Merge branch 'bing_issue#159_change_dir_for_runscript_in_create_env' into develop

.gitlab-ci.yml

@@ -9,7 +9,7 @@ Loading:
      - era5
     stage: build
     script: 
-        - echo "dataset testing"
+        - echo "Dataset testing"
         - cd /data_era5/2017
         - ls -ls
 
@@ -26,7 +26,7 @@ Preprocessing:
      - era5
     stage: build
     script: 
-        - echo "Building-preprocessing"
+        - echo "Building preprocessing"
 
 
 Training:
@@ -34,14 +34,34 @@ Training:
      - era5
     stage: build
     script: 
-        - echo "Building-Training"
+        - echo "Building training"
+
+
+Postprocessing:
+    tags:
+     - era5    
+    stage: build  
+    script: 
+        - echo "Building postprocessing"
+        - zypper --non-interactive install gcc gcc-c++ gcc-fortran
+        - zypper  --non-interactive install openmpi openmpi-devel
+        - zypper  --non-interactive install python3
+        - ls /usr/lib64/mpi/gcc/openmpi/bin
+        - export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+        - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpi/gcc/openmpi/bin
+        - export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin
+        - mpicxx -showme:link -pthread -L/usr/lib64/mpi/gcc/openmpi/bin -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
+        - pip install -r video_prediction_tools/env_setup/requirements_non_HPC.txt
+        - chmod +x ./video_prediction_tools/other_scripts/visualize_postprocess_era5_template.sh
+        - ./video_prediction_tools/other_scripts/visualize_postprocess_era5_template.sh   
+                                                                   
 
 test:
     tags: 
      - era5
     stage: build
     script:
-        - echo "model testing"
+        - echo "Model testing"
 #      - zypper --non-interactive install python3-pip
 #      - zypper --non-interactive install python-devel
 #      - pip install --upgrade pip

video_prediction_tools/env_setup/requirements_non_HPC.txt

@@ -4,7 +4,9 @@ pandas==0.25.3
 xarray==0.16.0
 basemap==1.3.0
 imageio==2.15.0     # although this numpy-version is in the container, we set it here to avoid any further installation
+numpy==1.17.3
 scikit-image==0.17.2
+#scikit-image==0.18.1
 opencv-python-headless==4.2.0.34
 netcdf4==1.5.8
 #metadata==0.2

video_prediction_tools/other_scripts/visualize_postprocess_era5_template.sh

@@ -13,8 +13,8 @@ lquick=1
 climate_file=/home/b.gong/data_era5/T2monthly/climatology_t2m_1991-2020.nc
 #select models
 model=convLSTM
-mkdir ${results_dir}
-python3 ../main_scripts/main_visualize_postprocess.py --checkpoint  ${checkpoint_dir} --mode test  \
+#mkdir ${results_dir}
+python3 ./video_prediction_tools/main_scripts/main_visualize_postprocess.py --checkpoint  ${checkpoint_dir} --mode test  \
                                                            --results_dir ${results_dir} --batch_size 4 \
                                                            --num_stochastic_samples 1 \
 							   --lquick_evaluation ${lquick} --climatology_file ${climate_file}

video_prediction_tools/utils/runscript_generator/config_postprocess.py

@@ -76,20 +76,28 @@ class Config_Postprocess(Config_runscript_base):
         self.model = os.path.basename(dir_base)
         # List the subdirectories...
         _ = Config_Postprocess.get_subdir_list(dir_base)
-        # ... and obtain the checkpoint directory
+        
+        # Chose the checkpoint directory
+        ckp_req_str = "Chose a checkpoint directory from the list above:"
+        ckp_req_err = NotADirectoryError("Could not find the passed directory.")
+        dir_base = Config_Postprocess.keyboard_interaction(ckp_req_str, Config_Postprocess.check_dir, ckp_req_err,
+                                                           prefix2arg=dir_base+"/", ntries=2)
+         # List the subdirectories...
+        _ = Config_Postprocess.get_subdir_list(dir_base) 
+        # ... and obtain the model directory with checkpoints
         trained_dir_req_str = "Choose a trained model from the experiment list above:"
         trained_err = FileNotFoundError("No trained model parameters found.")
-
         self.checkpoint_dir = Config_Postprocess.keyboard_interaction(trained_dir_req_str,
                                                                       Config_Postprocess.check_traindir,
                                                                       trained_err, ntries=3, prefix2arg=dir_base+"/")
 
+        
         # get the relevant information from checkpoint_dir in order to construct source_dir and results_dir
         # (following naming convention)
         cp_dir_split = Config_Postprocess.path_rec_split(self.checkpoint_dir)
         cp_dir_split = list(filter(None, cp_dir_split))                       # get rid of empty list elements
 
-        base_dir, exp_dir_base, exp_dir = "/"+os.path.join(*cp_dir_split[:-4]), cp_dir_split[-3], cp_dir_split[-1]
+        base_dir, exp_dir_base, exp_dir = "/"+os.path.join(*cp_dir_split[:-4]), cp_dir_split[-3], cp_dir_split[-2]
         self.runscript_target = self.rscrpt_tmpl_prefix + self.dataset + "_" + exp_dir + ".sh"
 
         # Set results_dir

video_prediction_tools/utils/runscript_generator/config_utils.py

@@ -31,9 +31,9 @@ class Config_runscript_base:
         self.VIRT_ENV_NAME = venv_name
         # runscript related attributes
         if lhpc:
-            self.runscript_dir = "../HPC_scripts"
+            self.runscript_dir = "../JSC_scripts"
         else:
-            self.runscript_dir = "../nonHPC_scripts"
+            self.runscript_dir = "../HPC_scripts"
 
         self.long_name_wrk_step = None
         self.rscrpt_tmpl_prefix = None

video_prediction_tools/utils/runscript_generator/setup_runscript_templates.sh

@@ -47,7 +47,7 @@ else
 fi
 
 echo "Start setting up templates under nonHPC_scripts/..."
-for f in "${BASE_DIR}"/nonHPC_scripts/*template.sh; do
+for f in "${BASE_DIR}"/HPC_scripts/*template.sh; do
   echo "Setting up ${f}..."
   fnew=${f%%.*}_${USER}.sh
   cp "${f}" "${fnew}"
@@ -56,7 +56,7 @@ done
 echo "Done!"
 
 echo "Start setting up templates under HPC_scripts/"
-for f in "${BASE_DIR}"/HPC_scripts/*template.sh; do
+for f in "${BASE_DIR}"/JSC_scripts/*template.sh; do
   echo "Setting up ${f}..."
   fnew=${f%%.*}_${USER}.sh
   cp "${f}" "${fnew}"