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WIP: Added json conversion of NWChem to workflow #557

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WIP: Added json conversion of NWChem to workflow #557

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cf24e7c
Added method to call json conversion script.
chetnieter Dec 7, 2016
70e29e3
Added redirect to nwchen submission script.
chetnieter Dec 8, 2016
dc65096
Moved json conversion to its own task.
chetnieter Dec 8, 2016
1d35945
Initial Dockerfile for nwchem-json container.
chetnieter Dec 12, 2016
23df0c4
Using docker container for nwchem json conversion.
chetnieter Dec 14, 2016
e8a050c
Passing in nwchem output filename on command line.
chetnieter Dec 15, 2016
0407b9e
Clean up before pausing work.
chetnieter Dec 16, 2016
c57d0ab
Merge branch 'master' into nwchem-json-generation
chetnieter Dec 18, 2016
a7bd2df
Changes from code review.
chetnieter Dec 19, 2016
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1 change: 1 addition & 0 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
backports.tempfile==1.0rc1
jsonschema==2.4.0
jsonpath-rw==1.4.0
jsonpath-rw-ext==1.0.0
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0 docker/Dockerfile → server/docker/nwchem/Dockerfile
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17 changes: 6 additions & 11 deletions server/taskflows/hpccloud/taskflow/nwchem/__init__.py
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Expand Up @@ -16,11 +16,11 @@
# See the License for the specific language governing permissions and
# limitations under the License.
###############################################################################
import tempfile
import json
import os
import subprocess
import shutil
from backports.tempfile import TemporaryDirectory
from jsonpath_rw import parse
from celery.exceptions import Retry

Expand Down Expand Up @@ -226,9 +226,8 @@ def create_json_output(task, upstream_result):
job_dir = job_directory(cluster, job)
out_file = '%s.out' % (job['name'])

try:
with TemporaryDirectory() as tmp_dir:
# Copy the nwchem output to server
tmp_dir = tempfile.mkdtemp()
cluster_path = os.path.join(job_dir, out_file)
local_path = os.path.join(tmp_dir, out_file)
with open(local_path, 'w') as local_fp:
Expand All @@ -244,9 +243,10 @@ def create_json_output(task, upstream_result):
stdout, stderr = p.communicate()

if p.returncode != 0:
print('Error running Docker container.')
print('STDOUT: ' + stdout)
print('STDERR: ' + stderr)
task
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@cjh1 cjh1 Jan 2, 2017

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Look like this is a typo?

task.logger.error('Error running Docker container.')
task.logger.error('STDOUT: ' + stdout)
task.logger.error('STDERR: ' + stderr)
raise Exception('Docker returned code {}.'.format(p.returncode))

# Copy json file back to cluster?
Expand All @@ -256,11 +256,6 @@ def create_json_output(task, upstream_result):
with open(local_path, 'r') as local_fp:
conn.put(local_fp, cluster_path)
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@cjh1 cjh1 Dec 16, 2016

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We don't need the JSON back on the cluster, it should just be uploaded to Girder

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@cjh1 cjh1 Jan 3, 2017

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@chetnieter We should factor out the docker run code into a set of function that can be reused by other taskflows.


# Delete temporary storage
finally:
if os.path.exists(tmp_dir):
shutil.rmtree(tmp_dir)

return upstream_result

@cumulus.taskflow.task
Expand Down