This page should contain a short guide on what the plugin does and a short example on how to use the plugin.
Use the following commands to install the plugin:
git clone https://github.com/aiidateam/aiida-diff . cd aiida-diff pip install -e . # also installs aiida, if missing (but not postgres) #pip install -e .[pre-commit,testing] # install extras for more features verdi quicksetup # better to set up a new profile verdi plugin list aiida.calculations # should now show your calculation plugins
verdi code setup with the
diff input plugin
to set up an AiiDA code for aiida-diff.
A quick demo of how to submit a calculation:
verdi daemon start # make sure the daemon is running cd examples verdi run test_submit.py # submit test calculation verdi calculation list -a # check status of calculation
If you have already set up your own aiida_diff code using
verdi code setup, you may want to try the following command:
diff-submit # uses aiida_diff.cli
AiiDA calculation plugin wrapping the diff executable. Simple AiiDA plugin wrapper for ‘diffing’ two files.
- code, Code, optional – The Code to use for this job. This input is required, unless the remote_folder input is specified, which means an existing job is being imported and no code will actually be run.
- file1, SinglefileData, required – First file to be compared.
- file2, SinglefileData, required – Second file to be compared.
- metadata, Namespace
- call_link_label, str, optional, non_db – The label to use for the CALL link if the process is called by another process.
- computer, Computer, optional, non_db – When using a “local” code, set the computer on which the calculation should be run.
- description, str, optional, non_db – Description to set on the process node.
- dry_run, bool, optional, non_db – When set to True will prepare the calculation job for submission but not actually launch it.
- label, str, optional, non_db – Label to set on the process node.
- options, Namespace
- account, str, optional, non_db – Set the account to use in for the queue on the remote computer
- additional_retrieve_list, (list, tuple), optional, non_db – List of relative file paths that should be retrieved in addition to what the plugin specifies.
- append_text, str, optional, non_db – Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
- custom_scheduler_commands, str, optional, non_db – Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the prepend_text is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
- environment_variables, dict, optional, non_db – Set a dictionary of custom environment variables for this calculation
- environment_variables_double_quotes, bool, optional, non_db – If set to True, use double quotes instead of single quotes to escape the environment variables specified in
- import_sys_environment, bool, optional, non_db – If set to true, the submission script will load the system environment variables
- input_filename, str, optional, non_db – Filename to which the input for the code that is to be run is written.
- max_memory_kb, int, optional, non_db – Set the maximum memory (in KiloBytes) to be asked to the scheduler
- max_wallclock_seconds, int, optional, non_db – Set the wallclock in seconds asked to the scheduler
- mpirun_extra_params, (list, tuple), optional, non_db – Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params extra_params … exec.x
- output_filename, str, optional, non_db
- parser_name, str, optional, non_db – Set a string for the output parser. Can be None if no output plugin is available or needed
- prepend_text, str, optional, non_db – Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
- priority, str, optional, non_db – Set the priority of the job to be queued
- qos, str, optional, non_db – Set the quality of service to use in for the queue on the remote computer
- queue_name, str, optional, non_db – Set the name of the queue on the remote computer
- rerunnable, bool, optional, non_db – Determines if the calculation can be requeued / rerun.
- resources, dict, required, non_db – Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
- scheduler_stderr, str, optional, non_db – Filename to which the content of stderr of the scheduler is written.
- scheduler_stdout, str, optional, non_db – Filename to which the content of stdout of the scheduler is written.
- stash, Namespace – Optional directives to stash files after the calculation job has completed.
- source_list, (tuple, list), optional, non_db – Sequence of relative filepaths representing files in the remote directory that should be stashed.
- stash_mode, str, optional, non_db – Mode with which to perform the stashing, should be value of `aiida.common.datastructures.StashMode.
- target_base, str, optional, non_db – The base location to where the files should be stashd. For example, for the copy stash mode, this should be an absolute filepath on the remote computer.
- submit_script_filename, str, optional, non_db – Filename to which the job submission script is written.
- withmpi, bool, optional, non_db – Set the calculation to use mpi
- store_provenance, bool, optional, non_db – If set to False provenance will not be stored in the database.
- parameters, DiffParameters, required – Command line parameters for diff
- remote_folder, RemoteData, optional – Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the CalcJob as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this RemoteData will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.
- diff, SinglefileData, required – diff between file1 and file2.
- remote_folder, RemoteData, required – Input files necessary to run the process will be stored in this folder node.
- remote_stash, RemoteStashData, optional – Contents of the stash.source_list option are stored in this remote folder after job completion.
- retrieved, FolderData, required – Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in CalcInfo.retrieve_list.