Merge pull request #3 from Dead-fisher/master

Add unittests. Make it running on localhost
deepmodeling · Jun 7, 2021 · 5f2a3ef · 5f2a3ef
2 parents f3afb51 + d1f62d6
commit 5f2a3ef
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,26 @@
+name: rid python package test
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  Unittest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup package
+      run: |
+          wget -q https://github.com/Dead-fisher/rid-kit/releases/download/v1.0/gromacs-dp-rid-0.0.5-float-gpu-Linux-x86_64.sh > download.log
+          sh gromacs-dp-rid-0.0.5-float-gpu-Linux-x86_64.sh
+          export PATH="$HOME/gromacs-dp-rid/bin:$PATH"
+          which python
+          pip install numpy
+          pip install sklearn
+          pip install dpdispatcher
+          pip install mock
+    - name: Run unittest
+      run: |
+        export PATH="$HOME/gromacs-dp-rid/bin:$PATH"
+        cd ./tests
+        python -m unittest
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,21 @@
+__pycache__
+*.pyc
+.nfs*
+rid.egg-info
+*.egg
+dist
+build
+.gitignore
+rid/old
+markdown.py
+examples/__pycache__
+examples/logs
+examples/test*
+examples/*.slurm
+examples/context.py
+examples/dpdisp.log
+example_for_plumed
+tests/dpdisp.log
+tests/scrip_tt.py
+tests/__pycache__
+rid.egg-info
diff --git a/README.md b/README.md
diff --git a/examples/cv.json → examples/jsons/cv.json b/examples/cv.json → examples/jsons/cv.json
diff --git a/examples/jsons/local.json b/examples/jsons/local.json
@@ -0,0 +1,89 @@
+{
+    "_comment": "system resources",
+
+
+    "enhcMD": {
+        "machine":{
+            "batch_type": "Shell",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "shell",
+            "number_node": 0,
+            "cpu_per_node": 0,
+            "gpu_per_node": 1,
+            "group_size": 1,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "post_enhc": {
+        "machine":{
+            "batch_type": "Shell",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "shell",
+            "number_node": 0,
+            "cpu_per_node": 0,
+            "gpu_per_node": 0,
+            "group_size": 1,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "resMD": {
+        "machine":{
+            "batch_type": "Shell",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "shell",
+            "number_node": 0,
+            "cpu_per_node": 0,
+            "gpu_per_node": 1,
+            "group_size": 10,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "cmpf": {
+        "machine":{
+            "batch_type": "Shell",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "shell",
+            "number_node": 0,
+            "cpu_per_node": 0,
+            "gpu_per_node": 0,
+            "group_size": 1000,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "train": {
+        "machine":{
+            "batch_type": "Shell",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "shell",
+            "number_node": 0,
+            "cpu_per_node": 0,
+            "gpu_per_node": 1,
+            "group_size": 1,
+            "if_cuda_multi_devices": false
+        }
+    }
+}
diff --git a/examples/jsons/machine.json b/examples/jsons/machine.json
@@ -0,0 +1,89 @@
+{
+    "_comment": "system resources",
+
+
+    "enhcMD": {
+        "machine":{
+            "batch_type": "Slurm",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "GPU_2080Ti",
+            "number_node": 1,
+            "cpu_per_node": 8,
+            "gpu_per_node": 1,
+            "group_size": 1,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "post_enhc": {
+        "machine":{
+            "batch_type": "Slurm",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "GPU_2080Ti",
+            "number_node": 1,
+            "cpu_per_node": 4,
+            "gpu_per_node": 0,
+            "group_size": 1,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "resMD": {
+        "machine":{
+            "batch_type": "Slurm",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "GPU_2080Ti",
+            "number_node": 1,
+            "cpu_per_node": 8,
+            "gpu_per_node": 1,
+            "group_size": 10,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "cmpf": {
+        "machine":{
+            "batch_type": "Shell",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": null,
+            "number_node": null,
+            "cpu_per_node": null,
+            "gpu_per_node": 0,
+            "group_size": 1000,
+            "if_cuda_multi_devices": false
+        }
+    },
+
+    "train": {
+        "machine":{
+            "batch_type": "Slurm",
+            "context_type": "LazyLocalContext",
+            "local_root": "./",
+            "remote_root": "./"
+        },
+        "resources":{
+            "queue_name": "GPU_2080Ti",
+            "number_node": 1,
+            "cpu_per_node": 8,
+            "gpu_per_node": 1,
+            "group_size": 1,
+            "if_cuda_multi_devices": false
+        }
+    }
+}
diff --git a/examples/rid.json → examples/jsons/rid.json b/examples/rid.json → examples/jsons/rid.json
@@ -18,7 +18,7 @@
   "bias_frame_freq": 25,
   "sel_threshold": 2,
   "cluster_threshold": 1.5,
-  "num_of_cluster_threshhold": 8,
+  "num_of_cluster_threshold": 8,
   "max_sel": 30,
   "bias_dt": 0.002,
   "bias_temperature": 300,
@@ -59,6 +59,8 @@
   "res_decay_steps": 120,
   "res_decay_rate": 0.96,
   "train_thread": 8,
+
+  "cleanup": false,
 
   "_comment": "That's all"
 }

diff --git a/examples/machine.json b/examples/machine.json
diff --git a/examples/main.py b/examples/main.py
@@ -11,7 +11,6 @@ def main(out_dir, mol_dir, rid_json, machine_json, cv_file, init_model, record_n
     fp = open(rid_json, 'r')
     jdata = json.load(fp)
     fp.close()
-    # record_file = out_dir + record_name
     record_file = os.path.join(out_dir, record_name)
     checkpoint = get_checkpoint(record_file)
     max_tasks = 10
@@ -21,7 +20,7 @@ def main(out_dir, mol_dir, rid_json, machine_json, cv_file, init_model, record_n
 
     if sum(checkpoint) < 0:
         print("prepare gen_rid")
-        gen_rid.gen_rid (out_dir, mol_dir, rid_json)
+        gen_rid (out_dir, mol_dir, rid_json)
 
     for iter_idx in range(iter_numb):
         if iter_idx > 0 :