diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index aeded1c8d507c7198eac969c545fec33d68d58d5..c5cfee3076cd043cc79be1621214ef5fa7e9731a 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/video_prediction_tools/env_setup/requirements_non_HPC.txt b/video_prediction_tools/env_setup/requirements_non_HPC.txt
index de100f9268b6112007f6b9a5df0549fe94718cfa..d72e87b47a762c93457e15ba1e202f76bcd148c0 100755
--- a/video_prediction_tools/env_setup/requirements_non_HPC.txt
+++ b/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
diff --git a/video_prediction_tools/other_scripts/visualize_postprocess_era5_template.sh b/video_prediction_tools/other_scripts/visualize_postprocess_era5_template.sh
index 8a063501382054535d8f50fb1c1fd8cd3e1fda7f..ee9a2fb0aa92d650e3578a5431f3312b7b97ddb2 100644
--- a/video_prediction_tools/other_scripts/visualize_postprocess_era5_template.sh
+++ b/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}
diff --git a/video_prediction_tools/utils/runscript_generator/config_postprocess.py b/video_prediction_tools/utils/runscript_generator/config_postprocess.py
index eff2694bbd1dc381726e54bb4fb46bf0af5ddb4c..544337834fd4a9a1241f8e20e2cf186d8a2265ce 100755
--- a/video_prediction_tools/utils/runscript_generator/config_postprocess.py
+++ b/video_prediction_tools/utils/runscript_generator/config_postprocess.py
@@ -76,24 +76,32 @@ 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
- self.results_dir = os.path.join(base_dir, "results", exp_dir_base, self.model, exp_dir)
+ self.results_dir = os.path.join(base_dir, "results", exp_dir_base,self.model, exp_dir)
return
# Decide if quick evaluation should be performed
diff --git a/video_prediction_tools/utils/runscript_generator/config_utils.py b/video_prediction_tools/utils/runscript_generator/config_utils.py
index e29ab9457615cbb6641aa27e0d5b9da2ac9bdc9f..4740f81e0b16519c6cc15394b14bdea77921e056 100755
--- a/video_prediction_tools/utils/runscript_generator/config_utils.py
+++ b/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
diff --git a/video_prediction_tools/utils/runscript_generator/setup_runscript_templates.sh b/video_prediction_tools/utils/runscript_generator/setup_runscript_templates.sh
index f47f6dcb390db9a14f09570e4e0d354aa7d50d9b..e89b6ba55790be1e3eca1db99faa14a6ad0c8cd0 100755
--- a/video_prediction_tools/utils/runscript_generator/setup_runscript_templates.sh
+++ b/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}"