Register here: http://gg.gg/ozw1u
MPI is the most complicated method of running in parallel but has the advantage of running over multiple nodes and so you are not limited by the core count on a node. With MPI you run with 256 cores, 512 cores or however many nodes the cluster allows. MPI uses message passing for it’s communication over the Infiniband network on HPC.
*There Are Not Enough Slots Available In The System To Satisfy Mpi Free
*There Are Not Enough Slots Available In The System To Satisfy Mpi Login
*There are not enough slots available in the system to satisfy the 4 slots that were requested by the application: pmd Either request fewer slots for your application, or make more slots available for use.
*These mechanisms are not ideal in the case of MPI-style jobs, in particular. The rlimit applied is the hvmem request multiplied by the slot count for the job on the host, but it is for each process in the job— the limit does not apply to the process tree as a whole.
*1General Information
*2Building MPICH
*3Compiling MPI Programs
*4Running MPI Programs
*5Debugging MPI Programs
*6TroubleshootingGeneral InformationQ: What is MPICH?
A: MPICH is a freely available, portable implementation of MPI, the Standard for message-passing libraries. It implements all versions of the MPI standard including MPI-1, MPI-2, MPI-2.1, MPI-2.2, and MPI-3.Q: What does MPICH stand for?
A: MPI stands for Message Passing Interface. The CH comes from Chameleon, the portability layer used in the original MPICH to provide portability to the existing message-passing systems.Q: Can MPI be used to program multicore systems?There Are Not Enough Slots Available In The System To Satisfy Mpi Free
A: There are two common ways to use MPI with multicore processors or multiprocessor nodes:
* Use one MPI process per core (here, a core is defined as a program counter and some set of arithmetic, logic, and load/store units).
* Use one MPI process per node (here, a node is defined as a collection of cores that share a single address space). Use threads or compiler-provided parallelism to exploit the multiple cores. OpenMP may be used with MPI; the loop-level parallelism of OpenMP may be used with any implementation of MPI (you do not need an MPI that supports MPI_THREAD_MULTIPLE when threads are used only for computational tasks). This is sometimes called the hybrid programming model.
MPICH automatically recognizes multicore architectures and optimizes communication for such platforms. No special configure option is required.Q: How do I build a Subversion checkout of MPICH on Unix?
A: Please see http://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH for the requirements and instructions.Q: Why can’t I build MPICH on Windows anymore?
Golden 7s slot machine. Unfortunately, due to the lack of developer resources, MPICH is not supported on Windows anymore including Cygwin. The last version of MPICH, which was supported on Windows, was MPICH2 1.4.1p1. There is minimal support left for this version, but you can find it on the downloads page:
Alternatively, Microsoft maintains a derivative of MPICH which should provide the features you need. You also find a link to that on the downloads page above. That version is much more likely to work on your system and will continue to be updated in the future. We recommend all Windows users migrate to using MS-MPI.Building MPICHQ: What are process managers?
A: Process managers are basically external (typically distributed) agents that spawn and manage parallel jobs. These process managers communicate with MPICH processes using a predefined interface called as PMI (process management interface). Since the interface is (informally) standardized within MPICH and its derivatives, you can use any process manager from MPICH or its derivatives with any MPI application built with MPICH or any of its derivatives, as long as they follow the same wire protocol. There are three known implementations of the PMI wire protocol: ’simple’, ’smpd’ and ’slurm’. By default, MPICH and all its derivatives use the ’simple’ PMI wire protocol, but MPICH can be configured to use ’smpd’ or ’slurm’ as well.
For example, MPICH provides several different process managers such as Hydra, MPD, Gforker and Remshell which follow the ’simple’ PMI wire protocol. MVAPICH2 provides a different process manager called ’mpirun’ that also follows the same wire protocol. OSC mpiexec follows the same wire protocol as well. You can mix and match an application built with any MPICH derivative with any process manager. For example, an application built with Intel MPI can run with OSC mpiexec or MVAPICH2’s mpirun or MPICH’s Gforker.
MPD has been the traditional default process manager for MPICH till the 1.2.x release series. Starting the 1.3.x series, Hydra is the default process manager.
SMPD is another process manager distributed with MPICH that uses the ’smpd’ PMI wire protocol. This is mainly used for running MPICH on Windows or a combination of UNIX and Windows machines. This will be deprecated in the future releases of MPICH in favour or Hydra. MPICH can be configured with SMPD using:
SLURM is an external process manager that uses MPICH’s PMI interface as well.Note that the default build of MPICH will work fine in SLURM environments. No extra steps are needed.
However, if you want to use the srun tool to launch jobs instead of the default mpiexec, you can configure MPICH as follows:
Once configured with slurm, no internal process manager is built for MPICH; the user is expected to use SLURM’s launch models (such as srun).
Q: Do I have to configure/make/install MPICH each time for each compiler I use?
A: No, in many cases you can build MPICH using one set of compilers and then use the libraries (and compilation scripts) with other compilers. However, this depends on the compilers producing compatible object files. Specifically, the compilers must
* Support the same basic datatypes with the same sizes. For example, the C compilers should use the same sizes for long long and long double.
* Map the names of routines in the source code to names in the object files in the object file in the same way. This can be a problem for Fortran and C++ compilers, though you can often force the Fortran compilers to use the same name mapping. More specifically, most Fortran compilers map names in the source code into all lower-case with one or two underscores appended to the name. To use the same MPICH library with all Fortran compilers, those compilers must make the same name mapping. There is one exception to this that is described below.
* Perform the same layout for C structures. The C langauge does not specify how structures are layed out in memory. For 100% compatibility, all compilers must follow the same rules. However, if you do not use any of the MPI_MIN_LOC or MPI_MAX_LOC datatypes, and you do not rely on the MPICH library to set the extent of a type created with MPI_Type_struct or MPI_Type_create_struct, you can often ignore this requirement.
* Require the same additional runtime libraries. Not all compilers will implement the same version of Unix, and some routines that MPICH uses may be present in only some of the run time libraries associated with specific compilers.
The above may seem like a stringent set of requirements, but in practice, many systems and compiler sets meet these needs, if for no other reason than that any software built with multiple libraries will have requirements similar to those of MPICH for compatibility.
If your compilers are completely compatible, down to the runtime libraries, you may use the compilation scripts (mpicc etc.) by either specifying the compiler on the command line, e.g.
or with the environment variables MPICH_CC etc. (this example assume a c-shell syntax):
If the compiler is compatible except for the runtime libraries, then this same format works as long as a configuration file that describes the necessary runtime libraries is created and placed into the appropriate directory (the ’sysconfdir’ directory in configure terms). See the installation manual for more details.
In some cases, MPICH is able to build the Fortran interfaces in a way that supports multiple mappings of names from the Fortran source code to the object file. This is done by using the ’multiple weak symbol’ support in some environments. For example, when using gcc under Linux, this is the default.
Q: How do I configure to use the Absoft Fortran compilers?
A: You can find build instructions on the Absoft web site at the bottom of the page http://www.absoft.com/Products/Compilers/Fortran/Linux/fortran95/MPich_Instructions.html
Q: When I configure MPICH, I get a message about FDZERO and the configure aborts.
A: FD_ZERO is part of the support for the select calls (see ``man select or ``man 2 select on Linux and many other Unix systems) . What this means is that your system (probably a Mac) has a broken version of the select call and related data types. This is an OS bug; the only repair is to update the OS to get past this bug. This test was added specifically to detect this error; if there was an easy way to work around it, we would have included it (we don’t just implement FD_ZERO ourselves because we don’t know what else is broken in this implementation of select).
If this configure works with gcc but not with xlc, then the problem is with the include files that xlc is using; since this is an OS call (even if emulated), all compilers should be using consistent if not identical include files. In this case, you may need to update xlc.
Q: When I use the g95 Fortran compiler on a 64-bit platform, some of the tests fail.
A: The g95 compiler incorrectly defines the default Fortran integer as a 64-bit integer while defining Fortran reals as 32-bit values (the Fortran standard requires that INTEGER and REAL be the same size). This was apparently done to allow a Fortran INTEGER to hold the value of a pointer, rather than requiring the programmer to select an INTEGER of a suitable KIND. To force the g95 compiler to correctly implement the Fortran standard, use the -i4 flag. For example, set the environment variable F90FLAGS before configuring MPICH:
G95 users should note that there (at this writing) are two distributions of g95 for 64-bit Linux platforms. One uses 32-bit integers and reals (and conforms to the Fortran standard) and one uses 32-bit integers and 64-bit reals. We recommend using the one that conforms to the standard (note that the standard specifies the ratio of sizes, not the absolute sizes, so a Fortran 95 compiler that used 64 bits for both INTEGER and REAL would also conform to the Fortran standard. However, such a compiler would need to use 128 bits for DOUBLE PRECISION quantities).
Q: Make fails with errors such as these:
A: Check if you have set the envirnoment variable CPPFLAGS. If so, unset it and use CXXFLAGS instead. Then rerun configure and make.
Q: When building the ssm channel, I get this error:
A: The ssm channel does not work on all platforms because they use special interprocess locks (often assembly) that may not work with some compilers or machine architectures. It works on Linux with gcc, Intel, and Pathscale compilers on various Intel architectures. It also works in Windows and Solaris environments.
This channel is now deprecated. Please use the ch3:nemesis channel, which is more portable and performs better than ssm.
Q: When using the Intel Fortran 90 compiler (version 9), the make fails with errors in compiling statement that reference MPI_ADDRESS_KIND.
A: Check the output of the configure step. If configure claims that ifort is a cross compiler, the likely problem is that programs compiled and linked with ifort cannot be run because of a missing shared library. Try to compile and run the following program (named conftest.f90):
If this program fails to run, then the problem is that your installation of ifort either has an error or you need to add additional values to your environment variables (such as LD_LIBRARY_PATH). Check your installation documentation for the ifort compiler. See http://softwareforums.intel.com/ISN/Community/en-US/search/SearchResults.aspx?q=libimf.so for an example of problems of this kind that users are having with version 9 of ifort.
If you do not need Fortran 90, you can configure with --disable-f90.
Q: The build fails when I use parallel make.
A: Prior to the 1.5a1 release, parallel make (often invoked with make -j4) would cause several job steps in the build process to update the same library file (libmpich.a) concurrently. Unfortunately, neither the ar nor the ranlib programs correctly handle this case, and the result is a corrupted library. For now, the solution is to not use a parallel make when building MPICH. However, all releases since 1.5a1 now support parallel make. If you are using a recent version of MPICH and seeing parallel build failures that do not occur with serial builds, please report the bug to us.Q: I get a configure error saying ’Incompatible Fortran and C Object File Types!’
A: This is a problem with the default compilers available on Mac OS: it provides a 32-bit C compiler and a 64-bit Fortran compiler (or the other way around). These two are not compatible with each other. Consider installing the same architecture compilers. Alternatively, if you do not need to build Fortran programs, you can disable it with the configure option --disable-f77 --disable-f90.
Compiling MPI ProgramsQ: I get compile errors saying ’SEEK_SET is #defined but must not be for the C++ binding of MPI’.
A: This is really a problem in the MPI-2 standard. And good or bad, the MPICH implementation has to adhere to it. The root cause of this error is that both stdio.h and the MPI C++ interface use SEEK_SET, SEEK_CUR, and SEEK_END. You can try adding:
before mpi.h is included, or add the definition
to the command line (this will cause the MPI versions of SEEK_SET etc. to be skipped).
Q: I get compile errors saying ’error C2555: ’MPI::Nullcomm::Clone’ : overriding virtual function differs from ’MPI::Comm::Clone’ only by return type or calling convention’.
A: This is caused by buggy C++ compilers not implementing part of the C++ standard. To work around this problem, add the definition:
to the CXXFLAGS variable or add a:
before including mpi.h
Running MPI ProgramsQ: I don’t like <WHATEVER> about mpd, or I’m having a problem with mpdboot, can you fix it?
A: Short answer: no.
Longer answer: For all releases since version 1.2, we recommend using the hydra process manager instead of mpd. The mpd process manager has many problems, as well as an annoying mpdboot step that is fragile and difficult to use correctly. The mpd process manager is deprecated at this point, and most reported bugs in it will not be fixed.
Q: Why did my application exited with a BAD TERMINATION error?
A: If the user application terminates abnormally, MPICH displays a message such as the following:
This means that the application has exited with a segmentation fault. This is typically an error in the application code, not in MPICH. We recommend debugging your application using a debugger such as ’ddd’, ’gdb’, ’totalview’ or ’padb’ if you run into this error. See the FAQ entry on debugging for more details.
Q: When I build MPICH with the Intel compilers, launching applications shows a libimf.so not found error
A: When MPICH (more specifically mpiexec and its helper minions, such as hydra_pmi_proxy) is built with the Intel compiler, a dependency is added to libimf.so. When you execute mpiexec, it expects the library dependency to be resolved on each node that you are using. If it cannot find the library on any of the nodes, the following error is reported:
This typically is a problem in the user environment setup. Specifically, your LD_LIBRARY_PATH is not setup correctly either for interactive logins or noninteractive logins, or both.
The above example shows that /soft/intel/13.1.3/lib/intel64 is the library path for interactive logins, but not for noninteractive logins, which can cause this error.
A simple way to fix this is to add the above path to libimf.so to your LD_LIBRARY_PATH in your shell init script (e.g., .bashrc).
Q: How do I pass environment variables to the processes of my parallel program?
A: The specific method depends on the process manager and version of mpiexec that you are using. See the appropriate specific section.
Q: How do I pass environment variables to the processes of my parallel program when using the mpd, hydra or gforker process manager?
A: By default, all the environment variables in the shell where mpiexec is run are passed to all processes of the application program. (The one exception is LD_LIBRARY_PATH when using MPD and the mpd’s are being run as root.) This default can be overridden in many ways, and individual environment variables can be passed to specific processes using arguments to mpiexec. A synopsis of the possible arguments can be listed by typing:
and further details are available in the Users Guide here: http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs.
Q: What determines the hosts on which my MPI processes run?
A: Where processes run, whether by default or by specifying them yourself, depends on the process manager being used.
If you are using the Hydra process manager, the host file can contain the number of processes you want on each node. More information on this can be found here.
If you are using the gforker process manager, then all MPI processes run on the same host where you are running mpiexec.
If you are using mpd, then before you run mpiexec, you will have started, or will have had started for you, a ring of processes called mpd’s (multi-purpose daemons), each running on its own host. It is likely, but not necessary, that each mpd will be running on a separate host. You can find out what this ring of hosts consists of by running the program mpdtrace. One of the mpd’s will be running on the ``local machine, the one where you will run mpiexec. The default placement of MPI processes, if one runs
is to start the first MPI process (rank 0) on the local machine and then to distribute the rest around the mpd ring one at a time. If there are more processes than mpd’s, then wraparound occurs. If there are more mpd’s than MPI processes, then some mpd’s will not run MPI processes. Thus any number of processes can be run on a ring of any size. While one is doing development, it is handy to run only one mpd, on the local machine. Then all the MPI processes will run locally as well.
The first modification to this default behavior is the -1 option to mpiexec (not a great argument name). If -1 is specified, as in
then the first application process will be started by the first mpd in the ring after the local host. (If there is only one mpd in the ring, then this will be on the local host.) This option is for use when a cluster of compute nodes has a ``head node wh
https://diarynote.indered.space
MPI is the most complicated method of running in parallel but has the advantage of running over multiple nodes and so you are not limited by the core count on a node. With MPI you run with 256 cores, 512 cores or however many nodes the cluster allows. MPI uses message passing for it’s communication over the Infiniband network on HPC.
*There Are Not Enough Slots Available In The System To Satisfy Mpi Free
*There Are Not Enough Slots Available In The System To Satisfy Mpi Login
*There are not enough slots available in the system to satisfy the 4 slots that were requested by the application: pmd Either request fewer slots for your application, or make more slots available for use.
*These mechanisms are not ideal in the case of MPI-style jobs, in particular. The rlimit applied is the hvmem request multiplied by the slot count for the job on the host, but it is for each process in the job— the limit does not apply to the process tree as a whole.
*1General Information
*2Building MPICH
*3Compiling MPI Programs
*4Running MPI Programs
*5Debugging MPI Programs
*6TroubleshootingGeneral InformationQ: What is MPICH?
A: MPICH is a freely available, portable implementation of MPI, the Standard for message-passing libraries. It implements all versions of the MPI standard including MPI-1, MPI-2, MPI-2.1, MPI-2.2, and MPI-3.Q: What does MPICH stand for?
A: MPI stands for Message Passing Interface. The CH comes from Chameleon, the portability layer used in the original MPICH to provide portability to the existing message-passing systems.Q: Can MPI be used to program multicore systems?There Are Not Enough Slots Available In The System To Satisfy Mpi Free
A: There are two common ways to use MPI with multicore processors or multiprocessor nodes:
* Use one MPI process per core (here, a core is defined as a program counter and some set of arithmetic, logic, and load/store units).
* Use one MPI process per node (here, a node is defined as a collection of cores that share a single address space). Use threads or compiler-provided parallelism to exploit the multiple cores. OpenMP may be used with MPI; the loop-level parallelism of OpenMP may be used with any implementation of MPI (you do not need an MPI that supports MPI_THREAD_MULTIPLE when threads are used only for computational tasks). This is sometimes called the hybrid programming model.
MPICH automatically recognizes multicore architectures and optimizes communication for such platforms. No special configure option is required.Q: How do I build a Subversion checkout of MPICH on Unix?
A: Please see http://wiki.mpich.org/mpich/index.php/Getting_And_Building_MPICH for the requirements and instructions.Q: Why can’t I build MPICH on Windows anymore?
Golden 7s slot machine. Unfortunately, due to the lack of developer resources, MPICH is not supported on Windows anymore including Cygwin. The last version of MPICH, which was supported on Windows, was MPICH2 1.4.1p1. There is minimal support left for this version, but you can find it on the downloads page:
Alternatively, Microsoft maintains a derivative of MPICH which should provide the features you need. You also find a link to that on the downloads page above. That version is much more likely to work on your system and will continue to be updated in the future. We recommend all Windows users migrate to using MS-MPI.Building MPICHQ: What are process managers?
A: Process managers are basically external (typically distributed) agents that spawn and manage parallel jobs. These process managers communicate with MPICH processes using a predefined interface called as PMI (process management interface). Since the interface is (informally) standardized within MPICH and its derivatives, you can use any process manager from MPICH or its derivatives with any MPI application built with MPICH or any of its derivatives, as long as they follow the same wire protocol. There are three known implementations of the PMI wire protocol: ’simple’, ’smpd’ and ’slurm’. By default, MPICH and all its derivatives use the ’simple’ PMI wire protocol, but MPICH can be configured to use ’smpd’ or ’slurm’ as well.
For example, MPICH provides several different process managers such as Hydra, MPD, Gforker and Remshell which follow the ’simple’ PMI wire protocol. MVAPICH2 provides a different process manager called ’mpirun’ that also follows the same wire protocol. OSC mpiexec follows the same wire protocol as well. You can mix and match an application built with any MPICH derivative with any process manager. For example, an application built with Intel MPI can run with OSC mpiexec or MVAPICH2’s mpirun or MPICH’s Gforker.
MPD has been the traditional default process manager for MPICH till the 1.2.x release series. Starting the 1.3.x series, Hydra is the default process manager.
SMPD is another process manager distributed with MPICH that uses the ’smpd’ PMI wire protocol. This is mainly used for running MPICH on Windows or a combination of UNIX and Windows machines. This will be deprecated in the future releases of MPICH in favour or Hydra. MPICH can be configured with SMPD using:
SLURM is an external process manager that uses MPICH’s PMI interface as well.Note that the default build of MPICH will work fine in SLURM environments. No extra steps are needed.
However, if you want to use the srun tool to launch jobs instead of the default mpiexec, you can configure MPICH as follows:
Once configured with slurm, no internal process manager is built for MPICH; the user is expected to use SLURM’s launch models (such as srun).
Q: Do I have to configure/make/install MPICH each time for each compiler I use?
A: No, in many cases you can build MPICH using one set of compilers and then use the libraries (and compilation scripts) with other compilers. However, this depends on the compilers producing compatible object files. Specifically, the compilers must
* Support the same basic datatypes with the same sizes. For example, the C compilers should use the same sizes for long long and long double.
* Map the names of routines in the source code to names in the object files in the object file in the same way. This can be a problem for Fortran and C++ compilers, though you can often force the Fortran compilers to use the same name mapping. More specifically, most Fortran compilers map names in the source code into all lower-case with one or two underscores appended to the name. To use the same MPICH library with all Fortran compilers, those compilers must make the same name mapping. There is one exception to this that is described below.
* Perform the same layout for C structures. The C langauge does not specify how structures are layed out in memory. For 100% compatibility, all compilers must follow the same rules. However, if you do not use any of the MPI_MIN_LOC or MPI_MAX_LOC datatypes, and you do not rely on the MPICH library to set the extent of a type created with MPI_Type_struct or MPI_Type_create_struct, you can often ignore this requirement.
* Require the same additional runtime libraries. Not all compilers will implement the same version of Unix, and some routines that MPICH uses may be present in only some of the run time libraries associated with specific compilers.
The above may seem like a stringent set of requirements, but in practice, many systems and compiler sets meet these needs, if for no other reason than that any software built with multiple libraries will have requirements similar to those of MPICH for compatibility.
If your compilers are completely compatible, down to the runtime libraries, you may use the compilation scripts (mpicc etc.) by either specifying the compiler on the command line, e.g.
or with the environment variables MPICH_CC etc. (this example assume a c-shell syntax):
If the compiler is compatible except for the runtime libraries, then this same format works as long as a configuration file that describes the necessary runtime libraries is created and placed into the appropriate directory (the ’sysconfdir’ directory in configure terms). See the installation manual for more details.
In some cases, MPICH is able to build the Fortran interfaces in a way that supports multiple mappings of names from the Fortran source code to the object file. This is done by using the ’multiple weak symbol’ support in some environments. For example, when using gcc under Linux, this is the default.
Q: How do I configure to use the Absoft Fortran compilers?
A: You can find build instructions on the Absoft web site at the bottom of the page http://www.absoft.com/Products/Compilers/Fortran/Linux/fortran95/MPich_Instructions.html
Q: When I configure MPICH, I get a message about FDZERO and the configure aborts.
A: FD_ZERO is part of the support for the select calls (see ``man select or ``man 2 select on Linux and many other Unix systems) . What this means is that your system (probably a Mac) has a broken version of the select call and related data types. This is an OS bug; the only repair is to update the OS to get past this bug. This test was added specifically to detect this error; if there was an easy way to work around it, we would have included it (we don’t just implement FD_ZERO ourselves because we don’t know what else is broken in this implementation of select).
If this configure works with gcc but not with xlc, then the problem is with the include files that xlc is using; since this is an OS call (even if emulated), all compilers should be using consistent if not identical include files. In this case, you may need to update xlc.
Q: When I use the g95 Fortran compiler on a 64-bit platform, some of the tests fail.
A: The g95 compiler incorrectly defines the default Fortran integer as a 64-bit integer while defining Fortran reals as 32-bit values (the Fortran standard requires that INTEGER and REAL be the same size). This was apparently done to allow a Fortran INTEGER to hold the value of a pointer, rather than requiring the programmer to select an INTEGER of a suitable KIND. To force the g95 compiler to correctly implement the Fortran standard, use the -i4 flag. For example, set the environment variable F90FLAGS before configuring MPICH:
G95 users should note that there (at this writing) are two distributions of g95 for 64-bit Linux platforms. One uses 32-bit integers and reals (and conforms to the Fortran standard) and one uses 32-bit integers and 64-bit reals. We recommend using the one that conforms to the standard (note that the standard specifies the ratio of sizes, not the absolute sizes, so a Fortran 95 compiler that used 64 bits for both INTEGER and REAL would also conform to the Fortran standard. However, such a compiler would need to use 128 bits for DOUBLE PRECISION quantities).
Q: Make fails with errors such as these:
A: Check if you have set the envirnoment variable CPPFLAGS. If so, unset it and use CXXFLAGS instead. Then rerun configure and make.
Q: When building the ssm channel, I get this error:
A: The ssm channel does not work on all platforms because they use special interprocess locks (often assembly) that may not work with some compilers or machine architectures. It works on Linux with gcc, Intel, and Pathscale compilers on various Intel architectures. It also works in Windows and Solaris environments.
This channel is now deprecated. Please use the ch3:nemesis channel, which is more portable and performs better than ssm.
Q: When using the Intel Fortran 90 compiler (version 9), the make fails with errors in compiling statement that reference MPI_ADDRESS_KIND.
A: Check the output of the configure step. If configure claims that ifort is a cross compiler, the likely problem is that programs compiled and linked with ifort cannot be run because of a missing shared library. Try to compile and run the following program (named conftest.f90):
If this program fails to run, then the problem is that your installation of ifort either has an error or you need to add additional values to your environment variables (such as LD_LIBRARY_PATH). Check your installation documentation for the ifort compiler. See http://softwareforums.intel.com/ISN/Community/en-US/search/SearchResults.aspx?q=libimf.so for an example of problems of this kind that users are having with version 9 of ifort.
If you do not need Fortran 90, you can configure with --disable-f90.
Q: The build fails when I use parallel make.
A: Prior to the 1.5a1 release, parallel make (often invoked with make -j4) would cause several job steps in the build process to update the same library file (libmpich.a) concurrently. Unfortunately, neither the ar nor the ranlib programs correctly handle this case, and the result is a corrupted library. For now, the solution is to not use a parallel make when building MPICH. However, all releases since 1.5a1 now support parallel make. If you are using a recent version of MPICH and seeing parallel build failures that do not occur with serial builds, please report the bug to us.Q: I get a configure error saying ’Incompatible Fortran and C Object File Types!’
A: This is a problem with the default compilers available on Mac OS: it provides a 32-bit C compiler and a 64-bit Fortran compiler (or the other way around). These two are not compatible with each other. Consider installing the same architecture compilers. Alternatively, if you do not need to build Fortran programs, you can disable it with the configure option --disable-f77 --disable-f90.
Compiling MPI ProgramsQ: I get compile errors saying ’SEEK_SET is #defined but must not be for the C++ binding of MPI’.
A: This is really a problem in the MPI-2 standard. And good or bad, the MPICH implementation has to adhere to it. The root cause of this error is that both stdio.h and the MPI C++ interface use SEEK_SET, SEEK_CUR, and SEEK_END. You can try adding:
before mpi.h is included, or add the definition
to the command line (this will cause the MPI versions of SEEK_SET etc. to be skipped).
Q: I get compile errors saying ’error C2555: ’MPI::Nullcomm::Clone’ : overriding virtual function differs from ’MPI::Comm::Clone’ only by return type or calling convention’.
A: This is caused by buggy C++ compilers not implementing part of the C++ standard. To work around this problem, add the definition:
to the CXXFLAGS variable or add a:
before including mpi.h
Running MPI ProgramsQ: I don’t like <WHATEVER> about mpd, or I’m having a problem with mpdboot, can you fix it?
A: Short answer: no.
Longer answer: For all releases since version 1.2, we recommend using the hydra process manager instead of mpd. The mpd process manager has many problems, as well as an annoying mpdboot step that is fragile and difficult to use correctly. The mpd process manager is deprecated at this point, and most reported bugs in it will not be fixed.
Q: Why did my application exited with a BAD TERMINATION error?
A: If the user application terminates abnormally, MPICH displays a message such as the following:
This means that the application has exited with a segmentation fault. This is typically an error in the application code, not in MPICH. We recommend debugging your application using a debugger such as ’ddd’, ’gdb’, ’totalview’ or ’padb’ if you run into this error. See the FAQ entry on debugging for more details.
Q: When I build MPICH with the Intel compilers, launching applications shows a libimf.so not found error
A: When MPICH (more specifically mpiexec and its helper minions, such as hydra_pmi_proxy) is built with the Intel compiler, a dependency is added to libimf.so. When you execute mpiexec, it expects the library dependency to be resolved on each node that you are using. If it cannot find the library on any of the nodes, the following error is reported:
This typically is a problem in the user environment setup. Specifically, your LD_LIBRARY_PATH is not setup correctly either for interactive logins or noninteractive logins, or both.
The above example shows that /soft/intel/13.1.3/lib/intel64 is the library path for interactive logins, but not for noninteractive logins, which can cause this error.
A simple way to fix this is to add the above path to libimf.so to your LD_LIBRARY_PATH in your shell init script (e.g., .bashrc).
Q: How do I pass environment variables to the processes of my parallel program?
A: The specific method depends on the process manager and version of mpiexec that you are using. See the appropriate specific section.
Q: How do I pass environment variables to the processes of my parallel program when using the mpd, hydra or gforker process manager?
A: By default, all the environment variables in the shell where mpiexec is run are passed to all processes of the application program. (The one exception is LD_LIBRARY_PATH when using MPD and the mpd’s are being run as root.) This default can be overridden in many ways, and individual environment variables can be passed to specific processes using arguments to mpiexec. A synopsis of the possible arguments can be listed by typing:
and further details are available in the Users Guide here: http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs.
Q: What determines the hosts on which my MPI processes run?
A: Where processes run, whether by default or by specifying them yourself, depends on the process manager being used.
If you are using the Hydra process manager, the host file can contain the number of processes you want on each node. More information on this can be found here.
If you are using the gforker process manager, then all MPI processes run on the same host where you are running mpiexec.
If you are using mpd, then before you run mpiexec, you will have started, or will have had started for you, a ring of processes called mpd’s (multi-purpose daemons), each running on its own host. It is likely, but not necessary, that each mpd will be running on a separate host. You can find out what this ring of hosts consists of by running the program mpdtrace. One of the mpd’s will be running on the ``local machine, the one where you will run mpiexec. The default placement of MPI processes, if one runs
is to start the first MPI process (rank 0) on the local machine and then to distribute the rest around the mpd ring one at a time. If there are more processes than mpd’s, then wraparound occurs. If there are more mpd’s than MPI processes, then some mpd’s will not run MPI processes. Thus any number of processes can be run on a ring of any size. While one is doing development, it is handy to run only one mpd, on the local machine. Then all the MPI processes will run locally as well.
The first modification to this default behavior is the -1 option to mpiexec (not a great argument name). If -1 is specified, as in
then the first application process will be started by the first mpd in the ring after the local host. (If there is only one mpd in the ring, then this will be on the local host.) This option is for use when a cluster of compute nodes has a ``head node wh
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