Advanced tutorial

This tutorial demonstrates more detailed functions and tools of JUBE. If you want a basic overview you should read the general JUBE tutorial first.

Schema validation

To validate your YAML based input files you can use schema validation. You can find jube.json in the contrib/schema folder.

To validate your XML based input files you can use DTD or schema validation. You can find jube.dtd, jube.xsd and jube.rnc in the contrib/schema folder. You have to add these schema information to your input files which you want to validate.

DTD usage:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE jube SYSTEM "<jube.dtd path>">
<jube>
...

Schema usage:

<?xml version="1.0" encoding="UTF-8"?>
<jube xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   xsi:noNamespaceSchemaLocation="<jube.xsd path>">
...

RELAX NG Compact Syntax (RNC for emacs nxml-mode) usage:

In order to use the provided rnc schema file schema/jube.rnc in emacs open an xml file and use C-c C-s C-f or M-x rng-set-schema-file-and-validate to choose the rnc file. You can also use M-x customize-variable rng-schema-locating-files after you loaded nxml-mode to customize the default search paths to include jube.rnc. After successful parsing emacs offers to automatically create a schema.xml file which looks like

<?xml version="1.0"?>
<locatingRules xmlns="http://thaiopensource.com/ns/locating-rules/1.0">
  <uri resource="jube-file.xml" uri="../schema/jube.rnc"/>
</locatingRules>

The next time you open the same xml file emacs will find the correct rnc for the validation based on schema.xml.

Example validation tools:

• eclipse (using DTD or schema)

• emacs (using RELAX NG)

• xmllint:

  • For validation (using the DTD):

    >>> xmllint --noout --valid <xml input file>
    

  • For validation (using the DTD and Schema):

    >>> xmllint --noout --valid --schema <schema file> <xml input file>
    

Scripting parameter

In some cases it is needed to create a parameter which is based on the value of another parameter. In this case you can use a scripting parameter.

The files used for this example can be found inside examples/scripting_parameter.

The input file scripting_parameter.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="scripting_parameter" outpath="bench_run">
    <comment>A scripting parameter example</comment>
    
    <!-- Configuration -->
    <parameterset name="param_set">
      <!-- Normal template -->
      <parameter name="number" type="int">1,2,4</parameter>
      <!-- A template created by a scripting parameter-->
      <parameter name="additional_number" mode="python" type="int">
        ",".join(str(a*${number}) for a in [1,2])
      </parameter>
      <!-- A scripting parameter -->
      <parameter name="number_mult" mode="python" type="float">
        ${number}*${additional_number}
      </parameter>
      <!-- Reuse another parameter -->
      <parameter name="text">Number: $number</parameter>
    </parameterset>
    
    <!-- Operation -->
    <step name="operation">
      <use>param_set</use> <!-- use existing parameterset -->
      <!-- shell commands -->
      <do>echo "number: $number, additional_number: $additional_number"</do>
      <do>echo "number_mult: $number_mult, text: $text"</do>
    </step>    
  </benchmark>
</jube>

The input file scripting_parameter.yaml:

name: scripting_parameter
outpath: bench_run
comment: A scripting parameter example

#Configuration
parameterset:
  name: param_set
  parameter:
    #Normal template
    - {name: number, type: int, _: "1,2,4"} 
    #A template created by a scripting parameter
    - {name: additional_number, mode: python, type: int, _: '",".join(str(a*${number}) for a in [1,2])'}
    #A scripting parameter
    - {name: number_mult, mode: python, type: float, _: "${number}*${additional_number}"}
    #Reuse another parameter
    - {name: text, _: "Number: $number"}

#Operation
step:
  name: operation
  use: param_set #use existing parameterset
  do:
    - 'echo "number: $number, additional_number: $additional_number"' 
    - 'echo "number_mult: $number_mult, text: $text"'

In this example we see four different parameters.

• number is a normal template which will be expanded to three different workpackages.

• additional_number is a scripting parameter which creates a new template and bases on number. The mode is set to the scripting language (python, perl and shell are allowed). The additional type is optional and declares the result type after evaluating the expression. The type is only used by the sort algorithm in the result step. It is not possible to create a template of different scripting parameters. Because of this second template we will get six different workpackages.

• number_mult is a small calculation. You can use any other existing parameters (which are used inside the same step).

• text is a normal parameter which uses the content of another parameter. For a simple concatenation parameter you do not need a scripting parameter.

For this example we will find the following output inside the run.log-file:

====== operation ======
>>> echo "number: 1, additional_number: 1"
>>> echo "number_mult: 1, text: Number: 1"
====== operation ======
>>> echo "number: 1, additional_number: 2"
>>> echo "number_mult: 2, text: Number: 1"
====== operation ======
>>> echo "number: 2, additional_number: 2"
>>> echo "number_mult: 4, text: Number: 2"
====== operation ======
>>> echo "number: 2, additional_number: 4"
>>> echo "number_mult: 8, text: Number: 2"
====== operation ======
>>> echo "number: 4, additional_number: 4"
>>> echo "number_mult: 16, text: Number: 4"
====== operation ======
>>> echo "number: 4, additional_number: 8"
>>> echo "number_mult: 32, text: Number: 4"

Implicit Perl or Python scripting inside the <do> or any other position is not possible. If you want to use some scripting expressions you have to create a new parameter.

Scripting pattern

Similar to the Scripting parameter, also different patterns, or patterns and parameters can be combined. For this a scripting pattern can be created by using the mode= attribute in the same way as it is used for the Scripting parameter.

All scripting patterns are evaluated at the end of the analyse part. Each scripting pattern is evaluated once. If there are multiple matches as described in the Statistic pattern values section, only the resulting statistical pattern is available (not each individual value). Scripting pattern do not create statistic values by themselves.

In addition the default= attribute can be used to set a default pattern value, if the value can’t be found during the analysis.

The files used for this example can be found inside examples/scripting_pattern.

The input file scripting_pattern.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="scripting_pattern" outpath="bench_run">
    <comment>A scripting_pattern example</comment>

    <!-- Configuration -->
    <parameterset name="param_set">
      <parameter name="value" type="int">0,1,2</parameter>
    </parameterset>

    <!-- Operation -->
    <step name="operation">
      <use>param_set</use>
      <do>echo "$value"</do>
    </step>

    <!-- Pattern to extract -->
    <patternset name="pattern_set">
      <!-- A normal pattern -->
      <pattern name="value_pat" type="int">$jube_pat_int</pattern>
      <!-- A combination of a pattern and a parameter -->
      <pattern name="dep_pat" type="int" mode="python">$value_pat+$value</pattern>
      <!-- This pattern is not available -->
      <pattern name="missing_pat" type="int">
        pattern_not_available: $jube_pat_int
      </pattern>
      <!-- The combination will fail (create NaN) -->
      <pattern name="missing_dep_pat" type="int" mode="python">
        $missing_pat*$value
      </pattern>
      <!-- Default value for missing pattern -->
      <pattern name="missing_pat_def" type="int" default="0">
        pattern_not_available: $jube_pat_int
      </pattern>
      <!-- Combination of default value and parameter -->
      <pattern name="missing_def_dep_pat" type="int" mode="python">
        $missing_pat_def*$value
      </pattern>
    </patternset>

    <analyser name="analyse">
      <use>pattern_set</use>
      <analyse step="operation">
        <file>stdout</file>
      </analyse>
    </analyser>

    <!-- result table creation -->
    <result>
      <use>analyse</use>
      <table name="result" style="pretty">
        <column>value</column>
        <column>value_pat</column>
        <column>dep_pat</column>
        <column>missing_pat</column>
        <column>missing_dep_pat</column>
        <column>missing_pat_def</column>
        <column>missing_def_dep_pat</column>
      </table>
    </result>
  </benchmark>
</jube>

The input file scripting_pattern.yaml:

name: scripting_pattern
outpath: bench_run
comment: A scripting_pattern example

#Configuration
parameterset:
  name: param_set
  parameter: {name: value, type: int, _: "0,1,2"}

#Operation
step:
  name: operation
  use: param_set
  do: echo "$value"

#Pattern to extract
patternset:
  name: pattern_set
  pattern:
    #A normal pattern
    - {name: value_pat, type: int, _: $jube_pat_int}
    #A combination of a pattern and a parameter
    - {name: dep_pat, type: int, mode: python, _: $value_pat+$value}
    #This pattern is not available
    - {name: missing_pat, type: int, _: "pattern_not_available: $jube_pat_int"}
    #The combination will fail (create NaN)
    - {name: missing_dep_pat, type: int, mode: python, _: $missing_pat*$value}
    #Default value for missing pattern
    - {name: missing_pat_def, type: int, default: 0, _: "pattern_not_available: $jube_pat_int"}
    #Combination of default value and parameter
    - {name: missing_def_dep_pat, type: int, mode: python, _: $missing_pat_def*$value}

analyser:
  name: analyse
  use: pattern_set
  analyse:
    step: operation
    file: stdout

#result table creation
result:
  use: analyse
  table:
    name: result
    style: pretty
    column: [value,value_pat,dep_pat,missing_pat,missing_dep_pat,missing_pat_def,missing_def_dep_pat]

It will create the following output:

| value | value_pat | dep_pat | missing_pat | missing_dep_pat | missing_pat_def | missing_def_dep_pat |
|-------|-----------|---------|-------------|-----------------|-----------------|---------------------|
|     0 |         0 |       0 |             |             nan |               0 |                   0 |
|     1 |         1 |       2 |             |             nan |               0 |                   0 |
|     2 |         2 |       4 |             |             nan |               0 |                   0 |

Statistic pattern values

Normally a pattern should only match a single entry in your result files. But sometimes there are multiple similar entries (e.g. if the benchmark uses some iteration feature).

JUBE will create the statistical values first, last, min, max, avg, std, cnt and sum automatically. To use these values, the user have to specify the pattern name followed by _<statistic_option>, e.g. pattern_name_last (the pattern_name itself will always be the first match).

An example for multiple matches and the statistic values can be found in examples/statistic.

The input file statistic.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="reduce_example" outpath="bench_run">
    <comment>A result reduce example</comment>

    <!-- Regex pattern -->
    <patternset name="pattern">
      <pattern name="number_pat" type="int">$jube_pat_int</pattern>
    </patternset>
    
    <!-- Operation -->
    <step name="write_some_numbers">
      <do>echo "1 2 3 4 5 6 7 8 9 10"</do> <!-- shell command -->
    </step>
    
    <!-- Analyse -->
    <analyser name="analyse">
      <use>pattern</use> <!-- use existing patternset -->
      <analyse step="write_some_numbers">
        <file>stdout</file> <!-- file which should be scanned -->
      </analyse>
    </analyser>
    
    <!-- Create result table -->
    <result>
      <use>analyse</use> <!-- use existing analyser -->
      <table name="result" style="pretty">
        <column>number_pat</column> <!-- first match -->
        <column>number_pat_first</column> <!-- first match -->
        <column>number_pat_last</column> <!-- last match -->
        <column>number_pat_min</column> <!-- min of all matches -->
        <column>number_pat_max</column> <!-- max of all matches -->
        <column>number_pat_sum</column> <!-- sum of all matches -->
        <column>number_pat_cnt</column> <!-- number of matches -->
        <column>number_pat_avg</column> <!-- avg of all matches -->
        <column format=".2f">number_pat_std</column> <!-- std of all matches -->
      </table>
    </result>
  </benchmark>
</jube>

The input file statistic.yaml:

name: reduce_example
outpath: bench_run
comment: A result reduce example

#Regex pattern
patternset:
  name: pattern
  pattern: {name: number_pat, type: int, _: $jube_pat_int}

#Operation 
step:
  name: write_some_numbers
  do: echo "1 2 3 4 5 6 7 8 9 10" #shell command

#Analyse
analyser:
  name: analyse
  use: pattern #use existing patternset
  analyse:
    step: write_some_numbers
    file: stdout #file which should be scanned

#Create result table
result:
  use: analyse #use existing analyser
  table:
    name: result
    style: pretty
    column:
      - number_pat #first match
      - number_pat_first #first match
      - number_pat_last #last match
      - number_pat_min #min of all matches
      - number_pat_max #max of all matches
      - number_pat_sum #sum of all matches
      - number_pat_cnt #number of matches
      - number_pat_avg #avg of all matches
      - {_: number_pat_std, format: .2f} #std of all matches

It will create the following output:

| number_pat | number_pat_last | number_pat_min | number_pat_max | number_pat_sum | number_pat_cnt | number_pat_avg | number_pat_std |
|------------|-----------------|----------------|----------------|----------------|----------------|----------------|----------------|
|          1 |              10 |              1 |             10 |             55 |             10 |            5.5 |           3.03 |

Jobsystem

In most cases you want to submit jobs by JUBE to your local jobsystem. You can use the normal file access and substitution system to prepare your jobfile and send it to the jobsystem. JUBE also provide some additional features.

The files used for this example can be found inside examples/jobsystem.

The input jobsystem file job.run.in for Torque/Moab (you can easily adapt your personal jobscript):

#!/bin/bash -x
#MSUB -l nodes=#NODES#:ppn=#PROCS_PER_NODE#
#MSUB -l walltime=#WALLTIME#
#MSUB -e #ERROR_FILEPATH#
#MSUB -o #OUT_FILEPATH#
#MSUB -M #MAIL_ADDRESS#
#MSUB -m #MAIL_MODE#

### start of jobscript

#EXEC#
touch #READY#

The JUBE input file jobsystem.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="jobsystem" outpath="bench_run">
    <comment>A jobsystem example</comment>
    
    <!-- benchmark configuration -->
    <parameterset name="param_set">
      <parameter name="number" type="int">1,2,4</parameter>
    </parameterset>
    
    <!-- Job configuration -->
    <parameterset name="executeset">
      <parameter name="submit_cmd">msub</parameter>
      <parameter name="job_file">job.run</parameter>
      <parameter name="nodes" type="int">1</parameter>
      <parameter name="walltime">00:01:00</parameter>
      <parameter name="ppn" type="int">4</parameter>      
      <parameter name="ready_file">ready</parameter>
      <parameter name="mail_mode">abe</parameter>
      <parameter name="mail_address"></parameter>
      <parameter name="err_file">stderr</parameter>
      <parameter name="out_file">stdout</parameter>
      <parameter name="exec">echo $number</parameter>
    </parameterset>
    
    <!-- Load jobfile -->
    <fileset name="files">
      <copy>${job_file}.in</copy>
    </fileset>
    
    <!-- Substitute jobfile -->
    <substituteset name="sub_job">
      <iofile in="${job_file}.in" out="$job_file" />
      <sub source="#NODES#" dest="$nodes" />
      <sub source="#PROCS_PER_NODE#" dest="$ppn" />
      <sub source="#WALLTIME#" dest="$walltime" />
      <sub source="#ERROR_FILEPATH#" dest="$err_file" />
      <sub source="#OUT_FILEPATH#" dest="$out_file" />
      <sub source="#MAIL_ADDRESS#" dest="$mail_address" />
      <sub source="#MAIL_MODE#" dest="$mail_mode" />
      <sub source="#EXEC#" dest="$exec" />
      <sub source="#READY#" dest="$ready_file" />
    </substituteset> 
         
    <!-- Operation -->
    <step name="submit" work_dir="$$SCRATCH/jobsystem_bench_${jube_benchmark_id}_${jube_wp_id}" >
      <use>param_set</use>
      <use>executeset</use>
      <use>files,sub_job</use>
      <do done_file="$ready_file">$submit_cmd $job_file</do> <!-- shell command -->
    </step>    
  </benchmark>
</jube>

The JUBE input file jobsystem.yaml:

name: jobsystem
outpath: bench_run
comment: A jobsystem example

parameterset:
  #benchmark configuration
  - name: param_set
    parameter: {name: number, type: int,  _: "1,2,4"} #comma separated integer must be quoted
  #Job configuration
  - name: executeset
    parameter:
      - {name: submit_cmd, "_": msub}
      - {name: job_file, "_": job.run}
      - {name: nodes, type: int, "_": 1}
      - {name: walltime, "_": "00:01:00"} #: must be quoted
      - {name: ppn, type: int, "_": 4}
      - {name: ready_file, "_": ready}
      - {name: mail_mode, "_": abe}
      - {name: mail_address}
      - {name: err_file, "_": stderr}
      - {name: out_file, "_": stdout}
      - {name: exec, "_": echo $number}

#Load jobfile
fileset:
  name: files
  copy: ${job_file}.in

substituteset:
  name: sub_job
  iofile: {in: "${job_file}.in", out: $job_file} #attributes with {} must be quoted
  sub:
    - {source: "#NODES#", dest: $nodes} 
    - {source: "#PROCS_PER_NODE#", dest: $ppn} 
    - {source: "#WALLTIME#", dest: $walltime}
    - {source: "#ERROR_FILEPATH#", dest: $err_file}
    - {source: "#OUT_FILEPATH#", dest: $out_file}
    - {source: "#MAIL_ADDRESS#", dest: $mail_address}
    - {source: "#MAIL_MODE#", dest: $mail_mode}
    - {source: "#EXEC#", dest: $exec}
    - {source: "#READY#", _: $ready_file } # _ can be used here as well instead of dest (should be used for multiline output)

#Operation
step:
  name: submit
  work_dir: "$$WORK/jobsystem_bench_${jube_benchmark_id}_${jube_wp_id}"
  use: [param_set,executeset,files,sub_job]
  do:
    done_file: $ready_file
    _: $submit_cmd $job_file #shell command

As you can see the jobfile is very general and several parameters will be used for replacement. By using a general jobfile and the substitution mechanism you can control your jobsystem directly out of your JUBE input file. $$ is used for Shell substitutions instead of JUBE substitution (see Environment handling).

The submit command is a normal Shell command so there are no special JUBE tags to submit a job.

There are two new attributes:

• done_file inside the <do> allows you to set a filename/path to a file which should be used by the jobfile to mark the end of execution. JUBE does not know when the job ends. Normally it will return when the Shell command was finished. When using a jobsystem the user usually have to wait until the jobfile is executed. If JUBE found a <do> containing a done_file attribute JUBE will return directly and will not continue automatically until the done_file exists. If you want to check the current status of your running steps and continue the benchmark process if possible you can type:

  >>> jube continue bench_run
  

  This will continue your benchmark execution (bench_run is the benchmarks directory in this example). The position of the done_file is relatively seen towards the work directory.

• work_dir can be used to change the sandbox work directory of a step. In normal cases JUBE checks that every work directory gets a unique name. When changing the directory the user must select a unique name by his own. For example he can use $jube_benchmark_id and $jube_wp_id, which are JUBE internal parameters and will be expanded to the current benchmark and workpackage ids. Files and directories out of a given <fileset> will be copied into the new work directory. Other automatic links, like the dependency links, will not be created!

You will see this Output after running the benchmark:

| stepname | all | open | wait | error | done |
|----------|-----|------|------|-------|------|
|   submit |   3 |    0 |    3 |     0 |    0 |

and this output after running the continue command (after the jobs where executed):

| stepname | all | open | wait | error | done |
|----------|-----|------|------|-------|------|
|   submit |   3 |    0 |    0 |     0 |    3 |

You have to run continue multiple times if not all done_file were written when running continue for the first time.

Include external data

As you have seen in the example before a benchmark can become very long. To structure your benchmark you can use multiple files and reuse existing sets. There are three different include features available.

The files used for this example can be found inside examples/include.

The include file include_data.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <parameterset name="param_set">
    <parameter name="number" type="int">1,2,4</parameter>
  </parameterset>
    
  <parameterset name="param_set2">
    <parameter name="text">Hello</parameter>
  </parameterset>
    
  <dos>
    <do>echo Test</do>
    <do>echo $number</do>
  </dos>
</jube>

The include file include_data.yaml:

parameterset: 
  - name: param_set
    parameter: {name: number, type: int, _: "1,2,4"}
  - name: param_set2
    parameter: {name: text, _: Hello}

dos:
  - echo Test
  - echo $number

All files which contain data to be included must use the XML-format. The include files can have a user specific structure (there can be no valid JUBE tags like <dos>), but the structure must be allowed by the searching mechanism (see below). The resulting file must have a valid JUBE structure.

The main file main.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="include" outpath="bench_run">
    <comment>A include example</comment>

    <!-- use parameterset out of an external file and add a additional parameter -->
    <parameterset name="param_set" init_with="include_data.xml">
      <parameter name="foo">bar</parameter>
    </parameterset>

    <!-- Operation -->
    <step name="say_hello">
      <use>param_set</use> <!-- use existing parameterset -->
      <use from="include_data.xml">param_set2</use> <!-- out of an external file -->
      <do>echo $foo</do> <!-- shell command -->
      <include from="include_data.xml" path="dos/do" /> <!-- include all available tag -->
    </step>    
  </benchmark>
</jube>

The main file main.yaml:

name: include
outpath: bench_run
comment: A include example

#use parameterset out of an external file and add a additional parameter
parameterset:
  name: param_set
  init_with: include_data.yaml
  parameter: {name: foo, _: bar}

#Operation
step:
  name: say_hello
  use:
   - param_set #use existing parameterset
   - from: include_data.yaml
     _: param_set2  #out of an external file
  do: 
    - echo $foo
    - !include include_data.yaml:["dos"]  #include all available tag

In these file there are three different include types:

The init_with can be used inside any set definition. Inside the given file the search mechanism will search for the same set (same type, same name), will parse its structure (this must be JUBE valid) and copy the content to main.xml. Inside main.xml you can add additional values or overwrite existing ones. If your include-set uses a different name inside your include file you can use init_with="filename.xml:old_name". It is possible to mix YAML based include files with XML files and vice versa.

The second method is the <use from="...">. This is mostly the same like the init_with structure, but in this case you are not able to add or overwrite some values. The external set will be used directly. There is no set-type inside the <use>, because of that, the set’s name must be unique inside the include-file. The remote file can use the YAML or the XML format.

The last method is the most generic include. The include mechanic is the only element in JUBE which works slightly different in YAML and XML based files.

In XML based files by using <include /> you can copy any XML-nodes you want to your main-XML file. The included file can provide tags which are not JUBE-conform but it must be a valid XML-file (e.g. only one root node allowed). The resulting main configuration file must be completely JUBE valid. The path is optional and can be used to select a specific node set (otherwise the root-node itself will be included). The <include /> is the only include-method that can be used to include any tag you want. The <include /> will copy all parts without any changes. The other include types will update path names, which were relative to the include-file position.

In YAML based files the prefix ! include is used followed by the file name. The file must be a YAML file, which will be opened and parsed. The second block :[“dos”] can be used to select any subset of data of the full dictionary, any Python syntax is allowed for this selection. Finally it is possible to also specify a third block which allows full Python list comprehensions. _ is the match of the selection before, e.g.: !include include_data.yaml:["dos"]:[i for i in _ if "Test" in i]. In contrast to the XML based include it isn’t possible to mix lists or dictionaries out of different files, each key can only handle a single include.

To run the benchmark you can use the normal command:

>>> jube run main.xml

It will search for the files to include inside four different positions, in the following order:

• inside a directory given over the command line interface:

  >>> jube run --include-path some_path another_path -- main.xml
  

• inside any path given by an <include-path>- or include-path:-tag in XML or YAML, respectively:

  <?xml version="1.0" encoding="UTF-8"?>
  <jube>
    <include-path>
      <path>some_path</path>
      <path>another_path</path>
    </include-path>
    ...
  </jube>
  

  ...
  include-path:
    path:
      - "some path"
      - "another path"
  ...
  

• inside any path given with the JUBE_INCLUDE_PATH environment variable (see Configuration):

  >>> export JUBE_INCLUDE_PATH=some_path:another_path
  

• inside the same directory of your main.xml

JUBE stops searching as soon as it finds the file to include, or gives an error if the file is not found.

Tagging

Tagging is an easy way to hide selected parts of your input file.

The files used for this example can be found inside examples/tagging.

The input file tagging.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <tags forced="true">
    <check_tags>deu|eng</check_tags>
    <tag name="deu">For german strings</tag>
    <tag name="eng">For english strings</tag>
  </tags>

  <benchmark name="tagging" outpath="bench_run">
    <comment>Tags as logical combination</comment>

    <!-- Configuration -->
    <parameterset name="param_set">
      <parameter name="hello_str" tag="!deu+eng">Hello</parameter>
      <parameter name="hello_str" tag="deu|!eng">Hallo</parameter>
      <parameter name="world_str" tag="eng">World</parameter>
    </parameterset>
    
    <!-- Operation -->
    <step name="say_hello">
      <use>param_set</use> <!-- use existing parameterset -->
      <do>echo '$hello_str $world_str'</do> <!-- shell command -->
    </step>    
  </benchmark>
</jube>

The input file tagging.yaml:

tags:
  check_tags: deu|eng  #check if tag deu or eng was set
  forced: True
  tag:
    - {name: deu, _: For german strings}
    - {name: eng, _: For english strings}

name: tagging
outpath: bench_run
comment: Tags as logical combination

#Configuration
parameterset:
  name: param_set
  parameter:
    - {name: hello_str, tag: "!deu+eng", _: Hello}
    - {name: hello_str, tag: deu|!eng, _: Hallo}
    - {name: world_str, tag: eng, _: World}

#Operation 
step:
  name: say_hello
  use: param_set #use existing parameterset
  do: echo '$hello_str $world_str' #shell command

The tag attribute and the check_tags tag allow you to define more complex boolean expressions. For example:

• ! can be used for negation (!deu stands for not deu)

• + can be used as an AND operator to combine tag values (e.g. XML: tag="!deu+eng"; YAML: tag: "!deu+eng").

• | can be used as an OR operator to combine tag values. (e.g. tag1 | tag2 means that one of the two (or both) tags must be set.)

• ^ can be used as am XOR operator to combine tag values. (e.g. tag1 ^ tag2 means that one of the two tags must be set, but not both.)

• Parentheses are also allowed

The tag attribute can be used within any <element> within the input file (except the <jube>). If several different tag attribute values are used in a script, they can be specified as a list separated by spaces from the command line.

To keep track of all tags, a description for each tag can be defined within the <tags>, where <check_tags> is also defined, using <tag name="...">Description</tag>. To force a description of all possible tags, the forced attribute can be set to true, so that an error is thrown if a tag is not documented.

All <elements> which contain a special tag="..." attribute will be hidden if the value of the tag evaluates to false. This means that JUBE will ignore the elements with these tags in its internal processing. Caution: This can lead to erroneous execution if you forget to set the necessary tags for execution, as JUBE will ignore e.g. a <parameter> provided with the corresponding tag attribute that evaluates to false.

Careful: This can lead to erroneous execution if you forget to set the necessary tags for execution, as JUBE will no longer consider e.g. parameters provided with the corresponding tag attribute.

To ensure that the user of the script specifies the necessary tag values that the script needs for successful execution, the check_tag element (added with JUBE version 2.6.0) can be used. It allows you to define tag values that must be specified when the script is called in order for it to run successfully. If none of the required tag combinations defined by check_tag are set by the user, an error message is displayed and the run is aborted.

In the example above, check_tags: deu|eng indicates that deu or eng must be set. When running the example using one of the specific tag values in <check_tags> (in this case --tag eng):

>>> jube run tagging.xml --tag eng

this results in the following output in the stdout file:

Hello World

Platform independent benchmarking

If you want to create platform independent benchmarks you can use the include features inside of JUBE.

All platform related sets must be declared in an includable file e.g. platform.xml. There can be multiple platform.xml in different directories to allow different platforms. By changing the include-path the benchmark changes its platform specific data.

An example benchmark structure is based on three include files:

• The main benchmark include file which contain all benchmark specific but platform independent data

• A mostly generic platform include file which contain benchmark independent but platform specific data (this can be created once and placed somewhere central on the system, it can be easily accessed using the JUBE_INCLUDE_PATH environment variable.

• A platform specific and benchmark specific include file which must be placed in a unique directory to allow inlcude-path usage

Inside the platform directory you will find some example benchmark independent platform configuration files for the supercomputers at Forschungszentrum Jülich.

To avoid writing long include-paths every time you run a platform independent benchmark, you can store the include-path inside your input file. This can be mixed using the tagging-feature:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <include-path>
    <path tag="plat1">some path</path>
    <path tag="plat2">another path</path>
    ...
  </include-path>
  ...
</jube>

Or in YAML:

...
include-path:
  path:
    - {tag: plat1,  _: "some path"}
    - {tag: plat2,  _: "another path"}
...

Now you can run your benchmark using:

>>> jube run filename.xml --tag plat1

Multiple benchmarks

Often you only have one benchmark inside your input file. But it is also possible to store multiple benchmarks inside the same input file:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="a" outpath="bench_runs">...</benchmark>
  <benchmark name="b" outpath="bench_runs">...</benchmark>
  ...
</jube>

- name: a
  # data for benchmark a
- name: b
  # data for benchmark b

All benchmarks can use the same global (as a child of <jube>) declared sets. Often it might be better to use an include feature instead. JUBE will run every benchmark in the given order. Every benchmark gets a unique benchmark id.

To select only one benchmark you can use:

>>> jube run filename.xml --only-bench a

or:

>>> jube run filename.xml --not-bench b

This information can also be stored inside the input file:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <selection>
    <only>a</only>
    <not>b</not>
  </selection>
  ...
</jube>

Shared operations

Sometimes you want to communicate between the different workpackages of a single step or you want a single operation to run only once for all workpackages. Here you can use shared steps.

The files used for this example can be found inside examples/shared.

The input file shared.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="shared" outpath="bench_run">
    <comment>A shared folder example</comment>
    
    <!-- Configuration -->
    <parameterset name="param_set">
      <parameter name="number" type="int">1,2,4</parameter>
    </parameterset>
    
    <!-- Operation -->
    <step name="a_step" shared="shared">
      <use>param_set</use>
      <!-- shell command will run three times -->
      <do>echo $jube_wp_id >> shared/all_ids</do>
      <!-- shell command will run one time -->
      <do shared="true">cat all_ids</do>
    </step>    
  </benchmark>
</jube>

The input file shared.yaml:

name: shared
outpath: bench_run
comment: A shared folder example

#Configuration
parameterset:
  name: param_set
  parameter: {name: number, type: int, _: "1,2,4"}

#Operation
step:
  name: a_step
  shared: shared
  use: param_set
  do:
    - echo $jube_wp_id >> shared/all_ids #shell command will run three times 
    - {shared: true, _: cat all_ids} #shell command will run one times 

The step must be marked using the shared attribute. The name, given inside this attribute, will be the name of a symbolic link, which will be created inside every single sandbox work directory pointing to a single shared folder. Every Workpackage can access this folder by using its own link. In this example every workpackage will write its own id into a shared file ($jube_wp_id is an internal variable, more of these you will find here).

To mark an operation to be a shared operation shared="true" inside the <do> must be used. The shared operation will start after all workpackages reached its execution position. The work directory for the shared operation is the shared folder itself.

You will get the following directory structure:

bench_run               # the given outpath
|
+- 000000               # the benchmark id
   |
   +- configuration.xml # the stored benchmark configuration
   +- workpackages.xml  # workpackage information
   +- 000000_a_step     # the first workpackage
      |
      +- done           # workpackage finished marker
      +- work           # user sandbox folder
         |
         +- stderr      # standard error messages of used shell commands
         +- stdout      # standard output of used shell commands
         +- shared      # symbolic link pointing to shared folder
   +- 000001_a_step     # workpackage information
   +- 000002_a_step     # workpackage information
   +- a_step_shared     # the shared folder
      |
      +- stdout         # standard output of used shell commands
      +- stderr         # standard error messages of used shell commands
      +- all_ids        # benchmark specific generated file

Environment handling

Shell environment handling can be very important to configure paths or parameter of your program.

The files used for this example can be found inside examples/environment.

The input file environment.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="environment" outpath="bench_run">
    <comment>An environment handling example</comment>
    
    <!-- Configuration -->
    <parameterset name="param_set">
      <parameter name="EXPORT_ME" export="true">VALUE</parameter>
    </parameterset>
    
    <!-- Operations -->
    <step name="first_step" export="true">
      <do>export SHELL_VAR=Hello</do> <!-- export a Shell var -->
      <do>echo "$$SHELL_VAR world"</do><!-- use exported Shell var --> 
    </step>
    
    <!-- Create a dependency between both steps -->
    <step name="second_step" depend="first_step">
      <use>param_set</use>
      <do>echo $$EXPORT_ME</do>
      <do>echo "$$SHELL_VAR again"</do> <!-- use exported Shell var out of privious step -->
    </step>    
  </benchmark>
</jube>

The input file environment.yaml:

name: environment
outpath: bench_run
comment: An environment handling example

#Configuration
parameterset:
  name: param_set
  parameter: {name: EXPORT_ME, export: true, _: VALUE}

step:
  #Operation
  - name: first_step
    export: true
    do:
      - export SHELL_VAR=Hello #export a Shell var
      - echo "$$SHELL_VAR world" #use exported Shell var

   #Create a dependency between both steps    
  - name: second_step
    depend: first_step
    use: param_set
    do:
      - echo $$EXPORT_ME
      - echo "$$SHELL_VAR again" #use exported Shell var out of privious step

In normal cases all <do> within one <step> shares the same environment. All exported variables of one <do> will be available inside the next <do> within the same <step>.

By using export="true" inside of a <parameter> you can export additional variables to your Shell environment. Be aware that this example uses $$ to explicitly use Shell substitution instead of JUBE substitution.

You can also export the complete environment of a step to a dependent step by using export="true" inside of <step>.

Parameter dependencies

Sometimes you need parameters which are based on other parameters or only a specific parameter combination makes sense and other combinations are useless or wrong. For this there are several techniques inside of JUBE to create such a more complex workflow.

The files used for this example can be found inside examples/parameter_dependencies.

The input file parameter_dependencies.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="parameter_dependencies" outpath="bench_run">
    <comment>A parameter_dependencies example</comment>

    <!-- Configuration -->
    <parameterset name="param_set">
      <parameter name="index" type="int">0,1</parameter>
      <parameter name="text" mode="python">["hello","world"][$index]</parameter>
    </parameterset>

    <parameterset name="depend_param_set0">
      <parameter name="number" type="int">3,5</parameter>
    </parameterset>

    <parameterset name="depend_param_set1">
      <parameter name="number" type="int">1,2,4</parameter>
    </parameterset>

    <!-- Operation -->
    <step name="operation">
      <use>param_set</use> <!-- use basic parameterset -->
      <use>depend_param_set$index</use> <!-- use dependent parameterset -->
      <use from="include_file.xml:depend_param_set0:depend_param_set1">
        depend_param_set$index
      </use>
      <do>echo "$text $number $number2"</do>
    </step>
  </benchmark>
</jube>

The input file parameter_dependencies.yaml:

name: parameter_dependencies
outpath: bench_run
comment: A parameter_dependencies example

#Configuration
parameterset:
  - name: param_set
    parameter:
      - {name: index, type: int,  _: "0,1"} #comma separated integer must be in quotations
      - {name: text, mode: python, _: '["hello","world"][$index]'} #attributes with " and [] must be in quotations
  - name: depend_param_set0
    parameter: {name: number, type: int,  _: "3,5"} #comma separated integer must be in quotations
  - name: depend_param_set1
    parameter: {name: number, type: int,  _: "1,2,4"} #comma separated integer must be in quotations

#Operation
step:
  name: operation
  use:
    - param_set #use basic parameterset
    - depend_param_set$index #use dependent parameterset
    - {from: 'include_file.yaml:depend_param_set0:depend_param_set1', _: depend_param_set$index}
  do: echo "$text $number $number2"

The include file include_file.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <parameterset name="depend_param_set0">
    <parameter name="number2" type="int">10</parameter>
  </parameterset>

  <parameterset name="depend_param_set1">
    <parameter name="number2" type="int">20</parameter>
  </parameterset>
</jube>

The include file include_file.yaml:

parameterset: 
  - name: depend_param_set0
    parameter: {name: number2, type: int, _: 10}
  - name: depend_param_set1
    parameter: {name: number2, type: int, _: 20}

The easiest way to handle dependencies is to define an index-parameter which can be used in other scripting parameters to combine all dependent parameter combinations.

Also complete sets can be marked as dependent towards a specific parameter by using this parameter in the <use>-tag. When using parametersets out of an other file the correct set-name must be given within the from attribute, because these sets will be loaded in a pre-processing step before the corresponding parameter will be evaluated. Also sets out of different files can be combined within the same <use> by using the file1:set1,file2:set2 syntax. The sets names must be unique.

Parameter update

Once a parameter is specified and evaluated the first time, its value will not change. Sometimes this behaviour can produce the wrong behaviour:

<parameter name="foo">$jube_wp_id</parameter>

In this example foo should hold the $jube_wp_id. If you have two steps, where one step depends on the other one foo will be available in both, but it will only be evaluated in the first one.

There is a simple workaround to change the update behaviour of a parameter by using the attribute update_mode:

• update_mode="never" No update (default behaviour)

• update_mode="use" Re-evaluate the parameter if the parameterset is explicitly used

• update_mode="step" Re-evaluate the parameter for each new step

• update_mode="cycle" Re-evaluate the parameter for each new cycleloop, but not at the begin of a new step

• update_mode="always" Combine step and cycle

Within a cycle loop no new workpackages can be created. Templates will be reevaluated, but they can not increase the number of existing workpackages within a cycle.

Within the result generation, the parameter value, which is presented in the result table is the value of the selected analysed step. If another parameter representation is needed as well, all other steps can be reached by using <parameter_name>_<step_name>.

The files used for this example can be found inside examples/parameter_update.

The input file parameter_update.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="parameter_updates" outpath="bench_run">
    <comment>A parameter_update example</comment>

    <!-- Configuration -->
    <parameterset name="foo">
      <parameter name="bar_never" mode="text" update_mode="never">
        iter_never: $jube_wp_id
      </parameter>
      <parameter name="bar_use" mode="text" update_mode="use">
        iter_use: $jube_wp_id
      </parameter>
      <parameter name="bar_step" mode="text" update_mode="step">
        iter_step: $jube_wp_id
      </parameter>
    </parameterset>

    <!-- Operation -->
    <step name="step1">
      <use>foo</use>
      <do>echo $bar_never</do>
      <do>echo $bar_use</do>
      <do>echo $bar_step</do>
    </step>

    <step name="step2" depend="step1">
      <use>foo</use>
      <do>echo $bar_never</do>
      <do>echo $bar_use</do>
      <do>echo $bar_step</do>
    </step>

    <step name="step3" depend="step2">
      <do>echo $bar_never</do>
      <do>echo $bar_use</do>
      <do>echo $bar_step</do>
    </step>
  </benchmark>
</jube>

The input file parameter_update.yaml:

name: parameter_updates
outpath: bench_run
comment: A parameter_update example

#Configuration
parameterset:
  name: foo
  parameter:
    - {name: bar_never, mode: text, update_mode: never, _: "iter_never: $jube_wp_id"} 
    - {name: bar_use, mode: text, update_mode: use, _: "iter_use: $jube_wp_id"} 
    - {name: bar_step, mode: text, update_mode: step, _: "iter_step: $jube_wp_id"}

#Operation
step:
  - name: step1
    use: foo
    do:
      - echo $bar_never
      - echo $bar_use
      - echo $bar_step
  - name: step2
    depend: step1
    use: foo
    do:
      - echo $bar_never
      - echo $bar_use
      - echo $bar_step
  - name: step3
    depend: step2
    do:
      - echo $bar_never
      - echo $bar_use
      - echo $bar_step

The use and influence of the three update modes update_mode="never", update_mode="use" and update_mode="step" is shown here. Keep in mind, that the steps have to be dependent from each other leading to identical outputs otherwise.

Step iteration

Especially in the context of benchmarking, an application should be executed multiple times to generate some meaningful statistical values. The handling of statistical values is described in Statistic pattern values. This allows you to aggregate multiple result lines if your application automatically support to run multiple times.

In addition there is also an iteration feature within JUBE to run a specific step and its parametrisation multiple times.

The files used for this example can be found inside examples/iterations.

The input file iterations.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="iterations" outpath="bench_run">
    <comment>A Iteration example</comment>

    <!-- Configuration -->
    <parameterset name="param_set">
      <parameter name="foo" type="int">1,2,4</parameter>
      <parameter name="bar" mode="text" update_mode="step">$foo iter:$jube_wp_iteration</parameter>
    </parameterset>

    <step name="first_step" iterations="2">
      <use>param_set</use> <!-- use existing parameterset -->
      <do>echo $bar</do> <!-- shell command -->
    </step>

    <step name="second_step" depend="first_step" iterations="2">
      <do>echo $bar</do> <!-- shell command -->
    </step>

    <!-- analyse without reduce -->
    <analyser name="analyse_no_reduce" reduce="false">
      <analyse step="second_step" />
    </analyser>

    <!-- Analyse with reduce -->
    <analyser name="analyse" reduce="true">
      <analyse step="second_step" />
    </analyser>

    <result>
      <use>analyse</use>
      <use>analyse_no_reduce</use>
      <table name="result" style="pretty">
        <column>jube_res_analyser</column>
        <column>jube_wp_id_first_step</column>
        <column>jube_wp_id</column>
        <column>jube_wp_iteration_first_step</column>
        <column>jube_wp_iteration</column>
        <column>foo</column>
      </table>
    </result>
  </benchmark>
</jube>

The input file iterations.yaml:

name: iterations
outpath: bench_run
comment: A Iteration example

#Configuration
parameterset:
  name: param_set
  parameter:
    - {name: foo, type: int, _: "1,2,4"}
    - {name: bar, update_mode: step, _: '$foo iter:$jube_wp_iteration'}

step:
  - name: first_step
    iterations: 2
    use: param_set #use existing parameterset
    do: echo $bar #shell command
  - name: second_step
    depend: first_step
    iterations: 2
    do: echo $bar #shell command

analyser:
  #analyse without reduce
  - name: analyse_no_reduce
    reduce: false
    analyse: 
      step: second_step
  #analyse with reduce
  - name: analyse
    reduce: true
    analyse:
      step: second_step

result:
  use: [analyse,analyse_no_reduce]
  table:
    name: result
    style: pretty
    column:
      - jube_res_analyser
      - jube_wp_id_first_step
      - jube_wp_id
      - jube_wp_iteration_first_step
      - jube_wp_iteration
      - foo

In this example, both steps 1 and 2 are executed 2 times for each parameter and dependency configuration. Because of the given parameter, step 1 is executed 6 times in total (3 parameter combinations x 2). Step 2 is executed 12 times (6 from the dependent step x 2). Each run will be executed in the normal way using its individual sandbox folder.

$jube_wp_iteration holds the individual iteration id. The update_mode is needed here to reevaluate the parameter bar in step 2.

In the analyser reduce=true or reduce=false can be enabled, to allow you to see all individual results or to aggregate all results of the same parameter combination. for the given step. If reduce=true is enabled (the default behaviour) the output of the individual runs, which uses the same parametrisation, are treated like a big continuous file before applying the statistical patterns.

| jube_res_analyser | jube_wp_id_first_step | jube_wp_id | jube_wp_iteration_first_step | jube_wp_iteration | foo |
|-------------------|-----------------------|------------|------------------------------|-------------------|-----|
| analyse_no_reduce |                     0 |          6 |                            0 |                 0 |   1 |
| analyse_no_reduce |                     0 |          7 |                            0 |                 1 |   1 |
| analyse_no_reduce |                     1 |          8 |                            1 |                 2 |   1 |
| analyse_no_reduce |                     1 |          9 |                            1 |                 3 |   1 |
| analyse_no_reduce |                     2 |         10 |                            0 |                 0 |   2 |
| analyse_no_reduce |                     2 |         11 |                            0 |                 1 |   2 |
| analyse_no_reduce |                     3 |         12 |                            1 |                 2 |   2 |
| analyse_no_reduce |                     3 |         13 |                            1 |                 3 |   2 |
| analyse_no_reduce |                     4 |         14 |                            0 |                 0 |   4 |
| analyse_no_reduce |                     4 |         15 |                            0 |                 1 |   4 |
| analyse_no_reduce |                     5 |         16 |                            1 |                 2 |   4 |
| analyse_no_reduce |                     5 |         17 |                            1 |                 3 |   4 |
|           analyse |                     5 |         16 |                            1 |                 2 |   4 |
|           analyse |                     0 |          7 |                            0 |                 1 |   1 |
|           analyse |                     1 |          8 |                            1 |                 2 |   1 |
|           analyse |                     2 |         10 |                            0 |                 0 |   2 |
|           analyse |                     3 |         12 |                            1 |                 2 |   2 |
|           analyse |                     4 |         15 |                            0 |                 1 |   4 |

Step cycle

Instead of having a new workpackage you can also redo the <do> commands inside a step using the cycle-feature. In contrast to the iterations, all executions for the cycle feature take place inside the same folder.

The files used for this example can be found inside examples/cycle.

The input file cycle.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="cycle" outpath="bench_run">
    <comment>A cycle example</comment>

    <step name="a_step" cycles="5">
      <do break_file="done">echo $jube_wp_cycle</do>
      <do active="$jube_wp_cycle==2">touch done</do>
    </step>

  </benchmark>
</jube>

The input file cycle.yaml:

---
benchmark: 
  - name: cycle
    outpath: bench_run
    comment: A cycle example

    step:
      - name: a_step
        cycles: 5
        do:
          - _: echo $jube_wp_cycle
            break_file: done
          - _: touch done
            active: $jube_wp_cycle==2
        

The cycles attribute allows to repeat all <do> commands within a step multiple times. The break_file can be used to cancel the loop and all following commands in the current cycle (the command itself is still executed). In the given example the output will be:

0
1
2
3

In contrast to the iterations, all executions for the cycle feature take place inside of the same folder.

Parallel workpackages

In a standard jube run a queue is filled with workpackages and then processed in serial. To enable parallel execution of independent workpackages, which belong to the expansions of a step, the argument procs of <step> can be used.

The files used for this example can be found inside examples/parallel_workpackages.

The input file parallel_workpackages.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="parallel_workpackages" outpath="bench_run">
    <comment>A parallel workpackages demo</comment>

    <parameterset name="param_set">
      <parameter name="i" type="int" mode="python">",".join([ str(i) for i in range(0,10)])</parameter>
    </parameterset>

    <step name="parallel_execution" suffix="${i}" procs="4">
      <use>param_set</use>
      <do>echo "${i}"</do>
      <do>N=1000000 ; a=1; k=0; while [ "$k" -lt $N ]; do echo $(( 2*k + 1 + $a )) ; k=$(( k + 1 )) ; done</do>
    </step>
  </benchmark>
</jube>

The input file parallel_workpackages.yaml:

name: parallel_workpackages
outpath: bench_run
comment: A parallel workpackages demo

parameterset:
  name: param_set
  parameter: {name: i, type: int, mode: python, _: "\",\".join([ str(i) for i in range(0,10)])"}
step:
  name: parallel_execution
  suffix: ${i}
  procs: 4
  use: param_set
  do:
  - "echo \"${i}\""
  - "N=1000000 ; a=1; k=0; while [ \"$k\" -lt $N ]; do echo $(( 2*k + 1 + $a )) ; k=$(( k + 1 )) ; done"

In the example above the expansion of the parameter i will lead to the creation of 10 workpackages of the step parallel_execution. Due to the given argument procs="4" JUBE will start 4 worker processes which will distribute the execution of the workpackages among themselves. N within the JUBE script represents the number of computation iterations to simulate a computational workload at hand. The parameters N, procs and the upper bound of range within this prototypical example can be alternated to study runtime, memory usage and load of CPUs.

Important hints:

• <do shared="true"> is not supported if procs is set for the corresponding step.

• If <step shared="..."> is set, then the user is responsible to avoid data races within the shared directory.

• Switching to an alternative work_dir for a step can also lead to data races if all expansions of the step access the same work_dir. Recommendation: Don’t use a shared work_dir in combination with procs.

• This feature is implemented based on the Python package multiprocessing and doesn’t support inter-node communication. That’s why the parallelisation is limited to a single shared memory compute node.

• Be considerate when working on a multi-user system with shared resources. The parallel feature of JUBE can easily exploit a whole compute node.

• Parallel execution of a JUBE script can lead to much higher memory demand compared to serial execution with procs=1. In this case it is advised to reduce procs leading to reduced memory usage.

Result database

Results can also be stored into a database to simplify result management.

The files used for this example can be found inside examples/result_database.

The input file result_database.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="result_database" outpath="bench_run">
    <comment>result database creation</comment>
    
    <parameterset name="param_set">
      <parameter name="number" type="int">1,2,4</parameter>
    </parameterset>
    
    <patternset name="pattern">
      <pattern name="number_pat" type="int">Number: $jube_pat_int</pattern>
    </patternset>

    <step name="write_number">
      <use>param_set</use>
      <do>echo "Number: $number"</do>
    </step>
    
    <analyser name="analyse">
      <use>pattern</use>
      <analyse step="write_number">
        <file>stdout</file>
      </analyse>
    </analyser>
    
    <result>
      <use>analyse</use>
      <!-- creating a database containing the columns "number" and "number_pat" -->
      <!-- one table of the name "results" is created within the database -->
      <!-- optionally, you can use the "file" attribute to specify an alternative storage location for the database -->
      <database name="results" primekeys="NUM">
        <key primekey="true">number</key>
        <key title="NUM">number_pat</key>
      </database>
    </result>
  </benchmark>
</jube>

The input file result_database.yaml:

name: result_database
outpath: bench_run
comment: result database creation

parameterset:
  name: param_set
  parameter: {name: number, type: int, _: "1,2,4"}

patternset:
  name: pattern
  pattern: {name: number_pat, type: int, _: "Number: $jube_pat_int"}

step:
  name: write_number
  use: param_set
  do: "echo \"Number: $number\""

analyser:
  name: analyse
  use: pattern
  analyse:
    step: write_number
    file: stdout

result:
  use: analyse
  database:
    # creating a database containing the columns "number" and "number_pat"
    # one table of the name "results" is created within the database
    # optionally, you can use the "file" attribute to specify an alternative storage location for the database
    name: results
    primekeys: "NUM"
    key:
    - {primekey: true, _: number}
    - {title: NUM, _: number_pat}

The default database will be located as follows and has the database tag name, which is here results, as root name concatenated with the appendix .dat:

bench_run
|
+- 000000
   |
   +- result
      |
      +- results.dat

The database tag takes the argument name. name is also the name of the table created within a database. If sqlite3 is installed the contents of the database can be shown with the following command line.

>>> sqlite3 -header -table bench_run/000000/result/results.dat 'SELECT * FROM results'
+--------+------------+
| number | number_pat |
+--------+------------+
| 1      | 1          |
| 2      | 2          |
| 4      | 4          |
+--------+------------+

The key tag adds columns to the database table having the same type as the corresponding parameter or pattern. Information of columns of the database table results can be shown as follows.

>>> sqlite3 -header -table bench_run/000000/result/results.dat 'PRAGMA table_info(results)'
+-----+------------+------+---------+------------+----+
| cid |    name    | type | notnull | dflt_value | pk |
+-----+------------+------+---------+------------+----+
| 0   | number     | int  | 0       |            | 1  |
| 1   | number_pat | int  | 0       |            | 2  |
+-----+------------+------+---------+------------+----+

The file argument takes a relative (to the current working directory) or absolute path to an alternative/user-defined location for the database file. Assuming that file="result_database.dat" was set in the above example, a file named result_database.dat would be created in the current working directory where jube result was invoked, containing a database named results, and the file bench_run/000000/result/results.dat would no longer contain the database, but the path specified in the file attributes.

Invocating jube result a second time will update the database specified by the file parameter. Without the primekey attribute of the key-tag, three additional rows would be added to the results table which are identical to the already existing three rows. Setting the primekey attribute of the key-tag to true adds the key to the primekeys, ensuring that a new row is only added to the database table if the column values specified in the primekeys do not match exactly in the database table. In this example, no new rows would be added. The use of the database attribute primekeys is deprecated. Instead, use the primekey attribute of the key. Updating primekeys is not supported.

To have a look into a database within a python script the python modules sqalchemy or pandas can be used.

Creating a do log

To increase reproducibility of the do statements within a workpackage of a step and to archive the environment during execution, a do log can be printed. A do log tries to mimic an executable script recreating the environment at execution time. The files used for this example can be found inside examples/do_log.

The input file do_log.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="do_log_example" outpath="bench_run">

    <parameterset name="param_set">
      <parameter name="number">1,2,3,4,5</parameter>
    </parameterset>
    
    <step name="execute" shared="shared" do_log_file="do_log">
      <use>param_set</use>
      <do>cp ../../../../loreipsum${number} shared</do>
      <do shared="true">grep -r -l "Hidden!" loreipsum*</do>
    </step>    

  </benchmark>
</jube>

The input file do_log.yaml:

- name: do_log_example
  outpath: bench_run

  parameterset: 
    - name: "param_set"
      parameter: 
        - {name: "number", _: "1,2,3,4,5"}

  step:
    name: execute
    use: 
      - param_set
    do_log_file: "do_log"
    shared: "shared"
    do:
      - cp ../../../../loreipsum${number} shared
      - {shared: "true", _: "grep -r -l \"Hidden!\" loreipsum*"}

In this example a hidden string is searched for within 5 files and the name of the file containing the hidden string is printed.

For the initial execution of this example within bench_run/000000/00000[0-4]_execute each can be found a do_log file. These files can be executed manually by prefixing it with /bin/sh. The scripts will reproduce the environment at execution time, the execution and the result output. Keep in mind that the shared grep will be executed by the benchmark with id 4 only.

The duplicate option

To simplify advanced tagging and parameter concatenation the duplicate option within parametersets or parameters can be stated.

The input file duplicate.xml:

<?xml version="1.0" encoding="UTF-8"?>
<jube>
  <benchmark name="parameter_duplicate_example" outpath="bench_run">
    <comment>parameter duplicate example</comment>
     
    <parameterset name="options" duplicate="concat">
      <parameter name="iterations"	     >1</parameter>
      <parameter name="iterations" tag="few" >2,3,4</parameter>
      <parameter name="iterations" tag="many">20,30,40</parameter>
    </parameterset>

    <parameterset name="result">
      <parameter name="sum" mode="python">int(${iterations}*(${iterations}+1)/2)</parameter>
    </parameterset>

    <step name="perform_iterations">
      <use>options,result</use>
      <do>echo $sum</do>
    </step>

  </benchmark>
</jube>

The input file duplicate.yaml:

name: parameter_duplicate_example
outpath: bench_run
comment: parameter duplicate example

parameterset:
  - name: options
    duplicate: concat
    parameter:
      - {name: iterations,            _: "1"}
      - {name: iterations, tag: few,  _: "2,3,4"}
      - {name: iterations, tag: many, _: "20,30,40"}
  - name: result
    parameter:
    - {name: sum, mode: "python", _: "int(${iterations}*(${iterations}+1)/2)"}
 
step:
  name: perform_iterations
  use: "options,result"
  do: "echo $sum"

In this example the duplicate option with the value concat is stated for a parameterset. This leads to a concatenation of parameter values of the same name. In combination with the tagging option for parameters the user can specify which options are included into the parameters. If the user states the tags few and many the parameter iterations takes the values 1,2,3,4,20,30,40.

The default option of duplicate for parametersets is replace which leads to a replacing of parameters if they are mentioned more than once. A third option for the duplicate option for parametersets is error. In this case the execution is aborted if a parameter is defined more than once.

The option duplicate can also be stated for parameters. In this case the parameters duplicate option is prioritized over the parametersets one. The possible values for parameters duplicate option are none, replace, concat and error. none is the default value and leads to the duplicate option being ignored for this parameter such that the parametersets duplicate option is taking precedence. The other three options have the same effect as in the parameterset.