- $ mpirun -np 25 python -c 'print 'hey' - There are not enough slots available in the system to satisfy the 25 slots that were requested by the application: python Either request fewer slots for your application, or make more slots available for use.
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Name
orterun, mpirun, mpiexec - Execute serial and parallel jobsin Open MPI. oshrun, shmemrun - Execute serial and parallel jobs in OpenSHMEM.
Note:mpirun, mpiexec, and orterun are all synonyms for each otheras well as oshrun, shmemrun in case Open SHMEM is installed. Using any ofthe names will produce the same behavior.
Synopsis
A 'slot' is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run: 1. Hostfile, via 'slots=N' clauses (N defaults to number of processor cores if not provided) 2. The -host command line parameter, via a ':N' suffix on the. Run started at:- Mon Apr 8 18:07:07 AEST 2019 - There are not enough slots available in the system to satisfy the 8 slots that were requested by the application: python Either request fewer slots for your application, or make more slots available for use. Attempt 3. 'There are not enough slots available in the system to satisfy the 1. Mpirun do the work, but there's no accounting for things in Yorkshire.
Single Process MultipleData (SPMD) Model:
mpirun [ options ] [ ]
Multiple InstructionMultiple Data (MIMD) Model:
mpirun [ global_options ] [ local_options1]
[ ] : [ local_options2 ]
[ ] : .. :
[ local_optionsN ]
[ ]
Note that in both models, invoking mpirun via an absolutepath name is equivalent to specifying the --prefix option with a
valueequivalent to the directory where mpirun resides, minus its last subdirectory. For example:% /usr/local/bin/mpirun ..
is equivalent to
% mpirun --prefix /usr/local
Quick Summary
If you are simply looking for how to run an MPI application,you probably want to use a command line of the following form:% mpirun[ -np X ] [ --hostfile ]
This will run X copies of in your current run-time environment(if running under a supported resource manager, Open MPI's mpirun will usuallyautomatically use the corresponding resource manager process starter, asopposed to, for example, rsh or ssh, which require the use of a hostfile,or will default to running all X copies on the localhost), scheduling (bydefault) in a round-robin fashion by CPU slot. See the rest of this pagefor more details.
Please note that mpirun automatically binds processesas of the start of the v1.8 series. Two binding patterns are used in theabsence of any further directives:
- Bind to core:
- when the number of processesis <= 2
- Bind to socket:
- when the number of processes is > 2
If your applicationuses threads, then you probably want to ensure that you are either notbound at all (by specifying --bind-to none), or bound to multiple cores usingan appropriate binding level or specific number of processing elementsper application process.
Options
mpirun will send the name of the directorywhere it was invoked on the local node to each of the remote nodes, andattempt to change to that directory. See the 'Current Working Directory'section below for further details.- The program executable. Thisis identified as the first non-recognized argument to mpirun.
- Passthese run-time arguments to every new process. These must always be thelast arguments to mpirun. If an app context file is used, will be ignored.
- -h, --help
- Display help for this command
- -q, --quiet
- Suppress informativemessages from orterun during application execution.
- -v, --verbose
- Be verbose
- -V, --version
- Print version number. If no other arguments are given, thiswill also cause orterun to exit.
- -display-map, --display-map
- Display a tableshowing the mapped location of each process prior to launch.
- -display-devel-map,--display-devel-map
- Display a more detailed table showing the mapped locationof each process prior to launch (usually of interest to developers).
- -display-allocation, --display-allocation
- Display the detected resource allocation.
Use one of the following options to specify which hosts (nodes) of thecluster to run on. Note that as of the start of the v1.8 release, mpirunwill launch a daemon onto each host in the allocation (as modified by thefollowing options) at the very beginning of execution, regardless of whetheror not application processes will eventually be mapped to execute there.This is done to allow collection of hardware topology information fromthe remote nodes, thus allowing us to map processes against known topology.However, it is a change from the behavior in prior releases where daemonswere only launched after mapping was complete, and thus only occurred onnodes where application processes would actually be executing.
- -H, -host,--host
- List of hosts on which to invoke processes.
- -hostfile,--hostfile
- Provide a hostfile to use.
- -machinefile, --machinefile
- Synonym for -hostfile.
- -cpu-set, --cpu-set
- Restrict launched processesto the specified logical cpus on each node. Note that the binding optionswill still apply within the specified envelope - e.g., you can elect to bindeach process to only one cpu within the specified cpu set.
The followingoptions specify the number of processes to launch. Note that none of theoptions imply a particular binding policy - e.g., requesting N processes foreach socket does not imply that the processes will be bound to the socket.
- -c, -n, --n, -np <#>
- Run this many copies of the program on the given nodes. This option indicates that the specified file is an executable programand not an application context. If no value is provided for the number ofcopies to execute (i.e., neither the '-np' nor its synonyms are provided onthe command line), Open MPI will automatically execute a copy of the programon each process slot (see below for description of a 'process slot'). Thisfeature, however, can only be used in the SPMD model and will return anerror (without beginning execution of the application) otherwise. -<>
- LaunchN times the number of objects of the specified type on each node.
- -npersocket,--npersocket <#persocket>
- On each node, launch this many processes times thenumber of processor sockets on the node. The -npersocket option also turnson the -bind-to-socket option. (deprecated in favor of --map-by ppr:n:socket)
- -npernode, --npernode <#pernode>
- On each node, launch this many processes.(deprecated in favor of --map-by ppr:n:node)
- -pernode, --pernode
- On each node,launch one process -- equivalent to -npernode 1. (deprecated in favor of --map-byppr:1:node)
To map processes:
- --map-by
- Map to the specified object,defaults to socket. Supported options include slot, hwthread, core, L1cache,L2cache, L3cache, socket, numa, board, node, sequential, distance, andppr. Any object can include modifiers by adding a : and any combinationof PE=n (bind n processing elements to each proc), SPAN (load balance theprocesses across the allocation), OVERSUBSCRIBE (allow more processes ona node than processing elements), and NOOVERSUBSCRIBE. This includes PPR,where the pattern would be terminated by another colon to separate it fromthe modifiers.
- -bycore, --bycore
- Map processes by core (deprecated in favorof --map-by core)
- -bysocket, --bysocket
- Map processes by socket (deprecatedin favor of --map-by socket)
- -nolocal, --nolocal
- Do not run any copies of thelaunched application on the same node as orterun is running. This optionwill override listing the localhost with --host or any other host-specifyingmechanism.
- -nooversubscribe, --nooversubscribe
- Do not oversubscribe any nodes;error (without starting any processes) if the requested number of processeswould cause oversubscription. This option implicitly sets 'max_slots' equalto the 'slots' value for each node.
- -bynode, --bynode
- Launch processes oneper node, cycling by node in a round-robin fashion. This spreads processesevenly among nodes and assigns MPI_COMM_WORLD ranks in a round-robin, 'bynode' manner.
To order processes' ranks in MPI_COMM_WORLD:
- --rank-by
- Rank in round-robin fashion according to the specified object, defaultsto slot. Supported options include slot, hwthread, core, L1cache, L2cache,L3cache, socket, numa, board, and node.
For process binding:
- --bind-to
- Bind processes to the specified object, defaults to core. Supportedoptions include slot, hwthread, core, l1cache, l2cache, l3cache, socket,numa, board, and none.
- -cpus-per-proc, --cpus-per-proc <#perproc>
- Bind each processto the specified number of cpus. (deprecated in favor of --map-by :PE=n)
- -cpus-per-rank, --cpus-per-rank <#perrank>
- Alias for -cpus-per-proc. (deprecated infavor of --map-by :PE=n)
- -bind-to-core, --bind-to-core
- Bind processes to cores(deprecated in favor of --bind-to core)
- -bind-to-socket, --bind-to-socket
- Bind processesto processor sockets (deprecated in favor of --bind-to socket)
- -bind-to-none,--bind-to-none
- Do not bind processes (deprecated in favor of --bind-to none)
- -report-bindings, --report-bindings
- Report any bindings for launched processes.
- -slot-list, --slot-list
- List of processor IDs to be used for bindingMPI processes. The specified bindings will be applied to all MPI processes.See explanation below for syntax.
For rankfiles:
- -rf, --rankfile
- Provide a rankfile file.
To manage standard I/O:
- -output-filename, --output-filename
- Redirect the stdout, stderr, and stddiag of all processes to aprocess-unique version of the specified filename. Any directories in thefilename will automatically be created. Each output file will consist offilename.id, where the id will be the processes' rank in MPI_COMM_WORLD,left-filled with zero's for correct ordering in listings.
- -stdin, --stdin
- The MPI_COMM_WORLD rank of the process that is to receive stdin. The defaultis to forward stdin to MPI_COMM_WORLD rank 0, but this option can be usedto forward stdin to any process. It is also acceptable to specify none,indicating that no processes are to receive stdin.
- -tag-output, --tag-output
- Tag each line of output to stdout, stderr, and stddiag with [jobid, MCW_rank]indicating the process jobid and MPI_COMM_WORLD rank of the process thatgenerated the output, and the channel which generated it.
- -timestamp-output,--timestamp-output
- Timestamp each line of output to stdout, stderr, and stddiag.
- -xml, --xml
- Provide all output to stdout, stderr, and stddiag in an xmlformat.
- -xterm, --xterm
- Display the output from the processes identifiedby their MPI_COMM_WORLD ranks in separate xterm windows. The ranks are specifiedas a comma-separated list of ranges, with a -1 indicating all. A separatewindow will be created for each specified process. Note: xterm will normallyterminate the window upon termination of the process running within it.However, by adding a '!' to the end of the list of specified ranks, theproper options will be provided to ensure that xterm keeps the window openafter the process terminates, thus allowing you to see the process' output.Each xterm window will subsequently need to be manually closed. Note: Insome environments, xterm may require that the executable be in the user'spath, or be specified in absolute or relative terms. Thus, it may be necessaryto specify a local executable as './foo' instead of just 'foo'. If xtermfails to find the executable, mpirun will hang, but still respond correctlyto a ctrl-c. If this happens, please check that the executable is being specifiedcorrectly and try again.
To manage files and runtime environment:
The parser for the -x option is not very sophisticated; it does not evenunderstand quoted values. Users are advised to set variables in the environment,and then use -x to export (not define) them.
Setting MCA parameters:
- -gmca, --gmca
- Pass global MCA parameters that are applicable toall contexts. is the parameter name; is the parameter value.
- -mca, --mca
- Send arguments to various MCA modules. See the 'MCA'section, below.
- -tune, --tune
- Specify a tune file to set argumentsfor various MCA modules and environment variables. See the 'Setting MCAparameters and environment variables from file' section, below.
Fordebugging:
- -debug, --debug
- Invoke the user-level debugger indicated by theorte_base_user_debugger MCA parameter.
- -debugger, --debugger
- Sequence ofdebuggers to search for when --debug is used (i.e. a synonym for orte_base_user_debuggerMCA parameter).
- -tv, --tv
- Launch processes under the TotalView debugger. Deprecatedbackwards compatibility flag. Synonym for --debug.
There are also otheroptions:
- --allow-run-as-root
- Allow mpirun to run when executed by the rootuser (mpirun defaults to aborting when launched as the root user).
- -aborted,--aborted <#>
- Set the maximum number of aborted processes to display.
- --app
- Provide an appfile, ignoring all other command line options.
- -cf,--cartofile
- Provide a cartography file.
- --hetero
- Indicates thatmultiple app_contexts are being provided that are a mix of 32/64-bit binaries.
- -leave-session-attached, --leave-session-attached
- Do not detach OmpiRTE daemonsused by this application. This allows error messages from the daemons aswell as the underlying environment (e.g., when failing to launch a daemon)to be output.
- -ompi-server, --ompi-server
- Specify the URI of theOpen MPI server (or the mpirun to be used as the server) , the name ofthe file (specified as file:filename) that contains that info, or the PID(specified as pid:#) of the mpirun to be used as the server.
The Open MPI server is used to support multi-application data exchangevia the MPI-2 MPI_Publish_name and MPI_Lookup_name functions. - -report-pid,--report-pid
- Print out mpirun's PID during startup. The channel mustbe either a '-' to indi cate that the pid is to be output to stdout, a '+' toindicate that the pid is to be outp ut to stderr, or a filename to whichthe pid is to be written.
- -report-uri, --report-uri
- Print out mpirun'sURI during startup. The channel must be either a '-' to indi cate that theURI is to be output to stdout, a '+' to indicate that the URI is to be output to stderr, or a filename to which the URI is to be written.
- -wait-for-server,--wait-for-server
- Pause mpirun before launching the job until ompi-server isdetected. This is useful in scripts where ompi-server may be started in thebackground, followed immediately by an mpirun command that wishes to connectto it. Mpirun will pause until either the specified ompi-server is contactedor the server-wait-time is exceeded.
- -server-wait-time, --server-wait-time
- The max amount of time (in seconds) mpirun should wait for the ompi-serverto start. The default is 10 seconds.
The following options are usefulfor developers; they are not generally useful to most ORTE and/or MPI users:
- -d, --debug-devel
- Enable debugging of the OmpiRTE (the run-time layer in OpenMPI). This is not generally useful for most users.
- --debug-daemons
- Enabledebugging of any OmpiRTE daemons used by this application.
- --debug-daemons-file
- Enable debugging of any OmpiRTE daemons used by this application, storingoutput in files.
- -launch-agent, --launch-agent
- Name of the executable thatis to be used to start processes on the remote nodes. The default is 'orted'.This option can be used to test new daemon concepts, or to pass optionsback to the daemons without having mpirun itself see them. For example,specifying a launch agent of orted -mca odls_base_verbose 5 allows the developerto ask the orted for debugging output without clutter from mpirun itself.
- --noprefix
- Disable the automatic --prefix behavior
There may be other optionslisted with mpirun --help.
Mpirun There Are Not Enough Slots Available In The Systems
Environment Variables
- MPIEXEC_TIMEOUT
- The maximumnumber of seconds that mpirun (mpiexec) will run. After this many seconds,mpirun will abort the launched job and exit.
Description
One invocationof mpirun starts an MPI application running under Open MPI. If the applicationis single process multiple data (SPMD), the application can be specifiedon the mpirun command line.If the application is multiple instructionmultiple data (MIMD), comprising of multiple programs, the set of programsand argument can be specified in one of two ways: Extended Command LineArguments, and Application Context.
An application context describes theMIMD program set including all arguments in a separate file. This fileessentially contains multiple mpirun command lines, less the command nameitself. The ability to specify different options for different instantiationsof a program is another reason to use an application context.
Extended commandline arguments allow for the description of the application layout on thecommand line using colons (:) to separate the specification of programsand arguments. Some options are globally set across all specified programs(e.g. --hostfile), while others are specific to a single program (e.g. -np).
Specifying Host Nodes
Host nodes can be identified on the mpirun commandline with the -host option or in a hostfile.
For example,
- mpirun -H aa,aa,bb./a.out
- launches two processes on node aa and one on bb.
Or, consider thehostfile
% cat myhostfile
aa slots=2
bb slots=2
cc slots=2
Here, we list both the host names (aa, bb, and cc) but also how many'slots' there are for each. Slots indicate how many processes can potentiallyexecute on a node. For best performance, the number of slots may be chosento be the number of cores on the node or the number of processor sockets. If the hostfile does not provide slots information, a default of 1 isassumed. When running under resource managers (e.g., SLURM, Torque, etc.),Open MPI will obtain both the hostnames and the number of slots directlyfrom the resource manger.
- mpirun -hostfile myhostfile ./a.out
- will launchtwo processes on each of the three nodes.
- mpirun -hostfile myhostfile -hostaa ./a.out
- will launch two processes, both on node aa.
- mpirun -hostfile myhostfile-host dd ./a.out
- will find no hosts to run on and abort with an error. Thatis, the specified host dd is not in the specified hostfile.
SpecifyingNumber of Processes
As we have just seen, the number of processes to runcan be set using the hostfile. Other mechanisms exist.The number of processeslaunched can be specified as a multiple of the number of nodes or processorsockets available. For example,
- mpirun -H aa,bb -npersocket 2 ./a.out
- launchesprocesses 0-3 on node aa and process 4-7 on node bb, where aa and bb areboth dual-socket nodes. The -npersocket option also turns on the -bind-to-socketoption, which is discussed in a later section.
- mpirun -H aa,bb -npernode2 ./a.out
- launches processes 0-1 on node aa and processes 2-3 on node bb.
- mpirun-H aa,bb -npernode 1 ./a.out
- launches one process per host node.
- mpirun -H aa,bb-pernode ./a.out
- is the same as -npernode 1.
Another alternative is to specifythe number of processes with the -np option. Consider now the hostfile
Note:mpirun, mpiexec, and orterun are all synonyms for each otheras well as oshrun, shmemrun in case Open SHMEM is installed. Using any ofthe names will produce the same behavior.
Synopsis
A 'slot' is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run: 1. Hostfile, via 'slots=N' clauses (N defaults to number of processor cores if not provided) 2. The -host command line parameter, via a ':N' suffix on the. Run started at:- Mon Apr 8 18:07:07 AEST 2019 - There are not enough slots available in the system to satisfy the 8 slots that were requested by the application: python Either request fewer slots for your application, or make more slots available for use. Attempt 3. 'There are not enough slots available in the system to satisfy the 1. Mpirun do the work, but there's no accounting for things in Yorkshire.
Single Process MultipleData (SPMD) Model:
mpirun [ options ] [ ]
Multiple InstructionMultiple Data (MIMD) Model:
mpirun [ global_options ] [ local_options1]
[ ] : [ local_options2 ]
[ ] : .. :
[ local_optionsN ]
[ ]
Note that in both models, invoking mpirun via an absolutepath name is equivalent to specifying the --prefix option with a
valueequivalent to the directory where mpirun resides, minus its last subdirectory. For example:% /usr/local/bin/mpirun ..
is equivalent to
% mpirun --prefix /usr/local
Quick Summary
If you are simply looking for how to run an MPI application,you probably want to use a command line of the following form:% mpirun[ -np X ] [ --hostfile ]
This will run X copies of in your current run-time environment(if running under a supported resource manager, Open MPI's mpirun will usuallyautomatically use the corresponding resource manager process starter, asopposed to, for example, rsh or ssh, which require the use of a hostfile,or will default to running all X copies on the localhost), scheduling (bydefault) in a round-robin fashion by CPU slot. See the rest of this pagefor more details.
Please note that mpirun automatically binds processesas of the start of the v1.8 series. Two binding patterns are used in theabsence of any further directives:
- Bind to core:
- when the number of processesis <= 2
- Bind to socket:
- when the number of processes is > 2
If your applicationuses threads, then you probably want to ensure that you are either notbound at all (by specifying --bind-to none), or bound to multiple cores usingan appropriate binding level or specific number of processing elementsper application process.
Options
mpirun will send the name of the directorywhere it was invoked on the local node to each of the remote nodes, andattempt to change to that directory. See the 'Current Working Directory'section below for further details.- The program executable. Thisis identified as the first non-recognized argument to mpirun.
- Passthese run-time arguments to every new process. These must always be thelast arguments to mpirun. If an app context file is used, will be ignored.
- -h, --help
- Display help for this command
- -q, --quiet
- Suppress informativemessages from orterun during application execution.
- -v, --verbose
- Be verbose
- -V, --version
- Print version number. If no other arguments are given, thiswill also cause orterun to exit.
- -display-map, --display-map
- Display a tableshowing the mapped location of each process prior to launch.
- -display-devel-map,--display-devel-map
- Display a more detailed table showing the mapped locationof each process prior to launch (usually of interest to developers).
- -display-allocation, --display-allocation
- Display the detected resource allocation.
Use one of the following options to specify which hosts (nodes) of thecluster to run on. Note that as of the start of the v1.8 release, mpirunwill launch a daemon onto each host in the allocation (as modified by thefollowing options) at the very beginning of execution, regardless of whetheror not application processes will eventually be mapped to execute there.This is done to allow collection of hardware topology information fromthe remote nodes, thus allowing us to map processes against known topology.However, it is a change from the behavior in prior releases where daemonswere only launched after mapping was complete, and thus only occurred onnodes where application processes would actually be executing.
- -H, -host,--host
- List of hosts on which to invoke processes.
- -hostfile,--hostfile
- Provide a hostfile to use.
- -machinefile, --machinefile
- Synonym for -hostfile.
- -cpu-set, --cpu-set
- Restrict launched processesto the specified logical cpus on each node. Note that the binding optionswill still apply within the specified envelope - e.g., you can elect to bindeach process to only one cpu within the specified cpu set.
The followingoptions specify the number of processes to launch. Note that none of theoptions imply a particular binding policy - e.g., requesting N processes foreach socket does not imply that the processes will be bound to the socket.
- -c, -n, --n, -np <#>
- Run this many copies of the program on the given nodes. This option indicates that the specified file is an executable programand not an application context. If no value is provided for the number ofcopies to execute (i.e., neither the '-np' nor its synonyms are provided onthe command line), Open MPI will automatically execute a copy of the programon each process slot (see below for description of a 'process slot'). Thisfeature, however, can only be used in the SPMD model and will return anerror (without beginning execution of the application) otherwise. -<>
- LaunchN times the number of objects of the specified type on each node.
- -npersocket,--npersocket <#persocket>
- On each node, launch this many processes times thenumber of processor sockets on the node. The -npersocket option also turnson the -bind-to-socket option. (deprecated in favor of --map-by ppr:n:socket)
- -npernode, --npernode <#pernode>
- On each node, launch this many processes.(deprecated in favor of --map-by ppr:n:node)
- -pernode, --pernode
- On each node,launch one process -- equivalent to -npernode 1. (deprecated in favor of --map-byppr:1:node)
To map processes:
- --map-by
- Map to the specified object,defaults to socket. Supported options include slot, hwthread, core, L1cache,L2cache, L3cache, socket, numa, board, node, sequential, distance, andppr. Any object can include modifiers by adding a : and any combinationof PE=n (bind n processing elements to each proc), SPAN (load balance theprocesses across the allocation), OVERSUBSCRIBE (allow more processes ona node than processing elements), and NOOVERSUBSCRIBE. This includes PPR,where the pattern would be terminated by another colon to separate it fromthe modifiers.
- -bycore, --bycore
- Map processes by core (deprecated in favorof --map-by core)
- -bysocket, --bysocket
- Map processes by socket (deprecatedin favor of --map-by socket)
- -nolocal, --nolocal
- Do not run any copies of thelaunched application on the same node as orterun is running. This optionwill override listing the localhost with --host or any other host-specifyingmechanism.
- -nooversubscribe, --nooversubscribe
- Do not oversubscribe any nodes;error (without starting any processes) if the requested number of processeswould cause oversubscription. This option implicitly sets 'max_slots' equalto the 'slots' value for each node.
- -bynode, --bynode
- Launch processes oneper node, cycling by node in a round-robin fashion. This spreads processesevenly among nodes and assigns MPI_COMM_WORLD ranks in a round-robin, 'bynode' manner.
To order processes' ranks in MPI_COMM_WORLD:
- --rank-by
- Rank in round-robin fashion according to the specified object, defaultsto slot. Supported options include slot, hwthread, core, L1cache, L2cache,L3cache, socket, numa, board, and node.
For process binding:
- --bind-to
- Bind processes to the specified object, defaults to core. Supportedoptions include slot, hwthread, core, l1cache, l2cache, l3cache, socket,numa, board, and none.
- -cpus-per-proc, --cpus-per-proc <#perproc>
- Bind each processto the specified number of cpus. (deprecated in favor of --map-by :PE=n)
- -cpus-per-rank, --cpus-per-rank <#perrank>
- Alias for -cpus-per-proc. (deprecated infavor of --map-by :PE=n)
- -bind-to-core, --bind-to-core
- Bind processes to cores(deprecated in favor of --bind-to core)
- -bind-to-socket, --bind-to-socket
- Bind processesto processor sockets (deprecated in favor of --bind-to socket)
- -bind-to-none,--bind-to-none
- Do not bind processes (deprecated in favor of --bind-to none)
- -report-bindings, --report-bindings
- Report any bindings for launched processes.
- -slot-list, --slot-list
- List of processor IDs to be used for bindingMPI processes. The specified bindings will be applied to all MPI processes.See explanation below for syntax.
For rankfiles:
- -rf, --rankfile
- Provide a rankfile file.
To manage standard I/O:
- -output-filename, --output-filename
- Redirect the stdout, stderr, and stddiag of all processes to aprocess-unique version of the specified filename. Any directories in thefilename will automatically be created. Each output file will consist offilename.id, where the id will be the processes' rank in MPI_COMM_WORLD,left-filled with zero's for correct ordering in listings.
- -stdin, --stdin
- The MPI_COMM_WORLD rank of the process that is to receive stdin. The defaultis to forward stdin to MPI_COMM_WORLD rank 0, but this option can be usedto forward stdin to any process. It is also acceptable to specify none,indicating that no processes are to receive stdin.
- -tag-output, --tag-output
- Tag each line of output to stdout, stderr, and stddiag with [jobid, MCW_rank]indicating the process jobid and MPI_COMM_WORLD rank of the process thatgenerated the output, and the channel which generated it.
- -timestamp-output,--timestamp-output
- Timestamp each line of output to stdout, stderr, and stddiag.
- -xml, --xml
- Provide all output to stdout, stderr, and stddiag in an xmlformat.
- -xterm, --xterm
- Display the output from the processes identifiedby their MPI_COMM_WORLD ranks in separate xterm windows. The ranks are specifiedas a comma-separated list of ranges, with a -1 indicating all. A separatewindow will be created for each specified process. Note: xterm will normallyterminate the window upon termination of the process running within it.However, by adding a '!' to the end of the list of specified ranks, theproper options will be provided to ensure that xterm keeps the window openafter the process terminates, thus allowing you to see the process' output.Each xterm window will subsequently need to be manually closed. Note: Insome environments, xterm may require that the executable be in the user'spath, or be specified in absolute or relative terms. Thus, it may be necessaryto specify a local executable as './foo' instead of just 'foo'. If xtermfails to find the executable, mpirun will hang, but still respond correctlyto a ctrl-c. If this happens, please check that the executable is being specifiedcorrectly and try again.
To manage files and runtime environment:
The parser for the -x option is not very sophisticated; it does not evenunderstand quoted values. Users are advised to set variables in the environment,and then use -x to export (not define) them.
Setting MCA parameters:
- -gmca, --gmca
- Pass global MCA parameters that are applicable toall contexts. is the parameter name; is the parameter value.
- -mca, --mca
- Send arguments to various MCA modules. See the 'MCA'section, below.
- -tune, --tune
- Specify a tune file to set argumentsfor various MCA modules and environment variables. See the 'Setting MCAparameters and environment variables from file' section, below.
Fordebugging:
- -debug, --debug
- Invoke the user-level debugger indicated by theorte_base_user_debugger MCA parameter.
- -debugger, --debugger
- Sequence ofdebuggers to search for when --debug is used (i.e. a synonym for orte_base_user_debuggerMCA parameter).
- -tv, --tv
- Launch processes under the TotalView debugger. Deprecatedbackwards compatibility flag. Synonym for --debug.
There are also otheroptions:
- --allow-run-as-root
- Allow mpirun to run when executed by the rootuser (mpirun defaults to aborting when launched as the root user).
- -aborted,--aborted <#>
- Set the maximum number of aborted processes to display.
- --app
- Provide an appfile, ignoring all other command line options.
- -cf,--cartofile
- Provide a cartography file.
- --hetero
- Indicates thatmultiple app_contexts are being provided that are a mix of 32/64-bit binaries.
- -leave-session-attached, --leave-session-attached
- Do not detach OmpiRTE daemonsused by this application. This allows error messages from the daemons aswell as the underlying environment (e.g., when failing to launch a daemon)to be output.
- -ompi-server, --ompi-server
- Specify the URI of theOpen MPI server (or the mpirun to be used as the server) , the name ofthe file (specified as file:filename) that contains that info, or the PID(specified as pid:#) of the mpirun to be used as the server.
The Open MPI server is used to support multi-application data exchangevia the MPI-2 MPI_Publish_name and MPI_Lookup_name functions. - -report-pid,--report-pid
- Print out mpirun's PID during startup. The channel mustbe either a '-' to indi cate that the pid is to be output to stdout, a '+' toindicate that the pid is to be outp ut to stderr, or a filename to whichthe pid is to be written.
- -report-uri, --report-uri
- Print out mpirun'sURI during startup. The channel must be either a '-' to indi cate that theURI is to be output to stdout, a '+' to indicate that the URI is to be output to stderr, or a filename to which the URI is to be written.
- -wait-for-server,--wait-for-server
- Pause mpirun before launching the job until ompi-server isdetected. This is useful in scripts where ompi-server may be started in thebackground, followed immediately by an mpirun command that wishes to connectto it. Mpirun will pause until either the specified ompi-server is contactedor the server-wait-time is exceeded.
- -server-wait-time, --server-wait-time
- The max amount of time (in seconds) mpirun should wait for the ompi-serverto start. The default is 10 seconds.
The following options are usefulfor developers; they are not generally useful to most ORTE and/or MPI users:
- -d, --debug-devel
- Enable debugging of the OmpiRTE (the run-time layer in OpenMPI). This is not generally useful for most users.
- --debug-daemons
- Enabledebugging of any OmpiRTE daemons used by this application.
- --debug-daemons-file
- Enable debugging of any OmpiRTE daemons used by this application, storingoutput in files.
- -launch-agent, --launch-agent
- Name of the executable thatis to be used to start processes on the remote nodes. The default is 'orted'.This option can be used to test new daemon concepts, or to pass optionsback to the daemons without having mpirun itself see them. For example,specifying a launch agent of orted -mca odls_base_verbose 5 allows the developerto ask the orted for debugging output without clutter from mpirun itself.
- --noprefix
- Disable the automatic --prefix behavior
There may be other optionslisted with mpirun --help.
Mpirun There Are Not Enough Slots Available In The Systems
Environment Variables
- MPIEXEC_TIMEOUT
- The maximumnumber of seconds that mpirun (mpiexec) will run. After this many seconds,mpirun will abort the launched job and exit.
Description
One invocationof mpirun starts an MPI application running under Open MPI. If the applicationis single process multiple data (SPMD), the application can be specifiedon the mpirun command line.If the application is multiple instructionmultiple data (MIMD), comprising of multiple programs, the set of programsand argument can be specified in one of two ways: Extended Command LineArguments, and Application Context.
An application context describes theMIMD program set including all arguments in a separate file. This fileessentially contains multiple mpirun command lines, less the command nameitself. The ability to specify different options for different instantiationsof a program is another reason to use an application context.
Extended commandline arguments allow for the description of the application layout on thecommand line using colons (:) to separate the specification of programsand arguments. Some options are globally set across all specified programs(e.g. --hostfile), while others are specific to a single program (e.g. -np).
Specifying Host Nodes
Host nodes can be identified on the mpirun commandline with the -host option or in a hostfile.For example,
- mpirun -H aa,aa,bb./a.out
- launches two processes on node aa and one on bb.
Or, consider thehostfile
% cat myhostfile
aa slots=2
bb slots=2
cc slots=2
Here, we list both the host names (aa, bb, and cc) but also how many'slots' there are for each. Slots indicate how many processes can potentiallyexecute on a node. For best performance, the number of slots may be chosento be the number of cores on the node or the number of processor sockets. If the hostfile does not provide slots information, a default of 1 isassumed. When running under resource managers (e.g., SLURM, Torque, etc.),Open MPI will obtain both the hostnames and the number of slots directlyfrom the resource manger.
- mpirun -hostfile myhostfile ./a.out
- will launchtwo processes on each of the three nodes.
- mpirun -hostfile myhostfile -hostaa ./a.out
- will launch two processes, both on node aa.
- mpirun -hostfile myhostfile-host dd ./a.out
- will find no hosts to run on and abort with an error. Thatis, the specified host dd is not in the specified hostfile.
SpecifyingNumber of Processes
As we have just seen, the number of processes to runcan be set using the hostfile. Other mechanisms exist.The number of processeslaunched can be specified as a multiple of the number of nodes or processorsockets available. For example,
- mpirun -H aa,bb -npersocket 2 ./a.out
- launchesprocesses 0-3 on node aa and process 4-7 on node bb, where aa and bb areboth dual-socket nodes. The -npersocket option also turns on the -bind-to-socketoption, which is discussed in a later section.
- mpirun -H aa,bb -npernode2 ./a.out
- launches processes 0-1 on node aa and processes 2-3 on node bb.
- mpirun-H aa,bb -npernode 1 ./a.out
- launches one process per host node.
- mpirun -H aa,bb-pernode ./a.out
- is the same as -npernode 1.
Another alternative is to specifythe number of processes with the -np option. Consider now the hostfile
% cat myhostfile
aa slots=4
bb slots=4
cc slots=4
Now,
- mpirun -hostfile myhostfile -np 6 ./a.out
- will launch processes 0-3on node aa and processes 4-5 on node bb. The remaining slots in the hostfilewill not be used since the -np option indicated that only 6 processes shouldbe launched.
Mapping Processes to Nodes: Using Policies
The examples aboveillustrate the default mapping of process processes to nodes. This mappingcan also be controlled with various mpirun options that describe mappingpolicies.Consider the same hostfile as above, again with -np 6:
node aa node bb node cc
mpirun 0 1 2 3 4 5
mpirun --map-by node 0 3 1 4 2 5
mpirun -nolocal 0 1 2 3 4 5
The --map-by node option will load balance the processes across the availablenodes, numbering each process in a round-robin fashion.
The -nolocal optionprevents any processes from being mapped onto the local host (in this casenode aa). While mpirun typically consumes few system resources, -nolocalcan be helpful for launching very large jobs where mpirun may actuallyneed to use noticeable amounts of memory and/or processing time.
Just as-np Bugs bunny slot machine. can specify fewer processes than there are slots, it can also oversubscribethe slots. For example, with the same hostfile:
- mpirun -hostfile myhostfile-np 14 ./a.out
- will launch processes 0-3 on node aa, 4-7 on bb, and 8-11 on cc. It will then add the remaining two processes to whichever nodes it chooses.
One can also specify limits to oversubscription. For example, with thesame hostfile:
- mpirun -hostfile myhostfile -np 14 -nooversubscribe ./a.out
- will produce an error since -nooversubscribe prevents oversubscription.
Limits to oversubscription can also be specified in the hostfile itself: % cat myhostfile
aa slots=4 max_slots=4
bb max_slots=4
cc slots=4
The max_slots field specifies such a limit. When it does, the slots valuedefaults to the limit. Now:
- mpirun -hostfile myhostfile -np 14 ./a.out
- causesthe first 12 processes to be launched as before, but the remaining twoprocesses will be forced onto node cc. The other two nodes are protectedby the hostfile against oversubscription by this job.
Using the --nooversubscribeoption can be helpful since Open MPI currently does not get 'max_slots'values from the resource manager.
Of course, -np can also be used with the-H or -host option. For example,
- mpirun -H aa,bb -np 8 ./a.out
- launches 8 processes. Since only two hosts are specified, after the first two processes aremapped, one to aa and one to bb, the remaining processes oversubscribethe specified hosts.
And here is a MIMD example:
- mpirun -H aa -np 1 hostname: -H bb,cc -np 2 uptime
- will launch process 0 running hostname on node aaand processes 1 and 2 each running uptime on nodes bb and cc, respectively.
Mapping, Ranking, and Binding: Oh My!
Open MPI employs a three-phase procedurefor assigning process locations and ranks:- mapping
- Assigns a default locationto each process
- ranking
- Assigns an MPI_COMM_WORLD rank value to each process
- binding
- Constrains each process to run on specific processors
The mappingstep is used to assign a default location to each process based on themapper being employed. Mapping by slot, node, and sequentially results inthe assignment of the processes to the node level. In contrast, mappingby object, allows the mapper to assign the process to an actual objecton each node.
Note: the location assigned to the process is independentof where it will be bound - the assignment is used solely as input to thebinding algorithm.
The mapping of process processes to nodes can be definednot just with general policies but also, if necessary, using arbitrarymappings that cannot be described by a simple policy. One can use the 'sequentialmapper,' which reads the hostfile line by line, assigning processes tonodes in whatever order the hostfile specifies. Use the -mca rmaps seq option. For example, using the same hostfile as before:
mpirun -hostfile myhostfile-mca rmaps seq ./a.out
will launch three processes, one on each of nodesaa, bb, and cc, respectively. The slot counts don't matter; one processis launched per line on whatever node is listed on the line.
Another wayto specify arbitrary mappings is with a rankfile, which gives you detailedcontrol over process binding as well. Rankfiles are discussed below.
Thesecond phase focuses on the ranking of the process within the job's MPI_COMM_WORLD. Open MPI separates this from the mapping procedure to allow more flexibilityin the relative placement of MPI processes. This is best illustrated byconsidering the following two cases where we used the —map-by ppr:2:socketoption:
node aa node bb
rank-by core 0 1 ! 2 3 4 5 ! 6 7
rank-by socket 0 2 ! 1 3 4 6 ! 5 7
rank-by socket:span 0 4 ! 1 5 2 6 ! 3 7
Ranking by core and by slot provide the identical result - a simple progressionof MPI_COMM_WORLD ranks across each node. Ranking by socket does a round-robinranking within each node until all processes have been assigned an MCWrank, and then progresses to the next node. Adding the span modifier tothe ranking directive causes the ranking algorithm to treat the entireallocation as a single entity - thus, the MCW ranks are assigned acrossall sockets before circling back around to the beginning.
The binding phaseactually binds each process to a given set of processors. This can improveperformance if the operating system is placing processes suboptimally.For example, it might oversubscribe some multi-core processor sockets, leavingother sockets idle; this can lead processes to contend unnecessarily forcommon resources. Or, it might spread processes out too widely; this canbe suboptimal if application performance is sensitive to interprocess communicationcosts. Binding can also keep the operating system from migrating processesexcessively, regardless of how optimally those processes were placed tobegin with.
The processors to be used for binding can be identified interms of topological groupings - e.g., binding to an l3cache will bind eachprocess to all processors within the scope of a single L3 cache withintheir assigned location. Thus, if a process is assigned by the mapper toa certain socket, then a —bind-to l3cache directive will cause the processto be bound to the processors that share a single L3 cache within thatsocket.
To help balance loads, the binding directive uses a round-robinmethod when binding to levels lower than used in the mapper. For example,consider the case where a job is mapped to the socket level, and then boundto core. Each socket will have multiple cores, so if multiple processesare mapped to a given socket, the binding algorithm will assign each processlocated to a socket to a unique core in a round-robin manner.
Alternatively,processes mapped by l2cache and then bound to socket will simply be boundto all the processors in the socket where they are located. In this manner,users can exert detailed control over relative MCW rank location and binding.
Finally, --report-bindings can be used to report bindings.
As an example,consider a node with two processor sockets, each comprising four cores. We run mpirun with -np 4 --report-bindings and the following additional options:
% mpirun .. --map-by core --bind-to core
[..] .. binding child [..,0] to cpus 0001
[..] .. binding child [..,1] to cpus 0002
[..] .. binding child [..,2] to cpus 0004
[..] .. binding child [..,3] to cpus 0008
% mpirun .. --map-by socket --bind-to socket
[..] .. binding child [..,0] to socket 0 cpus 000f
[..] .. binding child [..,1] to socket 1 cpus 00f0
[..] .. binding child [..,2] to socket 0 cpus 000f
[..] .. binding child [..,3] to socket 1 cpus 00f0
% mpirun .. --map-by core:PE=2 --bind-to core
[..] .. binding child [..,0] to cpus 0003
[..] .. binding child [..,1] to cpus 000c
[..] .. binding child [..,2] to cpus 0030
[..] .. binding child [..,3] to cpus 00c0
% mpirun .. --bind-to none
Here, --report-bindings shows the binding of each process as a mask. In thefirst case, the processes bind to successive cores as indicated by themasks 0001, 0002, 0004, and 0008. In the second case, processes bind toall cores on successive sockets as indicated by the masks 000f and 00f0.The processes cycle through the processor sockets in a round-robin fashionas many times as are needed. In the third case, the masks show us that2 cores have been bound per process. In the fourth case, binding is turnedoff and no bindings are reported.
Open MPI's support for process bindingdepends on the underlying operating system. Therefore, certain processbinding options may not be available on every system.
Process binding canalso be set with MCA parameters. Their usage is less convenient than thatof mpirun options. On the other hand, MCA parameters can be set not onlyon the mpirun command line, but alternatively in a system or user mca-params.conffile or as environment variables, as described in the MCA section below.Some examples include:
mpirun option MCA parameter key value
--map-by core rmaps_base_mapping_policy core
--map-by socket rmaps_base_mapping_policy socket
--rank-by core rmaps_base_ranking_policy core
--bind-to core hwloc_base_binding_policy core
--bind-to socket hwloc_base_binding_policy socket
--bind-to none hwloc_base_binding_policy none
Rankfiles
Rankfiles are text files that specify detailed informationabout how individual processes should be mapped to nodes, and to whichprocessor(s) they should be bound. Each line of a rankfile specifies thelocation of one process (for MPI jobs, the process' 'rank' refers to itsrank in MPI_COMM_WORLD). The general form of each line in the rankfileis: rank = slot=
For example:
$ cat myrankfile
rank 0=aa slot=1:0-2
rank 1=bb slot=0:0,1
rank 2=cc slot=1-2
$ mpirun -H aa,bb,cc,dd -rf myrankfile ./a.out
Means that
Rank 0 runs on node aa, bound to logical socket 1, cores0-2.
Rank 1 runs on node bb, bound to logical socket 0, cores 0 and 1.
Rank 2 runs on node cc, bound to logical cores 1 and 2.
Rankfiles can alternatively be used to specify physical processor locations.In this case, the syntax is somewhat different. Sockets are no longer recognized,and the slot number given must be the number of the physical PU as mostOS's do not assign a unique physical identifier to each core in the node.Thus, a proper physical rankfile looks something like the following:
$ cat myphysicalrankfile
rank 0=aa slot=1
rank 1=bb slot=8
rank 2=cc slot=6
This means that
Rank 0 will run on node aa, bound to the core thatcontains physical PU 1
Rank 1 will run on node bb, bound to the core that contains physicalPU 8
Rank 2 will run on node cc, bound to the core that contains physicalPU 6
Rankfiles are treated as logical by default, and the MCA parameter rmaps_rank_file_physicalmust be set to 1 to indicate that the rankfile is to be considered as physical.
The hostnames listed above are 'absolute,' meaning that actual resolveablehostnames are specified. However, hostnames can also be specified as 'relative,'meaning that they are specified in relation to an externally-specified listof hostnames (e.g., by mpirun's --host argument, a hostfile, or a job scheduler).
The 'relative' specification is of the form '+n', where X is an integerspecifying the Xth hostname in the set of all available hostnames, indexedfrom 0. For example:
$ cat myrankfile
rank 0=+n0 slot=1:0-2
rank 1=+n1 slot=0:0,1
rank 2=+n2 slot=1-2
$ mpirun -H aa,bb,cc,dd -rf myrankfile ./a.out
Starting with Open MPI v1.7, all socket/core slot locations are be specifiedas logical indexes (the Open MPI v1.6 series used physical indexes). Youcan use tools such as HWLOC's 'lstopo' to find the logical indexes of socketand cores.
Application Context or Executable Program?
To distinguish thetwo different forms, mpirun looks on the command line for --app option. Ifit is specified, then the file named on the command line is assumed tobe an application context. If it is not specified, then the file is assumedto be an executable program.Locating Files
If no relative or absolutepath is specified for a file, Open MPI will first look for files by searchingthe directories specified by the --path option. If there is no --path optionset or if the file is not found at the --path location, then Open MPI willsearch the user's PATH environment variable as defined on the source node(s).If a relative directory is specified, it must be relative to the initialworking directory determined by the specific starter used. For example whenusing the rsh or ssh starters, the initial directory is $HOME by default.Other starters may set the initial directory to the current working directoryfrom the invocation of mpirun.
Current Working Directory
The -wdir mpirunoption (and its synonym, -wd) allows the user to change to an arbitrarydirectory before the program is invoked. It can also be used in applicationcontext files to specify working directories on specific nodes and/or forspecific applications.If the -wdir option appears both in a context fileand on the command line, the context file directory will override the commandline value.
If the -wdir option is specified, Open MPI will attempt to changeto the specified directory on all of the remote nodes. If this fails, mpirunwill abort.
If the -wdir option is not specified, Open MPI will send thedirectory name where mpirun was invoked to each of the remote nodes. Theremote nodes will try to change to that directory. If they are unable (e.g.,if the directory does not exist on that node), then Open MPI will use thedefault directory determined by the starter.
All directory changing occursbefore the user's program is invoked; it does not wait until MPI_INIT iscalled.
Standard I/O
Open MPI directs UNIX standard input to /dev/nullon all processes except the MPI_COMM_WORLD rank 0 process. The MPI_COMM_WORLDrank 0 process inherits standard input from mpirun. Note: The node thatinvoked mpirun need not be the same as the node where the MPI_COMM_WORLDrank 0 process resides. Open MPI handles the redirection of mpirun's standardinput to the rank 0 process.Open MPI directs UNIX standard output and errorfrom remote nodes to the node that invoked mpirun and prints it on thestandard output/error of mpirun. Local processes inherit the standard output/errorof mpirun and transfer to it directly.
Thus it is possible to redirect standardI/O for Open MPI applications by using the typical shell redirection procedureon mpirun.
% mpirun -np 2 my_app < my_input > my_output
Note that in this example only the MPI_COMM_WORLD rank 0 process willreceive the stream from my_input on stdin. The stdin on all the other nodeswill be tied to /dev/null. However, the stdout from all nodes will be collectedinto the my_output file.
Signal Propagation
When orterun receives a SIGTERMand SIGINT, it will attempt to kill the entire job by sending all processesin the job a SIGTERM, waiting a small number of seconds, then sending allprocesses in the job a SIGKILL.SIGUSR1 and SIGUSR2 signals received byorterun are propagated to all processes in the job.
One can turn on forwardingof SIGSTOP and SIGCONT to the program executed by mpirun by setting theMCA parameter orte_forward_job_control to 1. A SIGTSTOP signal to mpirunwill then cause a SIGSTOP signal to be sent to all of the programs startedby mpirun and likewise a SIGCONT signal to mpirun will cause a SIGCONTsent.
Other signals are not currently propagated by orterun.
Process Termination/ Signal Handling
During the run of an MPI application, if any processdies abnormally (either exiting before invoking MPI_FINALIZE, or dyingas the result of a signal), mpirun will print out an error message andkill the rest of the MPI application.User signal handlers should probablyavoid trying to cleanup MPI state (Open MPI is currently not async-signal-safe;see MPI_Init_thread(3) for details about MPI_THREAD_MULTIPLE and threadsafety). For example, if a segmentation fault occurs in MPI_SEND (perhapsbecause a bad buffer was passed in) and a user signal handler is invoked,if this user handler attempts to invoke MPI_FINALIZE, Bad Things couldhappen since Open MPI was already 'in' MPI when the error occurred. Sincempirun will notice that the process died due to a signal, it is probablynot necessary (and safest) for the user to only clean up non-MPI state.
Process Environment
Processes in the MPI application inherit their environmentfrom the Open RTE daemon upon the node on which they are running. The environmentis typically inherited from the user's shell. On remote nodes, the exactenvironment is determined by the boot MCA module used. The rsh launch module,for example, uses either rsh/ssh to launch the Open RTE daemon on remotenodes, and typically executes one or more of the user's shell-setup filesbefore launching the Open RTE daemon. When running dynamically linked applicationswhich require the LD_LIBRARY_PATH environment variable to be set, caremust be taken to ensure that it is correctly set when booting Open MPI.See the 'Remote Execution' section for more details.
Remote Execution
Open MPI requires that the PATH environment variable be set to find executableson remote nodes (this is typically only necessary in rsh- or ssh-based environments-- batch/scheduled environments typically copy the current environment tothe execution of remote jobs, so if the current environment has PATH and/orLD_LIBRARY_PATH set properly, the remote nodes will also have it set properly). If Open MPI was compiled with shared library support, it may also be necessaryto have the LD_LIBRARY_PATH environment variable set on remote nodes aswell (especially to find the shared libraries required to run user MPIapplications).However, it is not always desirable or possible to edit shellstartup files to set PATH and/or LD_LIBRARY_PATH. The --prefix option isprovided for some simple configurations where this is not possible.
The--prefix option takes a single argument: the base directory on the remotenode where Open MPI is installed. Open MPI will use this directory to setthe remote PATH and LD_LIBRARY_PATH before executing any Open MPI or userapplications. This allows running Open MPI jobs without having pre-configuredthe PATH and LD_LIBRARY_PATH on the remote nodes.
Open MPI adds the basenameof the current node's 'bindir' (the directory where Open MPI's executablesare installed) to the prefix and uses that to set the PATH on the remotenode. Similarly, Open MPI adds the basename of the current node's 'libdir'(the directory where Open MPI's libraries are installed) to the prefix anduses that to set the LD_LIBRARY_PATH on the remote node. For example:
- Localbindir:
- /local/node/directory/bin
- Local libdir:
- /local/node/directory/lib64
If the following command line is used:
% mpirun --prefix /remote/node/directory
Open MPI will add '/remote/node/directory/bin' to the PATH and '/remote/node/directory/lib64'to the D_LIBRARY_PATH on the remote node before attempting to execute anything.
The --prefix option is not sufficient if the installation paths on the remotenode are different than the local node (e.g., if '/lib' is used on the localnode, but '/lib64' is used on the remote node), or if the installationpaths are something other than a subdirectory under a common prefix.
Notethat executing mpirun via an absolute pathname is equivalent to specifying--prefix without the last subdirectory in the absolute pathname to mpirun. For example:
% /usr/local/bin/mpirun ..
is equivalent to
% mpirun --prefix /usr/local
Exported Environment Variables
All environment variables that are namedin the form OMPI_* will automatically be exported to new processes on thelocal and remote nodes. Environmental parameters can also be set/forwardedto the new processes using the MCA parameter mca_base_env_list. The -x optionto mpirun has been deprecated, but the syntax of the MCA param followsthat prior example. While the syntax of the -x option and MCA param allowsthe definition of new variables, note that the parser for these optionsare currently not very sophisticated - it does not even understand quotedvalues. Users are advised to set variables in the environment and use theoption to export them; not to define them.Setting MCA Parameters
The-mca switch allows the passing of parameters to various MCA (Modular ComponentArchitecture) modules. MCA modules have direct impact on MPI programs becausethey allow tunable parameters to be set at run time (such as which BTLcommunication device driver to use, what parameters to pass to that BTL,etc.).The -mca switch takes two arguments: and . The argumentgenerally specifies which MCA module will receive the value. For example,the 'btl' is used to select which BTL to be used for transporting MPImessages. The argument is the value that is passed. For example:
- mpirun -mca btl tcp,self -np 1 foo
- Tells Open MPI to use the 'tcp' and 'self'BTLs, and to run a single copy of 'foo' an allocated node.
- mpirun -mca btlself -np 1 foo
- Tells Open MPI to use the 'self' BTL, and to run a singlecopy of 'foo' an allocated node.
The -mca switch can be used multiple timesto specify different and/or arguments. If the same is specifiedmore than once, the s are concatenated with a comma (',') separatingthem.
Note that the -mca switch is simply a shortcut for setting environmentvariables. The same effect may be accomplished by setting correspondingenvironment variables before running mpirun. The form of the environmentvariables that Open MPI sets is:
OMPI_MCA_=
Thus, the -mca switch overrides any previously set environment variables. The -mca settings similarly override MCA parameters set in the $OPAL_PREFIX/etc/openmpi-mca-params.confor $HOME/.openmpi/mca-params.conf file.
Unknown arguments are still setas environment variable -- they are not checked (by mpirun) for correctness.Illegal or incorrect arguments may or may not be reported -- it dependson the specific MCA module.
To find the available component types underthe MCA architecture, or to find the available parameters for a specificcomponent, use the ompi_info command. See the ompi_info(1) man page fordetailed information on the command.
Setting MCA parameters and environmentvariables from file.
The -tune command line option and its synonym -mca mca_base_envar_file_prefixallows a user to set mca parameters and environment variables with thesyntax described below. This option requires a single file or list of filesseparated by ',' to follow.A valid line in the file may contain zero ormany '-x', '-mca', or '--mca' arguments. The following patterns are supported:-mca var val -mca var 'val' -x var=val -x var. If any argument is duplicatedin the file, the last value read will be used.
MCA parameters and environmentspecified on the command line have higher precedence than variables specifiedin the file.
Running as root
The Open MPI team strongly advises againstexecuting mpirun as the root user. MPI applications should be run as regular(non-root) users.Reflecting this advice, mpirun will refuse to run as rootby default. To override this default, you can add the --allow-run-as-root optionto the mpirun command line.
Exit status
There is no standard definitionfor what mpirun should return as an exit status. After considerable discussion,we settled on the following method for assigning the mpirun exit status(note: in the following description, the 'primary' job is the initial applicationstarted by mpirun - all jobs that are spawned by that job are designated'secondary' jobs):- [bu]
- if all processes in the primary job normally terminatewith exit status 0, we return 0
- [bu]
- if one or more processes in the primaryjob normally terminate with non-zero exit status, we return the exit statusof the process with the lowest MPI_COMM_WORLD rank to have a non-zero status
- [bu]
- if all processes in the primary job normally terminate with exit status0, and one or more processes in a secondary job normally terminate withnon-zero exit status, we (a) return the exit status of the process withthe lowest MPI_COMM_WORLD rank in the lowest jobid to have a non-zero status,and (b) output a message summarizing the exit status of the primary andall secondary jobs.
- [bu]
- if the cmd line option --report-child-jobs-separatelyis set, we will return -only- the exit status of the primary job. Any non-zeroexit status in secondary jobs will be reported solely in a summary printstatement.
By default, OMPI records and notes that MPI processes exitedwith non-zero termination status. This is generally not considered an 'abnormaltermination' - i.e., OMPI will not abort an MPI job if one or more processesreturn a non-zero status. Instead, the default behavior simply reports thenumber of processes terminating with non-zero status upon completion ofthe job.
However, in some cases it can be desirable to have the job abortwhen any process terminates with non-zero status. For example, a non-MPI jobmight detect a bad result from a calculation and want to abort, but doesn'twant to generate a core file. Or an MPI job might continue past a call toMPI_Finalize, but indicate that all processes should abort due to somepost-MPI result.
It is not anticipated that this situation will occur frequently.However, in the interest of serving the broader community, OMPI now hasa means for allowing users to direct that jobs be aborted upon any processexiting with non-zero status. Setting the MCA parameter 'orte_abort_on_non_zero_status'to 1 will cause OMPI to abort all processes once any process exits withnon-zero status.
Terminations caused in this manner will be reported on the console asan 'abnormal termination', with the first process to so exit identifiedalong with its exit status.
Examples
Be sure also to see the examplesthroughout the sections above.- mpirun -np 4 -mca btl ib,tcp,self prog1
- Run4 copies of prog1 using the 'ib', 'tcp', and 'self' BTL's for the transportof MPI messages.
- mpirun -np 4 -mca btl tcp,sm,self
--mca btl_tcp_if_include eth0 prog1
Run 4 copies of prog1 using the 'tcp', 'sm' and 'self' BTLs for the transportof MPI messages, with TCP using only the eth0 interface to communicate. Note that other BTLs have similar if_include MCA parameters.
Mpirun There Are Not Enough Slots Available In The System Game
Return Value
mpirun returns 0 if all processes started by mpirun exitafter calling MPI_FINALIZE. A non-zero value is returned if an internalerror occurred in mpirun, or one or more processes exited before callingMPI_FINALIZE. If an internal error occurred in mpirun, the correspondingerror code is returned. In the event that one or more processes exit beforecalling MPI_FINALIZE, the return value of the MPI_COMM_WORLD rank of theprocess that mpirun first notices died before calling MPI_FINALIZE willbe returned. Note that, in general, this will be the first process thatdied but is not guaranteed to be so.Openmpi There Are Not Enough Slots Available In The System To Satisfy
See Also
MPI_Init_thread(3)Mpirun There Are Not Enough Slots Available In The System To Satisfy
From: Alexander Tzanov (Alexander.Tzanov_at_csi.cuny.edu)
Date: Wed Jun 24 2015 - 13:37:01 CDT
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HI Josh
Thanks for reply. I did not use charmrun in my scripts. However I downloaded and recompiled the newest version (06-2015) from your site with the same options as
before. Now the problem seems to me disapper and NAMD works fine on single node.
#!/bin/bash
#PBS -q production
#PBS -N apoa_job_nsf
#PBS -l select=1:ncpus=4:ngpus=2:mpiprocs=4
#PBS -l place=free
#PBS -V
cd $PBS_O_WORKDIR
NN=`cat $PBS_NODEFILE | wc -l`
echo 'Processors received = '$NN >> myout
MM=`cat $PBS_NODEFILE`
echo 'MM = '$MM >> myout
# Use 'mpirun' and point to the MPI parallel executable to run echo '>>>> Begin NAMD MPI Parallel Run ..'
mpirun -np 4 -machinefile $PBS_NODEFILE namd2 +idlepoll +devices 0,1 ./apoa1.namd > apoa1.out
Thanks. $PBS_NODEFILE reports correctly now:
Processors received = 4
MM = compute-0-21.ib compute-0-21.ib compute-0-21.ib compute-0-21.ib
Alex
On Jun 24, 2015, at 12:14 PM, Josh Vermaas > wrote:
What does your submit script look like? The error message looks like one from mpirun, not NAMD, so there may be something obvious going on if we were to see what options were given.
-Josh Vermaas
On 6/24/15 11:03 AM, Alexander Tzanov wrote:
Just to clarify a bit more:
NAMD cannot use more than one core on a node. If I run with one core per node,
the NAMD runs. If I ask for more than one core i.e. 4 cores, I got the error:
--------------------------------------------------------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
namd2
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
Thank you for your help.
Alex
On Jun 24, 2015, at 10:56 AM, Alexander Tzanov > wrote:
Dear all,
I am trying to run NAMD 2.10 with CUDA support on single virtual node. My CUDA is 6.5.14. I am running
on IB cluster which runs PBS pro ver. 12.1.0.131281. I want to run on a single virtual node with
4 CPU cores and 2 GPU (the CPU itself has 16 cores). I compiled NAMD with cuda support
(mpi, smp CHARMM++ underneath). However when the NAMD cannot address more than one core.
As a result I get error ' Not enough slots'. Does anyone see the problem and if so to share his/her experience.
Thank you
Alex
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