Support VPSC

[Gbowker]

See branch software/VPSC.
Detail:
Add support for VPSC as an additional option of task for crystal plasticity modelling.
I have begun development of this new feature, and will need as much support as possible to implement it. I expect many child issues to arise from this, but I thought it best to start the work on it sooner rather than later.
Thanks,

Guy

[Gbowker]

See commit 4b7b96a
Made a start transferring the functions from matflow-vpsc.
Please see the instruction manual for VPSC
Also see the Github repo for VPSC
Everything we require is already available.
The Aims and objectives we need to incorporate this are as follows:

• Aim: Get matflow to generate VPSC input files

  • objective: First run VPSC independant of matflow to learn input files required and where install on CSF3 is.
    NOTE: VPSC is implicit. To run a simulation, you may cannot define the input files to the command which runs the simulation as flags, they are implicitly determined from the .in file in the target directory you. run the simulation command within. in addition, you must have the compiled fortran executible in the target directory you wish to run and output the simulation results into.
    Update: VPSC8 has 4 required and 2 optional input files needed to run a simulation:
    1. REQUIRED: VPSC8.in file (must be all caps and always same name). This is master input file which contains paths to the others. Needs to beside the compiled vpsc8 exectutable.
    2. REQUIRED: .tex texture file. Contains texture of all grains as bunge-euler angles with volume fraction in plaintext.
    3. REQUIRED: .sx or .MTS single crystal file. Contains single crystal elastic, thermal and plastic parameters in plaintext.
    4. OPTIONAL: .c5 grain shape file. Contains dimensions of grains in units scaled to VE in plaintext.
    5. OPTIONAL: `` unable to determine this for now, Contains diffraction information.
    6. REQUIRED: .<int> where is some integer, Contains loadcases and loadsteps in plaintext.
    Update: Upon termination of the run, no master output file is produced. Stress, strain, and texture predictions are found in plaintext `STR_STR.OUT` and `TEX_PH1.OUT` files. It will take some work to convert the results in these to numpy arrays which can be passed between other tasks / subtasks!
  • objective: May need to first incorporate a VE generation task required for VPSC (such as neper) This will require it's own issue and pull request, stay tuned...
  • objective: Next, write demo-workflow tension_VPSC_Al replacing damask task inputs with VPSC ones.
  • objective: Add task schema for this task, linking the inputs to their file-generating scripts written by @mikesmic (stored in data/scripts/VPSC/)
  • objective: create vpsc-parse python environment using requirements.txt from the old matflow-vpsc.
  • objective: add this to a envs.yaml file named envs-vpsc.yaml and point config.yaml file to this new envs file.
  • Attempt matflow go tension_VPSC_Al and check if the task produced the input files required for the simulation in execute.

• Aim: Get matflow to simulate deformation using VPSC

  • objective: Create matflow environment in envs-vpsc.yaml which loads the installation of vpsc then runs it using the input files previously generated by the task.
  • objective: Need to know the command which initiates a VPSC simulation. (for damask its mpirun singularity run $IMG_PATH) parallelisation can be a later goal, for now getting it to run on one serial core alone is a good goal.
  • objective: Attempt matflow go tension_VPSC_Al and check if the simulation produced an output file in execute.

This is the plan for now, I will update it when we are further along and know more.
Any suggestions please feel free to edit this plan.
Thanks,
guy

[Gbowker]

Please see
hpcflow/matflow-environments#3
For my PR creating a matflow-env for vpsc. Its shaky at the moment as everything else has been nicely packaged using conda or the like. This should be easy to do for VPSC as it's just compiled fortran which becomes an executible.
My idea is that the compiled exe could be saved to RDS and made into a module so that matflow only need load the module and run the command vpsc. Becuase it's input files are implicit however matflow will need to be told to look for the input files in the PWD.

[Gbowker]

Update:
I've already created a module file with the compiled VPSC code. This is what is needed in the batch script to run it:

# Load any required modulefiles. A purge is used to start with a clean environment.
module purge

# Then load VPSC module
module use --append /mnt/eps01-rds/Fonseca-Lightform/shared/software/modulefiles
module load vpsc/8.0.0

# Begin VPSC8 simulation
$VPSC

[gcapes]

Should now be at the stage where you can create a workflow with a task to create a volume element, then this task schema with load case defined, and the rest taking default values. That should hopefully then run VPSC on the generated input files.

[gcapes]

I'm trying to run this demo workflow, and what I'm currently confused about is that vpsc/write_vpsc_in.py doesn't look to use the volume_element at all. The task schema is called simulate_VE_loading_vpsc, so the idea should be to simulate loading of the VE, right?

By way of comparison, matflow/data/scripts/damask/write_geom.py has volume_element as one of the input parameters. I don't see that VPSC is currently doing anything with the VE to create the VPSC8.in file. Have I missed something here?

[gcapes]

I'm currently getting an error (this is using MatFlow, version 0.3.0a218, on the vpsc branch).

...
  File "/net/scratch/mbexegc2/vpsc/.venv/lib/python3.12/site-packages/hpcflow/sdk/core/workflow.py", line 3869, in _add_submission
    sub_obj._set_environments()
  File "/net/scratch/mbexegc2/vpsc/.venv/lib/python3.12/site-packages/hpcflow/sdk/log.py", line 81, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/net/scratch/mbexegc2/vpsc/.venv/lib/python3.12/site-packages/hpcflow/sdk/submission/submission.py", line 203, in _set_environments
    raise MissingEnvironmentError(env_spec) from None
hpcflow.sdk.core.errors.MissingEnvironmentError: The environment 'damask_parse_env' is not defined on this machine, so the submission cannot be created.

But I do have a damask_parse_env defined in my environment file, which is pointed to in my config file.
@aplowman Any ideas on this one? Is there a new format/location that I need with this version of MatFlow?

My previously working matflow version was .0a200, which has just successfully submitted a tension_DAMASK_Al using the same environment/config files.