Merge pull request #46 from deepmodeling/devel-1.0

1.0.2-compatible with Bohrium App

apex/__init__.py

@@ -1,5 +1,5 @@
 import os
-__version__ = '1.0.1'
+__version__ = '1.0.2'
 LOCAL_PATH = os.getcwd()
 
 

apex/core/property/EOS.py

@@ -10,7 +10,7 @@
 import apex.core.calculator.lib.abacus as abacus
 import apex.core.calculator.lib.vasp as vasp
 import apex.core.calculator.lib.abacus_scf as abacus_scf
-from apex.core.Property import Property
+from apex.core.property.Property import Property
 from apex.core.refine import make_refine
 from apex.core.reproduce import make_repro, post_repro
 from dflow.python import upload_packages

apex/core/property/Elastic.py

@@ -14,7 +14,7 @@
 import apex.core.calculator.lib.abacus as abacus
 import apex.core.calculator.lib.vasp as vasp
 import apex.core.calculator.lib.abacus_scf as abacus_scf
-from apex.core.Property import Property
+from apex.core.property.Property import Property
 from apex.core.refine import make_refine
 from apex.core.calculator.lib.vasp import incar_upper
 from dflow.python import upload_packages

apex/core/property/Gamma.py

@@ -13,7 +13,7 @@
 
 import apex.core.calculator.lib.abacus as abacus
 import apex.core.calculator.lib.vasp as vasp
-from apex.core.Property import Property
+from apex.core.property.Property import Property
 from apex.core.refine import make_refine
 from apex.core.reproduce import make_repro, post_repro
 from apex.core.structure import StructureInfo

apex/core/property/Interstitial.py

@@ -3,7 +3,6 @@
 import logging
 import os
 import re
-import copy
 
 import numpy as np
 from monty.serialization import dumpfn, loadfn
@@ -12,7 +11,7 @@
 
 import apex.core.calculator.lib.abacus as abacus
 import apex.core.calculator.lib.lammps as lammps
-from apex.core.Property import Property
+from apex.core.property.Property import Property
 from apex.core.refine import make_refine
 from apex.core.reproduce import make_repro, post_repro
 from apex.core.structure import StructureInfo

apex/core/property/Surface.py

@@ -12,7 +12,7 @@
 
 import apex.core.calculator.lib.abacus as abacus
 import apex.core.calculator.lib.vasp as vasp
-from apex.core.Property import Property
+from apex.core.property.Property import Property
 from apex.core.refine import make_refine
 from apex.core.reproduce import make_repro, post_repro
 from dflow.python import upload_packages

apex/core/property/Vacancy.py

@@ -10,7 +10,7 @@
 from pymatgen.core.structure import Structure
 
 import apex.core.calculator.lib.abacus as abacus
-from apex.core.Property import Property
+from apex.core.property.Property import Property
 from apex.core.refine import make_refine
 from apex.core.reproduce import make_repro, post_repro
 from dflow.python import upload_packages

apex/flow.py

@@ -158,9 +158,10 @@ def _set_props_flow(
     def submit_relax(
             self,
             work_dir: Union[os.PathLike, str],
-            relax_parameter: dict
+            relax_parameter: dict,
+            labels: Optional[dict] = None
     ):
-        wf = Workflow(name='relaxation')
+        wf = Workflow(name='relaxation', labels=labels)
         relaxation = self._set_relax_flow(
             input_work_dir=upload_artifact(work_dir),
             relax_parameter=relax_parameter
@@ -177,14 +178,15 @@ def submit_relax(
     def submit_props(
             self,
             work_dir: Union[os.PathLike, str],
-            props_parameter: dict
+            props_parameter: dict,
+            labels: Optional[dict] = None
     ):
-        wf = Workflow(name='property')
-        property = self._set_props_flow(
+        wf = Workflow(name='property', labels=labels)
+        properties = self._set_props_flow(
             input_work_dir=upload_artifact(work_dir),
             props_parameter=props_parameter
         )
-        wf.add(property)
+        wf.add(properties)
         wf.submit()
         self.download(
             wf, step_name='property-cal',
@@ -197,19 +199,20 @@ def submit_joint(
             self,
             work_dir: Union[os.PathLike, str],
             relax_parameter: dict,
-            props_parameter: dict
+            props_parameter: dict,
+            labels: Optional[dict] = None
     ):
-        wf = Workflow(name='joint')
+        wf = Workflow(name='joint', labels=labels)
         relaxation = self._set_relax_flow(
             input_work_dir=upload_artifact(work_dir),
             relax_parameter=relax_parameter
         )
-        property = self._set_props_flow(
+        properties = self._set_props_flow(
             input_work_dir=relaxation.outputs.artifacts["output_all"],
             props_parameter=props_parameter
         )
         wf.add(relaxation)
-        wf.add(property)
+        wf.add(properties)
         wf.submit()
         self.download(
             wf, step_name='property-cal',

apex/submit.py

@@ -11,7 +11,6 @@
 from .flow import FlowFactory
 
 
-
 def judge_flow(parameter, specify) -> (Type[OP], str, str, dict, dict):
     # identify type of flow and input parameter file
     num_args = len(parameter)
@@ -81,40 +80,49 @@ def judge_flow(parameter, specify) -> (Type[OP], str, str, dict, dict):
     return run_op, task_type, flow_type, relax_param, props_param
 
 
-def submit(flow,
-           flow_type,
-           work_dir,
-           relax_param,
-           props_param,
-           conf=config,
-           s3_conf=s3_config):
+def submit(
+        flow,
+        flow_type,
+        work_dir,
+        relax_param,
+        props_param,
+        conf=config,
+        s3_conf=s3_config,
+        labels=None,
+):
     # reset dflow global config for sub-processes
     config.update(conf)
     s3_config.update(s3_conf)
 
     if flow_type == 'relax':
         flow.submit_relax(
             work_dir=work_dir,
-            relax_parameter=relax_param
+            relax_parameter=relax_param,
+            labels=labels
         )
     elif flow_type == 'props':
         flow.submit_props(
             work_dir=work_dir,
-            props_parameter=props_param
+            props_parameter=props_param,
+            labels=labels
         )
     elif flow_type == 'joint':
         flow.submit_joint(
             work_dir=work_dir,
             props_parameter=props_param,
-            relax_parameter=relax_param
+            relax_parameter=relax_param,
+            labels=labels
         )
 
 
-def submit_workflow(parameter,
-                    config_file,
-                    work_dir,
-                    flow_type,
-                    is_debug=False):
+def submit_workflow(
+        parameter,
+        config_file,
+        work_dir,
+        flow_type,
+        is_debug=False,
+        labels=None
+):
     try:
         config_dict = loadfn(config_file)
     except FileNotFoundError:
@@ -179,11 +187,11 @@ def submit_workflow(parameter,
         for ii in work_dir_list:
             res = pool.apply_async(
                 submit,
-                (flow, flow_type, ii, relax_param, props_param, config, s3_config)
+                (flow, flow_type, ii, relax_param, props_param, config, s3_config, labels)
             )
         pool.close()
         pool.join()
     elif len(work_dir_list) == 1:
-        submit(flow, flow_type, work_dir_list[0], relax_param, props_param)
+        submit(flow, flow_type, work_dir_list[0], relax_param, props_param, labels=labels)
 
     print('Completed!')

examples/abacus_demo/global_bohrium.json

@@ -4,7 +4,7 @@
     "email": "YOUR_EMAIL",
     "password": "YOUR_PASSWD",
     "program_id": 1234,
-    "apex_image_name":"registry.dp.tech/dptech/prod-11045/apex-dependencies:1.0.0",
+    "apex_image_name":"registry.dp.tech/dptech/prod-11045/apex-dependency:1.0",
     "abacus_image_name":"registry.dp.tech/dptech/prod-11461/abacus:phonopy",
     "abacus_run_command":"ulimit -s unlimited && ulimit -m unlimited && OMP_NUM_THREADS=1 mpirun -np 32 abacus > log",
     "batch_type": "Bohrium",

examples/lammps_demo/global_bohrium.json

@@ -4,7 +4,7 @@
     "email": "YOUR@EMAIL",
     "password": "YOURPASSWD",
     "program_id": 1234,
-    "apex_image_name":"registry.dp.tech/dptech/prod-11045/apex-dependencies:1.0.0",
+    "apex_image_name":"registry.dp.tech/dptech/prod-11045/apex-dependency:1.0",
     "lammps_image_name": "registry.dp.tech/dptech/prod-11045/deepmd-kit:deepmd-kit2.1.1_cuda11.6_gpu",
     "group_size": 2,
     "pool_size": 1,

examples/vasp_demo/global_bohrium.json

@@ -5,7 +5,7 @@
     "password": "YOUR_PASSWD",
     "program_id": 1234,
     "group_size": 2,
-    "apex_image_name":"registry.dp.tech/dptech/prod-11045/apex-dependencies:1.0.0",
+    "apex_image_name":"registry.dp.tech/dptech/prod-11045/apex-dependency:1.0",
     "vasp_image_name":"registry.dp.tech/dptech/vasp:5.4.4-dflow",
     "vasp_run_command":"bash -c \"source /opt/intel/oneapi/setvars.sh && ulimit -s unlimited && mpirun -n 32 /opt/vasp.5.4.4/bin/vasp_std \"",
     "batch_type": "Bohrium",

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="apex-flow",
-    version="1.0.1",
+    version="1.0.2",
     author="Zhuoyuan Li, Tongqi Wen",
     author_email="zhuoyli@outlook.com",
     description="Alloy Properties EXplorer using simulations",