORT, proc , ext_comm,&req)); } }; @@ -97,9 +97,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED_SHORT, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED_SHORT, proc , ext_comm,&req)); } }; @@ -109,9 +109,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_CHAR, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_CHAR, proc , ext_comm,&req)); } }; @@ -121,9 +121,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED_CHAR, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED_CHAR, proc , ext_comm,&req)); } }; @@ -133,9 +133,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED_LONG, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_UNSIGNED_LONG, proc , ext_comm,&req)); } }; @@ -145,9 +145,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_LONG, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_LONG, proc , ext_comm,&req)); } }; @@ -157,9 +157,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_FLOAT, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_FLOAT, proc , ext_comm,&req)); } }; @@ -169,9 +169,9 @@ template<> class MPI_IBcastW template<> class MPI_IBcastW { public: - static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req) + static inline void bcast(size_t proc ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_DOUBLE, proc , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Ibcast(v.getPointer(), v.size(),MPI_DOUBLE, proc , ext_comm,&req)); } }; @@ -195,15 +195,19 @@ struct bcast_inte_impl //! root processor size_t root; + //! MPI communicator + MPI_Comm ext_comm; + /*! \brief constructor * * \param v set of pointer buffers to set * */ inline bcast_inte_impl(vect & send, - openfpm::vector & req, - size_t root) - :send(send),req(req),root(root) + openfpm::vector & req, + size_t root, + MPI_Comm ext_comm) + :send(send),req(req),root(root),ext_comm(ext_comm) {}; //! It call the copy function for each property @@ -216,7 +220,7 @@ struct bcast_inte_impl req.add(); // gather - MPI_IBcastWB::bcast(root,&send.template get(0),send.size()*sizeof(send_type),req.last()); + MPI_IBcastWB::bcast(root,&send.template get(0),send.size()*sizeof(send_type),req.last(),ext_comm); } }; @@ -226,13 +230,14 @@ struct b_cast_helper template class layout_base > static void bcast_(openfpm::vector & req, openfpm::vector & v, - size_t root) + size_t root, + MPI_Comm ext_comm) { // Create one request req.add(); // gather - MPI_IBcastW::bcast(root,v,req.last()); + MPI_IBcastW::bcast(root,v,req.last(),ext_comm); } }; @@ -242,9 +247,10 @@ struct b_cast_helper template class layout_base > static void bcast_(openfpm::vector & req, openfpm::vector & v, - size_t root) + size_t root, + MPI_Comm ext_comm) { - bcast_inte_impl> bc(v,req,root); + bcast_inte_impl> bc(v,req,root,ext_comm); boost::mpl::for_each_ref>(bc); } diff --git a/src/MPI_wrapper/MPI_IallreduceW.hpp b/src/MPI_wrapper/MPI_IallreduceW.hpp index c34e01c..f53ba5a 100644 --- a/src/MPI_wrapper/MPI_IallreduceW.hpp +++ b/src/MPI_wrapper/MPI_IallreduceW.hpp @@ -19,7 +19,7 @@ template class MPI_IallreduceW { public: - static inline void reduce(T & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(T & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " cannot recognize " << typeid(T).name() << "\n"; } @@ -32,9 +32,9 @@ template class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(int & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(int & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_INT, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_INT, op, ext_comm,&req)); } }; @@ -44,9 +44,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(unsigned int & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(unsigned int & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED, op, ext_comm,&req)); } }; @@ -56,9 +56,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(short & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(short & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_SHORT, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_SHORT, op, ext_comm,&req)); } }; @@ -68,9 +68,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(unsigned short & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(unsigned short & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED_SHORT, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED_SHORT, op, ext_comm,&req)); } }; @@ -80,9 +80,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(char & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(char & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_CHAR, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_CHAR, op, ext_comm,&req)); } }; @@ -92,9 +92,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(unsigned char & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(unsigned char & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED_CHAR, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED_CHAR, op, ext_comm,&req)); } }; @@ -104,9 +104,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(size_t & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(size_t & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED_LONG, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_UNSIGNED_LONG, op, ext_comm,&req)); } }; @@ -116,9 +116,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(long int & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(long int & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_LONG, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_LONG, op, ext_comm,&req)); } }; @@ -128,9 +128,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(float & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(float & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_FLOAT, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_FLOAT, op, ext_comm,&req)); } }; @@ -140,9 +140,9 @@ template<> class MPI_IallreduceW template<> class MPI_IallreduceW { public: - static inline void reduce(double & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(double & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_DOUBLE, op, MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Iallreduce(MPI_IN_PLACE, &buf, 1,MPI_DOUBLE, op, ext_comm,&req)); } }; @@ -154,9 +154,9 @@ template<> class MPI_IallreduceW /*template<> class MPI_IallreduceW> { public: - static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_INT, op, MPI_COMM_WORLD,&req); + MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_INT, op, ext_comm,&req); } };*/ @@ -166,9 +166,9 @@ template<> class MPI_IallreduceW /*template<> class MPI_IallreduceW> { public: - static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_SHORT, op, MPI_COMM_WORLD,&req); + MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_SHORT, op, ext_comm,&req); } };*/ @@ -178,9 +178,9 @@ template<> class MPI_IallreduceW /*template<> class MPI_IallreduceW> { public: - static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_CHAR, op, MPI_COMM_WORLD,&req); + MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_CHAR, op, ext_comm,&req); } };*/ @@ -190,9 +190,9 @@ template<> class MPI_IallreduceW /*template<> class MPI_IallreduceW> { public: - static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_UNSIGNED_LONG, op, MPI_COMM_WORLD,&req); + MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_UNSIGNED_LONG, op, ext_comm,&req); } };*/ @@ -202,9 +202,9 @@ template<> class MPI_IallreduceW /*template<> class MPI_IallreduceW> { public: - static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_FLOAT, op, MPI_COMM_WORLD,&req); + MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_FLOAT, op, ext_comm,&req); } };*/ @@ -215,9 +215,9 @@ template<> class MPI_IallreduceW /*template<> class MPI_IallreduceW> { public: - static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req) + static inline void reduce(openfpm::vector & buf,MPI_Op op, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_DOUBLE, op, MPI_COMM_WORLD,&req); + MPI_Iallreduce(MPI_IN_PLACE, &buf.get(0), buf.size(),MPI_DOUBLE, op, ext_comm,&req); } };*/ diff --git a/src/MPI_wrapper/MPI_IrecvW.hpp b/src/MPI_wrapper/MPI_IrecvW.hpp index 266df27..4fef736 100644 --- a/src/MPI_wrapper/MPI_IrecvW.hpp +++ b/src/MPI_wrapper/MPI_IrecvW.hpp @@ -22,9 +22,9 @@ class MPI_IrecvWB * \param req MPI request * */ - static inline void recv(size_t proc , size_t tag ,void * buf, size_t sz, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,void * buf, size_t sz, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(buf,sz,MPI_BYTE, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(buf,sz,MPI_BYTE, proc, tag , ext_comm,&req)); } }; @@ -37,10 +37,15 @@ class MPI_IrecvWB template class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc, tag , ext_comm,&req)); } + + static inline void recv(size_t proc , size_t tag ,openfpm::vector_ofp & v, MPI_Request & req, MPI_Comm ext_comm) + { + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc, tag , ext_comm,&req)); + } }; @@ -50,9 +55,9 @@ template class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_INT, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_INT, proc, tag , ext_comm,&req)); } }; @@ -62,9 +67,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED, proc, tag , ext_comm,&req)); } }; @@ -74,9 +79,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_SHORT, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_SHORT, proc, tag , ext_comm,&req)); } }; @@ -86,9 +91,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED_SHORT, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED_SHORT, proc, tag , ext_comm,&req)); } }; @@ -98,9 +103,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_CHAR, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_CHAR, proc, tag , ext_comm,&req)); } }; @@ -110,9 +115,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED_CHAR, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED_CHAR, proc, tag , ext_comm,&req)); } }; @@ -122,9 +127,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED_LONG, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_UNSIGNED_LONG, proc, tag , ext_comm,&req)); } }; @@ -134,9 +139,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_LONG, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_LONG, proc, tag , ext_comm,&req)); } }; @@ -146,9 +151,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_FLOAT, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_FLOAT, proc, tag , ext_comm,&req)); } }; @@ -158,9 +163,9 @@ template<> class MPI_IrecvW template<> class MPI_IrecvW { public: - static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void recv(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_DOUBLE, proc, tag , MPI_COMM_WORLD,&req)); + MPI_SAFE_CALL(MPI_Irecv(v.getPointer(), v.size(),MPI_DOUBLE, proc, tag , ext_comm,&req)); } }; diff --git a/src/MPI_wrapper/MPI_IsendW.hpp b/src/MPI_wrapper/MPI_IsendW.hpp index 4c41962..bae7195 100644 --- a/src/MPI_wrapper/MPI_IsendW.hpp +++ b/src/MPI_wrapper/MPI_IsendW.hpp @@ -16,9 +16,9 @@ class MPI_IsendWB { public: - static inline void send(size_t proc , size_t tag ,const void * buf, size_t sz, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,const void * buf, size_t sz, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(buf, sz,MPI_BYTE, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(buf, sz,MPI_BYTE, proc, tag , ext_comm,&req); } }; @@ -31,12 +31,27 @@ class MPI_IsendWB template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc, tag , ext_comm,&req); } }; +/*! \brief General send for a vector of any type + * + * \tparam any type + * + */ + +template +class MPI_IsendW +{ +public: + static inline void send(size_t proc , size_t tag ,openfpm::vector_ofp & v, MPI_Request & req, MPI_Comm ext_comm) + { + MPI_Isend(v.getPointer(), v.size() * sizeof(T),MPI_BYTE, proc, tag , ext_comm,&req); + } +}; /*! \brief specialization for vector of integer * @@ -44,9 +59,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_INT, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_INT, proc, tag , ext_comm,&req); } }; @@ -56,9 +71,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED, proc, tag , ext_comm,&req); } }; @@ -68,9 +83,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_SHORT, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_SHORT, proc, tag , ext_comm,&req); } }; @@ -80,9 +95,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED_SHORT, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED_SHORT, proc, tag , ext_comm,&req); } }; @@ -92,9 +107,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_CHAR, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_CHAR, proc, tag , ext_comm,&req); } }; @@ -104,9 +119,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED_CHAR, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED_CHAR, proc, tag , ext_comm,&req); } }; @@ -116,9 +131,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED_LONG, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_UNSIGNED_LONG, proc, tag , ext_comm,&req); } }; @@ -128,9 +143,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_LONG, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_LONG, proc, tag , ext_comm,&req); } }; @@ -140,9 +155,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_FLOAT, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_FLOAT, proc, tag , ext_comm,&req); } }; @@ -152,9 +167,9 @@ template class MPI_IsendW template class MPI_IsendW { public: - static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req) + static inline void send(size_t proc , size_t tag ,openfpm::vector & v, MPI_Request & req, MPI_Comm ext_comm) { - MPI_Isend(v.getPointer(), v.size(),MPI_DOUBLE, proc, tag , MPI_COMM_WORLD,&req); + MPI_Isend(v.getPointer(), v.size(),MPI_DOUBLE, proc, tag , ext_comm,&req); } }; diff --git a/src/VCluster/InVis.cpp b/src/VCluster/InVis.cpp new file mode 100644 index 0000000..d599a9a --- /dev/null +++ b/src/VCluster/InVis.cpp @@ -0,0 +1,1002 @@ +/* + * InVis.cpp + * + * Created on: May 12, 2020 + * Author: Aryaman Gupta + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "timer.hpp" + +#include "InVis.hpp" +#include "memory/ShmBuffer.hpp" + +#define USE_VULKAN true +#define VERBOSE false +#define SAVE_FILES true + +MPI_Comm renComm; // non class variable = renderComm +MPI_Comm visualizationComm; // non class variable = visComm +MPI_Comm steeringComm; // non class variable = steerComm +int imgSize; +double avg_recent = 0.0; +long prevtime = 0; +int count = 0; +long totaltime = 0; +int timeVDIwrite = 0; +double alltoall_time = 0.0; +double gather_time = 0.0; +int numLayers = -1; + +void * recvBufCol = nullptr; +void * recvBufDepth = nullptr; +void * gather_recv = nullptr; + +timer t_alltoall; +timer t_gather; + +jmethodID streamMethod = nullptr; +jmethodID compositeMethod = nullptr; +jmethodID updateVisMethod = nullptr; + + +MPI_Request interact_req; +int * size_interact; + +InVis::InVis(int cPartners, MPI_Comm vComm, MPI_Comm rComm, MPI_Comm sComm, bool isMaster) { + vis_is_running = true; + windowSize = 700; + computePartners = cPartners; + imageSize = windowSize*windowSize*7; //RGBA + 4 bytes for depth + visComm = vComm; + renderComm = rComm; + steerComm = sComm; + renComm = rComm; + visualizationComm = vComm; + steeringComm = sComm; + if(renderComm != MPI_COMM_NULL) { + MPI_Comm_size(renderComm, &rCommSize); + std::cout << "RenderComm size is " << rCommSize << std::endl; + } + if(visComm != MPI_COMM_NULL) { + MPI_Comm_size(visComm, &vCommSize); + std::cout << "VisComm size is " << vCommSize << std::endl; + } + imgSize = imageSize; + + for(int i = 0; i< computePartners; i++) { + std::vector tmp; + gridBuffers.push_back(tmp); + } + + DIR *dir; + struct dirent *ent; + std::string classPath = "-Djava.class.path="; + std::string directory = "/home/aryaman/Repositories/scenery-insitu/target/dependency/"; + if ((dir = opendir ("/home/aryaman/Repositories/scenery-insitu/target/dependency")) != NULL) { + /* print all the files and directories within directory */ + while ((ent = readdir (dir)) != NULL) { + classPath.append(directory); + classPath.append(ent->d_name); + classPath.append(":"); + } + closedir (dir); + } else { + /* could not open directory */ + std::cerr << "ERROR: Could not open directory "<< directory <GetVersion(); + std::cout << ((ver >> 16) & 0x0f) << "." << (ver & 0x0f) << std::endl; + + + jclass localClass; + localClass = env->FindClass(className.c_str()); // try to find the class + if(localClass == nullptr) { + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: class "<< className << " not found !" <GetMethodID(localClass, "", "()V"); // find constructor + if (ctor == nullptr) { + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: constructor not found !" <NewObject(localClass, ctor); + if (!localObj) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: class object is null !"; + std::exit(EXIT_FAILURE); + } + } + + if (VERBOSE) std::cout << "Object of class has been constructed" << std::endl; + + clazz = reinterpret_cast(env->NewGlobalRef(localClass)); + obj = reinterpret_cast(env->NewGlobalRef(localObj)); + + env->DeleteLocalRef(localClass); + env->DeleteLocalRef(localObj); + + if (VERBOSE) std::cout << "Global references have been created and local ones deleted" << std::endl; +} + +void remove_memory() { //TODO: call when in situ needs to terminate + free(recvBufCol); + free(gather_recv); +} + +vis_type InVis::getVisType() { + ShmBuffer * buf = new ShmBuffer(datatype_path, 0, false); + buf->update_key(true); + ptr_with_size pws = buf->attach(); + int * ptr = (int *)pws.ptr; + if(*ptr == 1) { + return vis_type::grid; + } else if (*ptr == 2) { + return vis_type::particles; + } + else { + std::cerr<<"Found unidentified data when searching for data type flag"<AttachCurrentThread(reinterpret_cast(&env), NULL); + std::string pName; + if(pos) pName = "/"; + else pName = "/home"; + + ShmBuffer *buf; + buf = new ShmBuffer(pName, memKey, true); + double *str = NULL; + ptr_with_size pws{}; + jobject byteBuffer; + + while(true) { + buf->update_key(true); + pws = buf->attach(); + str = (double *)pws.ptr; + byteBuffer = (env)->NewDirectByteBuffer((void*) str, pws.size); + int temp = (env)-> GetDirectBufferCapacity(byteBuffer); + if (temp == -1) { + std::cout<<"Bytebuffer capacity was found to be -1. Size of mem returned was " << pws.size <<". This is for memKey " << memKey << " and pName: " << pName << std::endl; + } + if (VERBOSE) std::cout<<"Java method updatepos/updateprops has been called by thread with memkey " << memKey <<"! with buffer size "<CallVoidMethod(obj, methodID, byteBuffer, memKey); + if (VERBOSE) std::cout<<"Back after updating pos/props"<detach(false); //detach from the previous key + env->DeleteLocalRef(byteBuffer); + } + jvm->DetachCurrentThread(); +} + +void InVis::getMemoryPos() { + JNIEnv *env; + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + + jmethodID updatePosMethod = env->GetMethodID(clazz, "updatePos", "(Ljava/nio/ByteBuffer;I)V"); + if(updatePosMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function updatePos not found!"; +// std::exit(EXIT_FAILURE); + } + } + + std::vector threads; + + for(int i = 0; i < computePartners; i++){ + threads.emplace_back(&InVis::updateMemory, this, updatePosMethod, i, true); + } + + for(int i = 0; i < computePartners; i++) { + threads[i].join(); + } + jvm->DetachCurrentThread(); +} + +void InVis::getMemoryProps() { + JNIEnv *env; + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + + jmethodID updatePropsMethod = env->GetMethodID(clazz, "updateProps", "(Ljava/nio/ByteBuffer;I)V"); + if(updatePropsMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function updateProps not found!"; +// std::exit(EXIT_FAILURE); + } + } + + std::vector threads; + + for(int i = 0; i < computePartners; i++){ + threads.emplace_back(&InVis::updateMemory, this, updatePropsMethod, i, false); + } + + for(int i = 0; i < computePartners; i++) { + threads[i].join(); + } + jvm->DetachCurrentThread(); +} + +void sendImage(JNIEnv *e, jobject clazz, jobject image) { + if (VERBOSE) std::cout<< "In send image function" << std::endl; + jbyte *buf; + MPI_Request req; + MPI_Status stat; + buf = (jbyte *) e->GetDirectBufferAddress(image); + MPI_Isend((void *)buf, imgSize, MPI_BYTE, 0, 0, renComm, &req); + MPI_Wait(&req, &stat); //TODO: put wait before Isend or remove wait +} + +void InVis::receiveImages() { + JNIEnv *env; + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + + char buf[rCommSize - 1][imageSize]; + MPI_Request requests[rCommSize - 1]; + MPI_Status statuses[rCommSize - 1]; + jobjectArray bytebuffers; + jsize size = rCommSize - 1; + bytebuffers = (env)->NewObjectArray(size, (env)->FindClass("java/nio/ByteBuffer"), 0); + if (VERBOSE) std::cout << "Looking for function composite"<GetMethodID(clazz, "composite", "([Ljava/nio/ByteBuffer;I)V"); + if(compositeMethod == nullptr) { + if ((env)->ExceptionOccurred()) { + (env)->ExceptionDescribe(); + } else { + std::cout << "ERROR: function composite not found!"<NewDirectByteBuffer((void*) buf[i-1], imageSize); +// int temp = (env)-> GetDirectBufferCapacity(bb); +// std::cout<<"Bytebuffer containing color and depth is of size "<SetObjectArrayElement(bytebuffers, i-1, bb); + } + if (VERBOSE) std::cout << "Function composite will be called"< CallVoidMethod(obj, compositeMethod, bytebuffers, rCommSize); + } + jvm->DetachCurrentThread(); +} + +void InVis::updateCamera() { + JNIEnv *env; + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + jmethodID adjustCamMethod = env->GetMethodID(clazz, "adjustCamera", "()V"); + if(adjustCamMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function adjustCamera not found!"; +// std::exit(EXIT_FAILURE); + } + } + env->CallVoidMethod(obj, adjustCamMethod); + jvm->DetachCurrentThread(); +} + +void InVis::interactVis() { + JNIEnv *env; + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + + jmethodID updateVisMethod = env->GetMethodID(clazz, "updateVis", "(Ljava/nio/ByteBuffer;)V"); + if(updateVisMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function updateVis not found!"; +// std::exit(EXIT_FAILURE); + } + } + + int size = 0; + while(vis_is_running) { + if (VERBOSE) std::cout<<"Waiting for broadcast message"<NewDirectByteBuffer(buffer, size); + + env->CallVoidMethod(obj, updateVisMethod, bbMessage); + if(env->ExceptionOccurred()) { + env->ExceptionDescribe(); + env->ExceptionClear(); + } + if (VERBOSE) std::cout<<"Updated the camera!"<DeleteLocalRef(bbMessage); + } +} + +void InVis::getGridMemory() { + JNIEnv *env; + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + + jmethodID updateDataMethod = env->GetMethodID(clazz, "updateData", "(II[Ljava/nio/ByteBuffer;[I[I[I)V"); + if(updateDataMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function updateData not found!"; +// std::exit(EXIT_FAILURE); + } + } + +// std::cout<<"GOing to sleep"<update_key(true); + pws = GBoxBuf->attach(); + + size_t metaSize = pws.size - 512 - 32; + int numMetaElements = metaSize / sizeof(long); + if (VERBOSE) std::cout << "Got metadata for compute partner " << i << ". The size and no of elements are:" << metaSize << " and " << numMetaElements << std::endl; + long *metaData = (long*)pws.ptr; + + for(int j = 0; j < numMetaElements; j++) { + if (VERBOSE) std::cout< 3 + grid dimensions -> 6 + domain dimensions -> 6 + int numGrids = numMetaElements / elementsInGBox; + + int origins[3 * numGrids]; + jintArray jOrigins = env->NewIntArray(3 * numGrids); + int gridDims[6 * numGrids]; + jintArray jGridDims = env->NewIntArray(6 * numGrids); + int domainDims[6 * numGrids]; + jintArray jDomainDims = env->NewIntArray(6 * numGrids); + + jobjectArray bytebuffers; // Each element will be a direct byte buffer wrapping a grid that is controlled by this computePartner + jsize size = numGrids; + bytebuffers = (env)->NewObjectArray(size, (env)->FindClass("java/nio/ByteBuffer"), 0); + + int it = 0; + for(int j = 0; j < numGrids; j++) { + gridDims[j * 6] = (int)metaData[it]; + it ++; + gridDims[j * 6 + 1] = (int)metaData[it]; + it++; + gridDims[j * 6 + 2] = (int)metaData[it]; + it++; + gridDims[j * 6 + 3] = (int)metaData[it]; + it ++; + gridDims[j * 6 + 4] = (int)metaData[it]; + it++; + gridDims[j * 6 + 5] = (int)metaData[it]; + it++; + + domainDims[j * 6] = (int)metaData[it]; + it ++; + domainDims[j * 6 + 1] = (int)metaData[it]; + it++; + domainDims[j * 6 + 2] = (int)metaData[it]; + it++; + domainDims[j * 6 + 3] = (int)metaData[it]; + it ++; + domainDims[j * 6 + 4] = (int)metaData[it]; + it++; + domainDims[j * 6 + 5] = (int)metaData[it]; + it++; + + origins[j * 3] = (int)metaData[it]; + it ++; + origins[j * 3 + 1] = (int)metaData[it]; + it++; + origins[j * 3 + 2] = (int)metaData[it]; + it++; + + gridBuffers[i].push_back(new ShmBuffer(pName, j+1, true)); + gridBuffers[i][j]->update_key(true); + + ptr_with_size tmp = gridBuffers[i][j]->attach(); + + int width = abs(gridDims[j*6] - gridDims[j*6 + 3]) + 1; + + int height = abs(gridDims[j*6 + 1] - gridDims[j*6 + 4]) + 1; + + int depth = abs(gridDims[j*6 + 2] - gridDims[j*6 + 5]) + 1; + + int gridSize = width * height * depth; + + if (VERBOSE) std::cout<< "Grid " << j << " of computePartner " << i << " is of size " << gridSize << std::endl; + + jobject bb; + bb = env->NewDirectByteBuffer((void *)tmp.ptr, 2*gridSize); + env->SetObjectArrayElement(bytebuffers, j, bb); + int temp = (env)-> GetDirectBufferCapacity(bb); + if (VERBOSE) std::cout<<"Bytebuffer capacity was found to be " <DeleteLocalRef(bb); TODO: uncomment + } + + env->SetIntArrayRegion(jOrigins, 0, 3 * numGrids, origins); + env->SetIntArrayRegion(jGridDims, 0, 6 * numGrids, gridDims); + env->SetIntArrayRegion(jDomainDims, 0, 6 * numGrids, domainDims); + // the meta arguments for the java function updateData are now ready + if (VERBOSE) std::cout<<"the meta arguments for the java function updateData are now ready"<CallVoidMethod(obj, updateDataMethod, i, numGrids, bytebuffers, jOrigins, jGridDims, jDomainDims); + +// env->DeleteLocalRef(bytebuffers); +// env->DeleteLocalRef(jOrigins); +// env->DeleteLocalRef(jGridDims); +// env->DeleteLocalRef(jDomainDims); + } + jvm->DetachCurrentThread(); +} + +void distributeVDIs(JNIEnv *e, jobject clazzObject, jobject subVDICol, jobject subVDIDepth, jint sizePerProcess, jint commSize, jboolean generateVDIs) { + if (VERBOSE) std::cout<<"In distribute VDIs function. Comm size is "<GetDirectBufferAddress(subVDICol); + void *ptrDepth = nullptr; + if(!generateVDIs) { ptrDepth = e->GetDirectBufferAddress(subVDIDepth); } + + if(numLayers == -1) { + if (generateVDIs) { + numLayers = 3; // color + start depth + end depth + } else { + numLayers = 1; // only color, because depth is in a separate buffer + } + } + + if(recvBufCol == nullptr) { + std::cout<<"allocating in distributeVDIs"<0) {alltoall_time += t_alltoall.getwct();} + // MPI_Alltoall(ptrDepth, sizePerProcess*2, MPI_BYTE, recvBufDepth, sizePerProcess*2, MPI_BYTE, mpiComm); + + if(compositeMethod == nullptr) { + jclass clazz = e->GetObjectClass(clazzObject); + compositeMethod = e->GetMethodID(clazz, "compositeVDIs", "(Ljava/nio/ByteBuffer;Ljava/nio/ByteBuffer;I)V"); + } + + + jobject bbCol = e->NewDirectByteBuffer(recvBufCol, sizePerProcess * commSize * numLayers); + jobject bbDepth; + if(generateVDIs) { + bbDepth = e->NewDirectByteBuffer(recvBufDepth, 0); + } else { + bbDepth = e->NewDirectByteBuffer(recvBufDepth, sizePerProcess * commSize); + } + + if(e->ExceptionOccurred()) { + e->ExceptionDescribe(); + e->ExceptionClear(); + } + + if (VERBOSE) std::cout<<"Finished distributing the VDIs. Calling the Composite method now!"<CallVoidMethod(clazzObject, compositeMethod, bbCol, bbDepth, sizePerProcess); + if(e->ExceptionOccurred()) { + e->ExceptionDescribe(); + e->ExceptionClear(); + } +} + +void gatherCompositedVDIs(JNIEnv *e, jobject clazzObject, jobject compositedVDIColor, jint root, jint compositedVDILen, jint myRank, jint commSize, jboolean generateVDIs, jboolean saveFiles) { + + if (VERBOSE) std::cout<<"In Gather function " <GetDirectBufferAddress(compositedVDIColor); +// void *ptrDepth = e->GetDirectBufferAddress(compositedVDIDepth); +// std::cout << "Data received as parameter is: " << (char *)ptrCol << std::endl; +// void *recvBufDepth; + if (myRank == 0) { + if(gather_recv == nullptr) { + std::cout<<"allocating in gather"<0) {gather_time += t_gather.getwct();} + // MPI_Gather(ptrDepth, compositedVDILen*2, MPI_BYTE, recvBufDepth, compositedVDILen*2, MPI_BYTE, root, mpiComm); + //The data is here now! + +// int flag = 0; +// if(VERBOSE) std::cout<<"Testing if bcast has been received"<GetObjectClass(clazzObject); +// updateVisMethod = e->GetMethodID(clazz, "updateVis", "(Ljava/nio/ByteBuffer;)V"); +// } +// if(updateVisMethod == nullptr) { +// if (e->ExceptionOccurred()) { +// e->ExceptionDescribe(); +// } else { +// std::cout << "ERROR: function updateVis not found!"; +//// std::exit(EXIT_FAILURE); +// } +// } +// //Message has arrived +// if (VERBOSE) std::cout<<"Received the size of the broadcast message. It is: "<<*size_interact<NewDirectByteBuffer(buffer, *size_interact); +// +// e->CallVoidMethod(clazzObject, updateVisMethod, bbMessage); +// if(e->ExceptionOccurred()) { +// e->ExceptionDescribe(); +// e->ExceptionClear(); +// } +// if (VERBOSE) std::cout<<"Updated the camera!"<DeleteLocalRef(bbMessage); +// free(buffer); +// MPI_Ibcast(size_interact, 1, MPI_INT, 0, visualizationComm, &interact_req); +// } + + if(myRank == 0) { +// //send or store the VDI + if(generateVDIs) { + //TODO: implement streaming of VDIs + } else { + if(streamMethod == nullptr) { + jclass clazz = e->GetObjectClass(clazzObject); + streamMethod = e->GetMethodID(clazz, "streamImage", "(Ljava/nio/ByteBuffer;)V"); + } + + jobject bbImg = e->NewDirectByteBuffer(gather_recv, compositedVDILen * commSize); + + if(e->ExceptionOccurred()) { + e->ExceptionDescribe(); + e->ExceptionClear(); + } + + if (VERBOSE) std::cout<<"Streaming the composited image out now"<CallVoidMethod(clazzObject, streamMethod, bbImg); + if(e->ExceptionOccurred()) { + e->ExceptionDescribe(); + e->ExceptionClear(); + } + } + + //do benchmarking + if(count % 100 == 0) { + std::time_t t = std::time(0); + + long timetaken = 0; //for the last 100 VDIs/images + + if(prevtime == 0) { + //skip this step + } + else { + timetaken = t - prevtime; + totaltime += timetaken; + avg_recent += (double)timetaken; + double average_time = (double)totaltime/(double)count; + avg_recent = (double)avg_recent/100.0; + std::cout<<"Average time for the last 100 VDIs/images was: "<(gather_recv), compositedVDILen * commSize); +// b_streamDepth.write(static_cast(recvBufDepth), compositedVDILen * rCommSize * 2); + + if (b_stream.good()) { + std::cout<<"Writing was successful"<GetObjectClass(clazzObject); +// jmethodID updateMethod = e->GetMethodID(clazz, "updateVolumes", "()V"); +// +// e->CallVoidMethod(clazzObject, updateMethod); +// if(e->ExceptionOccurred()) { +// e->ExceptionDescribe(); +// e->ExceptionClear(); +// } + +} + +void broadcastVisMsg(JNIEnv *e, jobject clazzObject, jobject message_buffer, jint msg_size) { + if (VERBOSE) std::cout<<"Broadcasting vis message"<GetDirectBufferAddress(message_buffer); + + int size = msg_size; + + // Broadcast the message size +// MPI_Ibcast((void *)size_ptr, 1, MPI_INT, 0, visualizationComm, &interact_req); +// +// int flag = 0; +// +// MPI_Test(&interact_req, &flag, MPI_STATUS_IGNORE); +// +// while(flag == 0) +// { +// usleep(10000); +// } + + MPI_Bcast((void *) &size, 1, MPI_INT, 0, visualizationComm); + + // Broadcast the message + MPI_Bcast(message, msg_size, MPI_BYTE, 0, visualizationComm); +// free(message); +} + +void broadcastSteerMsg(JNIEnv *e, jobject clazzObject, jobject message_buffer) { + +} + +void InVis::doRender() { + JNIEnv *env; + jvm->GetEnv((void **)&env, JNI_VERSION_1_6); + + jmethodID mainMethod = env->GetMethodID(clazz, "main", "()V"); + if(mainMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function main not found!"; +// std::exit(EXIT_FAILURE); + } + } + env->CallVoidMethod(obj, mainMethod); + if(env->ExceptionOccurred()) { + env->ExceptionDescribe(); + env->ExceptionClear(); + } +} + +//void InVis::manageVisHead() { +// JNIEnv *env; +// jvm->GetEnv((void **)&env, JNI_VERSION_1_6); +// jfieldID winSizeField = env->GetFieldID(clazz, "windowSize", "I"); +// env->SetIntField(obj, winSizeField, windowSize); +// +// std::cout<<"starting thread: gather images"<DestroyJavaVM(); +//} + +void InVis::manageRenderer() { + JNIEnv *env; + jvm->GetEnv((void **)&env, JNI_VERSION_1_6); + jfieldID winSizeField = env->GetFieldID(clazz, "windowSize", "I"); + env->SetIntField(obj, winSizeField, windowSize); + + jfieldID compPartnersField = env->GetFieldID(clazz, "computePartners", "I"); + env->SetIntField(obj, compPartnersField, computePartners); + + if(vtype == vis_type::grid) { + jfieldID commSizeField = env->GetFieldID(clazz, "commSize", "I"); + env->SetIntField(obj, commSizeField, rCommSize); + } + + int renRank; + MPI_Comm_rank(renderComm, &renRank); + + jfieldID rankField = env->GetFieldID(clazz, "rank", "I"); + env->SetIntField(obj, rankField, renRank); + + jmethodID initArraysMethod = env->GetMethodID(clazz, "initializeArrays", "()V"); + + if(initArraysMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function initializeArrays not found!"; +// std::exit(EXIT_FAILURE); + } + } + env->CallVoidMethod(obj, initArraysMethod); + + if(vtype == vis_type::particles) { + jclass RendererClass; + if(USE_VULKAN) { + RendererClass = env->FindClass("graphics/scenery/backends/vulkan/VulkanRenderer"); // try to find the clas + } else { + RendererClass = env->FindClass("graphics/scenery/backends/opengl/OpenGLRenderer"); // try to find the class + } + + if(RendererClass == nullptr) { + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: Renderer class not found !" <RegisterNatives(RendererClass, methods, 1); + if(ret < 0) { // register it + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: Could not register natives for Renderer !" <RegisterNatives(clazz, methods, 2); + if(ret < 0) { // register it + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: Could not register natives for InVisVolume!" <DestroyJavaVM(); +} + +void InVis::manageMaster() { + JNIEnv *env; + jvm->GetEnv((void **)&env, JNI_VERSION_1_6); + + JNINativeMethod methods[] { { (char *)"transmitVisMsg", (char *)"(Ljava/nio/ByteBuffer;I)V", (void *)&broadcastVisMsg }, + { (char *)"transmitSteerMsg", (char *)"(Ljava/nio/ByteBuffer;I)V", (void *)&broadcastSteerMsg } + }; // mapping table + + int ret = env->RegisterNatives(clazz, methods, 2); + if(ret < 0) { // register it + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: Could not register natives for InSituMaster!" <GetMethodID(clazz, "listenForMessages", "()V"); + if(listenMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function listenForMessages not found!"; +// std::exit(EXIT_FAILURE); + } + } + env->CallVoidMethod(obj, listenMethod); + if(env->ExceptionOccurred()) { + env->ExceptionDescribe(); + env->ExceptionClear(); + } + +} diff --git a/src/VCluster/InVis.hpp b/src/VCluster/InVis.hpp new file mode 100644 index 0000000..b8cbc77 --- /dev/null +++ b/src/VCluster/InVis.hpp @@ -0,0 +1,74 @@ +/* + * InVis.hpp + * + * Created on: May 11, 2020 + * Author: Aryaman Gupta + */ + +#ifndef OPENFPM_PDATA_INVIS_HPP +#define OPENFPM_PDATA_INVIS_HPP + +#include +#include + +enum vis_type +{ + particles = 0x0, + grid = 0x1, +}; + +enum scale_vis +{ + no_scaling = 0x0, + global = 0x1, + fixed = 0x3, +}; + +enum vector_visualize +{ + magnitude = 0x0, + x_ = 0x1, + y_ = 0x2, + z_ = 0x3 +}; + +static std::string grid_shm_path = "/home/aryaman/temp"; +static std::string particle_pos_shm_path = "/"; +static std::string particle_prop_shm_path = "/home"; +static std::string datatype_path = "/home/aryaman/datatype"; + +class InVis +{ + int windowSize; + int computePartners; + int imageSize; + JavaVM *jvm; + jclass clazz; + jobject obj; + MPI_Comm visComm; + MPI_Comm renderComm; + MPI_Comm steerComm; + int rCommSize; + int vCommSize; + vis_type vtype; + std::vector> gridBuffers; + bool vis_is_running; + + + void updateMemory(jmethodID methodID, int memKey, bool pos); + void getMemoryPos(); + void getMemoryProps(); + void receiveImages(); + void updateCamera(); + void interactVis(); + void getGridMemory(); + void doRender(); + static vis_type getVisType(); + +public: + InVis(int cPartners, MPI_Comm vComm, MPI_Comm rcomm, MPI_Comm sComm, bool isMaster); + void manageRenderer(); + void manageMaster(); + }; + +#endif //OPENFPM_PDATA_InVis_HPP diff --git a/src/VCluster/InVisRenderer.cpp b/src/VCluster/InVisRenderer.cpp new file mode 100644 index 0000000..9cf6b2d --- /dev/null +++ b/src/VCluster/InVisRenderer.cpp @@ -0,0 +1,247 @@ +/* + * InVisRenderer.cpp + * + * Created on: May 12, 2020 + * Author: Aryaman Gupta + */ + +#include +#include +#include +#include +#include + +#include "ShmBuffer.hpp" + +#define windowSize 700 +#define computePartners 2 +#define imageSize windowSize*windowSize*7 + +int visRank = -1; +int commSize = -1; + +JavaVM *jvm; // Pointer to the JVM (Java Virtual Machine) + +void doRender(JNIEnv *env, jclass inVisClass, jobject inVisObject) { + jmethodID mainMethod = env->GetMethodID(inVisClass, "main", "()V"); + if(mainMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function main not found!"; +// std::exit(EXIT_FAILURE); + } + } + env->CallVoidMethod(inVisObject, mainMethod); +} + +void updateMemory(JNIEnv *env, jobject renderObject, jmethodID methodID, int memKey, bool pos) { + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + std::string pName; + if(pos) pName = "/"; + else pName = "/home"; + + ShmBuffer *buf; + buf = new ShmBuffer(pName, memKey, true); + double *str = NULL; + ptr_with_size pws{}; + jobject byteBuffer; + + while(true) { + buf->update_key(true); + pws = buf->attach(); + str = (double *)pws.ptr; + byteBuffer = (env)->NewDirectByteBuffer((void*) str, pws.size); + std::cout<<"Java method updatepos/updateprops has been called!"<CallVoidMethod(renderObject, methodID, byteBuffer, memKey); + std::cout<<"Back after updating pos/props"<detach(false); //detach from the previous key + } +} + +void getMemoryPos(JNIEnv *env, jclass renderClass, jobject renderObject) { + jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); + + jmethodID updatePosMethod = env->GetMethodID(renderClass, "updatePos", "(Ljava/nio/ByteBuffer;I)V"); + if(updatePosMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function updatePos not found!"; +// std::exit(EXIT_FAILURE); + } + } + + std::vector threads; + + for(int i = 0; i AttachCurrentThread(reinterpret_cast(&env), NULL); + + jmethodID updatePropsMethod = env->GetMethodID(renderClass, "updateProps", "(Ljava/nio/ByteBuffer;I)V"); + if(updatePropsMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function updateProps not found!"; +// std::exit(EXIT_FAILURE); + } + } + + std::vector threads; + + for(int i = 0; i < computePartners; i++){ + threads.emplace_back(&updateMemory, env, renderObject, updatePropsMethod, i, false); + } + + for(int i = 0; i < computePartners; i++) { + threads[i].join(); + } +} + +void sendImage(JNIEnv *e, jobject clazz, jobject image) { + jbyte *buf; + MPI_Request req; + MPI_Status stat; + buf = (jbyte *) e->GetDirectBufferAddress(image); + MPI_Isend((void *)buf, imageSize, MPI_BYTE, 0, 0, MPI_COMM_WORLD, &req); + MPI_Wait(&req, &stat); +} + +void manageVisRenderer() { + + JNIEnv *env; // Pointer to native interface + //================== prepare loading of Java VM ============================ + JavaVMInitArgs vm_args; // Initialization arguments + JavaVMOption *options = new JavaVMOption[2]; // JVM invocation options + options[0].optionString = (char *)"-Djava.class.path=" + 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+ // 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+ // options[1].optionString = (char *)"-Djava.library.path=/Users/argupta/Documents/scenery-insitu/src/test/kotlin/graphics/scenery/insitu/";fscenery + options[1].optionString = (char *) + "-Dscenery.Renderer=OpenGLRenderer"; + vm_args.version = JNI_VERSION_1_6; // minimum Java version + vm_args.nOptions = 2; // number of options + vm_args.options = options; + vm_args.ignoreUnrecognized = false; // invalid options make the JVM init fail + //=============== load and initialize Java VM and JNI interface ============= + jint rc = JNI_CreateJavaVM(&jvm, (void **) &env, &vm_args); // YES !! + std::cout<<"Hello world"<GetVersion(); + std::cout << ((ver >> 16) & 0x0f) << "." << (ver & 0x0f) << std::endl; + + int threadLevel; + MPI_Init_thread(NULL, NULL, MPI_THREAD_MULTIPLE, &threadLevel); + std::cout << "MPI initialized with thread level " << threadLevel << ". The desired level was " << MPI_THREAD_MULTIPLE << std::endl; + MPI_Comm_rank(MPI_COMM_WORLD, &visRank); + std::cout << "My rank is " << visRank << std::endl; + MPI_Comm_size(MPI_COMM_WORLD, &commSize); + std::cout<<"Communicator size is "<FindClass("graphics/scenery/insitu/InVisRenderer"); // try to find the class + if(rendererClass == nullptr) { + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: class not found !" <GetMethodID(rendererClass, "", "()V"); // FIND AN OBJECT CONSTRUCTOR + if (ctor == nullptr) { + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: constructor not found !" <NewObject(rendererClass, ctor); + if (!rendererObject) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: class object is null !"; + std::exit(EXIT_FAILURE); + } + } + + jfieldID winSizeField = env->GetFieldID(rendererClass, "windowSize", "I"); + env->SetIntField(rendererObject, winSizeField, windowSize); + + jfieldID compPartnersField = env->GetFieldID(rendererClass, "computePartners", "I"); + env->SetIntField(rendererObject, compPartnersField, computePartners); + + jmethodID initArraysMethod = env->GetMethodID(rendererClass, "initializeArrays", "()V"); + if(initArraysMethod == nullptr) { + if (env->ExceptionOccurred()) { + env->ExceptionDescribe(); + } else { + std::cout << "ERROR: function initializeArrays not found!"; +// std::exit(EXIT_FAILURE); + } + } + env->CallVoidMethod(rendererObject, initArraysMethod); + + jclass openGLRendererClass = env->FindClass("graphics/scenery/backends/opengl/OpenGLRenderer"); // try to find the class + if(openGLRendererClass == nullptr) { + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: OpenGLRenderer class not found !" <RegisterNatives(openGLRendererClass, methods, 1) < 0) { // register it + if( env->ExceptionOccurred() ) { + env->ExceptionDescribe(); + } else { + std::cerr << "ERROR: Could not register natives for OpenGLRenderer !" <DestroyJavaVM(); +} \ No newline at end of file diff --git a/src/VCluster/InVisRenderer.hpp b/src/VCluster/InVisRenderer.hpp new file mode 100644 index 0000000..3f71077 --- /dev/null +++ b/src/VCluster/InVisRenderer.hpp @@ -0,0 +1,30 @@ +/* + * InVisRenderer.hpp + * + * Created on: May 12, 2020 + * Author: Aryaman Gupta + */ + +#ifndef OPENFPM_PDATA_INVISRENDERER_HPP +#define OPENFPM_PDATA_INVISRENDERER_HPP + +#include + +#define windowSize 700 +#define computePartners 2 +#define imageSize windowSize*windowSize*7 + +class InVisRenderer +{ + JavaVM *jvm; + + void getMemoryPos(JNIEnv *env, jclass renderClass, jobject renderObject); + void getMemoryProps(JNIEnv *env, jclass renderClass, jobject renderObject); + void sendImage(JNIEnv *e, jobject clazz, jobject image); + void doRender(JNIEnv *env, jclass inVisClass, jobject inVisObject); + +public: + void manageVisRenderer(); +}; + +#endif //OPENFPM_PDATA_INVISRENDERER_HPP diff --git a/src/VCluster/InVisVolume.cpp b/src/VCluster/InVisVolume.cpp new file mode 100644 index 0000000..ccc1296 --- /dev/null +++ b/src/VCluster/InVisVolume.cpp @@ -0,0 +1,487 @@ +///* +// * InVisVolumeVolume.cpp +// * +// * Created on: June 18, 2020 +// * Author: Aryaman Gupta +// */ +// +//#include +//#include +//#include +//#include +//#include +//#include +//#include +//#include +// +//#include "InVisVolume.hpp" +//#include "memory/ShmBuffer.hpp" +// +//#define USE_VULKAN true +// +//MPI_Comm mpiComm; +////int imgSize; +//double avg_recent = 0.0; +//int prevtime = 0; +//int count = 0; +//int totaltime = 0; +//int timeVDIwrite = 0; +// +//InVisVolume::InVisVolume(int wSize, int cPartners, MPI_Comm vComm, bool isHead) { +// windowSize = wSize; +// computePartners = cPartners; +// imageSize = windowSize*windowSize*7; +// visComm = vComm; +// mpiComm = vComm; +// MPI_Comm_size(visComm, &commSize); +// std::cout<<"VisComm size is "< tmp; +// gridBuffers.push_back(tmp); +// } +// +// DIR *dir; +// struct dirent *ent; +// std::string classPath = "-Djava.class.path="; +// std::string directory = "/home/aryaman/Repositories/scenery-insitu/target/dependency/"; +// if ((dir = opendir ("/home/aryaman/Repositories/scenery-insitu/target/dependency")) != NULL) { +// /* print all the files and directories within directory */ +// while ((ent = readdir (dir)) != NULL) { +// classPath.append(directory); +// classPath.append(ent->d_name); +// classPath.append(":"); +// } +// closedir (dir); +// } else { +// /* could not open directory */ +// std::cerr << "ERROR: Could not open directory "<< directory <GetVersion(); +// std::cout << ((ver >> 16) & 0x0f) << "." << (ver & 0x0f) << std::endl; +// +// std::string className; +// if(isHead) className = "graphics/scenery/insitu/Head"; +// else className = "graphics/scenery/insitu/InVisVolumeRenderer"; +// +// jclass localClass; +// localClass = env->FindClass(className.c_str()); // try to find the class +// if(localClass == nullptr) { +// if( env->ExceptionOccurred() ) { +// env->ExceptionDescribe(); +// } else { +// std::cerr << "ERROR: class "<< className << " not found !" <GetMethodID(localClass, "", "()V"); // FIND AN OBJECT CONSTRUCTOR +// if (ctor == nullptr) { +// if( env->ExceptionOccurred() ) { +// env->ExceptionDescribe(); +// } else { +// std::cerr << "ERROR: constructor not found !" <NewObject(localClass, ctor); +// if (!localObj) { +// if (env->ExceptionOccurred()) { +// env->ExceptionDescribe(); +// } else { +// std::cout << "ERROR: class object is null !"; +// std::exit(EXIT_FAILURE); +// } +// } +// +//// std::cout << "Object of class has been constructed" << std::endl; +// +// clazz = reinterpret_cast(env->NewGlobalRef(localClass)); +// obj = reinterpret_cast(env->NewGlobalRef(localObj)); +// +// env->DeleteLocalRef(localClass); +// env->DeleteLocalRef(localObj); +// +//// std::cout << "Global references have been created and local ones deleted" << std::endl; +//} +// +//void InVisVolume::getMemory() { +// JNIEnv *env; +// jvm->AttachCurrentThread(reinterpret_cast(&env), NULL); +// +// jmethodID updateDataMethod = env->GetMethodID(clazz, "updateData", "(II[Ljava/nio/ByteBuffer;[I[I[I)V"); +// if(updateDataMethod == nullptr) { +// if (env->ExceptionOccurred()) { +// env->ExceptionDescribe(); +// } else { +// std::cout << "ERROR: function updateData not found!"; +//// std::exit(EXIT_FAILURE); +// } +// } +// +//// std::cout<<"GOing to sleep"<update_key(true); +// pws = GBoxBuf->attach(); +// +// size_t metaSize = pws.size - 512 - 32; +// int numMetaElements = metaSize / sizeof(long); +// std::cout << "Got metadata for compute partner " << i << ". The size and no of elements are:" << metaSize << " and " << numMetaElements << std::endl; +// long *metaData = (long*)pws.ptr; +// +// for(int j = 0; j < numMetaElements; j++) { +// std::cout< 3 + grid dimensions -> 6 + domain dimensions -> 6 +// int numGrids = numMetaElements / elementsInGBox; +// +// int origins[3 * numGrids]; +// jintArray jOrigins = env->NewIntArray(3 * numGrids); +// int gridDims[6 * numGrids]; +// jintArray jGridDims = env->NewIntArray(6 * numGrids); +// int domainDims[6 * numGrids]; +// jintArray jDomainDims = env->NewIntArray(6 * numGrids); +// +// jobjectArray bytebuffers; // Each element will be a direct byte buffer wrapping a grid that is controlled by this computePartner +// jsize size = numGrids; +// bytebuffers = (env)->NewObjectArray(size, (env)->FindClass("java/nio/ByteBuffer"), 0); +// +// int it = 0; +// for(int j = 0; j < numGrids; j++) { +// gridDims[j * 6] = (int)metaData[it]; +// it ++; +// gridDims[j * 6 + 1] = (int)metaData[it]; +// it++; +// gridDims[j * 6 + 2] = (int)metaData[it]; +// it++; +// gridDims[j * 6 + 3] = (int)metaData[it]; +// it ++; +// gridDims[j * 6 + 4] = (int)metaData[it]; +// it++; +// gridDims[j * 6 + 5] = (int)metaData[it]; +// it++; +// +// domainDims[j * 6] = (int)metaData[it]; +// it ++; +// domainDims[j * 6 + 1] = (int)metaData[it]; +// it++; +// domainDims[j * 6 + 2] = (int)metaData[it]; +// it++; +// domainDims[j * 6 + 3] = (int)metaData[it]; +// it ++; +// domainDims[j * 6 + 4] = (int)metaData[it]; +// it++; +// domainDims[j * 6 + 5] = (int)metaData[it]; +// it++; +// +// origins[j * 3] = (int)metaData[it]; +// it ++; +// origins[j * 3 + 1] = (int)metaData[it]; +// it++; +// origins[j * 3 + 2] = (int)metaData[it]; +// it++; +// +// gridBuffers[i].push_back(new ShmBuffer(pName, j+1, true)); +// gridBuffers[i][j]->update_key(true); +// +// ptr_with_size tmp = gridBuffers[i][j]->attach(); +// int width = abs(gridDims[j*6] - gridDims[j*6 + 3]) + 1; +// int height = abs(gridDims[j*6 + 1] - gridDims[j*6 + 4]) + 1; +// int depth = abs(gridDims[j*6 + 2] - gridDims[j*6 + 5]) + 1; +// int gridSize = width * height * depth; +// std::cout<< "Grid " << j << " of computePartner " << i << " is of size " << gridSize << std::endl; +// +// jobject bb; +// bb = env->NewDirectByteBuffer((void *)tmp.ptr, 2*gridSize); +// env->SetObjectArrayElement(bytebuffers, j, bb); +// int temp = (env)-> GetDirectBufferCapacity(bb); +// std::cout<<"Bytebuffer capacity was found to be " <DeleteLocalRef(bb); TODO: uncomment +// } +// +// env->SetIntArrayRegion(jOrigins, 0, 3 * numGrids, origins); +// env->SetIntArrayRegion(jGridDims, 0, 6 * numGrids, gridDims); +// env->SetIntArrayRegion(jDomainDims, 0, 6 * numGrids, domainDims); +// // the meta arguments for the java function updateData are now ready +// std::cout<<"the meta arguments for the java function updateData are now ready"<CallVoidMethod(obj, updateDataMethod, i, numGrids, bytebuffers, jOrigins, jGridDims, jDomainDims); +// +//// env->DeleteLocalRef(bytebuffers); +//// env->DeleteLocalRef(jOrigins); +//// env->DeleteLocalRef(jGridDims); +//// env->DeleteLocalRef(jDomainDims); +// } +// jvm->DetachCurrentThread(); +//} +// +//void InVisVolume::doRender() { +// JNIEnv *env; +// jvm->GetEnv((void **)&env, JNI_VERSION_1_6); +// +// jmethodID mainMethod = env->GetMethodID(clazz, "main", "()V"); +// if(mainMethod == nullptr) { +// if (env->ExceptionOccurred()) { +// env->ExceptionDescribe(); +// } else { +// std::cout << "ERROR: function main not found!"; +//// std::exit(EXIT_FAILURE); +// } +// } +// env->CallVoidMethod(obj, mainMethod); +// if(env->ExceptionOccurred()) { +// env->ExceptionDescribe(); +// env->ExceptionClear(); +// } +//} +// +// +//void distributeVDIs(JNIEnv *e, jobject clazzObject, jobject subVDICol, jint sizePerProcess, jint commSize) { +// +// void *ptrCol = e->GetDirectBufferAddress(subVDICol); +//// void *ptrDepth = e->GetDirectBufferAddress(subVDIDepth); +// +// void *recvBufCol = malloc(sizePerProcess * commSize * 3); +//// void *recvBufDepth = malloc(sizePerProcess * rCommSize * 2); +// +// MPI_Alltoall(ptrCol, sizePerProcess*3, MPI_BYTE, recvBufCol, sizePerProcess*3, MPI_BYTE, mpiComm); +//// MPI_Alltoall(ptrDepth, sizePerProcess*2, MPI_BYTE, recvBufDepth, sizePerProcess*2, MPI_BYTE, mpiComm); +// +// jclass clazz = e->GetObjectClass(clazzObject); +// jmethodID compositeMethod = e->GetMethodID(clazz, "compositeVDIs", "(Ljava/nio/ByteBuffer;I)V"); +// +// jobject bbCol = e->NewDirectByteBuffer(recvBufCol, sizePerProcess * commSize * 3); +//// jobject bbDepth = e->NewDirectByteBuffer(recvBufDepth, sizePerProcess * rCommSize * 2); +// +// if(e->ExceptionOccurred()) { +// e->ExceptionDescribe(); +// e->ExceptionClear(); +// } +// +// std::cout<<"Finished distributing the VDIs. Calling the Composite method now!"<CallVoidMethod(clazzObject, compositeMethod, bbCol, sizePerProcess); +// if(e->ExceptionOccurred()) { +// e->ExceptionDescribe(); +// e->ExceptionClear(); +// } +//} +// +//void gatherCompositedVDIs(JNIEnv *e, jobject clazzObject, jobject compositedVDIColor, jint root, jint compositedVDILen, jint myRank, jint commSize, jboolean saveFiles) { +// +// std::cout<<"In Gather function " <GetDirectBufferAddress(compositedVDIColor); +//// void *ptrDepth = e->GetDirectBufferAddress(compositedVDIDepth); +//// std::cout << "Data received as parameter is: " << (char *)ptrCol << std::endl; +// void *recvBufCol; +//// void *recvBufDepth; +// if (myRank == 0) { +// recvBufCol = malloc(compositedVDILen * commSize * 3); +//// recvBufDepth = malloc(compositedVDILen * rCommSize * 2); +// } +// else { +// recvBufCol = NULL; +//// recvBufDepth = NULL; +// } +// +// MPI_Gather(ptrCol, compositedVDILen*3, MPI_BYTE, recvBufCol, compositedVDILen*3, MPI_BYTE, root, mpiComm); +//// MPI_Gather(ptrDepth, compositedVDILen*2, MPI_BYTE, recvBufDepth, compositedVDILen*2, MPI_BYTE, root, mpiComm); +// //The data is here now! +// +// if(myRank == 0) { +//// //send or store the VDI +// std::time_t t = std::time(0); +// +// int timetaken = 0; +// if(prevtime == 0) { +// //skip this step +// } +// else { +// timetaken = t - prevtime; +// totaltime += timetaken; +// avg_recent += timetaken; +// count++; +// } +// if(count != 0 && count % 5 == 0) { +// double average_time = (double)totaltime/count; +// avg_recent = (double)avg_recent/5.0; +// std::cout<<"Average time for the last 5 VDIs was: "<(recvBufCol), compositedVDILen * commSize * 3); +//// b_streamDepth.write(static_cast(recvBufDepth), compositedVDILen * rCommSize * 2); +// +// if (b_stream.good()) { +// std::cout<<"Writing was successful"<GetObjectClass(clazzObject); +//// jmethodID updateMethod = e->GetMethodID(clazz, "updateVolumes", "()V"); +//// +//// e->CallVoidMethod(clazzObject, updateMethod); +//// if(e->ExceptionOccurred()) { +//// e->ExceptionDescribe(); +//// e->ExceptionClear(); +//// } +//} +// +//void InVisVolume::manageVolumeRenderer() { +// JNIEnv *env; +// jvm->GetEnv((void **)&env, JNI_VERSION_1_6); +// jfieldID winSizeField = env->GetFieldID(clazz, "windowSize", "I"); +// env->SetIntField(obj, winSizeField, windowSize); +// +// jfieldID compPartnersField = env->GetFieldID(clazz, "computePartners", "I"); +// env->SetIntField(obj, compPartnersField, computePartners); +// +// jfieldID commSizeField = env->GetFieldID(clazz, "rCommSize", "I"); +// env->SetIntField(obj, commSizeField, commSize); +// +// int visRank; +// MPI_Comm_rank(visComm, &visRank); +// +// jfieldID rankField = env->GetFieldID(clazz, "rank", "I"); +// env->SetIntField(obj, rankField, visRank); +// +// jmethodID initArraysMethod = env->GetMethodID(clazz, "initializeArrays", "()V"); +// +// if(initArraysMethod == nullptr) { +// if (env->ExceptionOccurred()) { +// env->ExceptionDescribe(); +// } else { +// std::cout << "ERROR: function initializeArrays not found!"; +//// std::exit(EXIT_FAILURE); +// } +// } +// env->CallVoidMethod(obj, initArraysMethod); +// +// JNINativeMethod methods[] { { (char *)"distributeVDIs", (char *)"(Ljava/nio/ByteBuffer;II)V", (void *)&distributeVDIs }, +// { (char *)"gatherCompositedVDIs", (char *)"(Ljava/nio/ByteBuffer;IIIIZ)V", (void *)&gatherCompositedVDIs } +// }; // mapping table +// +// if(env->RegisterNatives(clazz, methods, 2) < 0) { // register it +// if( env->ExceptionOccurred() ) { +// env->ExceptionDescribe(); +// } else { +// std::cerr << "ERROR: Could not register natives for InVisVolume!" <RegisterNatives(clazz, methods, 1) <DestroyJavaVM(); +//} diff --git a/src/VCluster/InVisVolume.hpp b/src/VCluster/InVisVolume.hpp new file mode 100644 index 0000000..fc18480 --- /dev/null +++ b/src/VCluster/InVisVolume.hpp @@ -0,0 +1,39 @@ +/* + * InVisVolume.hpp + * + * Created on: June 18, 2020 + * Author: Aryaman Gupta + */ + +#ifndef SRC_INVISVOLUME_HPP +#define SRC_INVISVOLUME_HPP + +#include +#include +#include + +class InVisVolume +{ + int windowSize; + int computePartners; + int imageSize; + JavaVM *jvm; + jclass clazz; + jobject obj; + MPI_Comm visComm; + int commSize; + std::vector> gridBuffers; + + void updateMemory(jmethodID methodID, int memKey, bool pos); + void getMemory(); + void receiveVDI(); + void updateCamera(); + void doRender(); + +public: + InVisVolume(int wSize, int cPartners, MPI_Comm vComm, bool isHead); + void manageVisHead(); + void manageVolumeRenderer(); +}; + +#endif //SRC_INVISVOLUME_HPP diff --git a/src/VCluster/VCluster.cpp b/src/VCluster/VCluster.cpp index c344810..3051319 100644 --- a/src/VCluster/VCluster.cpp +++ b/src/VCluster/VCluster.cpp @@ -8,12 +8,14 @@ #include "util/print_stack.hpp" #include "util/math_util_complex.hpp" +init_options global_option; Vcluster<> * global_v_cluster_private_heap = NULL; Vcluster * global_v_cluster_private_cuda = NULL; // std::vector sieve_spf; + // number of vcluster instances size_t n_vcluster = 0; bool ofp_initialized = false; diff --git a/src/VCluster/VCluster.hpp b/src/VCluster/VCluster.hpp index 14e8ddf..cd2dd4a 100644 --- a/src/VCluster/VCluster.hpp +++ b/src/VCluster/VCluster.hpp @@ -13,6 +13,8 @@ #include "VCluster_base.hpp" #include "VCluster_meta_function.hpp" #include "util/math_util_complex.hpp" +#include "InVisVolume.hpp" +#include "InVis.hpp" #ifdef CUDA_GPU extern CudaMemory mem_tmp; @@ -336,8 +338,8 @@ class Vcluster: public Vcluster_base * \param argv main set of arguments * */ - Vcluster(int *argc, char ***argv) - :Vcluster_base(argc,argv) + Vcluster(int *argc, char ***argv,MPI_Comm ext_comm = MPI_COMM_WORLD) + :Vcluster_base(argc,argv,ext_comm) { } @@ -878,34 +880,337 @@ class Vcluster: public Vcluster_base }; +enum init_options +{ + none = 0x0, + in_situ_visualization = 0x1, +}; +extern init_options global_option; // Function to initialize the global VCluster // extern Vcluster<> * global_v_cluster_private_heap; extern Vcluster * global_v_cluster_private_cuda; -/*! \brief Initialize a global instance of Runtime Virtual Cluster Machine +static inline void delete_global_v_cluster_private() +{ + delete global_v_cluster_private_heap; + delete global_v_cluster_private_cuda; +} + + +/*! \brief Finalize the library * - * Initialize a global instance of Runtime Virtual Cluster Machine + * This function MUST be called at the end of the program * */ +static inline void openfpm_finalize() +{ + if (global_option == init_options::in_situ_visualization) + { + MPI_Request bar_req; + MPI_Ibarrier(MPI_COMM_WORLD,&bar_req); + } + +#ifdef HAVE_PETSC + + PetscFinalize(); -static inline void init_global_v_cluster_private(int *argc, char ***argv) +#endif + + delete_global_v_cluster_private(); + ofp_initialized = false; + +#ifdef CUDA_GPU + + // Release memory + mem_tmp.destroy(); + mem_tmp.decRef(); + +#endif +} + +static void get_comm_ranks(MPI_Comm comm, openfpm::vector & world_ranks) { - if (global_v_cluster_private_heap == NULL) - {global_v_cluster_private_heap = new Vcluster<>(argc,argv);} + MPI_Group grp, world_grp; + + MPI_Comm_group(MPI_COMM_WORLD, &world_grp); + MPI_Comm_group(comm, &grp); + + int grp_size; + + MPI_Group_size(grp, &grp_size); + + openfpm::vector local_ranks; + + local_ranks.resize(grp_size); + world_ranks.resize(grp_size); + + for (int i = 0; i < grp_size; i++) + {local_ranks.get(i) = i;} - if (global_v_cluster_private_cuda == NULL) - {global_v_cluster_private_cuda = new Vcluster(argc,argv);} + MPI_Group_translate_ranks(grp, grp_size, (int *)local_ranks.getPointer(), world_grp, (int *)world_ranks.getPointer()); + + MPI_Group_free(&grp); + MPI_Group_free(&world_grp); } -static inline void delete_global_v_cluster_private() + +/*! \brief Initialize a global instance of Runtime Virtual Cluster Machine + * + * Initialize a global instance of Runtime Virtual Cluster Machine + * + */ + +static inline void init_global_v_cluster_private(int *argc, char ***argv, init_options option) { - delete global_v_cluster_private_heap; - delete global_v_cluster_private_cuda; + global_option = option; + if (option == init_options::in_situ_visualization) + { + int flag; + MPI_Initialized(&flag); + + if (flag == false) + { + int threadLevel; + MPI_Init_thread(argc, argv, MPI_THREAD_MULTIPLE, &threadLevel); + std::cout << "MPI initialized with thread level " << threadLevel << ". The desired level was " << MPI_THREAD_MULTIPLE << std::endl; + } + + MPI_Comm comm_compute; + MPI_Comm comm_render; + MPI_Comm comm_steer; + MPI_Comm comm_vis; + + int rank; + MPI_Comm_rank(MPI_COMM_WORLD,&rank); + + MPI_Comm nodeComm; + MPI_Comm_split_type( MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, rank, + MPI_INFO_NULL, &nodeComm ); + + openfpm::vector world_ranks; + get_comm_ranks(nodeComm,world_ranks); + + int nodeRank; + int len; + MPI_Comm_rank(nodeComm,&nodeRank); + + bool is_vis_process = false; + + if (rank != 0) + { + if (nodeRank == 0) + { + // The lowest ranked process on a given node (except head node); the rendering process of that node + char name[MPI_MAX_PROCESSOR_NAME]; + + // Vis process + MPI_Get_processor_name(name, &len); + + std::cout << "Node: " << name << " vis process: " << rank << std::endl; + + is_vis_process = true; + } + else + { + for (int i = 0 ; i < world_ranks.size() ; i++) + { + if (world_ranks.get(i) == 0 && (nodeRank == 1)) + { + char name[MPI_MAX_PROCESSOR_NAME]; + + // Vis process + MPI_Get_processor_name(name, &len); + + std::cout << "Vis process on node 0 " << name << " " << nodeRank << " " << rank << std::endl; + + is_vis_process = true; + } + } + } + } + +// if (nodeRank == 0) +// { +// // The lowest ranked process on a given node; the rendering process of that node +// //TODO: change it back to above +// char name[MPI_MAX_PROCESSOR_NAME]; +// +// // Vis process +// MPI_Get_processor_name(name, &len); +// +// std::cout << "Node: " << name << " vis process: " << rank << std::endl; +// +// is_vis_process = true; +// } + + int colorVis; + int colorSteer; + int colorComp; + int colorRen; + int colorPETSC; + + if(rank == 0) + { + //Rank 0 is part of both the vis communicator as well as the steering communicator + colorVis = 0; + colorSteer = 0; + //Rank 0 is not part of the compute, PETSC or rendering communicators + colorComp = MPI_UNDEFINED; + colorRen = MPI_UNDEFINED; + colorPETSC = 0; // PETSC does not seem to work with MPI_UNDEFINED + } else if (is_vis_process == true) + { + //All visualization processes are part of the vis and rendering communicators, + // but not part of the steering, PETSC or compute communicators + colorVis = 0; + colorRen = 0; + colorSteer = MPI_UNDEFINED; + colorComp = MPI_UNDEFINED; + colorPETSC = 0; // PETSC does not seem to work with MPI_UNDEFINED + } else + { + //All non-visualization processes are part of the steering and compute communicators, + // but not part of the vis or rendering communicators + colorSteer = 0; + colorComp = 0; + colorVis = MPI_UNDEFINED; + colorRen = MPI_UNDEFINED; + colorPETSC = 1; + } + + + MPI_Comm_split(MPI_COMM_WORLD, colorSteer, rank, &comm_steer); + MPI_Comm_split(MPI_COMM_WORLD, colorVis, rank, &comm_vis); + MPI_Comm_split(MPI_COMM_WORLD, colorComp, rank, &comm_compute); + MPI_Comm_split(MPI_COMM_WORLD, colorPETSC, rank, &PETSC_COMM_WORLD); + MPI_Comm_split(MPI_COMM_WORLD, colorRen, rank, &comm_render); + + +// if (rank == 0 || is_vis_process == true) +// { +// colorComp = MPI_UNDEFINED; +// MPI_Comm_split(MPI_COMM_WORLD, MPI_UNDEFINED,rank, &comm_compute); +// MPI_Comm_split(MPI_COMM_WORLD, 0, 0, &PETSC_COMM_WORLD); +// } +// else +// { +// MPI_Comm_split(MPI_COMM_WORLD,0,rank, &comm_compute); +// MPI_Comm_split(MPI_COMM_WORLD, 1, 0, &PETSC_COMM_WORLD); +// } +// +// if (rank == 0 || is_vis_process == false) +// { +// MPI_Comm_split(MPI_COMM_WORLD, MPI_UNDEFINED,rank, &comm_render); +// } +// else +// { +// MPI_Comm_split(MPI_COMM_WORLD,0,rank, &comm_render); +// } + +#ifdef HAVE_PETSC + +// PETSC_COMM_WORLD = comm_compute; + PetscInitialize(argc,argv,NULL,NULL); + +#endif + + if (is_vis_process == false && rank!=0) + { + if (global_v_cluster_private_heap == NULL) + {global_v_cluster_private_heap = new Vcluster<>(argc,argv,comm_compute);} + + if (global_v_cluster_private_cuda == NULL) + {global_v_cluster_private_cuda = new Vcluster(argc,argv,comm_compute);} + } + else if (is_vis_process == true) + { + int flag = false; + MPI_Request bar_req; + MPI_Ibarrier(MPI_COMM_WORLD,&bar_req); + //! barrier status + MPI_Status bar_stat; + + //How many simulation processes are running on this node? + int numSimProcesses; + int nodeCommSize; + MPI_Comm_size(nodeComm, &nodeCommSize); + + if(nodeRank != 0) + { + //This process' rank on its node is not 0. So it is on the head node + numSimProcesses = nodeCommSize - 2; // Vis Renderer + Master + } + else + { + numSimProcesses = nodeCommSize - 1; //All process apart from Vis Renderer are simulation processes + } + char name[MPI_MAX_PROCESSOR_NAME]; + MPI_Get_processor_name(name, &len); + + std::cout<<"Node size is " << nodeCommSize << " and no. of sim processes on node " << name << " are: " << numSimProcesses << std::endl; + + while(flag == false) + { + + int visRank; + MPI_Comm_rank(comm_vis, &visRank); + +// while (true) { +// sleep(100); +// } + + InVis *visSystem = new InVis(numSimProcesses, comm_vis, comm_render, MPI_COMM_NULL, false); + visSystem->manageRenderer(); + + MPI_SAFE_CALL(MPI_Test(&bar_req,&flag,&bar_stat)); + } + + openfpm_finalize(); + exit(0); + } + else // Master process (rank == 0) + { + int flag = false; + MPI_Request bar_req; + MPI_Ibarrier(MPI_COMM_WORLD,&bar_req); + //! barrier status + MPI_Status bar_stat; + +// int * a = static_cast(malloc(sizeof(int))); +// *a = 5; +// sleep(10); +// +// std::cout<<"Sending the bcast"<manageMaster(); + + + openfpm_finalize(); + exit(0); + } + } + else + { +#ifdef HAVE_PETSC + + PetscInitialize(argc,argv,NULL,NULL); + +#endif + if (global_v_cluster_private_heap == NULL) + {global_v_cluster_private_heap = new Vcluster<>(argc,argv);} + + if (global_v_cluster_private_cuda == NULL) + {global_v_cluster_private_cuda = new Vcluster(argc,argv);} + } } + template struct get_vcl { @@ -951,15 +1256,9 @@ static inline bool is_openfpm_init() * This function MUST be called before any other function * */ -static inline void openfpm_init(int *argc, char ***argv) +static inline void openfpm_init(int *argc, char ***argv, init_options option = init_options::none ) { -#ifdef HAVE_PETSC - - PetscInitialize(argc,argv,NULL,NULL); - -#endif - - init_global_v_cluster_private(argc,argv); + init_global_v_cluster_private(argc,argv,option); #ifdef SE_CLASS1 std::cout << "OpenFPM is compiled with debug mode LEVEL:1. Remember to remove SE_CLASS1 when you go in production" << std::endl; @@ -1000,30 +1299,6 @@ static inline void openfpm_init(int *argc, char ***argv) } -/*! \brief Finalize the library - * - * This function MUST be called at the end of the program - * - */ -static inline void openfpm_finalize() -{ -#ifdef HAVE_PETSC - - PetscFinalize(); - -#endif - - delete_global_v_cluster_private(); - ofp_initialized = false; - -#ifdef CUDA_GPU - - // Release memory - mem_tmp.destroy(); - mem_tmp.decRef(); - -#endif -} #endif diff --git a/src/VCluster/VCluster_base.hpp b/src/VCluster/VCluster_base.hpp index a6588d9..adfbaef 100644 --- a/src/VCluster/VCluster_base.hpp +++ b/src/VCluster/VCluster_base.hpp @@ -112,6 +112,9 @@ union red template class Vcluster_base { + //! external communicator + MPI_Comm ext_comm; + //! log file Vcluster_log log; @@ -238,8 +241,8 @@ class Vcluster_base * \param argv pointer to arguments vector passed to the program * */ - Vcluster_base(int *argc, char ***argv) - :NBX_cnt(0) + Vcluster_base(int *argc, char ***argv, MPI_Comm ext_comm) + :ext_comm(ext_comm),NBX_cnt(0) { #ifdef SE_CLASS2 check_new(this,8,VCLUSTER_EVENT,PRJ_VCLUSTER); @@ -259,7 +262,7 @@ class Vcluster_base // We try to get the local processors rank MPI_Comm shmcomm; - MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, + MPI_Comm_split_type(ext_comm, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &shmcomm); MPI_Comm_rank(shmcomm, &shmrank); @@ -268,8 +271,8 @@ class Vcluster_base // Get the total number of process // and the rank of this process - MPI_Comm_size(MPI_COMM_WORLD, &m_size); - MPI_Comm_rank(MPI_COMM_WORLD, &m_rank); + MPI_Comm_size(ext_comm, &m_size); + MPI_Comm_rank(ext_comm, &m_rank); #ifdef SE_CLASS2 process_v_cl = m_rank; @@ -379,7 +382,7 @@ class Vcluster_base */ MPI_Comm getMPIComm() { - return MPI_COMM_WORLD; + return ext_comm; } /*! \brief Get the total number of processors @@ -430,6 +433,15 @@ class Vcluster_base return m_rank; } + /*! \brief Get the rank within the node + * + * \return the rank of the process within the node + * + */ + size_t shmRank() + { + return shmrank; + } /*! \brief Sum the numbers across all processors and get the result * @@ -449,7 +461,7 @@ class Vcluster_base req.add(); // reduce - MPI_IallreduceW::reduce(num,MPI_SUM,req.last()); + MPI_IallreduceW::reduce(num,MPI_SUM,req.last(),ext_comm); } /*! \brief Get the maximum number across all processors (or reduction with infinity norm) @@ -468,7 +480,7 @@ class Vcluster_base req.add(); // reduce - MPI_IallreduceW::reduce(num,MPI_MAX,req.last()); + MPI_IallreduceW::reduce(num,MPI_MAX,req.last(),ext_comm); } /*! \brief Get the minimum number across all processors (or reduction with insinity norm) @@ -488,7 +500,7 @@ class Vcluster_base req.add(); // reduce - MPI_IallreduceW::reduce(num,MPI_MIN,req.last()); + MPI_IallreduceW::reduce(num,MPI_MIN,req.last(),ext_comm); } /*! \brief Send and receive multiple messages @@ -831,7 +843,7 @@ class Vcluster_base #endif tot_sent += sz[i]; - MPI_SAFE_CALL(MPI_Issend(ptr[i], sz[i], MPI_BYTE, prc[i], SEND_SPARSE + NBX_cnt*131072 + i, MPI_COMM_WORLD,&req.last())); + MPI_SAFE_CALL(MPI_Issend(ptr[i], sz[i], MPI_BYTE, prc[i], SEND_SPARSE + NBX_cnt*131072 + i, ext_comm,&req.last())); log.logSend(prc[i]); } } @@ -852,7 +864,7 @@ class Vcluster_base MPI_Status stat_t; int stat = false; - MPI_SAFE_CALL(MPI_Iprobe(MPI_ANY_SOURCE,MPI_ANY_TAG/*SEND_SPARSE + NBX_cnt*/,MPI_COMM_WORLD,&stat,&stat_t)); + MPI_SAFE_CALL(MPI_Iprobe(MPI_ANY_SOURCE,MPI_ANY_TAG/*SEND_SPARSE + NBX_cnt*/,ext_comm,&stat,&stat_t)); // If I have an incoming message and is related to this NBX communication if (stat == true) @@ -878,7 +890,7 @@ class Vcluster_base check_valid(ptr,msize); #endif tot_recv += msize; - MPI_SAFE_CALL(MPI_Recv(ptr,msize,MPI_BYTE,stat_t.MPI_SOURCE,stat_t.MPI_TAG,MPI_COMM_WORLD,&stat_t)); + MPI_SAFE_CALL(MPI_Recv(ptr,msize,MPI_BYTE,stat_t.MPI_SOURCE,stat_t.MPI_TAG,ext_comm,&stat_t)); #ifdef SE_CLASS2 check_valid(ptr,msize); @@ -898,7 +910,7 @@ class Vcluster_base // If all send has been completed if (flag == true) - {MPI_SAFE_CALL(MPI_Ibarrier(MPI_COMM_WORLD,&bar_req));reached_bar_req = true;} + {MPI_SAFE_CALL(MPI_Ibarrier(ext_comm,&bar_req));reached_bar_req = true;} } // Check if all processor reached the async barrier @@ -946,7 +958,7 @@ class Vcluster_base req.add(); // send - MPI_IsendWB::send(proc,SEND_RECV_BASE + tag,mem,sz,req.last()); + MPI_IsendWB::send(proc,SEND_RECV_BASE + tag,mem,sz,req.last(),ext_comm); return true; } @@ -981,11 +993,45 @@ class Vcluster_base req.add(); // send - MPI_IsendW::send(proc,SEND_RECV_BASE + tag,v,req.last()); + MPI_IsendW::send(proc,SEND_RECV_BASE + tag,v,req.last(),ext_comm); return true; } + /*! \brief Send data to a processor + * + * \warning In order to avoid deadlock every send must be coupled with a recv + * in case you want to send data without knowledge from the other side + * consider to use sendRecvMultipleMessages + * + * \warning operation is asynchronous execute must be called to ensure they are executed + * + * \see sendRecvMultipleMessages + * + * \param proc processor id + * \param tag id + * \param v buffer to send + * + * \return true if succeed false otherwise + * + */ + template bool send(size_t proc, size_t tag, openfpm::vector_ofp & v) + { +#ifdef SE_CLASS1 + checkType(); +#endif + + // send over MPI + + // Create one request + req.add(); + + // send + MPI_IsendW::send(proc,SEND_RECV_BASE + tag,v,req.last(),ext_comm); + + return true; + } + /*! \brief Recv data from a processor * * \warning In order to avoid deadlock every recv must be coupled with a send @@ -1012,7 +1058,7 @@ class Vcluster_base req.add(); // receive - MPI_IrecvWB::recv(proc,SEND_RECV_BASE + tag,v,sz,req.last()); + MPI_IrecvWB::recv(proc,SEND_RECV_BASE + tag,v,sz,req.last(),ext_comm); return true; } @@ -1046,11 +1092,45 @@ class Vcluster_base req.add(); // receive - MPI_IrecvW::recv(proc,SEND_RECV_BASE + tag,v,req.last()); + MPI_IrecvW::recv(proc,SEND_RECV_BASE + tag,v,req.last(),ext_comm); return true; } + /*! \brief Recv data from a processor + * + * \warning In order to avoid deadlock every recv must be coupled with a send + * in case you want to send data without knowledge from the other side + * consider to use sendrecvMultipleMessagesNBX + * + * \warning operation is asynchronous execute must be called to ensure they are executed + * + * \see sendrecvMultipleMessagesNBX + * + * \param proc processor id + * \param tag id + * \param v vector to send + * + * \return true if succeed false otherwise + * + */ + template bool recv(size_t proc, size_t tag, openfpm::vector_ofp & v) + { +#ifdef SE_CLASS1 + checkType(); +#endif + + // recv over MPI + + // Create one request + req.add(); + + // receive + MPI_IrecvW::recv(proc,SEND_RECV_BASE + tag,v,req.last(),ext_comm); + + return true; + } + /*! \brief Gather the data from all processors * * send a primitive data T receive the same primitive T from all the other processors @@ -1076,7 +1156,7 @@ class Vcluster_base v.resize(getProcessingUnits()); // gather - MPI_IAllGatherW::gather(&send,1,v.getPointer(),1,req.last()); + MPI_IAllGatherW::gather(&send,1,v.getPointer(),1,req.last(),ext_comm); return true; } @@ -1104,7 +1184,7 @@ class Vcluster_base checkType(); #endif - b_cast_helper::value == STD_VECTOR || is_layout_mlin>::value >::bcast_(req,v,root); + b_cast_helper::value == STD_VECTOR || is_layout_mlin>::value >::bcast_(req,v,root,ext_comm); return true; } diff --git a/src/VCluster/VCluster_unit_test_util.hpp b/src/VCluster/VCluster_unit_test_util.hpp index d26fa03..8ce0bf5 100644 --- a/src/VCluster/VCluster_unit_test_util.hpp +++ b/src/VCluster/VCluster_unit_test_util.hpp @@ -217,10 +217,8 @@ template void test_no_send_some_peer() } } -template void test_known() +template void test_known(Vcluster<> & vcl) { - Vcluster<> & vcl = create_vcluster(); - // send/recv messages global_rank = vcl.getProcessUnitID(); @@ -325,10 +323,8 @@ template void test_known() } } -template void test(unsigned int opt) +template void test(Vcluster<> & vcl, unsigned int opt) { - Vcluster<> & vcl = create_vcluster(); - // send/recv messages global_rank = vcl.getProcessUnitID(); diff --git a/src/VCluster/VCluster_unit_tests.cpp b/src/VCluster/VCluster_unit_tests.cpp index 444219d..446c503 100644 --- a/src/VCluster/VCluster_unit_tests.cpp +++ b/src/VCluster/VCluster_unit_tests.cpp @@ -191,7 +191,9 @@ BOOST_AUTO_TEST_CASE( VCluster_use_sendrecv) std::cout << "VCluster unit test start sendrecv" << "\n"; totp_check = false; - test(RECEIVE_UNKNOWN); + auto & v_cl = create_vcluster(); + + test(v_cl,RECEIVE_UNKNOWN); totp_check = false; test_no_send_some_peer(); @@ -203,8 +205,10 @@ BOOST_AUTO_TEST_CASE( VCluster_use_sendrecv_size_known) { std::cout << "VCluster unit test start sendrecv known size" << "\n"; + auto & v_cl = create_vcluster(); + totp_check = false; - test(RECEIVE_SIZE_UNKNOWN); + test(v_cl,RECEIVE_SIZE_UNKNOWN); totp_check = false; test_no_send_some_peer(); @@ -216,12 +220,32 @@ BOOST_AUTO_TEST_CASE( VCluster_use_sendrecv_known ) { std::cout << "VCluster unit test start known" << "\n"; - test_known(); + test_known(create_vcluster()); std::cout << "VCluster unit test stop known" << "\n"; } +BOOST_AUTO_TEST_CASE( VCluster_communicator_with_external_communicator ) +{ + std::cout << "VCluster unit test external communicator start" << std::endl; + + MPI_Comm com_compute; + int rank = create_vcluster().rank(); + if (rank == 0) + {MPI_Comm_split(MPI_COMM_WORLD, MPI_UNDEFINED,rank, &com_compute);} + else + {MPI_Comm_split(MPI_COMM_WORLD,0,rank, &com_compute);} + + if (rank != 0 ) + { + Vcluster<> v_cl(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv,com_compute); + test_known(v_cl); + test(v_cl,RECEIVE_SIZE_UNKNOWN); + } + + std::cout << "VCluster unit test external communicator stop" << std::endl; +} BOOST_AUTO_TEST_SUITE_END()