Closed gcapes closed 5 months ago
gcapes
commented
5 months ago Some errors fixed in 7249799, but I got a python syntax error. Now I'm using a newer version locally to debug faster, and I'm running into more 'new version' errors, some of which are now fixed, but I've not been able to copy the friction_conductance.inp file to the execute directory. Have asked Adam how command_files are supposed to work and what I'm doing wrong.
gcapes
commented
5 months ago This workflow is now working fine locally, but I'm having trouble getting the latest matflow installed and working correctly in my user space.
I get this, which I've sent to Adam for help
$ matflow go workflow.yaml
ERROR matflow.persistence: batch update exception!
Traceback (most recent call last):
File "/net/scratch2/mbexegc2/matflow-venv/bin/matflow", line 8, in <module>
sys.exit(cli())
^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/cli.py", line 156, in make_and_submit_workflow
out = app.make_and_submit_workflow(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/app.py", line 280, in <lambda>
return lambda *args, **kwargs: func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/app.py", line 1403, in _make_and_submit_workflow
submitted_js = wk.submit(
^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/core/workflow.py", line 2209, in submit
exceptions, submitted_js = self._submit(
^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/log.py", line 25, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/core/workflow.py", line 2131, in _submit
self._store._pending.commit_all()
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/log.py", line 25, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/persistence/pending.py", line 133, in commit_all
getattr(self, meth)()
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/log.py", line 25, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/persistence/pending.py", line 304, in commit_EAR_submission_indices
self.store._update_EAR_submission_indices(self.set_EAR_submission_indices)
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/log.py", line 25, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/hpcflow/sdk/persistence/zarr.py", line 615, in _update_EAR_submission_indices
arr[EAR_ID_i] = new_EAR_i.encode(attrs, self.ts_fmt)
~~~^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 1452, in __setitem__
self.set_basic_selection(pure_selection, value, fields=fields)
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 1548, in set_basic_selection
return self._set_basic_selection_nd(selection, value, fields=fields)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 1938, in _set_basic_selection_nd
self._set_selection(indexer, value, fields=fields)
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 2011, in _set_selection
self._chunk_setitems(lchunk_coords, lchunk_selection, chunk_values, fields=fields)
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 2202, in _chunk_setitems
cdatas = {
^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 2203, in <dictcomp>
key: self._process_for_setitem(key, sel, val, fields=fields)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/net/scratch2/mbexegc2/matflow-venv/lib/python3.11/site-packages/zarr/core.py", line 2285, in _process_for_setitem
chunk = value.astype(self._dtype, order=self._order, copy=False)
^^^^^^^^^^^^
AttributeError: 'list' object has no attribute 'astype'
I've sent the error and workflow to Adam - waiting to hear back.