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Table of Contents
prun - Execute serial and parallel jobs with the PMIx
Reference Server.
Single Process Multiple Data (SPMD) Model:
prun [ options ] <program> [ <args> ]
Multiple Instruction Multiple Data
(MIMD) Model:
prun [ global_options ] [ local_options1 ]
<program1> [ <args1> ] : [ local_options2 ]
<program2> [ <args2> ] : ... :
[ local_optionsN ]
<programN> [ <argsN> ]
Note that in both models, invoking prun via an absolute
path name is equivalent to specifying the --prefix option with a <dir> value
equivalent to the directory where prun resides, minus its last subdirectory.
For example:
% /usr/local/bin/prun ...
is equivalent to
% prun --prefix /usr/local
If you are simply looking for how to run an application,
you probably want to use a command line of the following form:
% prun
[ -np X ] [ --hostfile <filename> ] <program>
This will run X copies of <program> in your current run-time environment
(if running under a supported resource manager, PSRVR’s prun will usually
automatically use the corresponding resource manager process starter, as
opposed 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 (by
default) in a round-robin fashion by CPU slot. See the rest of this page
for more details.
Please note that prun automatically binds processes. Three
binding patterns are used in the absence of any further directives:
- Bind
to core:
- when the number of processes is <= 2
- Bind to socket:
- when the
number of processes is > 2
- Bind to none:
- when oversubscribed
If your
application uses threads, then you probably want to ensure that you are
either not bound at all (by specifying --bind-to none), or bound to multiple
cores using an appropriate binding level or specific number of processing
elements per application process.
prun will send the name of
the directory where it was invoked on the local node to each of the remote
nodes, and attempt to change to that directory. See the "Current Working
Directory" section below for further details.
- <program>
- The program executable.
This is identified as the first non-recognized argument to prun.
- <args>
- Pass
these run-time arguments to every new process. These must always be the
last arguments to prun. If an app context file is used, <args> will be ignored.
- -h, --help
- Display help for this command
- -q, --quiet
- Suppress informative
messages from prun during application execution.
- -v, --verbose
- Be verbose
- -V, --version
- Print version number. If no other arguments are given, this
will also cause prun to exit.
- -N <num>
Launch num processes per node on all allocated nodes (synonym for npernode).
- -display-map, --display-map
- Display a table showing the mapped location of
each process prior to launch.
- -display-allocation, --display-allocation
- Display
the detected resource allocation.
- -output-proctable, --output-proctable
- Output
the debugger proctable after launch.
- -max-vm-size, --max-vm-size <size>
- Number
of processes to run.
- -novm, --novm
- Execute without creating an allocation-spanning
virtual machine (only start daemons on nodes hosting application procs).
- -hnp, --hnp <arg0>
- Specify the URI of the psrvr process, or the name of the
file (specified as file:filename) that contains that info.
Use one of
the following options to specify which hosts (nodes) within the psrvr to
run on.
- -H, -host, --host <host1,host2,...,hostN>
- List of hosts on which to invoke
processes.
- -hostfile, --hostfile <hostfile>
- Provide a hostfile to use.
- -default-hostfile,
--default-hostfile <hostfile>
- Provide a default hostfile.
- -machinefile, --machinefile
<machinefile>
- Synonym for -hostfile.
- -cpu-set, --cpu-set <list>
- Restrict launched
processes to the specified logical cpus on each node (comma-separated list).
Note that the binding options will still apply within the specified envelope
- e.g., you can elect to bind each process to only one cpu within the specified
cpu set.
The following options specify the number of processes to launch.
Note that none of the options imply a particular binding policy - e.g., requesting
N processes for each 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
program and not an application context. If no value is provided for the
number of copies to execute (i.e., neither the "-np" nor its synonyms are
provided on the command line), prun will automatically execute a copy of
the program on each process slot (see below for description of a "process
slot"). This feature, however, can only be used in the SPMD model and will
return an error (without beginning execution of the application) otherwise.
-<>
- Launch N times the number of objects of the specified type on each node.
- -npersocket, --npersocket <#persocket>
- On each node, launch this many processes
times the number of processor sockets on the node. The -npersocket option
also turns on 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-by
ppr:1:node)
To map processes:
- --map-by <foo>
- Map to the specified object,
defaults to socket. Supported options include slot, hwthread, core, L1cache,
L2cache, L3cache, socket, numa, board, node, sequential, distance, and
ppr. Any object can include modifiers by adding a : and any combination
of PE=n (bind n processing elements to each proc), SPAN (load balance the
processes across the allocation), OVERSUBSCRIBE (allow more processes on
a node than processing elements), and NOOVERSUBSCRIBE. This includes PPR,
where the pattern would be terminated by another colon to separate it from
the modifiers.
- -bycore, --bycore
- Map processes by core (deprecated in favor
of --map-by core)
- -byslot, --byslot
- Map and rank processes round-robin by slot.
- -nolocal, --nolocal
- Do not run any copies of the launched application on
the same node as prun is running. This option will override listing the
localhost with --host or any other host-specifying mechanism.
- -nooversubscribe,
--nooversubscribe
- Do not oversubscribe any nodes; error (without starting
any processes) if the requested number of processes would cause oversubscription.
This option implicitly sets "max_slots" equal to the "slots" value for
each node. (Enabled by default).
- -oversubscribe, --oversubscribe
- Nodes are
allowed to be oversubscribed, even on a managed system, and overloading
of processing elements.
- -bynode, --bynode
- Launch processes one per node, cycling
by node in a round-robin fashion. This spreads processes evenly among nodes
and assigns ranks in a round-robin, "by node" manner.
- -cpu-list, --cpu-list <cpus>
- List of processor IDs to bind processes to [default=NULL].
To order
processes’ ranks:
- --rank-by <foo>
- Rank in round-robin fashion according to the
specified object, defaults to slot. Supported options include slot, hwthread,
core, L1cache, L2cache, L3cache, socket, numa, board, and node.
For
process binding:
- --bind-to <foo>
- Bind processes to the specified object, defaults
to core. Supported options include slot, hwthread, core, l1cache, l2cache,
l3cache, socket, numa, board, and none.
- -cpus-per-proc, --cpus-per-proc <#perproc>
- Bind each process to the specified number of cpus. (deprecated in favor
of --map-by <obj>:PE=n)
- -cpus-per-rank, --cpus-per-rank <#perrank>
- Alias for -cpus-per-proc.
(deprecated in favor of --map-by <obj>: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 processes to processor sockets (deprecated in favor of --bind-to socket)
- -report-bindings, --report-bindings
- Report any bindings for launched processes.
For rankfiles:
- -rf, --rankfile <rankfile>
- Provide a rankfile file.
To manage standard I/O:
- -output-filename, --output-filename <filename>
- Redirect
the stdout, stderr, and stddiag of all processes to a process-unique version
of the specified filename. Any directories in the filename will automatically
be created. Each output file will consist of filename.id, where the id will
be the processes’ rank, left-filled with zero’s for correct ordering in listings.
- -stdin, --stdin <rank>
- The rank of the process that is to receive stdin. The
default is to forward stdin to rank 0, but this option can be used to forward
stdin to any process. It is also acceptable to specify none, indicating
that no processes are to receive stdin.
- -merge-stderr-to-stdout, --merge-stderr-to-stdout
- Merge stderr to stdout for each process.
- -tag-output, --tag-output
- Tag each
line of output to stdout, stderr, and stddiag with [jobid, MCW_rank]<stdxxx>
indicating the process jobid and rank of the process that generated 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 xml format.
- -xml-file,
--xml-file <filename>
- Provide all output in XML format to the specified file.
- -xterm, --xterm <ranks>
- Display the output from the processes identified by
their ranks in separate xterm windows. The ranks are specified as a comma-separated
list of ranges, with a -1 indicating all. A separate window will be created
for each specified process. Note: xterm will normally terminate the window
upon termination of the process running within it. However, by adding a
"!" to the end of the list of specified ranks, the proper options will
be provided to ensure that xterm keeps the window open after the process
terminates, thus allowing you to see the process’ output. Each xterm window
will subsequently need to be manually closed. Note: In some environments,
xterm may require that the executable be in the user’s path, or be specified
in absolute or relative terms. Thus, it may be necessary to specify a local
executable as "./foo" instead of just "foo". If xterm fails to find the executable,
prun will hang, but still respond correctly to a ctrl-c. If this happens,
please check that the executable is being specified correctly and try again.
To manage files and runtime environment:
- -path, --path <path>
- <path> that
will be used when attempting to locate the requested executables. This
is used prior to using the local PATH setting.
- --prefix <dir>
- Prefix directory
that will be used to set the PATH and LD_LIBRARY_PATH on the remote node
before invoking the target process. See the "Remote Execution" section,
below.
- --noprefix
- Disable the automatic --prefix behavior
- -s, --preload-binary
- Copy the specified executable(s) to remote machines prior to starting remote
processes. The executables will be copied to the session directory and will
be deleted upon completion of the job.
- --preload-files <files>
- Preload the
comma separated list of files to the current working directory of the remote
machines where processes will be launched prior to starting those processes.
- -set-cwd-to-session-dir, --set-cwd-to-session-dir
- Set the working directory of the
started processes to their session directory.
- -wd <dir>
- Synonym for -wdir.
- -wdir <dir>
- Change to the directory <dir> before the user’s program executes.
See the "Current Working Directory" section for notes on relative paths.
Note: If the -wdir option appears both on the command line and in an application
context, the context will take precedence over the command line. Thus, if
the path to the desired wdir is different on the backend nodes, then it
must be specified as an absolute path that is correct for the backend node.
- -x <env>
- Export the specified environment variables to the remote nodes
before executing the program. Only one environment variable can be specified
per -x option. Existing environment variables can be specified or new variable
names specified with corresponding values. For example: % prun -x DISPLAY
-x OFILE=/tmp/out ...
The parser for the -x option is not very sophisticated; it does not even
understand quoted values. Users are advised to set variables in the environment,
and then use -x to export (not define) them.
Setting MCA parameters:
- -gpmca, --gpmca <key> <value>
- Pass global MCA parameters that are applicable
to all contexts. <key> is the parameter name; <value> is the parameter value.
- -pmca, --pmca <key> <value>
- Send arguments to various MCA modules. See the "MCA"
section, below.
- -am <arg0>
- Aggregate MCA parameter set file list.
- -tune,
--tune <tune_file>
- Specify a tune file to set arguments for various MCA modules
and environment variables. See the "Setting MCA parameters and environment
variables from file" section, below.
For debugging:
- -debug, --debug
- Invoke
the user-level debugger indicated by the orte_base_user_debugger MCA parameter.
- --get-stack-traces
- When paired with the --timeout option, prun will obtain
and print out stack traces from all launched processes that are still alive
when the timeout expires. Note that obtaining stack traces can take a little
time and produce a lot of output, especially for large process-count jobs.
- -debugger, --debugger <args>
- Sequence of debuggers to search for when --debug
is used (i.e. a synonym for orte_base_user_debugger MCA parameter).
- --timeout
<seconds>
- The maximum number of seconds that prun will run. After this many
seconds, prun will abort the launched job and exit with a non-zero exit
status. Using --timeout can be also useful when combined with the --get-stack-traces
option.
- -tv, --tv
- Launch processes under the TotalView debugger. Deprecated
backwards compatibility flag. Synonym for --debug.
There are also other
options:
- --allow-run-as-root
- Allow prun to run when executed by the root user
(prun defaults to aborting when launched as the root user).
- --app <appfile>
- Provide an appfile, ignoring all other command line options.
- -cf, --cartofile
<cartofile>
- Provide a cartography file.
- -continuous, --continuous
- Job is to
run until explicitly terminated.
- -disable-recovery, --disable-recovery
- Disable
recovery (resets all recovery options to off).
- -do-not-launch, --do-not-launch
- Perform all necessary operations to prepare to launch the application,
but do not actually launch it.
- -do-not-resolve, --do-not-resolve
- Do not attempt
to resolve interfaces.
- -enable-recovery, --enable-recovery
- Enable recovery
from process failure [Default = disabled].
- -index-argv-by-rank, --index-argv-by-rank
- Uniquely index argv[0] for each process using its rank.
- -max-restarts, --max-restarts
<num>
- Max number of times to restart a failed process.
- --ppr <list>
- Comma-separated
list of number of processes on a given resource type [default: none].
- -report-child-jobs-separately, --report-child-jobs-separately
- Return the exit status
of the primary job only.
- -report-events, --report-events <URI>
- Report events
to a tool listening at the specified URI.
- -report-pid, --report-pid <channel>
- Print out prun’s PID during startup. The channel must be either a ’-’ to indicate
that the pid is to be output to stdout, a ’+’ to indicate that the pid is
to be output to stderr, or a filename to which the pid is to be written.
- -report-uri, --report-uri <channel>
- Print out prun’s URI during startup. The channel
must be either a ’-’ to indicate that the URI 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.
- -show-progress, --show-progress
- Output a brief
periodic report on launch progress.
- -terminate, --terminate
- Terminate the
DVM.
- -use-hwthread-cpus, --use-hwthread-cpus
- Use hardware threads as independent
cpus.
- -use-regexp, --use-regexp
- Use regular expressions for launch.
The
following options are useful for developers; they are not generally useful
to most users:
- -d, --debug-devel
- Enable debugging. This is not generally useful
for most users.
- -display-devel-allocation, --display-devel-allocation
- Display
a detailed list of the allocation being used by this job.
- -display-devel-map,
--display-devel-map
- Display a more detailed table showing the mapped location
of each process prior to launch.
- -display-diffable-map, --display-diffable-map
- Display a diffable process map just before launch.
- -display-topo, --display-topo
- Display the topology as part of the process map just before launch.
- --report-state-on-timeout
- When paired with the --timeout command line option, report the run-time subsystem
state of each process when the timeout expires.
There may be other options
listed with prun --help.
One invocation of prun starts an
application running under PSRVR. If the application is single process multiple
data (SPMD), the application can be specified on the prun command line.
If the application is multiple instruction multiple data (MIMD), comprising
of multiple programs, the set of programs and argument can be specified
in one of two ways: Extended Command Line Arguments, and Application Context.
An application context describes the MIMD program set including all arguments
in a separate file. This file essentially contains multiple prun command
lines, less the command name itself. The ability to specify different options
for different instantiations of a program is another reason to use an application
context.
Extended command line arguments allow for the description of the
application layout on the command line using colons (:) to separate the
specification of programs and arguments. Some options are globally set across
all specified programs (e.g. --hostfile), while others are specific to a single
program (e.g. -np).
Host nodes can be identified on
the prun command line with the -host option or in a hostfile.
For example,
- prun -H aa,aa,bb ./a.out
- launches two processes on node aa and one on bb.
Or, consider the hostfile
% 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 potentially
execute on a node. For best performance, the number of slots may be chosen
to be the number of cores on the node or the number of processor sockets.
If the hostfile does not provide slots information, PSRVR will attempt
to discover the number of cores (or hwthreads, if the use-hwthreads-as-cpus
option is set) and set the number of slots to that value. This default behavior
also occurs when specifying the -host option with a single hostname. Thus,
the command
- prun -H aa ./a.out
- launches a number of processes equal to the
number of cores on node aa.
- prun -hostfile myhostfile ./a.out
- will launch
two processes on each of the three nodes.
- prun -hostfile myhostfile -host
aa ./a.out
- will launch two processes, both on node aa.
- prun -hostfile myhostfile
-host dd ./a.out
- will find no hosts to run on and abort with an error. That
is, the specified host dd is not in the specified hostfile.
When running
under resource managers (e.g., SLURM, Torque, etc.), PSRVR will obtain both
the hostnames and the number of slots directly from the resource manger.
As we have just seen, the number of processes
to run can be set using the hostfile. Other mechanisms exist.
The number
of processes launched can be specified as a multiple of the number of nodes
or processor sockets available. For example,
- prun -H aa,bb -npersocket 2
./a.out
- launches processes 0-3 on node aa and process 4-7 on node bb, where
aa and bb are both dual-socket nodes. The -npersocket option also turns on
the -bind-to-socket option, which is discussed in a later section.
- prun -H
aa,bb -npernode 2 ./a.out
- launches processes 0-1 on node aa and processes 2-3
on node bb.
- prun -H aa,bb -npernode 1 ./a.out
- launches one process per host
node.
- prun -H aa,bb -pernode ./a.out
- is the same as -npernode 1.
Another alternative
is to specify the number of processes with the -np option. Consider now
the hostfile
% cat myhostfile
aa slots=4
bb slots=4
cc slots=4
Now,
- prun -hostfile myhostfile -np 6 ./a.out
- will launch processes 0-3 on
node aa and processes 4-5 on node bb. The remaining slots in the hostfile
will not be used since the -np option indicated that only 6 processes should
be launched.
The examples above
illustrate the default mapping of process processes to nodes. This mapping
can also be controlled with various prun options that describe mapping
policies.
Consider the same hostfile as above, again with -np 6:
node aa node bb node cc
prun 0 1 2 3 4 5
prun --map-by node 0 3 1 4 2 5
prun -nolocal 0 1 2 3 4 5
The --map-by node option will load balance the processes across the available
nodes, numbering each process in a round-robin fashion.
The -nolocal option
prevents any processes from being mapped onto the local host (in this case
node aa). While prun typically consumes few system resources, -nolocal can
be helpful for launching very large jobs where prun may actually need to
use noticeable amounts of memory and/or processing time.
Just as -np can
specify fewer processes than there are slots, it can also oversubscribe
the slots. For example, with the same hostfile:
- prun -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 the
same hostfile:
- prun -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 value
defaults to the limit. Now:
- prun -hostfile myhostfile -np 14 ./a.out
- causes
the first 12 processes to be launched as before, but the remaining two
processes will be forced onto node cc. The other two nodes are protected
by the hostfile against oversubscription by this job.
Using the --nooversubscribe
option can be helpful since PSRVR 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,
- prun -H aa,bb -np 8 ./a.out
- launches 8 processes.
Since only two hosts are specified, after the first two processes are
mapped, one to aa and one to bb, the remaining processes oversubscribe
the specified hosts.
And here is a MIMD example:
- prun -H aa -np 1 hostname
: -H bb,cc -np 2 uptime
- will launch process 0 running hostname on node aa
and processes 1 and 2 each running uptime on nodes bb and cc, respectively.
PSRVR employs a three-phase procedure
for assigning process locations and ranks:
- mapping
- Assigns a default location
to each process
- ranking
- Assigns a rank value to each process
- binding
- Constrains each process to run on specific processors
The mapping step
is used to assign a default location to each process based on the mapper
being employed. Mapping by slot, node, and sequentially results in the assignment
of the processes to the node level. In contrast, mapping by object, allows
the mapper to assign the process to an actual object on each node.
Note:
the location assigned to the process is independent of where it will be
bound - the assignment is used solely as input to the binding algorithm.
The mapping of process processes to nodes can be defined not just with
general policies but also, if necessary, using arbitrary mappings that
cannot be described by a simple policy. One can use the "sequential mapper,"
which reads the hostfile line by line, assigning processes to nodes in
whatever order the hostfile specifies. Use the -pmca rmaps seq option. For
example, using the same hostfile as before:
prun -hostfile myhostfile -pmca
rmaps seq ./a.out
will launch three processes, one on each of nodes aa,
bb, and cc, respectively. The slot counts don’t matter; one process is launched
per line on whatever node is listed on the line.
Another way to specify
arbitrary mappings is with a rankfile, which gives you detailed control
over process binding as well. Rankfiles are discussed below.
The second
phase focuses on the ranking of the process within the job. PSRVR separates
this from the mapping procedure to allow more flexibility in the relative
placement of processes. This is best illustrated by considering the following
two cases where we used the —map-by ppr:2:socket option:
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 progression
of ranks across each node. Ranking by socket does a round-robin ranking within
each node until all processes have been assigned a rank, and then progresses
to the next node. Adding the span modifier to the ranking directive causes
the ranking algorithm to treat the entire allocation as a single entity
- thus, the MCW ranks are assigned across all sockets before circling back
around to the beginning.
The binding phase actually binds each process
to a given set of processors. This can improve performance if the operating
system is placing processes suboptimally. For example, it might oversubscribe
some multi-core processor sockets, leaving other sockets idle; this can
lead processes to contend unnecessarily for common resources. Or, it might
spread processes out too widely; this can be suboptimal if application
performance is sensitive to interprocess communication costs. Binding can
also keep the operating system from migrating processes excessively, regardless
of how optimally those processes were placed to begin with.
The processors
to be used for binding can be identified in terms of topological groupings
- e.g., binding to an l3cache will bind each process to all processors within
the scope of a single L3 cache within their assigned location. Thus, if
a process is assigned by the mapper to a certain socket, then a —bind-to
l3cache directive will cause the process to be bound to the processors
that share a single L3 cache within that socket.
To help balance loads,
the binding directive uses a round-robin method 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 bound to core. Each socket will have multiple
cores, so if multiple processes are mapped to a given socket, the binding
algorithm will assign each process located 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 bound to 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 prun with -np 4 --report-bindings
and the following additional options:
% prun ... --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
% prun ... --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
% prun ... --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
% prun ... --bind-to none
Here, --report-bindings shows the binding of each process as a mask. In the
first case, the processes bind to successive cores as indicated by the
masks 0001, 0002, 0004, and 0008. In the second case, processes bind to
all cores on successive sockets as indicated by the masks 000f and 00f0.
The processes cycle through the processor sockets in a round-robin fashion
as many times as are needed. In the third case, the masks show us that
2 cores have been bound per process. In the fourth case, binding is turned
off and no bindings are reported.
PSRVR’s support for process binding depends
on the underlying operating system. Therefore, certain process binding
options may not be available on every system.
Process binding can also
be set with MCA parameters. Their usage is less convenient than that of
prun options. On the other hand, MCA parameters can be set not only on the
prun command line, but alternatively in a system or user mca-params.conf
file or as environment variables, as described in the MCA section below.
Some examples include:
prun 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 are text files that specify detailed information
about how individual processes should be mapped to nodes, and to which
processor(s) they should be bound. Each line of a rankfile specifies the
location of one process. The general form of each line in the rankfile
is:
rank <N>=<hostname> slot=<slot list>
For example:
$ cat myrankfile
rank 0=aa slot=1:0-2
rank 1=bb slot=0:0,1
rank 2=cc slot=1-2
$ prun -H aa,bb,cc,dd -rf myrankfile ./a.out
Means that
Rank 0 runs on node aa, bound to logical socket 1, cores
0-2.
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 most
OS’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 that
contains physical PU 1
Rank 1 will run on node bb, bound to the core that contains physical
PU 8
Rank 2 will run on node cc, bound to the core that contains physical
PU 6
Rankfiles are treated as logical by default, and the MCA parameter rmaps_rank_file_physical
must be set to 1 to indicate that the rankfile is to be considered as physical.
The hostnames listed above are "absolute," meaning that actual resolveable
hostnames are specified. However, hostnames can also be specified as "relative,"
meaning that they are specified in relation to an externally-specified list
of hostnames (e.g., by prun’s --host argument, a hostfile, or a job scheduler).
The "relative" specification is of the form "+n<X>", where X is an integer
specifying the Xth hostname in the set of all available hostnames, indexed
from 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
$ prun -H aa,bb,cc,dd -rf myrankfile ./a.out
All socket/core slot locations are be specified as logical indexes. You
can use tools such as HWLOC’s "lstopo" to find the logical indexes of socket
and cores.
To distinguish the
two different forms, prun looks on the command line for --app option. If
it is specified, then the file named on the command line is assumed to
be an application context. If it is not specified, then the file is assumed
to be an executable program.
If no relative or absolute
path is specified for a file, prun will first look for files by searching
the directories specified by the --path option. If there is no --path option
set or if the file is not found at the --path location, then prun will search
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 initial working
directory determined by the specific starter used. For example when using
the rsh or ssh starters, the initial directory is $HOME by default. Other
starters may set the initial directory to the current working directory
from the invocation of prun.
The -wdir prun
option (and its synonym, -wd) allows the user to change to an arbitrary
directory before the program is invoked. It can also be used in application
context files to specify working directories on specific nodes and/or for
specific applications.
If the -wdir option appears both in a context file
and on the command line, the context file directory will override the command
line value.
If the -wdir option is specified, prun will attempt to change
to the specified directory on all of the remote nodes. If this fails, prun
will abort.
If the -wdir option is not specified, prun will send the directory
name where prun was invoked to each of the remote nodes. The remote nodes
will try to change to that directory. If they are unable (e.g., if the directory
does not exist on that node), then prun will use the default directory
determined by the starter.
All directory changing occurs before the user’s
program is invoked.
PSRVR directs UNIX standard input to
/dev/null on all processes except the rank 0 process. The rank 0 process
inherits standard input from prun. Note: The node that invoked prun need
not be the same as the node where the rank 0 process resides. PSRVR handles
the redirection of prun’s standard input to the rank 0 process.
PSRVR directs
UNIX standard output and error from remote nodes to the node that invoked
prun and prints it on the standard output/error of prun. Local processes
inherit the standard output/error of prun and transfer to it directly.
Thus
it is possible to redirect standard I/O for applications by using the typical
shell redirection procedure on prun.
% prun -np 2 my_app < my_input
> my_output
Note that in this example only the rank 0 process will receive the stream
from my_input on stdin. The stdin on all the other nodes will be tied to
/dev/null. However, the stdout from all nodes will be collected into the
my_output file.
When prun receives a SIGTERM and SIGINT,
it will attempt to kill the entire job by sending all processes in the
job a SIGTERM, waiting a small number of seconds, then sending all processes
in the job a SIGKILL.
SIGUSR1 and SIGUSR2 signals received by prun are
propagated to all processes in the job.
A SIGTSTOP signal to prun will
cause a SIGSTOP signal to be sent to all of the programs started by prun
and likewise a SIGCONT signal to prun will cause a SIGCONT sent.
Other
signals are not currently propagated by prun.
During the run of an application, if any process dies abnormally
(either exiting before invoking PMIx_Finalize, or dying as the result of
a signal), prun will print out an error message and kill the rest of the
application.
Processes in the application inherit
their environment from the PSRVR daemon upon the node on which they are
running. The environment is typically inherited from the user’s shell. On
remote nodes, the exact environment is determined by the boot MCA module
used. The rsh launch module, for example, uses either rsh/ssh to launch
the PSRVR daemon on remote nodes, and typically executes one or more of
the user’s shell-setup files before launching the daemon. When running dynamically
linked applications which require the LD_LIBRARY_PATH environment variable
to be set, care must be taken to ensure that it is correctly set when booting
PSRVR.
See the "Remote Execution" section for more details.
PSRVR requires that the PATH environment variable be set to find executables
on remote nodes (this is typically only necessary in rsh- or ssh-based environments
-- batch/scheduled environments typically copy the current environment to
the execution of remote jobs, so if the current environment has PATH and/or
LD_LIBRARY_PATH set properly, the remote nodes will also have it set properly).
If PSRVR was compiled with shared library support, it may also be necessary
to have the LD_LIBRARY_PATH environment variable set on remote nodes as
well (especially to find the shared libraries required to run user applications).
However, it is not always desirable or possible to edit shell startup files
to set PATH and/or LD_LIBRARY_PATH. The --prefix option is provided for some
simple configurations where this is not possible.
The --prefix option takes
a single argument: the base directory on the remote node where PSRVR is
installed. PSRVR will use this directory to set the remote PATH and LD_LIBRARY_PATH
before executing any user applications. This allows running jobs without
having pre-configured the PATH and LD_LIBRARY_PATH on the remote nodes.
PSRVR
adds the basename of the current node’s "bindir" (the directory where PSRVR’s
executables are installed) to the prefix and uses that to set the PATH
on the remote node. Similarly, PSRVR adds the basename of the current node’s
"libdir" (the directory where PSRVR’s libraries are installed) to the prefix
and uses that to set the LD_LIBRARY_PATH on the remote node. For example:
- Local bindir:
- /local/node/directory/bin
- Local libdir:
- /local/node/directory/lib64
If the following command line is used:
% prun --prefix /remote/node/directory
PSRVR 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 remote
node are different than the local node (e.g., if "/lib" is used on the local
node, but "/lib64" is used on the remote node), or if the installation
paths are something other than a subdirectory under a common prefix.
Note
that executing prun via an absolute pathname is equivalent to specifying
--prefix without the last subdirectory in the absolute pathname to prun.
For example:
% /usr/local/bin/prun ...
is equivalent to
% prun --prefix /usr/local
All environment variables that are named
in the form PMIX_* will automatically be exported to new processes on the
local and remote nodes. Environmental parameters can also be set/forwarded
to the new processes using the MCA parameter mca_base_env_list. While the
syntax of the -x option and MCA param allows the definition of new variables,
note that the parser for these options are currently not very sophisticated
- it does not even understand quoted values. Users are advised to set variables
in the environment and use the option to export them; not to define them.
The -pmca switch allows the passing of parameters
to various MCA (Modular Component Architecture) modules. MCA modules have
direct impact on programs because they allow tunable parameters to be set
at run time (such as which BTL communication device driver to use, what
parameters to pass to that BTL, etc.).
The -pmca switch takes two arguments:
<key> and <value>. The <key> argument generally specifies which MCA module will
receive the value. For example, the <key> "btl" is used to select which BTL
to be used for transporting messages. The <value> argument is the value that
is passed. For example:
- prun -pmca btl tcp,self -np 1 foo
- Tells PSRVR to
use the "tcp" and "self" BTLs, and to run a single copy of "foo" on an
allocated node.
- prun -pmca btl self -np 1 foo
- Tells PSRVR to use the "self"
BTL, and to run a single copy of "foo" on an allocated node.
The -pmca switch
can be used multiple times to specify different <key> and/or <value> arguments.
If the same <key> is specified more than once, the <value>s are concatenated
with a comma (",") separating them.
Note that the -pmca switch is simply
a shortcut for setting environment variables. The same effect may be accomplished
by setting corresponding environment variables before running prun. The
form of the environment variables that PSRVR sets is:
PMIX_MCA_<key>=<value>
Thus, the -pmca switch overrides any previously set environment variables.
The -pmca settings similarly override MCA parameters set in the $OPAL_PREFIX/etc/psrvr-mca-params.conf
or $HOME/.psrvr/mca-params.conf file.
Unknown <key> arguments are still set
as environment variable -- they are not checked (by prun) for correctness.
Illegal or incorrect <value> arguments may or may not be reported -- it depends
on the specific MCA module.
To find the available component types under
the MCA architecture, or to find the available parameters for a specific
component, use the pinfo command. See the pinfo(1) man page for detailed
information on the command.
The -tune command line option and its synonym -pmca mca_base_envar_file_prefix
allows a user to set mca parameters and environment variables with the
syntax described below. This option requires a single file or list of files
separated by "," to follow.
A valid line in the file may contain zero or
many "-x", "-pmca", or “--pmca” arguments. The following patterns are supported:
-pmca var val -pmca var "val" -x var=val -x var. If any argument is duplicated
in the file, the last value read will be used.
MCA parameters and environment
specified on the command line have higher precedence than variables specified
in the file.
The PSRVR team strongly advises against
executing prun as the root user. Applications should be run as regular (non-root)
users.
Reflecting this advice, prun will refuse to run as root by default.
To override this default, you can add the --allow-run-as-root option to the
prun command line.
There is no standard definition for what
prun should return as an exit status. After considerable discussion, we
settled on the following method for assigning the prun exit status (note:
in the following description, the "primary" job is the initial application
started by prun - all jobs that are spawned by that job are designated "secondary"
jobs):
- [bu]
- if all processes in the primary job normally terminate with
exit status 0, we return 0
- [bu]
- if one or more processes in the primary
job normally terminate with non-zero exit status, we return the exit status
of the process with the lowest rank to have a non-zero status
- [bu]
- if all
processes in the primary job normally terminate with exit status 0, and
one or more processes in a secondary job normally terminate with non-zero
exit status, we (a) return the exit status of the process with the lowest
rank in the lowest jobid to have a non-zero status, and (b) output a message
summarizing the exit status of the primary and all secondary jobs.
- [bu]
- if
the cmd line option --report-child-jobs-separately is set, we will return -only-
the exit status of the primary job. Any non-zero exit status in secondary
jobs will be reported solely in a summary print statement.
By default,
PSRVR records and notes that processes exited with non-zero termination
status. This is generally not considered an "abnormal termination" - i.e.,
PSRVR will not abort a job if one or more processes return a non-zero status.
Instead, the default behavior simply reports the number of processes terminating
with non-zero status upon completion of the job.
However, in some cases it
can be desirable to have the job abort when any process terminates with
non-zero status. For example, a non-PMIx job might detect a bad result from
a calculation and want to abort, but doesn’t want to generate a core file.
Or a PMIx job might continue past a call to PMIx_Finalize, but indicate
that all processes should abort due to some post-PMIx result.
It is not anticipated
that this situation will occur frequently. However, in the interest of serving
the broader community, PSRVR now has a means for allowing users to direct
that jobs be aborted upon any process exiting with non-zero status. Setting
the MCA parameter "orte_abort_on_non_zero_status" to 1 will cause PSRVR
to abort all processes once any process exits with non-zero status.
Terminations caused in this manner will be reported on the console as
an "abnormal termination", with the first process to so exit identified
along with its exit status.
prun returns 0 if all processes
started by prun exit after calling PMIx_Finalize. A non-zero value is returned
if an internal error occurred in prun, or one or more processes exited
before calling PMIx_Finalize. If an internal error occurred in prun, the
corresponding error code is returned. In the event that one or more processes
exit before calling PMIx_Finalize, the return value of the rank of the
process that prun first notices died before calling PMIx_Finalize will
be returned. Note that, in general, this will be the first process that
died but is not guaranteed to be so.
If the --timeout command line option
is used and the timeout expires before the job completes (thereby forcing
prun to kill the job) prun will return an exit status equivalent to the
value of ETIMEDOUT (which is typically 110 on Linux and OS X systems).
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