Open MPI main development repository (BSD license)
https://github.com/open-mpi/ompi
d7456c3d89
Copy the Doxyfile to orte so people can generate just that documentation. Adjust the properties on that directory so it ignores the resulting doxygen output tree. This should go over to the release branch(es) This commit was SVN r9625. |
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Copyright (c) 2004-2006 The Trustees of Indiana University and Indiana University Research and Technology Corporation. All rights reserved. Copyright (c) 2004-2006 The University of Tennessee and The University of Tennessee Research Foundation. All rights reserved. Copyright (c) 2004-2006 High Performance Computing Center Stuttgart, University of Stuttgart. All rights reserved. Copyright (c) 2004-2006 The Regents of the University of California. All rights reserved. $COPYRIGHT$ Additional copyrights may follow $HEADER$ =========================================================================== The best way to report bugs, send comments, or ask questions is to sign up on the user's and/or developer's mailing list (for user-level and developer-level questions; when in doubt, send to the user's list): users@open-mpi.org devel@open-mpi.org Because of spam, only subscribers are allowed to post to these lists (ensure that you subscribe with and post from exactly the same e-mail address -- joe@example.com is considered different than joe@mycomputer.example.com!). Visit these pages to subscribe to the lists: http://www.open-mpi.org/mailman/listinfo.cgi/users http://www.open-mpi.org/mailman/listinfo.cgi/devel Thanks for your time. =========================================================================== The following abbreviated list of release notes applies to this code base as of this writing (27 Feb 2006): - Open MPI includes support for a wide variety of supplemental hardware and software package. When configuring Open MPI, you may need to supply additional flags to the "configure" script in order to tell Open MPI where the header files, libraries, and any other required files are located. As such, running "configure" by itself may include support for all the devices (etc.) that you expect, especially if their support headers / libraries are installed in non-standard locations. Network interconnects are an easy example to discuss -- Myrinet and Infiniband, for example, both have supplemental headers and libraries that must be found before Open MPI can build support for them. You must specify where these files are with the appropriate options to configure. See the listing of configure command-line switches, below, for more details. - The Open MPI installation must be in your PATH on all nodes (and potentially LD_LIBRARY_PATH, if libmpi is a shared library). - LAM/MPI-like mpirun notation of "C" and "N" is not yet supported. - Striping MPI messages across multiple networks is supported (and happens automatically when multiple networks are available), but needs performance tuning. - The run-time systems that are currently supported are: - rsh / ssh - Recent versions of BProc (e.g., Clustermatic) - PBS Pro, Open PBS, Torque (i.e., anything who supports the TM interface) - SLURM - XGrid - Yod - The majority of Open MPI's documentation is here in this file and on the web site FAQ (http://www.open-mpi.org/). This will eventually be supplemented with cohesive installation and user documentation files. - Systems that have been tested are: - Linux, 32 bit, with gcc - Linux, 64 bit (x86), with gcc - OS X (10.3), 32 bit, with gcc - OS X (10.4), 32 bit, with gcc - Other systems have been lightly (but not fully tested): - Other compilers on Linux, 32 and 64 bit - Other 64 bit platforms (Linux and AIX on PPC64, SPARC) - Building shared libraries on AIX with the xlc compilers is only supported if you supply the following command line option to configure: LDFLAGS=-Wl,-brtl. - At least some versions of the Intel 8.1 compiler seg fault while compiling certain Open MPI source code files. As such, it is not supported. - Early versions of the Portland Group 6.0 compiler have problems creating the C++ MPI bindings as a shared library (e.g., v6.0-1). Tests with later versions show that this has been fixed (e.g., v6.0-5). - The Portland Group compilers require the "-Msignextend" compiler flag to extend the sign bit when converting from a shorter to longer integer. This is is different than other compilers (such as GNU). When compiling Open MPI with the Portland compiler suite, the following flags should be passed to Open MPI's configure script: shell$ ./configure CFLAGS=-Msignextend CXXFLAGS=-signextent \ --with-wrapper-cflags=-Msignextend \ --with-wrapper-cxxflags=-Msignextend ... This will both compile Open MPI with the proper compile flags and also automatically add "-Msignextend" when the C and C++ MPI wrapper compilers are used to compile user MPI applications. - Open MPI will build bindings suitable for all common forms of Fortran 77 compiler symbol mangling on platforms that support it (e.g., Linux). On platforms that do not support weak symbols (e.g., OS X), Open MPI will build Fortran 77 bindings just for the compiler that Open MPI was configured with. Hence, on platforms that support it, if you configure Open MPI with a Fortran 77 compiler that uses one symbol mangling scheme, you can successfully compile and link MPI Fortran 77 applications with a Fortran 77 compiler that uses a different symbol mangling scheme. NOTE: For platforms that support the multi-Fortran-compiler bindings (i.e., weak symbols are supported), due to limitations in the MPI standard and in Fortran compilers, it is not possible to hide these differences in all cases. Specifically, the following two cases may not be portable between different Fortran compilers: 1. The C constants MPI_F_STATUS_IGNORE and MPI_F_STATUSES_IGNORE will only compare properly to Fortran applications that were created with Fortran compilers that that use the same name-mangling scheme as the Fortran compiler that Open MPI was configured with. 2. Fortran compilers may have different values for the logical .TRUE. constant. As such, any MPI function that uses the Fortran LOGICAL type may only get .TRUE. values back that correspond to the the .TRUE. value of the Fortran compiler that Open MPI was configured with. Note that some Fortran compilers allow forcing .TRUE. to be 1 and .FALSE. to be 0. For example, the Portland Group compilers provide the "-Munixlogical" option, and Intel compilers (version >= 8.) provide the "-fpscomp logicals" option. You can use the ompi_info command to see the Fortran compiler that Open MPI was configured with. - The MPI and run-time layers do not free all used memory properly during MPI_FINALIZE. - Running on nodes with different endian and/or different datatype sizes within a single parallel application is not supported in this release. - MPI_THREAD_MULTIPLE support is included, but is only lightly tested. - Asynchronous message passing progress support is not included in this release. - Due to limitations in the Libtool 1.5 series, Fortran 90 MPI bindings support can only be built as a static library. It is expected that Libtool 2.0 (and therefore future releases of Open MPI) will be able to support shared libraries for the Fortran 90 bindings. - On Linux, if either the malloc_hooks or malloc_interpose memory hooks are enabled, it will not be possible to link against a static libc.a. libmpi can still be built statically - it is only the final application link step that can not be static. If applications must be statically linked, it is recommended you compile Open MPI with the --without-memory-manager configure option. - The XGrid support is experimental - see the Open MPI FAQ and this post on the Open MPI user's mailing list for more information: http://www.open-mpi.org/community/lists/users/2006/01/0539.php - The MX library limits the maximum message fragment size for both on-node and off-node messages. As of MX v1.0.3, the inter-node maximum fragment size is 32k, and the intra-node maximum fragment size is 16k -- fragments sent larger than these sizes will fail. Open MPI automatically fragments large messages; it currently limits its first fragment size on MX networks to the lower of these two values -- 16k. As such, increasing the value of the MCA parameter named "btl_mx_first_frag_size" larger than 16k may cause failures in some cases (i.e., when using MX to send large messages to processes on the same node); it will cause failures in all cases if it is set above 32k. Note that this only affects the *first* fragment of messages; latter fragments do not have this size restriction. The MCA parameter btl_mx_max_send_size can be used to vary the maximum size of subsequent fragments. - The current version of the Open MPI point-to-point engine does not yet support hardware-level MPI message matching. As such, MPI message matching must be performed in software, artificially increasing latency for short messages on certain networks (such as MX and hardware-supported Portals). Future versions of Open MPI will support hardware matching on networks that provide it, and will eliminate the extra overhead of software MPI message matching where possible. =========================================================================== Building Open MPI ----------------- Open MPI uses a traditional configure script paired with "make" to build. Typical installs can be of the pattern: --------------------------------------------------------------------------- shell$ ./configure [...options...] shell$ make all install --------------------------------------------------------------------------- There are many available configure options (see "./configure --help" for a full list); a summary of the more commonly used ones follows: --prefix=<directory> Install Open MPI into the base directory named <directory>. Hence, Open MPI will place its executables in <directory>/bin, its header files in <directory>/include, its libraries in <directory>/lib, etc. --with-gm=<directory> Specify the directory where the GM libraries and header files are located. This enables GM support in Open MPI. --with-mx=<directory> Specify the directory where the MX libraries and header files are located. This enables MX support in Open MPI. --with-mvapi=<directory> Specify the directory where the mVAPI libraries and header files are located. This enables mVAPI support in Open MPI. --with-openib=<directory> Specify the directory where the Open IB libraries and header files are located. This enables mVAPI support in Open MPI. --with-tm=<directory> Specify the directory where the TM libraries and header files are located. This enables PBS / Torque support in Open MPI. --with-mpi-param_check(=value) "value" can be one of: always, never, runtime. If no value is specified, or this option is not used, "always" is the default. Using --without-mpi-param-check is equivalent to "never". - always: the parameters of MPI functions are always checked for errors - never: the parameters of MPI functions are never checked for errors - runtime: whether the parameters of MPI functions are checked depends on the value of the MCA parameter mpi_param_check (default: yes). --with-threads=value Since thread support (both support for MPI_THREAD_MULTIPLE and asynchronous progress) is only partially tested, it is disabled by default. To enable threading, use "--with-threads=posix". This is most useful when combined with --enable-mpi-threads and/or --enable-progress-threads. --enable-mpi-threads Allows the MPI thread level MPI_THREAD_MULTIPLE. See --with-threads; this is currently disabled by default. --enable-progress-threads Allows asynchronous progress in some transports. See --with-threads; this is currently disabled by default. --disable-mpi-cxx Disable building the C++ MPI bindings. Note that this does *not* disable the C++ checks during configure; some of Open MPI's tools are written in C++ and therefore require a C++ compiler to be built. --disable-mpi-f77 Disable building the Fortran 77 MPI bindings. --disable-mpi-f90 Disable building the Fortran 90 MPI bindings. Also related to the --with-f90-max-array-dim option. --with-f90-max-array-dim=<DIM> The F90 MPI bindings are strictly typed, even including the number of dimensions for arrays for MPI choice buffer parameters. Open MPI generates these bindings at compile time with a maximum number of dimensions as specified by this parameter. The default value is 4. --disable-shared By default, libmpi is built as a shared library, and all components are built as dynamic shared objects (DSOs). This switch disables this default; it is really only useful when used with --enable-static. --enable-static Build libmpi as a static library, and statically link in all components. There are several other options available -- see "./configure --help". Changing the compilers that Open MPI uses to build itself uses the standard Autoconf mechanism of setting special environment variables either before invoking configure or on the configure command line. The following environment variables are recognized by configure: CC - C compiler to use CFLAGS - Compile flags to pass to the C compiler CPPFLAGS - Preprocessor flags to pass to the C compiler CXX - C++ compiler to use CXXFLAGS - Compile flags to pass to the C++ compiler CXXCPPFLAGS - Preprocessor flags to pass to the C++ compiler F77 - Fortran 77 compiler to use FFLAGS - Compile flags to pass to the Fortran 77 compiler FC - Fortran 90 compiler to use FCFLAGS - Compile flags to pass to the Fortran 90 compiler LDFLAGS - Linker flags to pass to all compilers LIBS - Libraries to pass to all compilers (it is rarely necessary for users to need to specify additional LIBS) For example: shell$ ./configure CC=mycc CXX=myc++ F77=myf77 F90=myf90 ... It is required that the compilers specified be compile and link compatible, meaning that object files created by one compiler must be able to be linked with object files from the other compilers and produce correctly functioning executables. Open MPI supports all the "make" targets that are provided by GNU Automake, such as: all - build the entire Open MPI package install - install Open MPI uninstall - remove all traces of Open MPI from the $prefix clean - clean out the build tree Once Open MPI has been built and installed, it is safe to run "make clean" and/or remove the entire build tree. VPATH builds are fully supported. Generally speaking, the only thing that users need to do to use Open MPI is ensure that <prefix>/bin is in their PATH and <prefix>/lib is in their LD_LIBRARY_PATH. Users may need to ensure to set the PATH and LD_LIBRARY_PATH in their shell setup files (e.g., .bashrc, .cshrc) so that rsh/ssh-based logins will be able to find the Open MPI executables. =========================================================================== Checking Your Open MPI Installation ----------------------------------- The "ompi_info" command can be used to check the status of your Open MPI installation (located in <prefix>/bin/ompi_info). Running it with no arguments provides a summary of information about your Open MPI installation. Note that the ompi_info command is extremely helpful in determining which components are installed as well as listing all the run-time settable parameters that are available in each component (as well as their default values). The following options may be helpful: --all Show a *lot* of information about your Open MPI installation. --parsable Display all the information in an easily grep/cut/awk/sed-able format. --param <framework> <component> A <framework> of "all" and a <component> of "all" will show all parameters to all components. Otherwise, the parameters of all the components in a specific framework, or just the parameters of a specific component can be displayed by using an appropriate <framework> and/or <component> name. Changing the values of these parameters is explained in the "The Modular Component Architecture (MCA)" section, below. =========================================================================== Compiling Open MPI Applications ------------------------------- Open MPI provides "wrapper" compilers that should be used for compiling MPI applications: C: mpicc C++: mpiCC (or mpic++ if your filesystem is case-insensitive) Fortran 77: mpif77 Fortran 90: mpif90 For example: shell$ mpicc hello_world_mpi.c -o hello_world_mpi -g shell$ All the wrapper compilers do is add a variety of compiler and linker flags to the command line and then invoke a back-end compiler. To be specific: the wrapper compilers do not parse source code at all; they are solely command-line manipulators, and have nothing to do with the actual compilation or linking of programs. The end result is an MPI executable that is properly linked to all the relevant libraries. =========================================================================== Running Open MPI Applications ----------------------------- Open MPI supports both mpirun and mpiexec (they are exactly equivalent). For example: shell$ mpirun -np 2 hello_world_mpi or shell$ mpiexec -np 1 hello_world_mpi : -np 1 hello_world_mpi are equivalent. Some of mpiexec's switches (such as -host and -arch) are not yet functional, although they will not error if you try to use them. The rsh starter accepts a -hostfile parameter (the option "-machinefile" is equivalent); you can specify a -hostfile parameter indicating an standard mpirun-style hostfile (one hostname per line): shell$ mpirun -hostfile my_hostfile -np 2 hello_world_mpi If you intend to run more than one process on a node, the hostfile can use the "slots" attribute. If "slots" is not specified, a count of 1 is assumed. For example, using the following hostfile: --------------------------------------------------------------------------- node1.example.com node2.example.com node3.example.com slots=2 node4.example.com slots=4 --------------------------------------------------------------------------- shell$ mpirun -hostfile my_hostfile -np 8 hello_world_mpi will launch MPI_COMM_WORLD rank 0 on node1, rank 1 on node2, ranks 2 and 3 on node3, and ranks 4 through 7 on node4. Other starters, such as the batch scheduling environments, do not require hostfiles (and will ignore the hostfile if it is supplied). Note that the values of component parameters can be changed on the mpirun / mpiexec command line. This is explained in the section below, "The Modular Component Architecture (MCA)". =========================================================================== The Modular Component Architecture (MCA) The MCA is the backbone of Open MPI -- most services and functionality are implemented through MCA components. Here is a list of all the component frameworks in Open MPI: --------------------------------------------------------------------------- MPI component frameworks: ------------------------- allocator - Memory allocator bml - BTL management layer btl - MPI point-to-point byte transfer layer coll - MPI collective algorithms io - MPI-2 I/O mpool - Memory pooling pml - MPI point-to-point management layer ptl - (Outdated / deprecated) MPI point-to-point transport layer rcache - Memory registration cache topo - MPI topology routines Back-end run-time environment component frameworks: --------------------------------------------------- errmgr - RTE error manager gpr - General purpose registry iof - I/O forwarding ns - Name server oob - Out of band messaging pls - Process launch system ras - Resource allocation system rds - Resource discovery system rmaps - Resource mapping system rmgr - Resource manager rml - RTE message layer schema - Name schemas sds - Startup / discovery service soh - State of health monitor Miscellaneous frameworks: ------------------------- maffinity - Memory affinity memory - Memory subsystem hooks paffinity - Processor affinity timer - High-resolution timers --------------------------------------------------------------------------- Each framework typically has one or more components that are used at run-time. For example, the btl framework is used by MPI to send bytes across underlying networks. The tcp btl, for example, sends messages across TCP-based networks; the gm btl sends messages across GM Myrinet-based networks. Each component typically has some tunable parameters that can be changed at run-time. Use the ompi_info command to check a component to see what its tunable parameters are. For example: shell$ ompi_info --param btl tcp shows all the parameters (and default values) for the tcp btl component. These values can be overridden at run-time in several ways. At run-time, the following locations are examined (in order) for new values of parameters: 1. <prefix>/etc/openmpi-mca-params.conf This file is intended to set any system-wide default MCA parameter values -- it will apply, by default, to all users who use this Open MPI installation. The default file that is installed contains many comments explaining its format. 2. $HOME/.openmpi/mca-params.conf If this file exists, it should be in the same format as <prefix>/etc/openmpi-mca-params.conf. It is intended to provide per-user default parameter values. 3. environment variables of the form OMPI_MCA_<name> set equal to a <value> Where <name> is the name of the parameter. For example, set the variable named OMPI_MCA_btl_tcp_frag_size to the value 65536 (Bourne-style shells): shell$ OMPI_MCA_btl_tcp_frag_size=65536 shell$ export OMPI_MCA_btl_tcp_frag_size 4. the mpirun command line: --mca <name> <value> Where <name> is the name of the parameter. For example: shell$ mpirun --mca btl_tcp_frag_size 65536 -np 2 hello_world_mpi These locations are checked in order. For example, a parameter value passed on the mpirun command line will override an environment variable; an environment variable will override the system-wide defaults. =========================================================================== Common Questions ---------------- Many common questions about building and using Open MPI are answered on the FAQ: http://www.open-mpi.org/faq/ =========================================================================== Got more questions? ------------------- Found a bug? Got a question? Want to make a suggestion? Want to contribute to Open MPI? Please let us know! User-level questions and comments should generally be sent to the user's mailing list (users@open-mpi.org). Because of spam, only subscribers are allowed to post to this list (ensure that you subscribe with and post from *exactly* the same e-mail address -- joe@example.com is considered different than joe@mycomputer.example.com!). Visit this page to subscribe to the user's list: http://www.open-mpi.org/mailman/listinfo.cgi/users Developer-level bug reports, questions, and comments should generally be sent to the developer's mailing list (devel@open-mpi.org). Please do not post the same question to both lists. As with the user's list, only subscribers are allowed to post to the developer's list. Visit the following web page to subscribe: http://www.open-mpi.org/mailman/listinfo.cgi/devel When submitting bug reports to either list, be sure to include the following information in your mail (please compress!): - the stdout and stderr from Open MPI's configure - the top-level config.log file - the stdout and stderr from building Open MPI - the output from "ompi_info --all" (if possible) For Bourne-type shells, here's one way to capture this information: shell$ ./configure ... 2>&1 | tee config.out [...lots of configure output...] shell$ make 2>&1 | tee make.out [...lots of make output...] shell$ mkdir ompi-output shell$ cp config.out config.log make.out ompi-output shell$ ompi_info --all |& tee ompi-output/ompi-info.out shell$ tar cvf ompi-output.tar ompi-output [...output from tar...] shell$ gzip ompi-output.tar For C shell-type shells, the procedure is only slightly different: shell% ./configure ... |& tee config.out [...lots of configure output...] shell% make |& tee make.out [...lots of make output...] shell% mkdir ompi-output shell% cp config.out config.log make.out ompi-output shell% ompi_info --all |& tee ompi-output/ompi-info.out shell% tar cvf ompi-output.tar ompi-output [...output from tar...] shell% gzip ompi-output.tar In either case, attach the resulting ompi-output.tar.gz file to your mail. This provides the Open MPI developers with a lot of information about your installation and can greatly assist us in helping with your problem. Be sure to also include any other useful files (in the ompi-output.tar.gz tarball), such as output showing specific errors.