11.18. pegasus-kickstart

Pegasus remote job wrapper

pegasus-kickstart [-n tr] [-N dv] [-H] [-R site] [-W | -w dir]
                  [-L lbl -T iso] [-s p | @fn] [-S p | @fn] [-i fn]
                  [-o fn] [-e fn] [-X] [-l fn sz] [-F] (-I fn | app [appflags])
pegasus-kickstart -V

11.18.1. Description

pegasus-kickstart is a wrapper program which manages and monitors the execution of jobs on remote resources.

Sitting in between the remote scheduler and the application process, it is possible for pegasus-kickstart to gather additional information about the process’ run-time behavior and resource usage, including the exit status of jobs. This information is important for Pegasus invocation tracking as well as detecting Globus GRAM job failures.

pegasus-kickstart allows the optional execution of jobs before and after the main application job that run in chained execution with the main application job. See section SUBJOBS for details about this feature.

It also allows stdin, stdout, and stderr to be redirected from/to specific files.

All jobs with relative path specifications to the application are part of search relative to the current working directory (yes, this is unsafe), and by prepending each component from the PATH environment variable. The first match is used. Jobs that use absolute pathnames, starting in a slash, are exempt. Using an absolute path to your executable is the safe and recommended option.

pegasus-kickstart rewrites the command line of any job (pre, post and main) with variable substitutions from Unix environment variables. See section VARIABLE REWRITING below for details on this feature.

11.18.2. Options

-n tr

In order to associate the minimal performance information of the job with the invocation records, the jobs needs to carry which transformation was responsible for producing it. The format is the textual notation for fully-qualified definition names, like namespace::name:version, with only the name portion being mandatory.

There is no default. If no value is given, “null” will be reported.

-N dv

The jobs may carry which instantiation of a transformation was responsible for producing it. The format is the textual notation for fully-qualified definition names, like namespace::name:version, with only the name portion being mandatory.

There is no default. If no value is given, “null” will be reported.

-H

This option avoids pegasus-kickstart writing the XML preamble (entity), if you need to combine multiple pegasus-kickstart records into one document.

Additionally, if specified, the environment and the resource usage segments will not be written, assuming that a in a concatenated record version, the initial run will have captured those settings.

-R site

In order to provide the greater picture, pegasus-kickstart can reflect the site handle (resource identifier) into its output.

There is no default. If no value is given, the attribute will not be generated.

-L lbl; -T iso

These optional arguments denote the workflow label (from DAX) and the workflow’s last modification time (from DAX). The label lbl can be any sensible string of up to 32 characters, but should use C identifier characters. The timestamp iso must be an ISO 8601 compliant time-stamp.

-S l=p

If stat information on any file is required before any jobs were started, logical to physical file mappings to stat can be passed using the -S option. The LFN and PFN are concatenated by an equals (=) sign. The LFN is optional: If no equals sign is found, the argument is taken as sole PFN specification without LFN.

This option may be specified multiple times. To reduce and overcome command line length limits, if the argument is prefixed with an at (@) sign, the argument is taken to be a textual file of LFN to PFN mappings. The optionality mentioned above applies. Each line inside the file argument is the name of a file to stat. Comments (#) and empty lines are permitted.

Each PFN will incur a statcall record (element) with attribute id set to value initial. The optional lfn attribute is set to the LFN stat’ed. The filename is part of the statinfo record inside.

There is no default.

-s fn

If stat information on any file is required after all jobs have finished, logical to physical file mappings to stat can be passed using the -s option. The LFN and PFN are concatenated by an equals (=) sign. The LFN is optional: If no equals sign is found, the argument is taken as sole PFN specification without LFN.

This option may be specified multiple times. To reduce and overcome commandline length limits, if the argument is prefixed with an at (@) sign, the argument is taken to be a textual file of LFN to PFN mappings. The optionality mentioned above applies. Each line inside the file argument is the name of a file to stat. Comments (#) and empty lines are permitted.

Each PFN will incur a statcall record (element) with attribute id set to value final. The optional lfn attribute is set to the LFN stat’ed. The filename is part of the statinfo record inside.

There is no default.

-i fn

This option allows pegasus-kickstart to re-connect the stdin of the application that it starts. Use a single hyphen to share stdin with the one provided to pegasus-kickstart.

The default is to connect stdin to /dev/null.

-o fn

This option allows pegasus-kickstart to re-connect the stdout of the application that it starts. The mode is used whenever an application produces meaningful results on its stdout that need to be tracked by Pegasus. The real stdout of Globus jobs is staged via GASS (GT2) or RFT (GT4). The real stdout is used to propagate the invocation record back to the submit site. Use the single hyphen to share the application’s stdout with the one that is provided to pegasus-kickstart. In that case, the output from pegasus-kickstart will interleave with application output. For this reason, such a mode is not recommended.

In order to provide an un-captured stdout as part of the results, it is the default to connect the stdout of the application to a temporary file. The content of this temporary file will be transferred as payload data in the pegasus-kickstart results. The content size is subject to payload limits, see the -B option. If the content grows large, only the last portion will become part of the payload. If the temporary file grows too large, it may flood the worker node’s temporary space. The temporary file will be deleted after pegasus-kickstart finishes.

If the filename is prefixed with an exclamation point, the file will be opened in append mode instead of overwrite mode. Note that you may need to escape the exclamation point from the shell.

The default is to connect stdout to a temporary file.

-e fn

This option allows pegasus-kickstart to re-connect the stderr of the application that it starts. This option is used whenever an application produces meaningful results on stderr that needs tracking by Pegasus. The real stderr of Globus jobs is staged via GASS (GT2) or RFT (GT4). It is used to propagate abnormal behavior from both, pegasus-kickstart and the application that it starts, though its main use is to propagate application dependent data and heartbeats. Use a single hyphen to share stderr with the stderr that is provided to pegasus-kickstart. This is the backward compatible behavior.

In order to provide an un-captured stderr as part of the results, by default the stderr of the application will be connected to a temporary file. Its content is transferred as payload data in the pegasus-kickstart results. If too large, only the last portion will become part of the payload. If the temporary file grows too large, it may flood the worker node’s temporary space. The temporary file will be deleted after pegasus-kickstart finishes.

If the filename is prefixed with an exclamation point, the file will be opened in append mode instead of overwrite mode. Note that you may need to escape the exclamation point from the shell.

The default is to connect stderr to a temporary file.

-l logfn

allows to append the performance data to the specified file. Thus, multiple XML documents may end up in the same file, including their XML preamble. stdout is normally used to stream back the results. Usually, this is a GASS-staged stream. Use a single hyphen to generate the output on the stdout that was provided to pegasus-kickstart, the default behavior.

Default is to append the invocation record onto the provided stdout.

-w dir

permits the explicit setting of a new working directory once pegasus-kickstart is started. This is useful in a remote scheduling environment, when the chosen working directory is not visible on the job submitting host. If the directory does not exist, pegasus-kickstart will fail. This option is mutually exclusive with the -W dir option.

Default is to use the working directory that the application was started in. This is usually set up by a remote scheduling environment.

-W dir

permits the explicit creation and setting of a new working directory once pegasus-kickstart is started. This is useful in a remote scheduling environment, when the chosen working directory is not visible on the job submitting host. If the directory does not exist, pegasus-kickstart will attempt to create it, and then change into it. Both, creation and directory change may still fail. This option is mutually exclusive with the -w dir option.

Default is to use the working directory that the application was started in. This is usually set up by a remote scheduling environment.

-X

make an application executable, no matter what. It is a work-around code for a weakness of globus-url-copy which does not copy the permissions of the source to the destination. Thus, if an executable is staged-in using GridFTP, it will have the wrong permissions. Specifying the -X flag will attempt to change the mode to include the necessary x (and r) bits to make the application executable.

Default is not to change the mode of the application. Note that this feature can be misused by hackers, as it is attempted to call chmod on whatever path is specified.

-B sz

Changes the amount of stdout and stderr data to include in the output. The last sz bytes of the stdout and stderr of the process will be copied into kickstart’s output. All other data will be discarded. The special value all can be used to capture all the stdout/stderr of the process. The default is 256KB.

-F

This flag will issue an explicit fsync() call on kickstart’s own stdout file. Typically you won’t need this flag. Albeit, certain shared file system situations may improve when adding a flush after the written invocation record.

The default is to just use kickstart’s NFS alleviation strategy by locking and unlocking stdout.

-I fn

In this mode, the application name and any arguments to the application are specified inside of file fn. The file contains one argument per line. Escaping from Globus, Condor and shell meta characters is not required. This mode permits to use the maximum possible command line length of the underlying operating system, e.g. 128k for Linux. Using the -I mode stops any further command line processing of pegasus-kickstart command lines.

Default is to use the app flags mode, where the application is specified explicitly on the command-line.

-f

This flag causes kickstart to output full information, including the environment and resource limits under which the job ran, and any useful auxilliary statcalls. If the job fails, then -f is implied.

-k S

This flag causes kickstart to send the job a SIGTERM if it is still running after S seconds. The default value is 0, which disables the timeout.

-K S

This flag causes kickstart to send the job a SIGKILL if it is still running S seconds after recieving a SIGTERM sent as a result of the -k flag. The default value is 5. If -k is not set, or is set to 0, then this flag is ignored.

-t

This flag causes kickstart to use ptrace() to collect resource usage info for the process by intercepting the process start and stop events. This flag only exists when kickstart is compiled for Linux.

-z

This flag causes kickstart to use ptrace() to intercept system calls and report a list of files accessed and I/O performed. This flag only exists when kickstart is compiled for Linux.

-Z

This flag causes kickstart to use LD_PRELOAD to intercept library calls and report a list of files accessed and I/O performed. This flag only exists when kickstart is compiled for Linux. There are several environment variables documented below that control what file accesses are traced.

-q

This flag causes kickstart to omit the <data> part of the <statcall> records when the job exits successfully. This is designed to reduce the size of the output logs for large workflows.

-c

This flag causes kickstart to output <data> from stdout and stderr as a CDATA section instead of quoting it.

app

The path to the application has to be completely specified. The application is a mandatory option.

appflags

Application may or may not have additional flags.

11.18.3. Return Value

pegasus-kickstart will return the return value of the main job. In addition, the error code 127 signals that the call to exec failed, and 126 that reconnecting the stdio failed. A job failing with the same exit codes is indistinguishable from pegasus-kickstart failures.

11.18.4. See Also

pegasus-plan(1), condor_submit_dag(1), condor_submit(1), getrusage(3c).

11.18.5. Subjobs

Subjobs are a new feature and may have a few wrinkles left.

In order to allow specific setups and assertion checks for compute nodes, pegasus-kickstart allows the optional execution of a prejob. This prejob is anything that the remote compute node is capable of executing. For modern Unix systems, this includes #! scripts interpreter invocations, as long as the x bits on the executed file are set. The main job is run if and only if the prejob returned regularly with an exit code of zero.

With similar restrictions, the optional execution of a postjob is chained to the success of the main job. The postjob will be run, if the main job terminated normally with an exit code of zero.

In addition, a user may specify a setup and a cleanup job. The setup job sets up the remote execution environment. The cleanup job may tear down and clean-up after any job ran. Failure to run the setup job has no impact on subsequent jobs. The cleanup is a job that will even be attempted to run for all failed jobs. No job information is passed. If you need to invoke multiple setup or clean-up jobs, bundle them into a script, and invoke the clean-up script. Failure of the clean-up job is not meant to affect the progress of the remote workflow (DAGMan). This may change in the future.

The setup-, pre-, and post- and cleanup-job run on the same compute node as the main job to execute. However, since they run in separate processes as children of pegasus-kickstart, they are unable to influence each others nor the main jobs environment settings.

All jobs and their arguments are subject to variable substitutions as explained in the next section.

To specify the prejob, insert the the application invocation and any optional commandline argument into the environment variable KICKSTART_PREJOB. If you are invoking from a shell, you might want to use single quotes to protect against the shell. If you are invoking from Globus, you can append the RSL string feature. From Condor, you can use Condor’s notion of environment settings. In Pegasus use the profile command to set generic scripts that will work on multiple sites, or the transformation catalog to set environment variables in a pool-specific fashion. Please remember that the execution of the main job is chained to the success of the prejob.

To set up the postjob, use the environment variable KICKSTART_POSTJOB to point to an application with potential arguments to execute. The same restrictions as for the prejob apply. Please note that the execution of the post job is chained to the main job.

To provide the independent setup job, use the environment variable KICKSTART_SETUP. The exit code of the setup job has no influence on the remaining chain of jobs. To provide an independent cleanup job, use the environment variable KICKSTART_CLEANUP to point to an application with possible arguments to execute. The same restrictions as for prejob and postjob apply. The cleanup is run regardless of the exit status of any other jobs.

11.18.6. Variable Rewriting

Variable substitution is a new feature and may have a few wrinkles left.

The variable substitution employs simple rules from the Bourne shell syntax. Simple quoting rules for backslashed characters, double quotes and single quotes are obeyed. Thus, in order to pass a dollar sign to as argument to your job, it must be escaped with a backslash from the variable rewriting.

For pre- and postjobs, double quotes allow the preservation of whitespace and the insertion of special characters like \a (alarm), \b (backspace), \n (newline), \r (carriage return), \t (horizontal tab), and \v (vertical tab). Octal modes are not allowed. Variables are still substituted in double quotes. Single quotes inside double quotes have no special meaning.

Inside single quotes, no variables are expanded. The backslash only escapes a single quote or backslash.

Backticks are not supported.

Variables are only substituted once. You cannot have variables in variables. If you need this feature, please request it.

Outside quotes, arguments from the pre- and postjob are split on linear whitespace. The backslash makes the next character verbatim.

Variables that are rewritten must start with a dollar sign either outside quotes or inside double quotes. The dollar may be followed by a valid identifier. A valid identifier starts with a letter or the underscore. A valid identifier may contain further letters, digits or underscores. The identifier is case sensitive.

The alternative use is to enclose the identifier inside curly braces. In this case, almost any character is allowed for the identifier, including whitespace. This is the only curly brace expansion. No other Bourne magic involving curly braces is supported.

One of the advantages of variable substitution is, for example, the ability to specify the application as $HOME/bin/app1 in the transformation catalog, and thus to gridstart. As long as your home directory on any compute node has a bin directory that contains the application, the transformation catalog does not need to care about the true location of the application path on each pool. Even better, an administrator may decide to move your home directory to a different place. As long as the compute node is set up correctly, you don’t have to adjust any Pegasus data.

Mind that variable substitution is an expert feature, as some degree of tricky quoting is required to protect substitutable variables and quotes from Globus, Condor and Pegasus in that order. Note that Condor uses the dollar sign for its own variables.

The variable substitution assumptions for the main job differ slightly from the prejob and postjob for technical reasons. The pre- and postjob command lines are passed as one string. However, the main jobs command line is already split into pieces by the time it reaches pegasus-kickstart. Thus, any whitespace on the main job’s command line must be preserved, and further argument splitting avoided.

It is highly recommended to experiment on the Unix command line with the echo and env applications to obtain a feeling for the different quoting mechanisms needed to achieve variable substitution.

11.18.7. Example

You can run the pegasus-kickstart executable locally to verify that it is functioning well. In the initial phase, the format of the performance data may be slightly adjusted.

$ env KICKSTART_PREJOB='/bin/usleep 250000' \\
  KICKSTART_POSTJOB='/bin/date -u' \\
  pegasus-kickstart -l xx \\$PEGASUS_HOME/bin/keg -T1 -o-
$ cat xx
<?xml version="1.0" encoding="ISO-8859-1"?>
  ...
  </statcall>
</invocation>

Please take note a few things in the above example:

The output from the postjob is appended to the output of the main job on stdout. The output could potentially be separated into different data sections through different temporary files. If you truly need the separation, request that feature.

The log file is reported with a size of zero, because the log file did indeed barely exist at the time the data structure was (re-) initialized. With regular GASS output, it will report the status of the socket file descriptor, though.

The file descriptors reported for the temporary files are from the perspective of pegasus-kickstart. Since the temporary files have the close-on-exec flag set, pegasus-kickstarts file descriptors are invisible to the job processes. Still, the ‘stdio of the job processes are connected to the temporary files.

Even this output already appears large. The output may already be too large to guarantee that the append operation on networked pipes (GASS, NFS) are atomically written.

The current format of the performance data is as follows:

11.18.8. Timeouts

Kickstart sets timeouts for the job based on the -k and -K flags. The -k flag sets the time kickstart will wait before it sends the job a SIGTERM, and the -K flag sets the time kickstart will wait after delivering a SIGTERM until it delivers a SIGKILL. The -K timeout is designed to give the job some time to write a checkpoint, which it can trigger by handling the SIGTERM. If the job runs for longer than the timeout specified using -k, then then the job exits with a non-zero exit status.

If the job has KICKSTART_SETUP, KICKSTART_PREJOB, or KICKSTART_POSTJOB, then their runtimes are included in the timeout and they will be sent SIGTERM/SIGKILL in the same manner as the main job. If KICKSTART_CLEANUP is set, then it will run regardless of whether processes from the other stages were signalled. If KICKSTART_SETUP is specified, and it runs longer than the timeout, then it will be signalled, and the other stages will be skipped.

11.18.9. Output Format

Refer to https://pegasus.isi.edu/documentation/schemas/iv-2.2/iv-2.2.html for an up-to-date description of elements and their attributes. Check with https://pegasus.isi.edu/documentation for invocation schemas with a higher version number.

11.18.10. Restrictions

There is no version for the Condor standard universe. It is simply not possible within the constraints of Condor.

Due to its very nature, pegasus-kickstart will also prove difficult to port outside the Unix environment.

Any of the pre-, main-, cleanup and postjob are unable to influence one another’s visible environment.

Do not use a Pegasus transformation with just the name null and no namespace nor version.

First Condor, and then Unix, place a limit on the length of the command line. The additional space required for the gridstart invocation may silently overflow the maximum space, and cause applications to fail. If you suspect to work with many argument, try an argument-file based approach.

A job failing with exit code 126 or 127 is indistinguishable from pegasus-kickstart failing with the same exit codes. Sometimes, careful examination of the returned data can help.

If the logfile is collected into a shared file, due to the size of the data, simultaneous appends on a shared filesystem from different machines may still mangle data. Currently, file locking is not even attempted, although all data is written atomically from the perspective of pegasus-kickstart.

The upper limit of characters of command line characters is currently not checked by pegasus-kickstart. Thus, some variable substitutions could potentially result in a command line that is larger than permissible.

If the output or error file is opened in append mode, but the application decides to truncate its output file, as in the above example by opening /dev/fd/1 inside keg, the resulting file will still be truncated. This is correct behavior, but sometimes not obvious.

11.18.11. Files

/usr/share/pegasus/schema/iv-2.2.xsd: is the suggested location of the latest XML schema describing the data on the submit host.

11.18.12. Metadata

Kickstart creates a file to which the job should write metadata “key=value” pairs. The contents of the file are inserted into the invocation record by Kickstart, and transferred with the job’s stdio. If the job is run under Pegasus, then pegasus-monitord will parse this metadata and merge it with the metadata for the job in the Pegasus workflow database. Kickstart uses the environment variable KICKSTART_METADATA to tell the job to which file it should write its metadata.

11.18.13. Environment Variables

Note: Pegasus 4.6 deprecated the “GRIDSTART” prefix for environment variables and replaced it with “KICKSTART”. The “GRIDSTART” versions of the old variables should still work.

KICKSTART_TMP: is the hightest priority to look for a temporary directory, if specified. This rather special variable was introduced to overcome some peculiarities with the FNAL cluster.
TMP: is the next hightest priority to look for a temporary directory, if specified.
TEMP: is the next priority for an environment variable denoting a temporary files directory.
TMPDIR: is next in the checklist. If none of these are found, either the stdio definition P_tmpdir is taken, or the fixed string /tmp.
KICKSTART_SETUP: contains a string that starts a job to be executed unconditionally before any other jobs, see above for a detailed description.
KICKSTART_PREJOB: contains a string that starts a job to be executed before the main job, see above for a detailed description.
KICKSTART_POSTJOB: contains a string that starts a job to be executed conditionally after the main job, see above for a detailed description.
KICKSTART_CLEANUP: contains a string that starts a job to be executed unconditionally after any of the previous jobs, see above for a detailed description.
KICKSTART_PREPEND_PATH: the value of this variable is prepended to the PATH variable seen by Kickstart and passed to the job. The modified PATH is also used to look up executables for the main job and any pre/post/setup/cleanup jobs.
KICKSTART_WRAPPER: the value of this variable is prepended to the job arguments. It can be used to wrap the task with a wrapper or launcher. For example, you can set it to “mpiexec -n 128” to run an MPI job, or you can set it to “tau_exec” to profile the job with TAU.

KICKSTART_TRACE_ALL If this variable is set, then the -Z option will trace everything, including stdio and directories. By default, stdio and directories are ignored.

KICKSTART_TRACE_CWD If this variable is set, then the -Z option will only trace files in the current working directory of the process.

KICKSTART_TRACE_MATCH: If this variable is set, then the -Z option will only trace files that match one of the patterns specified. The value of this variable should be a list of fnmatch() patterns separated by :.

KICKSTART_TRACE_IGNORE This is the inverse of KICKSTART_TRACE_MATCH. Any files matching one of the patterns will be ignored, and all other files will be traced.

KICKSTART_METADATA Kickstart passes this environment variable to the job. The value of the variable is the path to the metadata file to which the job should write its metadata. See the METADATA section for more information.

11.18.14. History

As you may have noticed, pegasus-kickstart had the name kickstart in previous incantations. We are slowly moving to the new name to avoid clashes in a larger OS installation setting. However, there is no pertinent need to change the internal name, too, as no name clashes are expected.

11.18.15. Notes

sha256 implementation by Dr Brian Gladman, Worcester, UK. Please see the source code at https://github.com/pegasus-isi for the full copyright notice.