Canfar job limit

docs/source/canfar.md

@@ -56,16 +56,28 @@ it is recommended to perform some or all of the testing steps (1. - 4.).
 
 ## Monitoring
 
+
+### Status and output of submitted job 
+
 Monitoring of the currently active remote session can be performed using the session IDs `session_IDs.txt` written by the
 remote session script `curl_canfar_local.sh`. In the patch main directory, run
 ```bash
+curl_canfar_monitor.sh events
+```
+to display the remotely started docker image status, and
+```bash
 curl_canfar_monitor.sh logs
 ```
-to print `stdout` of the remotely run pipeline script, and
+to print `stdout` of the remotely run pipeline script.
+
+### Number of submitted running jobs
+
+The script
 ```bash
-curl_canfar_monitor.sh events
+stats_headless_canfar.py
 ```
-to display the remotely started docker image status.
+returns the number of actively running headless jobs.
+
 
 ## Post-hoc summary
 
@@ -74,3 +86,9 @@ In the patch main directory, run
 summary_run PATCH
 ```
 to print a summary with missing image IDs per job and module.
+
+## Deleting jobs
+
+```bash
+ for id in `cat session_IDs.txt`; do echo $id; curl -X DELETE -E /arc/home/kilbinger/.ssl/cadcproxy.pem https://ws-uv.canfar.net/skaha/v0/session/$id;  done
+ ```

environment.yml

@@ -22,6 +22,7 @@ dependencies:
     - PyQt5
     - pyqtgraph
     - reproject
+    - skaha
     - sip_tpv
     - sf_tools
     - sqlitedict

example/cfis/config_Gie_vos.ini

@@ -98,4 +98,6 @@ RETRIEVE = vos
 N_TRY = 3
 
 # Retrieve command options, optional
-RETRIEVE_OPTIONS = --certfile=$VM_HOME/.ssl/cadcproxy.pem
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
+
+CHECK_EXISTING_DIR = $SP_RUN/data_exp

example/cfis/config_GitFeGie_vos.ini

@@ -84,7 +84,7 @@ OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
 RETRIEVE = vos
 
 # Copy command options, optional
-RETRIEVE_OPTIONS = --certfile=$VM_HOME/.ssl/cadcproxy.pem
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
 
 CHECK_EXISTING_DIR = $SP_RUN/output/run_sp_Git/get_images_runner_run_1/output
 
@@ -152,4 +152,4 @@ RETRIEVE = vos
 N_TRY = 3
 
 # Retrieve command options, optional
-RETRIEVE_OPTIONS = --certfile=$VM_HOME/.ssl/cadcproxy.pem
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem

example/cfis/config_GitFe_symlink.ini

@@ -0,0 +1,105 @@
+# ShapePipe configuration file for: get images and find exposures
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_GitFe
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = get_images_runner, find_exposures_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get tiles
+[GET_IMAGES_RUNNER]
+
+FILE_PATTERN = tile_numbers
+
+FILE_EXT = .txt
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = 
+
+# Paths
+
+# Input path where original images are stored. Can be local path or vos url.
+# Single string or list of strings
+INPUT_PATH = $SP_RUN/data_tiles, $SP_RUN/data_tiles
+
+# Input file pattern including tile number as dummy template
+INPUT_FILE_PATTERN = CFIS.000.000.r, CFIS.000.000.r.weight
+
+# Input file extensions
+INPUT_FILE_EXT = .fits, .fits.fz
+
+# Input numbering scheme, python regexp
+INPUT_NUMBERING = \d{3}\.\d{3}
+
+# Output file pattern without number
+OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
+
+# Copy/download method, one in 'vos', 'symlink'
+RETRIEVE = symlink
+
+# Copy command options, optional
+RETRIEVE_OPTIONS = -L
+
+
+[FIND_EXPOSURES_RUNNER]
+
+INPUT_MODULE = get_images_runner
+
+FILE_PATTERN = CFIS_image
+
+FILE_EXT = .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# Column number of exposure name in FITS header
+COLNUM = 3
+
+# Prefix to remove from exposure name
+EXP_PREFIX = p

example/cfis/config_Git_vos.ini

@@ -0,0 +1,93 @@
+# ShapePipe configuration file for: get images
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Git
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = get_images_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get tiles
+[GET_IMAGES_RUNNER]
+
+FILE_PATTERN = tile_numbers
+
+FILE_EXT = .txt
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = 
+
+# Paths
+
+# Input path where original images are stored. Can be local path or vos url.
+# Single string or list of strings
+INPUT_PATH = vos:cfis/tiles_DR5, vos:cfis/tiles_DR5
+
+# Input file pattern including tile number as dummy template
+INPUT_FILE_PATTERN = CFIS.000.000.r, CFIS.000.000.r.weight
+
+# Input file extensions
+INPUT_FILE_EXT = .fits, .fits.fz
+
+# Input numbering scheme, python regexp
+INPUT_NUMBERING = \d{3}\.\d{3}
+
+# Output file pattern without number
+OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
+
+# Copy/download method, one in 'vos', 'symlink'
+RETRIEVE = vos
+
+# If RETRIEVE=vos, number of attempts to download
+# Optional, default=3
+N_TRY = 3
+
+# Copy command options, optional
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
+
+CHECK_EXISTING_DIR = $SP_RUN/data_tiles