script naming

README.md

@@ -102,70 +102,75 @@ write_adcirc_configurations(
 This code will generate a directory `hera_shinnecock_ike/` with the following structure:
 
 ```
-hera_shinnecock_ike/
-├── coldstart/
-│   ├── fort.13
-│   ├── fort.14
-│   └── fort.15
-├── runs/
-│   └── test_case_1/
-│       ├── fort.13
-│       ├── fort.14
-│       └── fort.15
-├── config.rc.coldstart
-├── config.rc.hotstart
-├── model_configure.coldstart
-├── model_configure.hotstart
-├── nems.configure.coldstart
-├── nems.configure.hotstart
-├── hera_adcprep.job
-├── hera_nems_adcirc.job.coldstart
-├── hera_nems_adcirc.job.hotstart
-└── run_hera.sh
+📦 hera_shinnecock_ike/
+┣ 📂 coldstart/
+┃  ┣ 📜 fort.13
+┃  ┣ 📜 fort.14
+┃  ┗ 📜 fort.15
+┣ 📂 runs/
+┃  ┗ 📂 test_case_1/
+┃    ┣ 📜 fort.13
+┃    ┣ 📜 fort.14
+┃    ┗ 📜 fort.15
+┣ 📜 config.rc.coldstart
+┣ 📜 config.rc.hotstart
+┣ 📜 model_configure.coldstart
+┣ 📜 model_configure.hotstart
+┣ 📜 nems.configure.coldstart
+┣ 📜 nems.configure.hotstart
+┣ 📜 job_adcprep_hera.job
+┣ 📜 job_nems_adcirc_hera.job.coldstart
+┣ 📜 job_nems_adcirc_hera.job.hotstart
+┗ 📜 run_hera.sh
 ```
 
 _**Note:** the required NEMS configuration files (`nems.configure`, `model_configure`) do not yet exist in the run
 directories (`coldstart/`, `runs/test_case_1/`). These will be populated in the next step._
 
 ### 2. run job submission script `run_<platform>.sh`
 
-Run `sh run_hera.sh` to submit the jobs as a batch. This will create symbolic links to populate configuration directories
-within the structure, as so:
+Run `run_hera.sh`:
+
+```bash
+sh run_hera.sh
+``` 
+
+This will first create symbolic links to populate configuration directories,
 
 ```
-hera_shinnecock_ike/
-├── coldstart/
-│   ├── fort.13
-│   ├── fort.14
-│   ├── fort.15
-│   ├── config.rc -> ../config.rc.coldstart
-│   ├── model_configure -> ../model_configure.coldstart
-│   ├── nems.configure -> ../nems.configure.coldstart
-│   ├── hera_adcprep.job -> ../hera_adcprep.job
-│   └── hera_nems_adcirc.job -> ../hera_nems_adcirc.job.coldstart
-├── runs/
-│   └── test_case_1/
-│       ├── fort.13
-│       ├── fort.14
-│       ├── fort.15
-│       ├── config.rc -> ../../config.rc.hotstart
-│       ├── model_configure -> ../../model_configure.hotstart
-│       ├── nems.configure -> ../../nems.configure.hotstart
-│       ├── hera_adcprep.job -> ../../hera_adcprep.job
-│       └── hera_nems_adcirc.job -> ../../hera_nems_adcirc.job.hotstart
-├── config.rc.coldstart
-├── config.rc.hotstart
-├── model_configure.coldstart
-├── model_configure.hotstart
-├── nems.configure.coldstart
-├── nems.configure.hotstart
-├── hera_adcprep.job
-├── hera_nems_adcirc.job.coldstart
-├── hera_nems_adcirc.job.hotstart
-└── run_hera.sh
+📦 hera_shinnecock_ike/
+┣ 📂 coldstart/
+┃  ┣ 📜 fort.13
+┃  ┣ 📜 fort.14
+┃  ┣ 📜 fort.15
+┃  ┣ 🔗 config.rc -> ../config.rc.coldstart
+┃  ┣ 🔗 model_configure -> ../model_configure.hotstart
+┃  ┣ 🔗 nems.configure -> ../nems.configure.coldstart
+┃  ┣ 🔗 hera_adcprep.job -> ../job_adcprep_hera.job
+┃  ┗ 🔗 hera_nems_adcirc.job -> ../job_nems_adcirc_hera.job.coldstart
+┣ 📂 runs/
+┃  ┗ 📂 test_case_1/
+┃    ┣ 📜 fort.13
+┃    ┣ 📜 fort.14
+┃    ┣ 📜 fort.15
+┃    ┣ 🔗 config.rc -> ../../config.rc.hotstart
+┃    ┣ 🔗 model_configure -> ../../model_configure.hotstart
+┃    ┣ 🔗 nems.configure -> ../../nems.configure.hotstart
+┃    ┣ 🔗 hera_adcprep.job -> ../../job_adcprep_hera.job
+┃    ┗ 🔗 hera_nems_adcirc.job -> ../../job_nems_adcirc_hera.job.hotstart
+┣ 📜 config.rc.coldstart
+┣ 📜 config.rc.hotstart
+┣ 📜 model_configure.coldstart
+┣ 📜 model_configure.hotstart
+┣ 📜 nems.configure.coldstart
+┣ 📜 nems.configure.hotstart
+┣ 📜 job_adcprep_hera.job
+┣ 📜 job_nems_adcirc_hera.job.coldstart
+┣ 📜 job_nems_adcirc_hera.job.hotstart
+┗ 📜 run_hera.sh
 ```
 
-The script then submits the requested jobs to the queue:
+and then submit the requested jobs to the queue:
 
 ```bash
    JOBID                  NAME CPUS NODE                      DEPENDENCY ACCOUNT PARTITION          SUBMIT_TIME           START_TIME             END_TIME

coupledmodeldriver/adcirc.py

@@ -1,10 +1,8 @@
 import copy
 from datetime import timedelta
-from glob import glob
 import os
 from os import PathLike
 from pathlib import Path
-import re
 
 from adcircpy import AdcircMesh, AdcircRun
 from adcircpy.forcing.base import Forcing
@@ -147,7 +145,7 @@ def write_adcirc_configurations(
         slurm_log_filename=f'{adcprep_run_name}.out.log',
     )
     adcprep_script.write(
-        output_directory / f'{adcprep_script.platform.value}_adcprep.job', overwrite=True
+        output_directory / f'job_adcprep_{adcprep_script.platform.value}.job', overwrite=True
     )
 
     if spinup is not None:
@@ -190,7 +188,7 @@ def write_adcirc_configurations(
         )
 
     coldstart_run_script.write(
-        output_directory / f'{coldstart_run_script.platform.value}_nems_adcirc.job.coldstart',
+        output_directory / f'job_nems_adcirc_{coldstart_run_script.platform.value}.job.coldstart',
         overwrite=True,
     )
 
@@ -215,11 +213,8 @@ def write_adcirc_configurations(
             slurm_log_filename=f'{adcirc_hotstart_run_name}.out.log',
         )
 
-        hotstart_run_script.write(
-            output_directory
-            / f'{hotstart_run_script.platform.value}_nems_adcirc.job.hotstart',
-            overwrite=True,
-        )
+        hotstart_run_script.write(output_directory / f'job_nems_adcirc_{hotstart_run_script.platform.value}.job.hotstart',
+                                  overwrite=True)
 
     slurm = SlurmConfig(
         account=slurm_account,
@@ -275,19 +270,5 @@ def write_adcirc_configurations(
         driver.mesh.set_attribute(attribute_name, value)
         driver.write(run_directory, overwrite=True, coldstart=None, hotstart='fort.15', driver=None)
 
-    pattern = re.compile(' p*adcirc')
-    replacement = ' NEMS.x'
-    for job_filename in glob(str(output_directory / '**' / 'slurm.job'), recursive=True):
-        with open(job_filename) as job_file:
-            text = job_file.read()
-        matched = pattern.search(text)
-        if matched:
-            LOGGER.debug(
-                f'replacing `{matched.group(0)}` with `{replacement}`' f' in "{job_filename}"'
-            )
-            text = re.sub(pattern, replacement, text)
-            with open(job_filename, 'w') as job_file:
-                job_file.write(text)
-
     run_script = RunScript(platform)
     run_script.write(output_directory / f'run_{platform.value}.sh', overwrite=True)

coupledmodeldriver/job_script.py

@@ -193,7 +193,7 @@ def __str__(self) -> str:
 
         if self.platform != Platform.LOCAL:
             lines.extend(
-                [self.slurm_header, '', 'set -e', '', ]
+                [self.slurm_header, '', 'set -e', '']
             )
 
         if self.modules is not None:
@@ -384,21 +384,24 @@ def __init__(self, platform: Platform):
 
     def __str__(self) -> str:
         lines = [
-            'DIRECTORY="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"',
+            'DIRECTORY="$(',
+            '    cd "$(dirname "$0")" >/dev/null 2>&1',
+            '    pwd -P',
+            ')"',
             '',
             '# prepare single coldstart directory',
             f'cd $DIRECTORY/coldstart',
-            f'ln -sf ../{self.platform.value}_adcprep.job adcprep.job',
-            f'ln -sf ../{self.platform.value}_nems_adcirc.job.coldstart nems_adcirc.job',
+            f'ln -sf ../job_adcprep_{self.platform.value}.job adcprep.job',
+            f'ln -sf ../job_nems_adcirc_{self.platform.value}.job.coldstart nems_adcirc.job',
             'cd $DIRECTORY',
             '',
             '# prepare every hotstart directory',
             bash_for_loop(
                 'for hotstart in $DIRECTORY//runs/*/',
                 [
                     'cd "$hotstart"',
-                    f'ln -sf ../../{self.platform.value}_adcprep.job adcprep.job',
-                    f'ln -sf ../../{self.platform.value}_nems_adcirc.job.hotstart nems_adcirc.job',
+                    f'ln -sf ../../job_adcprep_{self.platform.value}.job adcprep.job',
+                    f'ln -sf ../../job_nems_adcirc_{self.platform.value}.job.hotstart nems_adcirc.job',
                     'cd $DIRECTORY/',
                 ]
             ),
@@ -475,7 +478,7 @@ def write(self, filename: PathLike, overwrite: bool = False):
             filename = Path(filename)
 
         if filename.is_dir():
-            filename = filename / f'run.sh'
+            filename = filename / f'run_{self.platform.value}.sh'
 
         output = f'{self}\n'
         if overwrite or not filename.exists():

tests/data/reference/hera_shinnecock_ike/coldstart/fort.15

@@ -1,4 +1,4 @@
-created on 2021-02-18 14:49                                     ! RUNDES
+created on 2021-02-18 15:59                                     ! RUNDES
  Shinacock Inlet Coarse Grid                                    ! RUNID
 1                                                               ! NFOVER
 1                                                               ! NABOUT

tests/data/reference/hera_shinnecock_ike/config.rc.coldstart

@@ -1,2 +1,2 @@
-# `config.rc` generated with NEMSpy 0.3.1.post8.dev0+91de88b
+# `config.rc` generated with NEMSpy 0.3.1.post9.dev0+5c0cf20
 

tests/data/reference/hera_shinnecock_ike/config.rc.hotstart

@@ -1,4 +1,4 @@
-# `config.rc` generated with NEMSpy 0.3.1.post8.dev0+91de88b
+# `config.rc` generated with NEMSpy 0.3.1.post9.dev0+5c0cf20
  atm_dir: input/shinnecock_ike/forcings
  atm_nam: wind_atm_fin_ch_time_vec.nc
  wav_dir: input/shinnecock_ike/forcings

tests/data/reference/hera_shinnecock_ike/model_configure.coldstart

@@ -1,4 +1,4 @@
-# `model_configure` generated with NEMSpy 0.3.1.post8.dev0+91de88b
+# `model_configure` generated with NEMSpy 0.3.1.post9.dev0+5c0cf20
 total_member:            1
 print_esmf:              .true.
 namelist:                atm_namelist

tests/data/reference/hera_shinnecock_ike/model_configure.hotstart

@@ -1,4 +1,4 @@
-# `model_configure` generated with NEMSpy 0.3.1.post8.dev0+91de88b
+# `model_configure` generated with NEMSpy 0.3.1.post9.dev0+5c0cf20
 total_member:            1
 print_esmf:              .true.
 namelist:                atm_namelist

tests/data/reference/hera_shinnecock_ike/nems.configure.coldstart

@@ -1,4 +1,4 @@
-# `nems.configure` generated with NEMSpy 0.3.1.post8.dev0+91de88b
+# `nems.configure` generated with NEMSpy 0.3.1.post9.dev0+5c0cf20
 # EARTH #
 EARTH_component_list: OCN
 EARTH_attributes::

tests/data/reference/hera_shinnecock_ike/nems.configure.hotstart

@@ -1,4 +1,4 @@
-# `nems.configure` generated with NEMSpy 0.3.1.post8.dev0+91de88b
+# `nems.configure` generated with NEMSpy 0.3.1.post9.dev0+5c0cf20
 # EARTH #
 EARTH_component_list: ATM WAV OCN
 EARTH_attributes::

tests/data/reference/hera_shinnecock_ike/run_hera.sh

@@ -1,16 +1,19 @@
-DIRECTORY="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"
+DIRECTORY="$(
+    cd "$(dirname "$0")" >/dev/null 2>&1
+    pwd -P
+)"
 
 # prepare single coldstart directory
 cd $DIRECTORY/coldstart
-ln -sf ../hera_adcprep.job adcprep.job
-ln -sf ../hera_nems_adcirc.job.coldstart nems_adcirc.job
+ln -sf ../job_adcprep_hera.job adcprep.job
+ln -sf ../job_nems_adcirc_hera.job.coldstart nems_adcirc.job
 cd $DIRECTORY
 
 # prepare every hotstart directory
 for hotstart in $DIRECTORY//runs/*/; do
     cd "$hotstart"
-    ln -sf ../../hera_adcprep.job adcprep.job
-    ln -sf ../../hera_nems_adcirc.job.hotstart nems_adcirc.job
+    ln -sf ../../job_adcprep_hera.job adcprep.job
+    ln -sf ../../job_nems_adcirc_hera.job.hotstart nems_adcirc.job
     cd $DIRECTORY/
 done