Submitting a Job

The condor_submit command takes a job description file as input and submits the job to HTCondor. In the submit description file, HTCondor finds everything it needs to know about the job. Items such as the name of the executable to run, the initial working directory, and command-line arguments to the program all go into the submit description file. condor_submit creates a job ClassAd based upon the information, and HTCondor works toward running the job.

It is easy to submit multiple runs of a program to HTCondor with a single submit description file. To run the same program many times with different input data sets, arrange the data files accordingly so that each run reads its own input, and each run writes its own output. Each individual run may have its own initial working directory, files mapped for stdin, stdout, stderr, command-line arguments, and shell environment.

The condor_submit manual page contains a complete and full description of how to use condor_submit. It also includes descriptions of all of the many commands that may be placed into a submit description file. In addition, the index lists entries for each command under the heading of Submit Commands.

Sample submit description files

In addition to the examples of submit description files given here, there are more in the condor_submit manual page.

Example 1

Example 1 is one of the simplest submit description files possible. It queues the program myexe for execution somewhere in the pool. As this submit description file does not request a specific operating system to run on, HTCondor will use the default, which is to run the job on a machine which has the same architecture and operating system it was submitted from.

Before submitting a job to HTCondor, it is a good idea to test it first locally, by running it from a command shell. This example job might look like this when run from the shell prompt.

$ ./myexe SomeArgument

The corresponding submit description file might look like the following

# Example 1
# Simple HTCondor submit description file
# Everything with a leading # is a comment

executable   = myexe
arguments    = SomeArgument

output       = outputfile
error        = errorfile
log          = myexe.log

request_cpus   = 1
request_memory = 1024
request_disk   = 10240

should_transfer_files = yes

queue

The standard output for this job will go to the file outputfile, as specified by the output command. Likewise, the standard error output will go to errorfile.

HTCondor will append events about the job to a log file wih the requested name``myexe.log``. When the job finishes, its exit conditions and resource usage will also be noted in the log file. This file’s contents are an excellent way to figure out what happened to jobs.

HTCondor needs to know how many machine resources to allocate to this job. The request_ lines describe that this job should be allocated 1 cpu core, 1024 megabytes of memory and 10240 kilobytes of scratch disk space.

Finally, the queue statement tells HTCondor that you are done describing the job, and to send it to the queue for processing.

Example 2

The submit description file for Example 2 queues 150 runs of program foo. This job requires machines which have at least 4 GiB of physical memory, one cpu core and 16 Gb of scratch disk. Each of the 150 runs of the program is given its own HTCondor process number, starting with 0. $(Process) is expanded by HTCondor to the actual number used by each instance of the job. So, stdout, and stderr will refer to out.0, and err.0 for the first run of the program, out.1, and err.1 for the second run of the program, and so forth. A log file containing entries about when and where HTCondor runs, checkpoints, and migrates processes for all the 150 queued programs will be written into the single file foo.log. If there are 150 or more available slots in your pool, all 150 instances might be run at the same time, otherwise, HTCondor will run as many as it can concurrently.

Each instance of this program works on one input file. The name of this input file is passed to the program as the only argument. We prepare 150 copies of this input file in the current directory, and name them input_file.0, input_file.1 … up to input_file.149. Using transfer_input_files, we tell HTCondor which input file to send to each instance of the program.

# Example 2: Show off some fancy features,
# including the use of pre-defined macros.

executable     = foo
arguments      = input_file.$(Process)

request_memory = 4096
request_cpus   = 1
request_disk   = 16383

error   = err.$(Process)
output  = out.$(Process)
log     = foo.log

should_transfer_files = yes
transfer_input_files = input_file.$(Process)

# submit 150 instances of this job
queue 150

Submitting many similar jobs with one queue command

A wide variety of job submissions can be specified with extra information to the queue submit command. This flexibility eliminates the need for a job wrapper or Perl script for many submissions.

The form of the queue command defines variables and expands values, identifying a set of jobs. Square brackets identify an optional item.

queue [<int expr> ]

queue [<int expr> ] [<varname> ] in [slice ] <list of items>

queue [<int expr> ] [<varname> ] matching [files | dirs ] [slice ] <list of items with file globbing>

queue [<int expr> ] [<list of varnames> ] from [slice ] <file name> | <list of items>

All optional items have defaults:

  • If <int expr> is not specified, it defaults to the value 1.

  • If <varname> or <list of varnames> is not specified, it defaults to the single variable called ITEM.

  • If slice is not specified, it defaults to all elements within the list. This is the Python slice [::], with a step value of 1.

  • If neither files nor dirs is specified in a specification using the from key word, then both files and directories are considered when globbing.

The list of items uses syntax in one of two forms. One form is a comma and/or space separated list; the items are placed on the same line as the queue command. The second form separates items by placing each list item on its own line, and delimits the list with parentheses. The opening parenthesis goes on the same line as the queue command. The closing parenthesis goes on its own line. The queue command specified with the key word from will always use the second form of this syntax. Example 3 below uses this second form of syntax. Finally, the key word from accepts a shell command in place of file name, followed by a pipe | (example 4).

The optional slice specifies a subset of the list of items using the Python syntax for a slice. Negative step values are not permitted.

Here are a set of examples.

Example 1

transfer_input_files = $(filename)
arguments            = -infile $(filename)
queue filename matching files *.dat

The use of file globbing expands the list of items to be all files in the current directory that end in .dat. Only files, and not directories are considered due to the specification of files. One job is queued for each file in the list of items. For this example, assume that the three files initial.dat, middle.dat, and ending.dat form the list of items after expansion; macro filename is assigned the value of one of these file names for each job queued. That macro value is then substituted into the arguments and transfer_input_files commands. The queue command expands to

transfer_input_files = initial.dat
arguments            = -infile initial.dat
queue
transfer_input_files = middle.dat
arguments            = -infile middle.dat
queue
transfer_input_files = ending.dat
arguments            = -infile ending.dat
queue

Example 2

queue 1 input in A, B, C

Variable input is set to each of the 3 items in the list, and one job is queued for each. For this example the queue command expands to

input = A
queue
input = B
queue
input = C
queue

Example 3

queue input, arguments from (
  file1, -a -b 26
  file2, -c -d 92
)

Using the from form of the options, each of the two variables specified is given a value from the list of items. For this example the queue command expands to

input = file1
arguments = -a -b 26
queue
input = file2
arguments = -c -d 92
queue

Example 4

queue from seq 7 9 |

feeds the list of items to queue with the output of seq 7 9:

item = 7
queue
item = 8
queue
item = 9
queue

Variables in the Submit Description File

There are automatic variables for use within the submit description file.

$(Cluster) or $(ClusterId)

Each set of queued jobs from a specific user, submitted from a single submit host, sharing an executable have the same value of $(Cluster) or $(ClusterId). The first cluster of jobs are assigned to cluster 0, and the value is incremented by one for each new cluster of jobs. $(Cluster) or $(ClusterId) will have the same value as the job ClassAd attribute ClusterId.

$(Process) or $(ProcId)

Within a cluster of jobs, each takes on its own unique $(Process) or $(ProcId) value. The first job has value 0. $(Process) or $(ProcId) will have the same value as the job ClassAd attribute ProcId.

$$(a_machine_classad_attribue)

When the machine is matched to this job for it to run on, any dollar-dollar expressions are looked up from the machine ad, and then expanded. This lets you put the value of some machine ad attribute into your job. For example, if you to pass the actual amount of memory a slot has provisioned as an argument to the job, you could add arguments = --mem $$(Memory)

arguments = --mem $$(Memory)

or, if you wanted to put the name of the machine the job ran on into the output file name, you could add

$$([ an_evaluated_classad_expression ])

This dollar-dollar-bracket syntax is useful when you need to perform some math on a value before passing it to your job. For example, if want to pass 90% of the allocated memory as an argument to your job, the submit file can have

and when the job is matched to a machine, condor will evaluate this expression in the context of both the job and machine ad

$(ARCH)

The Architecture that HTCondor is running on, or the ARCH variable in the config file. Example might be X86_64.

$(OPSYS) $(OPSYSVER) $(OPSYSANDVER) $(OPSYSMAJORVER)

These submit file macros are availle at submit time, and mimic the classad attributes of the same names.

$(SUBMIT_FILE)

The name of the submit_file as passed to the condor_submit command.

$(SUBMIT_TIME)

The Unix epoch time submit was run. Note, this may be useful for naming output files.

$(Year) $(Month) $(Day)

These integer values are derived from the $(SUBMIT_FILE) macro above.

$(Item)

The default name of the variable when no <varname> is provided in a queue command.

$(ItemIndex)

Represents an index within a list of items. When no slice is specified, the first $(ItemIndex) is 0. When a slice is specified, $(ItemIndex) is the index of the item within the original list.

$(Step)

For the <int expr> specified, $(Step) counts, starting at 0.

$(Row)

When a list of items is specified by placing each item on its own line in the submit description file, $(Row) identifies which line the item is on. The first item (first line of the list) is $(Row) 0. The second item (second line of the list) is $(Row) 1. When a list of items are specified with all items on the same line, $(Row) is the same as $(ItemIndex).

Here is an example of a queue command for which the values of these automatic variables are identified.

Example 1

This example queues six jobs.

queue 3 in (A, B)
  • $(Process) takes on the six values 0, 1, 2, 3, 4, and 5.

  • Because there is no specification for the <varname> within this queue command, variable $(Item) is defined. It has the value A for the first three jobs queued, and it has the value B for the second three jobs queued.

  • $(Step) takes on the three values 0, 1, and 2 for the three jobs with $(Item)=A, and it takes on the same three values 0, 1, and 2 for the three jobs with $(Item)=B.

  • $(ItemIndex) is 0 for all three jobs with $(Item)=A, and it is 1 for all three jobs with $(Item)=B.

  • $(Row) has the same value as $(ItemIndex) for this example.

Including Submit Commands Defined Elsewhere

Externally defined submit commands can be incorporated into the submit description file using the syntax

include : <what-to-include>

The <what-to-include> specification may specify a single file, where the contents of the file will be incorporated into the submit description file at the point within the file where the include is. Or, <what-to-include> may cause a program to be executed, where the output of the program is incorporated into the submit description file. The specification of <what-to-include> has the bar character (|) following the name of the program to be executed.

The include key word is case insensitive. There are no requirements for white space characters surrounding the colon character.

Included submit commands may contain further nested include specifications, which are also parsed, evaluated, and incorporated. Levels of nesting on included files are limited, such that infinite nesting is discovered and thwarted, while still permitting nesting.

Consider the example

include : ./list-infiles.sh |

In this example, the bar character at the end of the line causes the script list-infiles.sh to be invoked, and the output of the script is parsed and incorporated into the submit description file. If this bash script is in the PATH when submit is run, and contains

#!/bin/sh

echo "transfer_input_files = `ls -m infiles/*.dat`"
exit 0

then the output of this script has specified the set of input files to transfer to the execute host. For example, if directory infiles contains the three files A.dat, B.dat, and C.dat, then the submit command

transfer_input_files = infiles/A.dat, infiles/B.dat, infiles/C.dat

is incorporated into the submit description file.

Using Conditionals in the Submit Description File

Conditional if/else semantics are available in a limited form. The syntax:

if <simple condition>
   <statement>
   . . .
   <statement>
else
   <statement>
   . . .
   <statement>
endif

An else key word and statements are not required, such that simple if semantics are implemented. The <simple condition> does not permit compound conditions. It optionally contains the exclamation point character (!) to represent the not operation, followed by

  • the defined keyword followed by the name of a variable. If the variable is defined, the statement(s) are incorporated into the expanded input. If the variable is not defined, the statement(s) are not incorporated into the expanded input. As an example,

    if defined MY_UNDEFINED_VARIABLE
       X = 12
    else
       X = -1
    endif
    

    results in X = -1, when MY_UNDEFINED_VARIABLE is not yet defined.

  • the version keyword, representing the version number of of the daemon or tool currently reading this conditional. This keyword is followed by an HTCondor version number. That version number can be of the form x.y.z or x.y. The version of the daemon or tool is compared to the specified version number. The comparison operators are

    • == for equality. Current version 8.2.3 is equal to 8.2.

    • >= to see if the current version number is greater than or equal to. Current version 8.2.3 is greater than 8.2.2, and current version 8.2.3 is greater than or equal to 8.2.

    • <= to see if the current version number is less than or equal to. Current version 8.2.0 is less than 8.2.2, and current version 8.2.3 is less than or equal to 8.2.

    As an example,

    if version >= 8.1.6
       DO_X = True
    else
       DO_Y = True
    endif
    

    results in defining DO_X as True if the current version of the daemon or tool reading this if statement is 8.1.6 or a more recent version.

  • True or yes or the value 1. The statement(s) are incorporated.

  • False or no or the value 0 The statement(s) are not incorporated.

  • $(<variable>) may be used where the immediately evaluated value is a simple boolean value. A value that evaluates to the empty string is considered False, otherwise a value that does not evaluate to a simple boolean value is a syntax error.

The syntax

if <simple condition>
   <statement>
   . . .
   <statement>
elif <simple condition>
   <statement>
   . . .
   <statement>
endif

is the same as syntax

if <simple condition>
   <statement>
   . . .
   <statement>
else
   if <simple condition>
      <statement>
      . . .
      <statement>
   endif
endif

Here is an example use of a conditional in the submit description file. A portion of the sample.sub submit description file uses the if/else syntax to define command line arguments in one of two ways:

if defined X
  arguments = -n $(X)
else
  arguments = -n 1 -debug
endif

Submit variable X is defined on the condor_submit command line with

$ condor_submit  X=3  sample.sub

This command line incorporates the submit command X = 3 into the submission before parsing the submit description file. For this submission, the command line arguments of the submitted job become

arguments = -n 3

If the job were instead submitted with the command line

$ condor_submit  sample.sub

then the command line arguments of the submitted job become

arguments = -n 1 -debug

Function Macros in the Submit Description File

A set of predefined functions increase flexibility. Both submit description files and configuration files are read using the same parser, so these functions may be used in both submit description files and configuration files.

Case is significant in the function’s name, so use the same letter case as given in these definitions.

$CHOICE(index, listname) or $CHOICE(index, item1, item2, ...)

An item within the list is returned. The list is represented by a parameter name, or the list items are the parameters. The index parameter determines which item. The first item in the list is at index 0. If the index is out of bounds for the list contents, an error occurs.

$ENV(environment-variable-name[:default-value])

Evaluates to the value of environment variable environment-variable-name. If there is no environment variable with that name, Evaluates to UNDEFINED unless the optional :default-value is used; in which case it evaluates to default-value. For example,

A = $ENV(HOME)

binds A to the value of the HOME environment variable.

$F[fpduwnxbqa](filename)

One or more of the lower case letters may be combined to form the function name and thus, its functionality. Each letter operates on the filename in its own way.

  • f convert relative path to full path by prefixing the current working directory to it. This option works only in condor_submit files.

  • p refers to the entire directory portion of filename, with a trailing slash or backslash character. Whether a slash or backslash is used depends on the platform of the machine. The slash will be recognized on Linux platforms; either a slash or backslash will be recognized on Windows platforms, and the parser will use the same character specified.

  • d refers to the last portion of the directory within the path, if specified. It will have a trailing slash or backslash, as appropriate to the platform of the machine. The slash will be recognized on Linux platforms; either a slash or backslash will be recognized on Windows platforms, and the parser will use the same character specified unless u or w is used. if b is used the trailing slash or backslash will be omitted.

  • u convert path separators to Unix style slash characters

  • w convert path separators to Windows style backslash characters

  • n refers to the file name at the end of any path, but without any file name extension. As an example, the return value from $Fn(/tmp/simulate.exe) will be simulate (without the .exe extension).

  • x refers to a file name extension, with the associated period (.). As an example, the return value from $Fn(/tmp/simulate.exe) will be .exe.

  • b when combined with the d option, causes the trailing slash or backslash to be omitted. When combined with the x option, causes the leading period (.) to be omitted.

  • q causes the return value to be enclosed within quotes. Double quote marks are used unless a is also specified.

  • a When combined with the q option, causes the return value to be enclosed within single quotes.

$DIRNAME(filename) is the same as $Fp(filename)

$BASENAME(filename) is the same as $Fnx(filename)

$INT(item-to-convert) or $INT(item-to-convert, format-specifier)

Expands, evaluates, and returns a string version of item-to-convert. The format-specifier has the same syntax as a C language or Perl format specifier. If no format-specifier is specified, “%d” is used as the format specifier.

$RANDOM_CHOICE(choice1, choice2, choice3, ...)

A random choice of one of the parameters in the list of parameters is made. For example, if one of the integers 0-8 (inclusive) should be randomly chosen:

$RANDOM_CHOICE(0,1,2,3,4,5,6,7,8)
$RANDOM_INTEGER(min, max [, step])

A random integer within the range min and max, inclusive, is selected. The optional step parameter controls the stride within the range, and it defaults to the value 1. For example, to randomly chose an even integer in the range 0-8 (inclusive):

$RANDOM_INTEGER(0, 8, 2)
$REAL(item-to-convert) or $REAL(item-to-convert, format-specifier)

Expands, evaluates, and returns a string version of item-to-convert for a floating point type. The format-specifier is a C language or Perl format specifier. If no format-specifier is specified, “%16G” is used as a format specifier.

$SUBSTR(name, start-index) or $SUBSTR(name, start-index, length)

Expands name and returns a substring of it. The first character of the string is at index 0. The first character of the substring is at index start-index. If the optional length is not specified, then the substring includes characters up to the end of the string. A negative value of start-index works back from the end of the string. A negative value of length eliminates use of characters from the end of the string. Here are some examples that all assume

Name = abcdef
  • $SUBSTR(Name, 2) is cdef.

  • $SUBSTR(Name, 0, -2) is abcd.

  • $SUBSTR(Name, 1, 3) is bcd.

  • $SUBSTR(Name, -1) is f.

  • $SUBSTR(Name, 4, -3) is the empty string, as there are no characters in the substring for this request.

Here are example uses of the function macros in a submit description file. Note that these are not complete submit description files, but only the portions that promote understanding of use cases of the function macros.

Example 1

Generate a range of numerical values for a set of jobs, where values other than those given by $(Process) are desired.

MyIndex     = $(Process) + 1
initial_dir = run-$INT(MyIndex,%04d)

Assuming that there are three jobs queued, such that $(Process) becomes 0, 1, and 2, initial_dir will evaluate to the directories run-0001, run-0002, and run-0003.

Example 2

This variation on Example 1 generates a file name extension which is a 3-digit integer value.

Values     = $(Process) * 10
Extension  = $INT(Values,%03d)
input      = X.$(Extension)

Assuming that there are four jobs queued, such that $(Process) becomes 0, 1, 2, and 3, Extension will evaluate to 000, 010, 020, and 030, leading to files defined for input of X.000, X.010, X.020, and X.030.

Example 3

This example uses both the file globbing of the queue command and a macro function to specify a job input file that is within a subdirectory on the submit host, but will be placed into a single, flat directory on the execute host.

arguments            = $Fnx(FILE)
transfer_input_files = $(FILE)
queue FILE matching (
    samplerun/*.dat
)

Assume that two files that end in .dat, A.dat and B.dat, are within the directory samplerun. Macro FILE expands to samplerun/A.dat and samplerun/B.dat for the two jobs queued. The input files transferred are samplerun/A.dat and samplerun/B.dat on the submit host. The $Fnx() function macro expands to the complete file name with any leading directory specification stripped, such that the command line argument for one of the jobs will be A.dat and the command line argument for the other job will be B.dat.

About Requirements and Rank

The requirements and rank commands in the submit description file are powerful and flexible. Using them effectively requires care, and this section presents those details.

Both requirements and rank need to be specified as valid HTCondor ClassAd expressions, however, default values are set by the condor_submit program if these are not defined in the submit description file. From the condor_submit manual page and the above examples, you see that writing ClassAd expressions is intuitive, especially if you are familiar with the programming language C. There are some pretty nifty expressions you can write with ClassAds. A complete description of ClassAds and their expressions can be found in the HTCondor’s ClassAd Mechanism section.

All of the commands in the submit description file are case insensitive, except for the ClassAd attribute string values. ClassAd attribute names are case insensitive, but ClassAd string values are case preserving.

Note that the comparison operators (<, >, <=, >=, and ==) compare strings case insensitively. The special comparison operators =?= and =!= compare strings case sensitively.

A requirements or rank command in the submit description file may utilize attributes that appear in a machine or a job ClassAd. Within the submit description file (for a job) the prefix MY. (on a ClassAd attribute name) causes a reference to the job ClassAd attribute, and the prefix TARGET. causes a reference to a potential machine or matched machine ClassAd attribute.

The condor_status command displays statistics about machines within the pool. The -l option displays the machine ClassAd attributes for all machines in the HTCondor pool. The job ClassAds, if there are jobs in the queue, can be seen with the condor_q -l command. This shows all the defined attributes for current jobs in the queue.

A list of defined ClassAd attributes for job ClassAds is given in the Appendix on the Job ClassAd Attributes page. A list of defined ClassAd attributes for machine ClassAds is given in the Appendix on the Machine ClassAd Attributes page.

Rank Expression Examples

When considering the match between a job and a machine, rank is used to choose a match from among all machines that satisfy the job’s requirements and are available to the user, after accounting for the user’s priority and the machine’s rank of the job. The rank expressions, simple or complex, define a numerical value that expresses preferences.

The job’s Rank expression evaluates to one of three values. It can be UNDEFINED, ERROR, or a floating point value. If Rank evaluates to a floating point value, the best match will be the one with the largest, positive value. If no Rank is given in the submit description file, then HTCondor substitutes a default value of 0.0 when considering machines to match. If the job’s Rank of a given machine evaluates to UNDEFINED or ERROR, this same value of 0.0 is used. Therefore, the machine is still considered for a match, but has no ranking above any other.

A boolean expression evaluates to the numerical value of 1.0 if true, and 0.0 if false.

The following Rank expressions provide examples to follow.

For a job that desires the machine with the most available memory:

Rank = memory

For a job that prefers to run on a friend’s machine on Saturdays and Sundays:

Rank = ( (clockday == 0) || (clockday == 6) )
       && (machine == "friend.cs.wisc.edu")

For a job that prefers to run on one of three specific machines:

Rank = (machine == "friend1.cs.wisc.edu") ||
       (machine == "friend2.cs.wisc.edu") ||
       (machine == "friend3.cs.wisc.edu")

For a job that wants the machine with the best floating point performance (on Linpack benchmarks):

Rank = kflops

This particular example highlights a difficulty with Rank expression evaluation as currently defined. While all machines have floating point processing ability, not all machines will have the kflops attribute defined. For machines where this attribute is not defined, Rank will evaluate to the value UNDEFINED, and HTCondor will use a default rank of the machine of 0.0. The Rank attribute will only rank machines where the attribute is defined. Therefore, the machine with the highest floating point performance may not be the one given the highest rank.

So, it is wise when writing a Rank expression to check if the expression’s evaluation will lead to the expected resulting ranking of machines. This can be accomplished using the condor_status command with the -constraint argument. This allows the user to see a list of machines that fit a constraint. To see which machines in the pool have kflops defined, use

$ condor_status -constraint kflops

Alternatively, to see a list of machines where kflops is not defined, use

$ condor_status -constraint "kflops=?=undefined"

For a job that prefers specific machines in a specific order:

Rank = ((machine == "friend1.cs.wisc.edu")*3) +
       ((machine == "friend2.cs.wisc.edu")*2) +
        (machine == "friend3.cs.wisc.edu")

If the machine being ranked is friend1.cs.wisc.edu, then the expression

(machine == "friend1.cs.wisc.edu")

is true, and gives the value 1.0. The expressions

(machine == "friend2.cs.wisc.edu")

and

(machine == "friend3.cs.wisc.edu")

are false, and give the value 0.0. Therefore, Rank evaluates to the value 3.0. In this way, machine friend1.cs.wisc.edu is ranked higher than machine friend2.cs.wisc.edu, machine friend2.cs.wisc.edu is ranked higher than machine friend3.cs.wisc.edu, and all three of these machines are ranked higher than others.

Submitting Jobs Using a Shared File System

If vanilla, java, or parallel universe jobs are submitted without using the File Transfer mechanism, HTCondor must use a shared file system to access input and output files. In this case, the job must be able to access the data files from any machine on which it could potentially run.

As an example, suppose a job is submitted from blackbird.cs.wisc.edu, and the job requires a particular data file called /u/p/s/psilord/data.txt. If the job were to run on cardinal.cs.wisc.edu, the file /u/p/s/psilord/data.txt must be available through either NFS or AFS for the job to run correctly.

HTCondor allows users to ensure their jobs have access to the right shared files by using the FileSystemDomain and UidDomain machine ClassAd attributes. These attributes specify which machines have access to the same shared file systems. All machines that mount the same shared directories in the same locations are considered to belong to the same file system domain. Similarly, all machines that share the same user information (in particular, the same UID, which is important for file systems like NFS) are considered part of the same UID domain.

The default configuration for HTCondor places each machine in its own UID domain and file system domain, using the full host name of the machine as the name of the domains. So, if a pool does have access to a shared file system, the pool administrator must correctly configure HTCondor such that all the machines mounting the same files have the same FileSystemDomain configuration. Similarly, all machines that share common user information must be configured to have the same UidDomain configuration.

When a job relies on a shared file system, HTCondor uses the requirements expression to ensure that the job runs on a machine in the correct UidDomain and FileSystemDomain. In this case, the default requirements expression specifies that the job must run on a machine with the same UidDomain and FileSystemDomain as the machine from which the job is submitted. This default is almost always correct. However, in a pool spanning multiple UidDomains and/or FileSystemDomains, the user may need to specify a different requirements expression to have the job run on the correct machines.

For example, imagine a pool made up of both desktop workstations and a dedicated compute cluster. Most of the pool, including the compute cluster, has access to a shared file system, but some of the desktop machines do not. In this case, the administrators would probably define the FileSystemDomain to be cs.wisc.edu for all the machines that mounted the shared files, and to the full host name for each machine that did not. An example is jimi.cs.wisc.edu.

In this example, a user wants to submit vanilla universe jobs from her own desktop machine (jimi.cs.wisc.edu) which does not mount the shared file system (and is therefore in its own file system domain, in its own world). But, she wants the jobs to be able to run on more than just her own machine (in particular, the compute cluster), so she puts the program and input files onto the shared file system. When she submits the jobs, she needs to tell HTCondor to send them to machines that have access to that shared data, so she specifies a different requirements expression than the default:

Requirements = TARGET.UidDomain == "cs.wisc.edu" && \
               TARGET.FileSystemDomain == "cs.wisc.edu"

WARNING: If there is no shared file system, or the HTCondor pool administrator does not configure the FileSystemDomain setting correctly (the default is that each machine in a pool is in its own file system and UID domain), a user submits a job that cannot use remote system calls (for example, a vanilla universe job), and the user does not enable HTCondor’s File Transfer mechanism, the job will only run on the machine from which it was submitted.

Jobs That Require Credentials

If the HTCondor pool administrator has configured the submit machine with one or more credential monitors, jobs submitted on that machine may automatically be provided with credentials and/or it may be possible for users to request and obtain credentials for their jobs.

Suppose the administrator has configured the submit machine such that users may obtain credentials from a storage service called “CloudBoxDrive.” A job that needs credentials from CloudBoxDrive should contain the submit command

use_oauth_services = cloudboxdrive

Upon submitting this job for the first time, the user will be directed to a webpage hosted on the submit machine which will guide the user through the process of obtaining a CloudBoxDrive credential. The credential is then stored securely on the submit machine. (Note: depending on which credential monitor is used, the original job may have to be re-submitted at this point.) (Also note that at no point is the user’s password stored on the submit machine.) Once a credential is stored on the submit machine, as long as it remains valid, it is transferred securely to all subsequently submitted jobs that contain use_oauth_services = cloudboxdrive.

When a job that contains credentials runs on an execute machine, the job’s executable will have the environment variable _CONDOR_CREDS set, which points to the location of all of the credentials inside the job’s sandbox. For credentials obtained via the use_oauth_services submit file command, the “access token” is stored under $_CONDOR_CREDS in a JSON-encoded file named with the name of the service provider and with the extension .use. For the “CloudBoxDrive” example, the access token would be located in $_CONDOR_CREDS/cloudboxdrive.use.

The HTCondor file transfer mechanism has built-in plugins for using user-obtained credentials to transfer files from some specific storage providers, see File Transfer Using a URL.

Some credential providers may require the user to provide a description of the permissions (often called “scopes”) a user needs for a specific credential. Credential permission scoping is possible using the <service name>_oauth_permissions submit file command. For example, suppose our CloudBoxDrive service has a /public directory, and the documentation for the service said that users must specify a read:<directory> scope in order to be able to read data out of <directory>. The submit file would need to contain

use_oauth_services = cloudboxdrive
cloudboxdrive_oauth_permissions = read:/public

Some credential providers may also require the user to provide the name of the resource (or “audience”) that a credential should allow access to. Resource naming is done using the <service name>_oauth_resource submit file command. For example, if our CloudBoxDrive service has servers located at some unversities and the documentation says that we should pick one near us and specify it as the audience, the submit file might look like

use_oauth_services = cloudboxdrive
cloudboxdrive_oauth_permissions = read:/public
cloudboxdrive_oauth_resource = https://cloudboxdrive.myuni.edu

It is possible for a single job to request and/or use credentials from multiple services by listing each service in the use_oauth_services command. Suppose the nearby university has a SciTokens service that provides credentials to access the localstorage.myuni.edu machine, and the HTCondor pool administrator has configured the submit machine to allow users to obtain credentials from this service, and that a user has write access to the /foo directory on the storage machine. A submit file that would result in a job that contains credentials that can read from CloudBoxDrive and write to the local university storage might look like

use_oauth_services = cloudboxdrive, myuni

cloudboxdrive_oauth_permissions = read:/public
cloudboxdrive_oauth_resource = https://cloudboxdrive.myuni.edu

myuni_oauth_permissions = write:/foo
myuni_oauth_resource = https://localstorage.myuni.edu

A single job can also request multiple credentials from the same service provider by affixing handles to the <service>_oauth_permissions and (if necessary) <service>_oauth_resource commands. For example, if a user wants separate read and write credentials for CloudBoxDrive

use_oauth_services = cloudboxdrive
cloudboxdrive_oauth_permissions_readpublic = read:/public
cloudboxdrive_oauth_permissions_writeprivate = write:/private

cloudboxdrive_oauth_resource_readpublic = https://cloudboxdrive.myuni.edu
cloudboxdrive_oauth_resource_writeprivate = https://cloudboxdrive.myuni.edu

Submitting the above would result in a job with respective access tokens located in $_CONDOR_CREDS/cloudboxdrive_readpublic.use and $_CONDOR_CREDS/cloudboxdrive_writeprivate.use.

Note that the permissions and resource settings for each handle (and for no handle) are stored separately from the job so multiple jobs from the same user running at the same time or for a period of time consecutively may not use a different set of permissions and resource settings for the same service and handle. If that is attempted, a new job submission will fail with instructions on how to resolve the conflict, but the safest thing is to choose a unique handle.

If a service provider does not require permissions or resources to be specified, a user can still request multiple credentials by affixing handles to <service>_oauth_permissions commands with empty values

use_oauth_services = cloudboxdrive
cloudboxdrive_oauth_permissions_personal =
cloudboxdrive_oauth_permissions_public =

Jobs That Require GPUs

A job that needs GPUs to run identifies the number of GPUs needed in the submit description file by adding the submit command

request_GPUs = <n>

where <n> is replaced by the integer quantity of GPUs required for the job. For example, a job that needs 1 GPU uses

request_GPUs = 1

Because there are different capabilities among GPUs, the job might need to further qualify which GPU of available ones is required. Do this by specifying or adding a clause to an existing Requirements submit command. As an example, assume that the job needs a speed and capacity of a CUDA GPU that meets or exceeds the value 1.2. In the submit description file, place

request_GPUs = 1
requirements = (CUDACapability >= 1.2) && $(requirements:True)

Access to GPU resources by an HTCondor job needs special configuration of the machines that offer GPUs. Details of how to set up the configuration are in the Policy Configuration for Execute Hosts and for Submit Hosts section.

Interactive Jobs

An interactive job is a Condor job that is provisioned and scheduled like any other vanilla universe Condor job onto an execute machine within the pool. The result of a running interactive job is a shell prompt issued on the execute machine where the job runs. The user that submitted the interactive job may then use the shell as desired, perhaps to interactively run an instance of what is to become a Condor job. This might aid in checking that the set up and execution environment are correct, or it might provide information on the RAM or disk space needed. This job (shell) continues until the user logs out or any other policy implementation causes the job to stop running. A useful feature of the interactive job is that the users and jobs are accounted for within Condor’s scheduling and priority system.

Neither the submit nor the execute host for interactive jobs may be on Windows platforms.

The current working directory of the shell will be the initial working directory of the running job. The shell type will be the default for the user that submits the job. At the shell prompt, X11 forwarding is enabled.

Each interactive job will have a job ClassAd attribute of

InteractiveJob = True

Submission of an interactive job specifies the option -interactive on the condor_submit command line.

A submit description file may be specified for this interactive job. Within this submit description file, a specification of these 5 commands will be either ignored or altered:

  1. executable

  2. transfer_executable

  3. arguments

  4. universe . The interactive job is a vanilla universe job.

  5. queue <n>. In this case the value of <n> is ignored; exactly one interactive job is queued.

The submit description file may specify anything else needed for the interactive job, such as files to transfer.

If no submit description file is specified for the job, a default one is utilized as identified by the value of the configuration variable INTERACTIVE_SUBMIT_FILE .

Here are examples of situations where interactive jobs may be of benefit.

  • An application that cannot be batch processed might be run as an interactive job. Where input or output cannot be captured in a file and the executable may not be modified, the interactive nature of the job may still be run on a pool machine, and within the purview of Condor.

  • A pool machine with specialized hardware that requires interactive handling can be scheduled with an interactive job that utilizes the hardware.

  • The debugging and set up of complex jobs or environments may benefit from an interactive session. This interactive session provides the opportunity to run scripts or applications, and as errors are identified, they can be corrected on the spot.

  • Development may have an interactive nature, and proceed more quickly when done on a pool machine. It may also be that the development platforms required reside within Condor’s purview as execute hosts.

Submitting Lots of Jobs

When submitting a lot of jobs with a single submit file, you can dramatically speed up submission and reduce the load on the condor_schedd by submitting the jobs as a late materialization job factory.

A submission of this form sends a single ClassAd, called the Cluster ad, to the condor_schedd, as well as instructions to create the individual jobs as variations on that Cluster ad. These instructions are sent as a submit digest and optional itemdata. The submit digest is the submit file stripped down to just the statements that vary between jobs. The itemdata is the arguments to the Queue statement when the arguments are more than just a count of jobs.

The condor_schedd will use the submit digest and the itemdata to create the individual job ClassAds when they are needed. Materialization is controlled by two values stored in the Cluster classad, and by optional limits configured in the condor_schedd.

The max_idle limit specifies the maximum number of non-running jobs that should be materialized in the condor_schedd at any one time. One or more jobs will materialize whenever a job enters the Run state and the number of non-running jobs that are still in the condor_schedd is less than this limit. This limit is stored in the Cluster ad in the JobMaterializeMaxIdle attribute.

The max_materialize limit specifies an overall limit on the number of jobs that can be materialized in the condor_schedd at any one time. One or more jobs will materialize when a job leaves the condor_schedd and the number of materialized jobs remaining is less than this limit. This limit is stored in the Cluster ad in the JobMaterializeLimit attribute.

Late materialization can be used as a way for a user to submit millions of jobs without hitting the MAX_JOBS_PER_OWNER or MAX_JOBS_PER_SUBMISSION limits in the condor_schedd, since the condor_schedd will enforce these limits by applying them to the max_materialize and max_idle values specified in the Cluster ad.

To give an example, the following submit file:

executable     = foo
arguments      = input_file.$(Process)

request_memory = 4096
request_cpus   = 1
request_disk   = 16383

error   = err.$(Process)
output  = out.$(Process)
log     = foo.log

should_transfer_files = yes
transfer_input_files = input_file.$(Process)

# submit as a factory with an idle jobs limit
max_idle = 100

# submit 15,000 instances of this job
queue 15*1000

When submitted as a late materialization factory, the submit digest for this factory will contain only the submit statments that vary between jobs, and the collapsed queue statement like this:

arguments = input_file.$(Process)
error = err.$(Process)
output = out.$(Process)
transfer_input_files = input_file.$(Process)

queue 15000

Materialization log events

When a Late Materialization job factory is submitted to the condor_schedd, a Cluster submitted event will be written to the UserLog of the Cluster ad. This will be the same log file used by the first job materialized by the factory. To avoid confustion, it is recommended that you use the same log file for all jobs in the factory.

When the Late Materialization job factory is removed from the condor_schedd, a Cluster removed event will be written to the UserLog of the Cluster ad. This event will indicate how many jobs were materialized before the factory was removed.

If Late Materialization of jobs is paused due to an error in materialization or because condor_hold was used to hold the cluster id, a Job Materialization Paused event will be written to the UserLog of the Cluster ad. This event will indicate the reason for the pause.

When condor_release is used to release the the cluster id of a Late Materialization job factory, and materialization was paused because of a previous use of condor_hold, a Job Materialization Resumed event will be written to the UserLog of the Cluster ad.

Limitations

Currently, not all features of condor_submit will work with late materialization. The following limitations apply:

  • Only a single Queue statement is allowed, lines from the submit file after the first Queue statement will be ignored.

  • the $RANDOM_INTEGER and $RANDOM_CHOICE macro functions will expand at submit time to produce the Cluster ad, but these macro functions will not be included in the submit digest and so will have the same value for all jobs.

  • Spooling of input files does not work with late materialization.

  • SUBMIT_REQUIREMENT_* and JOB_TRANSFORM_* configuration parameters in the condor_schedd are applied to jobs as they are materialized, but not to the Cluster ad as it is submitted. So a SUBMIT_REQUIREMENT might not fail at submit time, causing the user to think that they had met the submit requirements when in fact the jobs would fail to materialize at some time in the future. This can be confusing because a factory that has no materialized jobs is not visible in the normal condor_q output. The only way to see late materialization job factories is to use the -factory option with condor_q

Displaying the Factory

condor_q can be use to show late materialization job factories in the condor_schedd by using the -factory option.

> condor_q -factory
-- Schedd: submit.example.org : <192.168.101.101:9618?... @ 12/01/20 13:35:00
ID     OWNER          SUBMITTED  LIMIT PRESNT   RUN    IDLE   HOLD NEXTID MODE DIGEST
77.    bob         12/01  13:30  15000    130     30     80     20   1230      /var/lib/condor/spool/77/condor_submit.77.digest

The factory above shows that 30 jobs are currently running, 80 are idle, 20 are held and that the next job to materialize will be job 77.1230. The total of Idle + Held jobs is 100, which is equal to the max_idle value specified in the submit file.

The path to the submit digest file is shown. This file is used to reload the factory when the condor_schedd is restarted. If the factory is unable to materialize jobs because of an error, the MODE field will show Held or Errs to indicate there is a problem. Errs indicates a problem reloading the factory, Held indicates a problem materializing jobs.

In case of a factory problem, use condor_q -factory -long to see the the factory information and the JobMaterializePauseReason attribute.

Removing a Factory

The Late materialization job factory will be remove from the schedd automatically once all of the jobs have materialized and completed. To remove the factory without first completing all of the jobs use condor_rm with the ClusterId of the factory as the argument.

Editing a Factory

The submit digest for a Late Materialization job factory cannot be changed after submission, but the Cluster ad for the factory can be edited using condor_qedit. Any condor_qedit command that has the ClusterId as a edit target will edit all currently materialized jobs, as well as editing the Cluster ad so that all jobs that materialize in the future will also be edited.