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GLOBAL ARRAYS ~~~~~~~~~~~~~ DISCLAIMER ========== This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, APPARATUS, PRODUCT, SOFTWARE, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS. ACKNOWLEDGMENT ============== This software and its documentation were produced with United States Government support under Contract Number DE-AC06-76RLO-1830 awarded by the United States Department of Energy. The United States Government retains a paid-up non-exclusive, irrevocable worldwide license to reproduce, prepare derivative works, perform publicly and display publicly by or for the US Government, including the right to distribute to other US Government contractors. The primary current source of funding for development of GA is the DoE-2000 ACTS project. GA is a part of the ACTS toolkit: http://acts.nersc.gov FOR THE IMPATIENT ================= The command:: ./configure && make && make install should compile the static GA library (libga.a) to use sockets and install headers and libraries to /usr/local/include and /usr/local/lib, respectively. Please refer to the INSTALL file for generic build instructions. That is a good place to start if you are new to using "configure; make; make install" types of builds. Detailed instructions are covered later in this file. QUESTIONS/HELP/SUPPORT/BUG-REPORT ================================= email: email@example.com If you encounter any problems, please first refer to the file NOTES located in the same directory and see the GA support webpage: http://www.emsl.pnl.gov/docs/global/support.html Please don't hesitate to send us an email. An archive of emails is available at: http://groups.google.com/group/hpctools WHERE IS THE DOCUMENTATION? =========================== The GA webpage has the most current versions of the Fortran and C documentation and the User's Manual in the HTML format: http://www.emsl.pnl.gov/docs/global/ ABOUT THIS SOFTWARE =================== This directory contains the Global Arrays (GA), Aggregate Remote Memory Copy Interface (ARMCI) run-time library, and Memory Allocator (MA), parallel I/O libraries (DRA,EAF,SF), TCGMSG, and TCGMSG-MPI packages bundled together. Global Arrays is a portable Non-Uniform Memory Access (NUMA) shared-memory programming environment for distributed and shared memory computers. It augments the message-passing model by providing a shared-memory like access to distributed dense arrays. ARMCI provides one-sided remote memory operations used by GA. DRA (Disk Resident Arrays) is a parallel I/O library that maintains dense 2-dim arrays on disk. SF (Shared Files) is a parallel I/O library that allows noncollective I/O to a parallel file. EAF (Exclusive Access Files) is parallel I/O library that supports I/O to private files. TCGMSG is a simple, efficient, but becoming obsolete message-passing library. TCGMSG-MPI is a TCGMSG interface implementation on top of MPI and ARMCI. MA is a dynamic memory allocator/manager for Fortran and C programs. GA++ is a C++ binding for global arrays. See file 'COPYRIGHT' for copying conditions. See file 'INSTALL' for compilation and installation instructions (generic). See file 'NEWS' for a list of major changes in the current release. See file 'AUTHORS' for the names of anyone who has contributed to GA. See file 'NOTES' for a few platform-specific symptoms and fixes. DIRECTORY STRUCTURE (ALPHABETICALLY) ==================================== - armci + config (configuration makefile includes) + doc (documentation for ARMCI library) + lib (compatibility source files for missing system features) + src (source code for ARMCI library) - build-aux (autotools support scripts) - cca (common component architecture) - compat (compatibility source files for missing system features) - doc (documentation) - ga++ (C++ Bindings for Global Arrays) + doc (contains sample Doxyfile for Doxygen doc generator) + src (source code for GA C++ bindings) + testing (test programs) - gaf2c (Fortran-to-C compatibility library and tests) - global + doc (paper & documentation in PostScript, HTML & plain text) + src (source code for GA library) + testing (GA test programs and performance results) + trace (library and programs to generate and process tracefiles) + X (xregion visualization program for GA) - LinAlg (linear algebra software used by GA) + lapack+blas - m4 (autoconf macros) - ma (Memory Allocator) + man - pario + dra (Disk Resident Array Library code) + eaf (Exclusive Access Files Library code) + elio ("device" layer for other parallel I/O models) + sf (Shared Files Library code) - tcgmsg (simple, legacy message-passing library) + ipcv4.0 + ipcv5.0 + tcgmsg-mpi (TCGMSG on top of MPI) HOW TO BUILD THE PACKAGE? ========================= Please refer to the INSTALL file for generic build instructions. That is a good place to start if you are new to using "configure; make; make install" types of builds. The following will cover platform-specific considerations as well as the various optional features of GA. Customizations to the GA build via the configure script are discussed next. Configuration Options --------------------- There are many options available when configuring GA. Although configure can be safely run within this distributions' root folder, we recommend performing an out-of-source (aka VPATH) build. This will cleanly separate the generated Makefiles and compiled object files and libraries from the source code. This will allow, for example, one build using sockets versus another build using OpenIB for the communication layer to use the same source tree e.g.:: mkdir bld_mpi_sockets && cd bld_mpi_sockets && ../configure mkdir bld_mpi_openib && cd bld_mpi_openib && ../configure --with-openib Regardless of your choice to perform a VPATH build, the following should hopefully elucidate the myriad options to configure. Only the options requiring additional details are documented here. ./configure --help will certainly list more options in addition to limited documentation. --disable-f77 Disable Fortran code. This used to be the old GA_C_CORE or NOFORT environment variables which enabled the C++ bindings. However, it is severely broken. There are certain cases where Fortran code is required but this will not inhibit the building of the C++ bindings. In the future we may be able to eliminate the need for the Fortran compiler/linker. Use at your own risk (of missing symbols at link-time.) --enable-cxx Build C++ interface. This will require the C++ linker to locate the Fortran libraries (handled automatically) but user C++ code will require the same considerations (C++ linker, Fortran libraries.) --disable-opt Don't use hard-coded optimization flags. GA is a highly-optimized piece of software. There are certain optimization levels or flags that are known to break the software. If you experience mysterious faults, consider rebuilding without optimization by using this option. --enable-peigs Enable Parallel Eigensystem Solver interface. This will build the stubs required to call into the peigs library (external). --enable-checkpoint Enable checkpointing. Untested. For use with old X-based visualization tool. --enable-profile Enable profiling. Not sure what this does, sorry. --enable-trace Enable tracing. Not sure what this does, sorry. --enable-thread-safety **unsupported** Turn on thread safety. --enable-underscoring Force single underscore for all external Fortran symbols. Usually, configure is able to detect the name mangling scheme of the detected Fortran compiler and will default to using what is detected. This includes any variation of zero, one, or two underscores or whether UPPERCASE or lowercase symbols are used. If you want to force a single underscore which was the default of older GA builds, use this option. Otherwise, you can use the FFLAGS environment variable to override the Fortran compiler's or platform's defaults e.g. configure FFLAGS=-fno-underscoring. --enable-i4 Use 4 bytes for Fortran INTEGER size. Otherwise, the default INTEGER size is set to the results of the C sizeof(void*) operator. --enable-i8 Use 8 bytes for Fortran INTEGER size. Otherwise, the default INTEGER size is set to the results of the C sizeof(void*) operator. --enable-shared Build shared libraries [default=no]. Useful, for example, if you plan on wrapping GA with an interpreted language such as Python. Otherwise, some systems only support static libraries (or vice versa) but static libraries are the default. For most of the external software packages an optional argument is allowed (represented as ARG below.) **ARG can be omitted** or can be one or more whitespace-separated directories, linker or preprocessor directives. For example:: --with-mpi="/path/to/mpi -lmylib -I/mydir" --with-mpi=/path/to/mpi/base --with-mpi=-lmpich The messaging libraries supported include MPI, TCGMSG, and TCGMSG over MPI. If you omit their respective --with-* option, MPI is the default. GA can be built to work with MPI or TCGMSG. Since the TCGMSG package is small (comparing to portable MPI implementations), compiles fast, it is still bundled with the GA package. --with-mpi=ARG Select MPI as the messaging library (default). If you omit ARG, we attempt to locate the MPI compiler wrappers. If you supply anything for ARG, we will parse ARG as indicated above. --with-tcgmsg Select TCGMSG as the messaging library; if --with-mpi is also specified then TCGMSG over MPI is used. --with-vampir=ARG Enable VAMPIR performance tracing. http://www.vampir.eu --with-blas=ARG Use external BLAS library; attempt to detect sizeof(INTEGER) used to compile BLAS; if not found, an internal BLAS is built --with-blas4=ARG Use external BLAS library compiled with sizeof(INTEGER)==4 --with-blas8=ARG Use external BLAS library compiled with sizeof(INTEGER)==8 --with-lapack=ARG Use external LAPACK library. If not found, an internal one is built. --with-scalapack=ARG Use external ScaLAPACK library. The ARMCI networks supported are listed next. Our ability to automatically locate required headers libraries is currently inadequate. Therefore, you will likely need to specify the optional ARG pointing to the necessary directories and/or libraries. sockets is the default ARMCI network if nothing else is specified. --with-bgml=ARG select armci network as IBM BG/L --with-cray-shmem=ARG select armci network as Cray XT shmem --with-dcmf=ARG select armci network as IBM BG/P Deep Computing Message Framework --with-lapi=ARG select armci network as IBM LAPI --with-mpi-spawn=ARG select armci network as MPI-2 dynamic process mgmt --with-openib=ARG select armci network as Infiniband OpenIB --with-portals=ARG select armci network as Cray XT portals --with-sockets=ARG select armci network as Ethernet TCP/IP (default) There are some influential environment variables as documented in configure --help, however there are a few that are special to GA. - THREAD_LIBRARY See --enable-thread-safety. I don't know what this does, sorry. - F77_INT_FLAG Fortran compiler flag to set the default INTEGER size. We know about certain Fortran flags that set the default INTEGER size, but there will certainly be some new (or old) ones that we don't know about. If the configure test to determine the correct flag fails, please try setting this variable and rerunning configure. - F2C_HIDDEN_STRING_LENGTH_AFTER_ARGS If cross compiling, set to either "yes" (default) or "no" (after string). For compatibility between Fortran and C, a Fortran subroutine written in C that takes a character string must take an additional argument (one per character string) indicating the length of the string. This 'hidden' argument appears either immediately after the string in the argument list or after all other arguments to the function. This is compiler dependent. We attempt to detect this behavior automatically, but in the case of cross-compiled systems it may be necessary to specify the less usual after string convention the gaf2c/testarg program crashes. Special Notes for BLAS ---------------------- BLAS, being a Fortran library, can be compiled with a default INTEGER size of 4 or a promoted INTEGER size of 8. Experience has shown us that most of the time the default size of INTEGER used is 4. In some cases, however, you may have an external BLAS library which is using 8-byte INTEGERs. In order to correctly interface with an external BLAS library, GA must know the size of INTEGER used by the BLAS library. configure has the following BLAS-related options: --with-blas, --with-blas4, and --with-blas8. The latter two will force the INTEGER size to 4- or 8-bytes, respectively. The first option, --with-blas, defaults to 4-byte INTEGERS *however* in the two special cases of using ACML or MKL, it is possible to detect 8-byte INTEGERs automatically. As documented in the ACML manual, if the path to the library has "_int64" then 8-byte INTEGERs are used. As documented in the MKL manual, if the library is "ilp64", then 8-byte INTEGERs are used. You may always override --with-blas by specifying the INTEGER size using one of the two more specific options. Cross-Compilation Issues ------------------------ Certain platforms cross-compile from a login node for a compute node, or one might choose to cross-compile for other reasons. Cross-compiling requires the use of the --host option to configure which indicates to configure that certain run-time tests should not be executed. See INSTALL for details on use of the --host option. Two of our target platforms are known to require cross-compilation, Cray XT and IBM Blue Gene. Cray XT +++++++ It has been noted that configure still succeeds without the use of the --host flag. If you experience problems without --host, we recommend:: configure --host=x86_64-unknown-linux-gnu And if that doesn't work (cross-compilation is not detected) you must then *force* cross-compilation using both --host and --build together:: configure --host=x86_64-unknown-linux-gnu --build=x86_64-unknown-linux-gnu BlueGene/P ++++++++++ Currently the only way to detect the BGP platform and compile correctly is to use:: configure --host=powerpc-bgp-linux The rest of the configure options apply as usual e.g. --with-dcmf in this case. Compiler Selection ------------------ Unless otherwise noted you can try to overwrite the default compiler names detected by configure by defining F77, CC, and CXX for Fortran (77), C, and C++ compilers, respectively. Or when using the MPI compilers MPIF77, MPICC, and MPICXX for MPI Fortran (77), C, and C++ compilers, respectively:: configure F77=f90 CC=gcc configure MPIF77=mpif90 MPICC=mpicc Although you can change the compiler at make-time it will likely fail. Many platform-specific compiler flags are detected at configure-time based on the compiler selection. If changing compilers, we recommend rerunning configure as above. After Configuration ------------------- By this point we assume you have successfully run configure either from the base distribution directory or from a separate build directory (aka VPATH build.) You are now ready to run 'make'. You can optionally run parallel make using the "-j" option which significantly speeds up the build. If using the MPI compiler wrappers, occasionally using "-j" will cause build failures because the MPI compiler wrapper creates a temporary symlink to the mpif.h header. In that case, you won't be able to use the "-j" option. Further, the influential environment variables used at configure-time can be overridden at make-time in case problems are encountered. For example:: ./configure CFLAGS=-Wimplicit ... make CFLAGS="-Wimplicit -g -O0" One particularly influential make variable is "V" which controls the verbosity of the make output. This variable corresponds to the --dis/enable-silent-riles configure-time option, but I often prefer the make-time variable:: make V=0 (configure --enable-silent-rules) make V=1 (configure --disable-silent-rules) Test Programs ------------- Running "make checkprogs" will build most test and example programs. Note that not all tests are built -- some tests depend on certain features being detected or enabled during configure. These programs are not intented to be examples of good GA coding practices because they often include private headers. However, they help us debug or time our GA library. Test Suite ++++++++++ Running "make check" will build most test and example programs (See "make checkprogs" notes above) in addition to running the test suite. The test suite runs both the serial and parallel tests. The test suite must know how to launch the parallel tests via the MPIEXEC variable. Please read your MPI flavor's documentation on how to launch, or if using TCGMSG you will use the "parallel" tool. For example, the following is the command to launch the test suite when compiled with OpenMPI:: make check MPIEXEC="mpiexec -np 4" All tests have a per-test log file containing the output of the test. So if the test is global/testing/test.x, the log file would be global/testing/test.log. The output of failed tests is collected in the top-level log summary test-suite.log. The test suite will recurse into the ARMCI directory and run the ARMCI test suite first. If the ARMCI test suite fails, the GA test suite will not run (the assumption here is that you should fix bugs in the dependent library first.) To run only the GA test suite, type "make check-ga" with the appropriate MPIEXEC variable. How to Run GA Test Programs? ---------------------------- Depends on the system. MPPs like Intel iPSC/860, Delta, Paragon, IBM SPx, Cray T3/E have their own commands for submitting parallel jobs. On workstations and clusters, GA are run like ordinary message-passing programs:: To run GA programs with MPI, you need to built the package to be compatible with MPI (see README in ./global and documentation in ./global/doc/ ) and run it as any other MPI program. The GA package has been tested only with a limited number of MPI implementations (MPICH, and vendor's: Intel, IBM, Sun, HP, and SGI). TCGMSG `parallel' command (built automaticaly in ./tcgmsg/ipcv4.0/parallel if needed) is used to start a job on clusters if you are using TCGMSG as your message-passing library. On the workstations, GA-based programs that use TCGMSG can be run with a single process without the `parallel' command -- just by typing program name -- useful for debugging. Other Issues ============ a. LINUX64 supports ALPHA, Itanium, Opteron, and Em64T processors only. b. The SGI_N32 version is recommended on all newer SGI boxes including the O2, Octane, Origin, Indigo2, and PowerChallenge systems unless the system has lots of memory and your program uses huge arrays (>4GB) in which case 64-bit addressing is required (SGITFP version). In addition, TARGET_CPU environment variable can be used to choose the optimal compiler flags for R8000 and R10000 processors. c. In 64 bit platforms, if you are using blas libraries that takes integer as 8 bytes, then set the following environment variables: setenv BLAS_I8 yes setenv BLAS_LIB specify_your_blas_library e.g.setenv BLAS_LIB -L/usr/lib/libblas.a d. To turn Async I/O on under Linux, set environment variable USE_LINUXAIO=y Performance Tuning ------------------ global/src/gaconfig.h has a varible called AVOID_MA_STORAGE. If defined, this variable forces GA to use ARMCI memory which can lead to better performance on platforms on which memory needs to be registered for fast communication. Setting an environment variable MA_USE_ARMCI_MEM forces MA library to use ARMCI memory, communication via which can be faster on networks like GM, VIA and InfiniBand.