Data Provenance
In order to achieve Reproducibility and Replicability with your experiments using COMPSs, the runtime includes the capacity of recording details of the application’s execution, also known as Data Provenance. This is supported for both Python and Java COMPSs applications.
When the provenance option is activated, the runtime records every access to a file or directory specified in the application, as well as its direction (IN, OUT, INOUT). In addition to this, other information such as the parameters passed as inputs in the command line that submitted the application, its source files, workflow image and profiling statistics, authors and their institutions, … are also stored. All this information is later used to record the Data Provenance of your workflow using the RO-Crate specification, and with the assistance of the ro-crate-py library. RO-Crate is based on JSON-LD (JavaScript Object Notation for Linked Data), is much simpler than other standards and tools created to record Provenance, and that is why it has been adopted in a number of communities. Using RO-Crate to register the execution’s information ensures not only to register correctly the Provenance of a COMPSs application run, but also compatibility with some existing portals that already embrace RO-Crate as their core format for representing metadata, such as WorkflowHub.
Software dependencies
Provenance generation in COMPSs depends on the ro-crate-py library,
thus, it must be installed before the provenance option can be used. Depending on the target system, different
options are available using pip:
If the installation is in a laptop or machine you manage, you can use the command:
$ pip install rocrate
If you do not manage the target machine, you can install the library in your own user space using:
$ pip install rocrate --user
This would typically install the library in ~/.local/. Another option is to specify the target directory with:
$ pip install -t install_path rocrate
Our implementation has been tested with ro-crate-py version 0.7.0 and earlier.
Previous needed information
There are certain pieces of information which must be included when registering the provenance of a workflow that
the COMPSs runtime cannot automatically infer, such as the authors of an application. For specifying all these
fields that are needed to generate an RO-Crate but cannot be automatically obtained, we have created a simple YAML
structure where the user can specify them. They need to provide in their working directory (i.e., where the application
is going to be run) a YAML file named ro-crate-info.yaml that follows the next template structure:
COMPSs Workflow Information:
name: Name of your COMPSs application
description: Detailed description of your COMPSs application
license: Apache-2.0 #Provide better a URL, but these strings are accepted:
# https://about.workflowhub.eu/Workflow-RO-Crate/#supported-licenses
sources_dir: [path_to/dir_1, path_to/dir_2] # Optional: List of directories containing the application source files.
# Relative or absolute paths can be used
sources_main_file: my_main_file.py # Optional: Name of the main file of the application, located in one of the
# sources_dir. Relative paths from a sources_dir entry, or absolute paths can be used
files: [main_file.py, aux_file_1.py, aux_file_2.py] # List of application files
# Relative or absolute paths can be used
Authors:
- name: Author_1 Name
e-mail: author_1@email.com
orcid: https://orcid.org/XXXX-XXXX-XXXX-XXXX
organisation_name: Institution_1 name
ror: https://ror.org/XXXXXXXXX # Find them in ror.org
- name: Author_2 Name
e-mail: author2@email.com
orcid: https://orcid.org/YYYY-YYYY-YYYY-YYYY
organisation_name: Institution_2 name
ror: https://ror.org/YYYYYYYYY # Find them in ror.org
Warning
If no YAML file is provided, the runtime will fail to generate provenance, and will automatically generate an
ro-crate-info_TEMPLATE.yaml file that the user can edit to add their details.
As you can see, there are two main blocks in the YAML:
COMPSs Workflow Information: Where details on the application are provided.
Authors: Where authors’ details are given.
More specifically, in the COMPSs Workflow Information section:
The
nameanddescriptionfields are free text, where a long name and description of the application must be provided.The
licensefield is preferred to be specified by providing an URL to the license, but a set of predefined strings are also supported, and can be found here: https://about.workflowhub.eu/Workflow-RO-Crate/#supported-licensessources_dircan be a single path, or a list of paths where application source files can be found. Our script will add ALL files (i.e., not only source files, but any file found) and sub-directories inside each of the paths specified. The sub-directories structure is respected when the files are added in the crate (inside a sub-directoryapplication_sources).sources_main_fileis the name of the main source file of the application, and may be specified if the user wants to select a particular file as such. The COMPSs runtime detects automatically the main source of an application, therefore this is a way to override the detected file. The file can be specified with a relative path inside one of the directories listed insources_dir. An absolute path can also be used.filesis a single or a list of all the source files of the application (typically all.pyfiles for Python applications, or.java,.class,.jarfiles for Java ones). Both relative and absolute paths can be used. All files specified here will be added in the root of the sub-directoryapplication_sourcesfrom the resulting crate. If the script is unable to automatically identify the main source file of the application, the first file of this list may be considered as such.
The sources_dir and files terms are complementary to each other. An ro-crate-info.yaml could use the term
files alone or sources_dir alone, but also both, if the user is willing to add a number of sub-directories
with source files, but also several files by hand.
Warning
The term sources_main_file can only be used when sources_dir is defined. While the runtime is able to detect
automatically the main file from application execution, this would enable to modify that automatic selection in case
of need.
And in the Authors section:
name,e-mailandorganisation_nameare strings corresponding to the author’s name, e-mail and their institution. They are free text, but thee-mailfield must follow theuser@domain.topformat.orcidrefers to the ORCID identifier of the author. The IDs can be found and created at https://orcid.org/rorrefers to the Research Organization Registry (ROR) identifier for an institution. They can be found at http://ror.org/
Tip
It is very important that the list of source files (defined with sources_dir or files), orcid and
ror terms are correctly defined, since the
runtime will only register information for the list of source files defined, and the orcid and ror are
used as unique identifiers in the RO-Crate specification.
In the following lines, we provide a YAML example for an out-of-core Matrix Multiplication PyCOMPSs application, distributed with license Apache v2.0, with 2 source files, and authored by 3 persons from two different institutions.
COMPSs Workflow Information:
name: COMPSs Matrix Multiplication, out-of-core using files
description: Hypermatrix size 2x2 blocks, block size 2x2 elements
license: Apache-2.0 #Provide better a URL, but these strings are accepted:
# https://about.workflowhub.eu/Workflow-RO-Crate/#supported-licenses
files: [matmul_directory.py, matmul_tasks.py]
Authors:
- name: Raül Sirvent
e-mail: Raul.Sirvent@bsc.es
orcid: https://orcid.org/0000-0003-0606-2512
organisation_name: Barcelona Supercomputing Center
ror: https://ror.org/05sd8tv96
- name: Rosa M. Badia
e-mail: Rosa.M.Badia@bsc.es
orcid: https://orcid.org/0000-0003-2941-5499
organisation_name: Barcelona Supercomputing Center
ror: https://ror.org/05sd8tv96
- name: Adam Hospital
e-mail: adam.hospital@irbbarcelona.org
orcid: https://orcid.org/0000-0002-8291-8071
organisation_name: IRB Barcelona
ror: https://ror.org/01z1gye03
Also, another example of a COMPSs Java K-means application, where the usage of the sources_dir term can be seen.
We add to the crate the sub-directories that contain the .jar and .java files correspondingly.
COMPSs Workflow Information:
name: COMPSs K-means
description: K-means clustering is a method of cluster analysis that aims to partition ''n'' points into ''k''
clusters in which each point belongs to the cluster with the nearest mean. It follows an iterative refinement
strategy to find the centers of natural clusters in the data.
license: https://opensource.org/licenses/Apache-2.0 #Provide better a URL, but these strings are accepted:
# https://about.workflowhub.eu/Workflow-RO-Crate/#supported-licenses
sources_dir: [jar/, src/]
Authors:
- name: Raül Sirvent
e-mail: Raul.Sirvent@bsc.es
orcid: https://orcid.org/0000-0003-0606-2512
organisation_name: Barcelona Supercomputing Center
ror: https://ror.org/05sd8tv96
Usage
The way of activating the recording of Data Provenance with COMPSs is very simple.
One must only enable the -p or --provenance flag when using runcomps or
enqueue_compss to run or submit a COMPSs application, respectively.
As shown in the help option:
$ runcompss -h
(...)
--provenance, -p Generate COMPSs workflow provenance data in RO-Crate format from YAML file. Automatically
activates -graph and -output_profile.
Default: false
Warning
As stated in the help, provenance automatically activates both --graph and --output_profile options.
Consider that the graph image generation can take some extra seconds at the end of the execution of your
application, therefore, adjust the --exec_time accordingly.
In the case of extremely large workflows (e.g., a workflow with tenths of thousands of task nodes, or tenths of thousands of files used as inputs or outputs), the extra time needed to generate the data provenance with RO-Crate may be a problem in systems with strict run time constraints. In these cases, the workflow execution may end correctly, but the extra processing to generate the provenance may be killed by the system if it exceeds a certain limit, and the provenance will not be created correctly.
For this or any other similar situation, our data provenance generation script can be triggered offline at any moment after the workflow has executed correctly, thanks to our design. From the working directory of the application, the following commands may be used:
$ $COMPSS_HOME/Runtime/scripts/utils/compss_gengraph svg $BASE_LOG_DIR/monitor/complete_graph.dot
$ python $COMPSS_HOME/Runtime/scripts/system/provenance/generate_COMPSs_RO-Crate.py ro-crate-info.yaml $BASE_LOG_DIR/dataprovenance.log
In these commands, COMPSS_HOME is where your COMPSs installation is located, and BASE_LOG_DIR points to the path where the
application run logs are stored (see Section Logs
for more details on where to locate these logs). compss_gengraph
generates the workflow image to be added to the crate, but if its generation time is a concern, or the user does not
want it to be included in the crate, the command can be skipped. The second command runs the
generate_COMPSs_RO-Crate.py Python script, that uses the information provided by the user in ro-crate-info.yaml
combined with the file accesses information registered by the COMPSs runtime in the dataprovenance.log file. The
result is a sub-directory COMPSs_RO-Crate_[uuid]/ that contains the data provenance of the run (see next sub-section
for a detailed description).
Result
Once the application has finished, a new sub-folder under the application’s Working Directory
will be created with the name COMPSs_RO-Crate_[uuid]/, which is also known as crate. The contents of the
folder include all the elements needed to reproduce a COMPSs execution, and
are:
Application Source Files: As detailed by the user in the
ro-crate-info.yamlfile, with the termssources_dirand/orfiles. They have to include the main source file and all auxiliary files that the application needs (e.g.:.py,.java,.classor.jar). Optionally, the termsources_main_filecan be used to manually select the main source file of the application. All application files are added to a sub-folder in the crate namedapplication_sources, where thesources_dirlocations are included with their same folder tree structure. The files included with thefilesterm are added to the root of theapplication_sourcessub-folder in the crate.complete_graph.svg: The image of the workflow generated by the COMPSs runtime, as generated with the
runcompss -gor--graphoption.App_Profile.json: A set of statistics of the application run recorded by the COMPSs runtime, as if the
runcompss --output_profile=<path>option was enabled. It includes, for each resource and method executed: number of executions of the specific method, as well as maximum, average and minimum run time. The name of the file can be customized using the--output_profile=<path>option.compss_command_line_arguments.txt: Stores the options passed by the command line when the application was submitted. This is very important for reproducing a COMPSs application, since input parameters could even potentially change the resulting workflow generated by the COMPSs runtime.
ro-crate-metadata.json: The RO-Crate JSON main file describing the contents of this directory (crate) in the RO-Crate specification format. You can find examples in the following Sections.
Warning
All previous file names (complete_graph.svg, App_Profile.json and compss_command_line_arguments.txt)
are automatically used to generate new files when using the -p or --provenance option.
Avoid using these file names among
your own files to avoid unwanted overwritings. You can change the resulting App_Profile.json name by using
the --output_profile=/path_to/file flag.
Log and time statistics
When the provenance generation is activated, and after the application has finished, the data provenance generation
script will be automatically triggered. A number of log messages related to provenance can bee seen, which return
interesting information regarding the provenance generation process. They can all be filtered by doing a grep in
the output log of the application using the PROVENANCE expression.
PROVENANCE | GENERATING GRAPH FOR DATA PROVENANCE
Output file: /Users/rsirvent/.COMPSs/matmul_directory.py_07//monitor/complete_graph.svg
INFO: Generating Graph with legend
DONE
PROVENANCE | ENDED GENERATING GRAPH FOR DATA PROVENANCE. TIME: 0
This first block indicates that the workflow image in SVG format is being generated. When this part finishes, the time in seconds will be reported. As mentioned earlier, complex workflows can lead to large graph generation times.
PROVENANCE | RUNNING DATA PROVENANCE SCRIPT
PROVENANCE | Number of source files detected: 2
PROVENANCE | COMPSs version: 3.0.rc2210, main_entity is: /Users/rsirvent/COMPSs-DP/matmul_directory/matmul_directory.py, out_profile is: App_Profile.json
This second block details how many source files have been detected from the sources_dir and files terms defined
in the ro-crate-py.yaml file. It also shows the COMPSs version detected, the mainEntity detected (i.e., the
source file that contains the main method from the COMPSs application), and the name of the file containing the
execution profile of the application.
PROVENANCE | RO-CRATE data_provenance.log processing TIME (process_accessed_files): 0.00011706352233886719 s
PROVENANCE | RO-CRATE adding physical files TIME (add_file_to_crate): 0.001096963882446289 s
PROVENANCE | RO-CRATE adding input files' references TIME (add_file_not_in_crate): 0.001238107681274414 s
PROVENANCE | RO-CRATE adding output files' references TIME (add_file_not_in_crate): 0.00026798248291015625 s
The third block provides a set of times to understand if any overhead is caused by the script. The first time is the time taken to process the data_provenance.log. The second is the time taken to add the files that are included physically in the crate (this is, source files, workflow image, …). And the third and the fourth are the times spent by the script to add all input and output files of the workflow as references in the RO-Crate, respectively.
PROVENANCE | COMPSs RO-Crate created successfully in subfolder COMPSs_RO-Crate_aaf0cb82-a500-4c28-bbc8-439c37c2e210/
PROVENANCE | RO-CRATE dump TIME: 0.004969120025634766 s
PROVENANCE | RO-CRATE GENERATION TOTAL EXECUTION TIME: 0.014089107513427734 s
PROVENANCE | ENDED DATA PROVENANCE SCRIPT
The fourth and final block details the name of the sub-folder where the RO-Crate has been generated, while stating
the time to record the ro-crate-metadata.json file to disk, and the total time execution of the whole script.
ro-crate-metadata.json PyCOMPSs example (Laptop)
In the RO-Crate specification, the root file containing the metadata referring to the crate created is named
ro-crate-metadata.json. In these lines, we provide an example of an ro-crate-metadata.json file resulting from
a PyCOMPSs application execution in a laptop, specifically an out-of-core matrix multiplication example that includes matrices
A and B as inputs in an inputs/ sub-directory, and matrix C as the result of their multiplication
(which in the code is also passed as input, to have a matrix initialized with 0s).
For all the specific details on the fields provided in the JSON file, please refer to the
RO-Crate specification Website. Intuitively, if you search through
the JSON file you can find several interesting terms:
creator: List of authors, identified by their ORCID.
publisher: Organisations of the authors.
hasPart in ./: lists all the files and directories this workflow needs and generates, and also the ones included in the crate. The URIs point to the hostname where the application has been run, thus, tells the user where the inputs and outputs can be found (in this example, a BSC laptop).
ComputationalWorkflow: Main file of the application (in the example,
application_sources/matmul_directory.py). Includes theinputsandoutputsneeded and generated by the workflow, and a reference to the generated workflow image in theimagefield.version: The COMPSs specific version and build used to run this application. In the example:
3.0.rc2210. This is a very important field to achieve reproducibility or replicability, since COMPSs features may vary their behaviour in different versions of the programming model runtime.
We encourage the reader to navigate through this ro-crate-metadata.json file example to get familiar with its
contents. Many of the fields are easily and directly understandable.
{
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "./",
"@type": "Dataset",
"creator": [
{
"@id": "https://orcid.org/0000-0003-0606-2512"
},
{
"@id": "https://orcid.org/0000-0002-8291-8071"
},
{
"@id": "https://orcid.org/0000-0003-2941-5499"
}
],
"datePublished": "2022-10-24T08:52:07+00:00",
"description": "Hypermatrix size 2x2 blocks, block size 2x2 elements",
"hasPart": [
{
"@id": "application_sources/matmul_directory.py"
},
{
"@id": "complete_graph.svg"
},
{
"@id": "App_Profile.json"
},
{
"@id": "compss_command_line_arguments.txt"
},
{
"@id": "application_sources/matmul_tasks.py"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.1.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.1.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.1"
}
],
"license": "Apache-2.0",
"mainEntity": {
"@id": "application_sources/matmul_directory.py"
},
"name": "COMPSs Matrix Multiplication, out-of-core using files",
"publisher": [
{
"@id": "https://ror.org/05sd8tv96"
},
{
"@id": "https://ror.org/01z1gye03"
}
]
},
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
]
},
{
"@id": "https://orcid.org/0000-0003-0606-2512",
"@type": "Person",
"affiliation": {
"@id": "https://ror.org/05sd8tv96"
},
"contactPoint": {
"@id": "mailto:Raul.Sirvent@bsc.es"
},
"name": "Ra\u00fcl Sirvent"
},
{
"@id": "mailto:Raul.Sirvent@bsc.es",
"@type": "ContactPoint",
"contactType": "Author",
"email": "Raul.Sirvent@bsc.es",
"identifier": "Raul.Sirvent@bsc.es",
"url": "https://orcid.org/0000-0003-0606-2512"
},
{
"@id": "https://ror.org/05sd8tv96",
"@type": "Organization",
"name": "Barcelona Supercomputing Center"
},
{
"@id": "https://orcid.org/0000-0003-2941-5499",
"@type": "Person",
"affiliation": {
"@id": "https://ror.org/05sd8tv96"
},
"contactPoint": {
"@id": "mailto:Rosa.M.Badia@bsc.es"
},
"name": "Rosa M. Badia"
},
{
"@id": "mailto:Rosa.M.Badia@bsc.es",
"@type": "ContactPoint",
"contactType": "Author",
"email": "Rosa.M.Badia@bsc.es",
"identifier": "Rosa.M.Badia@bsc.es",
"url": "https://orcid.org/0000-0003-2941-5499"
},
{
"@id": "https://orcid.org/0000-0002-8291-8071",
"@type": "Person",
"affiliation": {
"@id": "https://ror.org/01z1gye03"
},
"contactPoint": {
"@id": "mailto:adam.hospital@irbbarcelona.org"
},
"name": "Adam Hospital"
},
{
"@id": "mailto:adam.hospital@irbbarcelona.org",
"@type": "ContactPoint",
"contactType": "Author",
"email": "adam.hospital@irbbarcelona.org",
"identifier": "adam.hospital@irbbarcelona.org",
"url": "https://orcid.org/0000-0002-8291-8071"
},
{
"@id": "https://ror.org/01z1gye03",
"@type": "Organization",
"name": "IRB Barcelona"
},
{
"@id": "application_sources/matmul_directory.py",
"@type": [
"File",
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"contentSize": 2151,
"description": "Main file of the COMPSs workflow source files",
"encodingFormat": "text/plain",
"image": {
"@id": "complete_graph.svg"
},
"input": [
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.1"
}
],
"name": "matmul_directory.py",
"output": [
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.1"
}
],
"programmingLanguage": {
"@id": "#compss"
}
},
{
"@id": "#compss",
"@type": "ComputerLanguage",
"alternateName": "COMPSs",
"citation": "https://doi.org/10.1007/s10723-013-9272-5",
"name": "COMPSs Programming Model",
"url": "http://compss.bsc.es/",
"version": "3.0.rc2210"
},
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/92",
"@type": "WebSite",
"name": "Scalable Vector Graphics"
},
{
"@id": "complete_graph.svg",
"@type": [
"File",
"ImageObject",
"WorkflowSketch"
],
"about": {
"@id": "application_sources/matmul_directory.py"
},
"contentSize": 6163,
"description": "The graph diagram of the workflow, automatically generated by COMPSs runtime",
"encodingFormat": [
[
"image/svg+xml",
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/92"
}
]
],
"name": "complete_graph.svg"
},
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/817",
"@type": "WebSite",
"name": "JSON Data Interchange Format"
},
{
"@id": "App_Profile.json",
"@type": "File",
"contentSize": 248,
"description": "COMPSs application Tasks profile",
"encodingFormat": [
"application/json",
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/817"
}
],
"name": "App_Profile.json"
},
{
"@id": "compss_command_line_arguments.txt",
"@type": "File",
"contentSize": 24,
"description": "COMPSs command line execution command, including parameters passed",
"encodingFormat": "text/plain",
"name": "compss_command_line_arguments.txt"
},
{
"@id": "application_sources/matmul_tasks.py",
"@type": "File",
"contentSize": 1721,
"description": "Auxiliary File",
"encodingFormat": "text/plain",
"name": "matmul_tasks.py"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.0.0",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "A.0.0",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.0.1",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "A.0.1",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.1.0",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "A.1.0",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.1.1",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "A.1.1",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.0.0",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "B.0.0",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.0.1",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "B.0.1",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.1.0",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "B.1.0",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.1.1",
"@type": "File",
"contentSize": 16,
"dateModified": "2022-05-17T10:14:33",
"name": "B.1.1",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/",
"@type": "Dataset",
"dateModified": "2022-05-17T10:14:33",
"hasPart": [
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/A/A.1.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.0.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.0.1"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.1.0"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/inputs/B/B.1.1"
}
],
"name": "inputs",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.0",
"@type": "File",
"contentSize": 20,
"dateModified": "2022-10-24T08:52:02",
"name": "C.0.0",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.0.1",
"@type": "File",
"contentSize": 20,
"dateModified": "2022-10-24T08:52:02",
"name": "C.0.1",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.0",
"@type": "File",
"contentSize": 20,
"dateModified": "2022-10-24T08:52:02",
"name": "C.1.0",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
},
{
"@id": "file://bsccs742.int.bsc.es/Users/rsirvent/COMPSs-DP/matmul_directory/C.1.1",
"@type": "File",
"contentSize": 20,
"dateModified": "2022-10-24T08:52:02",
"name": "C.1.1",
"sdDatePublished": "2022-10-24T08:52:07+00:00"
}
]
}
ro-crate-metadata.json Java COMPSs example (MN4 supercomputer)
In this second ro-crate-metadata.json example, we want to illustrate the provenance result of a Java COMPSs
application execution in the MareNostrum 4 supercomputer. We show the execution of a matrix LU factorization
for out-of-core sparse matrices implemented with COMPSs and using the Java programming language. In this algorithm,
matrix A is both input and output of the workflow, since the factorization overwrites the original value of A.
In addition, we have used a 4x4 blocks hyper-matrix (i.e., the matrix is divided in 16 blocks, that contain 16
elements each) and, if a block is all 0s, the corresponding file will not be
created in the file system (in the example, this happens for blocks A.0.3, A.1.3, A.3.0 and A.3.1).
Apart from the terms already mentioned in the previous example (creator, publisher, hasPart,
ComputationalWorkflow, version), if we first observe the ro-crate-info.yaml file:
COMPSs Workflow Information:
name: COMPSs Sparse LU
description: The Sparse LU application computes an LU matrix factorization on a sparse blocked matrix. The matrix size (number of blocks) and the block size are parameters of the application.
license: Apache-2.0 #Provide better a URL, but these strings are accepted:
# https://about.workflowhub.eu/Workflow-RO-Crate/#supported-licenses
sources_dir: [src, jar, xml]
files: [Readme, pom.xml, ro-crate-info.yaml]
Authors:
- name: Raül Sirvent
e-mail: Raul.Sirvent@bsc.es
orcid: https://orcid.org/0000-0003-0606-2512
organisation_name: Barcelona Supercomputing Center
ror: https://ror.org/05sd8tv96
We can see that we have specified several directories to be added as source files: the src folder that contains the
.java and .class files, the jar folder with the sparseLU.jar file, and the xml folder with extra
xml configuration files. Besides, we also add the Readme, pom.xml, and the ro-crate-info.yaml file itself,
so they are packed in the resulting crate. This example also shows that the script is able to select the correct
SparseLU.java main file from the ones specified as sources_dir, although three files use the same file name (i.e.,
they implement 3 versions of the same algorithm: using files, arrays or objects).
It is also interesting to note the differences in the URIs used to reference input and output files when provenance is
run in a supercomputer, instead of a laptop (as shown in the previous example). Since we do not add explicitly the input
and output files of a workflow (because they could be extremely large), our crate only includes references to them,
which are ment as pointers to where files can be found, rather than a publicly accessible URI reference. Therefore,
while in the PyCOMPSs previous example files could be found in the bsccs742.int.bsc.es laptop, in this Java COMPSs
example files can be found in s02r2b45-ib0 hostname, which is an internal hostname of MN4. This means that, for
reproducibility purposes, a new user would have to request input and output files to bsccs742.int.bsc.es
laptop’s owner in the first case, or request access to the MN4 paths specified by the corresponding URIs, in the
second case.
{
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "./",
"@type": "Dataset",
"creator": [
{
"@id": "https://orcid.org/0000-0003-0606-2512"
}
],
"datePublished": "2022-10-24T09:31:39+00:00",
"description": "The Sparse LU application computes an LU matrix factorization on a sparse blocked matrix. The matrix size (number of blocks) and the block size are parameters of the application.",
"hasPart": [
{
"@id": "application_sources/src/main/java/sparseLU/files/Block.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUItf.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUImpl.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLU.java"
},
{
"@id": "complete_graph.svg"
},
{
"@id": "App_Profile.json"
},
{
"@id": "compss_command_line_arguments.txt"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/Block.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUItf.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUImpl.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLU.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/objects/Block.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/objects/SparseLUItf.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/objects/SparseLU.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/objects/Block.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/objects/SparseLUItf.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/objects/SparseLU.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/arrays/SparseLUItf.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/arrays/SparseLUImpl.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/arrays/SparseLU.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/arrays/SparseLUItf.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/arrays/SparseLUImpl.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/arrays/SparseLU.class"
},
{
"@id": "application_sources/jar/sparseLU.jar"
},
{
"@id": "application_sources/xml/resources.xml"
},
{
"@id": "application_sources/xml/project.xml"
},
{
"@id": "application_sources/Readme"
},
{
"@id": "application_sources/pom.xml"
},
{
"@id": "application_sources/ro-crate-info.yaml"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.3"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.3.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.3.3"
}
],
"license": "Apache-2.0",
"mainEntity": {
"@id": "application_sources/src/main/java/sparseLU/files/SparseLU.java"
},
"name": "COMPSs Sparse LU",
"publisher": [
{
"@id": "https://ror.org/05sd8tv96"
}
]
},
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
]
},
{
"@id": "https://orcid.org/0000-0003-0606-2512",
"@type": "Person",
"affiliation": {
"@id": "https://ror.org/05sd8tv96"
},
"contactPoint": {
"@id": "mailto:Raul.Sirvent@bsc.es"
},
"name": "Ra\u00fcl Sirvent"
},
{
"@id": "mailto:Raul.Sirvent@bsc.es",
"@type": "ContactPoint",
"contactType": "Author",
"email": "Raul.Sirvent@bsc.es",
"identifier": "Raul.Sirvent@bsc.es",
"url": "https://orcid.org/0000-0003-0606-2512"
},
{
"@id": "https://ror.org/05sd8tv96",
"@type": "Organization",
"name": "Barcelona Supercomputing Center"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/Block.java",
"@type": "File",
"contentSize": 5589,
"description": "Auxiliary File",
"encodingFormat": "text/plain",
"name": "Block.java"
},
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/x-fmt/415",
"@type": "WebSite",
"name": "Java Compiled Object Code"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUItf.class",
"@type": "File",
"contentSize": 904,
"description": "Auxiliary File",
"encodingFormat": [
[
"Java .class",
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/x-fmt/415"
}
]
],
"name": "SparseLUItf.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUImpl.java",
"@type": "File",
"contentSize": 2431,
"description": "Auxiliary File",
"encodingFormat": "text/plain",
"name": "SparseLUImpl.java"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLU.java",
"@type": [
"File",
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"contentSize": 6602,
"description": "Main file of the COMPSs workflow source files",
"encodingFormat": "text/plain",
"image": {
"@id": "complete_graph.svg"
},
"input": [
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.3"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.3.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.3.3"
}
],
"name": "SparseLU.java",
"output": [
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.0.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.1.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.0"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.1"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.2.3"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.3.2"
},
{
"@id": "file://s02r2b45-ib0/gpfs/home/bsc19/bsc19057/COMPSs-DP/tutorial_apps/java/sparseLU/A.3.3"
}
],
"programmingLanguage": {
"@id": "#compss"
}
},
{
"@id": "#compss",
"@type": "ComputerLanguage",
"alternateName": "COMPSs",
"citation": "https://doi.org/10.1007/s10723-013-9272-5",
"name": "COMPSs Programming Model",
"url": "http://compss.bsc.es/",
"version": "3.0.rc2210"
},
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/92",
"@type": "WebSite",
"name": "Scalable Vector Graphics"
},
{
"@id": "complete_graph.svg",
"@type": [
"File",
"ImageObject",
"WorkflowSketch"
],
"about": {
"@id": "application_sources/src/main/java/sparseLU/files/SparseLU.java"
},
"contentSize": 21106,
"description": "The graph diagram of the workflow, automatically generated by COMPSs runtime",
"encodingFormat": [
[
"image/svg+xml",
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/92"
}
]
],
"name": "complete_graph.svg"
},
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/817",
"@type": "WebSite",
"name": "JSON Data Interchange Format"
},
{
"@id": "App_Profile.json",
"@type": "File",
"contentSize": 1584,
"description": "COMPSs application Tasks profile",
"encodingFormat": [
"application/json",
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/817"
}
],
"name": "App_Profile.json"
},
{
"@id": "compss_command_line_arguments.txt",
"@type": "File",
"contentSize": 28,
"description": "COMPSs command line execution command, including parameters passed",
"encodingFormat": "text/plain",
"name": "compss_command_line_arguments.txt"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/Block.class",
"@type": "File",
"contentSize": 4135,
"description": "Auxiliary File",
"encodingFormat": [
[
"Java .class",
{
"@id": "https://www.nationalarchives.gov.uk/PRONOM/x-fmt/415"
}
]
],
"name": "Block.class"
},
{
"@id": "application_sources/src/main/java/sparseLU/files/SparseLUItf.java",
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