diff --git a/notebooks/FragenAntworten.ipynb b/notebooks/FragenAntworten.ipynb index 8fdb26488353e2dc7443906ff9f9665f9c0ff66c..9033ec647bc3c4bc8f0b1ef00b9d0b0a03a7d9fb 100644 --- a/notebooks/FragenAntworten.ipynb +++ b/notebooks/FragenAntworten.ipynb @@ -84,7 +84,7 @@ "- [Tim Kreuzer](https://www.fz-juelich.de/SharedDocs/Personen/IAS/JSC/EN/staff/kreuzer_t.html) (Jülich Supercomputing Centre) (Infrastruktur für das wissenschaftliche Rechens, Webapplikation, Automatisierung der Rechnungen) \n", "- [Prof. Dr. Gordon Pipa](https://www.ikw.uni-osnabrueck.de/en/research_groups/neuroinformatics/people/prof_dr_gordon_pipa.html) (Uni Osnabrück) (Konzeption und wissenschaftliche Leitung)\n", "- [Pascal Nieters](https://www.ikw.uni-osnabrueck.de/en/research_groups/neuroinformatics/people/msc_pascal_nieters.html) (Uni Osnabrück) (Umsetzung, Daten Analyse und Konzeption, Darstellung der Ergebnisse)\n", - "- [Dr. Daniel Rohe](https://www.fz-juelich.de/SharedDocs/Kontaktdaten/Mitarbeiter/R/Rohe_d_rohe_fz_juelich_de.html?nn=2458612) (Jülich Supercomputing Centre) (Organisation und Diskussion)\n" + "- Dr. Daniel Rohe (Jülich Supercomputing Centre) (Organisation und Diskussion)\n" ] } ], diff --git a/src/gridjob_produce_plots.slurm b/src/gridjob_produce_plots.slurm index 1597cc8be73275bdaeee4e90854df1046d07f26f..65893ea39d2e91a73a6f9a5dcabfd77af190e063 100644 --- a/src/gridjob_produce_plots.slurm +++ b/src/gridjob_produce_plots.slurm @@ -8,9 +8,9 @@ #SBATCH --output=/p/project/covid19dynstat/autostart/runs/%A_o.txt #SBATCH --error=/p/project/covid19dynstat/autostart/runs/%A_e.txt #SBATCH --time=2:00:00 -#SBATCH --mail-type=ALL +#SBATCH --mail-type=FAIL #SBATCH --mail-user=t.kreuzer@fz-juelich.de -#SBATCH --dependency=afterany:8491614 +#SBATCH --dependency=afterok:3265 # select project jutil env activate -p covid19dynstat diff --git a/src/gridjob_produce_plots.slurm.sh b/src/gridjob_produce_plots.slurm.sh index 064696f0fb01a64cc3bfe64c75d3e94f2b639acb..090361bc734d4385372501076052107e93dfd1b2 100755 --- a/src/gridjob_produce_plots.slurm.sh +++ b/src/gridjob_produce_plots.slurm.sh @@ -10,7 +10,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python scriptsi diff --git a/src/gridjob_produce_plots_loop.slurm.sh b/src/gridjob_produce_plots_loop.slurm.sh index b4653233669a6c0f054129e5745093ff9d8c40dd..425877232f8ae441b2288ba36917a65e2a6b4d1a 100755 --- a/src/gridjob_produce_plots_loop.slurm.sh +++ b/src/gridjob_produce_plots_loop.slurm.sh @@ -10,7 +10,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python scriptsi diff --git a/src/gridjob_sample_ia.slurm.sh b/src/gridjob_sample_ia.slurm.sh index d1aec15676a3a66872f53a753af1c4e33aa2b609..6db447ee54968a7d4446573dacbc637959790d9a 100755 --- a/src/gridjob_sample_ia.slurm.sh +++ b/src/gridjob_sample_ia.slurm.sh @@ -8,7 +8,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python scripts diff --git a/src/gridjob_sample_ia_window.slurm b/src/gridjob_sample_ia_window.slurm index d6e7ecf9efa062a5997ca59a0e1f49fb6c2da5fb..255fcb13e93a60dd161992ba4e4b9b9ec4be08eb 100644 --- a/src/gridjob_sample_ia_window.slurm +++ b/src/gridjob_sample_ia_window.slurm @@ -5,7 +5,7 @@ #SBATCH --array=1-100:4 #SBATCH --ntasks-per-node=4 #SBATCH --nodes=1 -#SBATCH --time=24:00:00 +#SBATCH --time=1:30:00 #SBATCH --output=/p/project/covid19dynstat/autostart/runs/%A_o.txt #SBATCH --error=/p/project/covid19dynstat/autostart/runs/%A_e.txt # ATTENTION: @@ -16,4 +16,4 @@ jutil env activate -p covid19dynstat # run tasks -srun --exclusive -n ${SLURM_NTASKS} gridjob_sample_ia_window_183.slurm.sh \ No newline at end of file +srun --exclusive -n ${SLURM_NTASKS} gridjob_sample_ia_window_183.slurm.sh diff --git a/src/gridjob_sample_ia_window.slurm.sh b/src/gridjob_sample_ia_window.slurm.sh index f3ccd874bf5ac56590cc6b780259144132d6bcc1..674f9428814dbfdbee7f4d463801030152d4da68 100755 --- a/src/gridjob_sample_ia_window.slurm.sh +++ b/src/gridjob_sample_ia_window.slurm.sh @@ -10,7 +10,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python scrip diff --git a/src/gridjob_sample_posterior.slurm.sh b/src/gridjob_sample_posterior.slurm.sh index 862c4cdfa2890fd41efc766d939e0fa53a0ff1a9..280c727f1ede8bab7a7e527e81988e754300f38d 100644 --- a/src/gridjob_sample_posterior.slurm.sh +++ b/src/gridjob_sample_posterior.slurm.sh @@ -8,7 +8,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python scripts diff --git a/src/gridjob_sample_window_posterior.slurm b/src/gridjob_sample_window_posterior.slurm index 4dbec00165741197a9baa348f352e5bbf1489ecd..ddd7ac7746f06671e54c469acd3d774a53f41630 100644 --- a/src/gridjob_sample_window_posterior.slurm +++ b/src/gridjob_sample_window_posterior.slurm @@ -7,10 +7,10 @@ #SBATCH --nodes=1 #SBATCH --output=/p/project/covid19dynstat/autostart/runs/%A_o.txt #SBATCH --error=/p/project/covid19dynstat/autostart/runs/%A_e.txt -#SBATCH --time=24:00:00 -#SBATCH --mail-type=ALL +#SBATCH --time=10:00:00 +#SBATCH --mail-type=FAIL #SBATCH --mail-user=t.kreuzer@fz-juelich.de -#SBATCH --dependency=afterany:8491604 +#SBATCH --dependency=afterok:3240 # select project jutil env activate -p covid19dynstat diff --git a/src/gridjob_sample_window_posterior.slurm.sh b/src/gridjob_sample_window_posterior.slurm.sh index 92ac383f707e9c9c2eba262bbedb9abd0fb8c0b6..6c97af65889b018534571aae2b1c5083c1118da6 100755 --- a/src/gridjob_sample_window_posterior.slurm.sh +++ b/src/gridjob_sample_window_posterior.slurm.sh @@ -8,7 +8,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python script diff --git a/src/gridjob_sample_window_posterior_loop.slurm.sh b/src/gridjob_sample_window_posterior_loop.slurm.sh index cbf89149c54a3f2f46da79e20816a1f9b82428b8..996870b3290e139d2b0bac628d131fd1fe5270d0 100755 --- a/src/gridjob_sample_window_posterior_loop.slurm.sh +++ b/src/gridjob_sample_window_posterior_loop.slurm.sh @@ -8,7 +8,7 @@ mkdir -p ${TASK_DIR} echo "TASK ${TASK_ID}: Running in job-array ${SLURM_ARRAY_JOB_ID} on `hostname` and dump output to ${TASK_DIR}" # activate virtual python environment -source ${PROJECT}/.local/share/venvs/covid19dynstat_v01/bin/activate +source ${PROJECT}/.local/share/venvs/covid19dynstat_jusuf/bin/activate # run code export SGE_TASK_ID=${TASK_ID} # needed for later python script diff --git a/src/plot_curves_window.py b/src/plot_curves_window.py index 57cfdb951bb1c86343baa8619850e9418c96c9bd..828921c85169d94648fad442122df0800b2dcb3e 100644 --- a/src/plot_curves_window.py +++ b/src/plot_curves_window.py @@ -45,7 +45,7 @@ def curves(start, county, n_weeks=3, model_i=35, save_plot=False): # check for metadata file: - if True:#not os.path.isfile("../figures/{}_{}_{}/metadata.csv".format(year, month, day)): + if not os.path.isfile("../figures/{}_{}_{}/metadata.csv".format(year, month, day)): ids = [] for key in counties: ids.append(int(key)) diff --git a/src/produce_plots.py b/src/produce_plots.py index 5ed033840a856b42dc201ab032838b04ba52fa5d..9e7f3dbfd114a0cf07be2ba6efe40ebbc168e190 100644 --- a/src/produce_plots.py +++ b/src/produce_plots.py @@ -13,6 +13,8 @@ start_day = pd.Timestamp('2020-01-28') + pd.Timedelta(days=start) year = str(start_day)[:4] month = str(start_day)[5:7] day = str(start_day)[8:10] +#figures_path = "../figures/{}_{}_{}/".format(year, month, day) +#shared_path = "../../../shared_assets/figures/{}_{}_{}/".format(year, month, day) figures_path = "/p/project/covid19dynstat/autostart/BSTIM-Covid19_Window_Final/figures/{}_{}_{}/".format(year, month, day) shared_path = "/p/project/covid19dynstat/shared_assets/figures/{}_{}_{}/".format(year, month, day) @@ -28,6 +30,7 @@ interaction_kernel(start, save_plot=True) # DIe Metadata CSV sotieren. metadata_date_path = os.path.join(figures_path, "metadata.csv") +#metadata_total_path = "../../../shared_assets/metadata.csv" metadata_total_path = "/p/project/covid19dynstat/shared_assets/metadata.csv" metadata_date_df = pd.read_csv(metadata_date_path)