Gibbs workflow error

Atomate
1

Hi,

Running the Gibbs workflow in the atomate tutorial I, I get the following error on the Elastic Tensor Fitting Firework:

Traceback (most recent call last):

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/fireworks/core/rocket.py”, line 253, in run

m_action = t.run_task(my_spec)

File “/global/u2/a/ardunn/tutorials/atomate_dev/codes/atomate/atomate/vasp/firetasks/parse_outputs.py”, line 547, in run_task

coll.insert_one(gibbs_dict)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/collection.py”, line 670, in insert_one

bypass_doc_val=bypass_document_validation),

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/collection.py”, line 575, in _insert

check_keys, manipulate, write_concern, op_id, bypass_doc_val)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/collection.py”, line 556, in _insert_one

check_keys=check_keys)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/pool.py”, line 482, in command

self._raise_connection_failure(error)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/pool.py”, line 610, in _raise_connection_failure

raise error

InvalidDocument: Cannot encode object: array([-10.88950285])

All other fireworks (all transmuters, bulk optimization) launch and finish successfully . Has anyone else had this problem and/or know how to fix it?

If I’m not mistaken, this happens sometimes when trying to store numpy arrays with pymongo.

Thanks,

Alex

2

Yes this would happen when trying to stick a numpy array in pymongo

Feel free to open a ticket in atomate Github issues. The quick fix is to use monty’s jsanitize() on the object but it would be better if someone actually converted the numpy arrays to list first. Probably Kiran or Brandon would be the one to do it.

Best,

Anubhav

···

On Mon, Sep 11, 2017 at 2:17 PM, [email protected] wrote:

Hi,

Running the Gibbs workflow in the atomate tutorial I, I get the following error on the Elastic Tensor Fitting Firework:

Traceback (most recent call last):

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/fireworks/core/rocket.py”, line 253, in run

m_action = t.run_task(my_spec)

File “/global/u2/a/ardunn/tutorials/atomate_dev/codes/atomate/atomate/vasp/firetasks/parse_outputs.py”, line 547, in run_task

coll.insert_one(gibbs_dict)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/collection.py”, line 670, in insert_one

bypass_doc_val=bypass_document_validation),

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/collection.py”, line 575, in _insert

check_keys, manipulate, write_concern, op_id, bypass_doc_val)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/collection.py”, line 556, in _insert_one

check_keys=check_keys)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/pool.py”, line 482, in command

self._raise_connection_failure(error)

File “/global/homes/a/ardunn/.conda/envs/atomate_dev_env/lib/python2.7/site-packages/pymongo/pool.py”, line 610, in _raise_connection_failure

raise error

InvalidDocument: Cannot encode object: array([-10.88950285])

All other fireworks (all transmuters, bulk optimization) launch and finish successfully . Has anyone else had this problem and/or know how to fix it?

If I’m not mistaken, this happens sometimes when trying to store numpy arrays with pymongo.

Thanks,

Alex

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Best,
Anubhav