link instead of copy in staging jobs

parm/stage/analysis.yaml.j2

@@ -6,7 +6,7 @@ analysis:
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
         {% endfor %}
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}

parm/stage/atmosphere_cold.yaml.j2

@@ -5,7 +5,7 @@ atmosphere_cold:
         {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_INPUT_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}

parm/stage/atmosphere_ens_perturbations.yaml.j2

@@ -5,7 +5,7 @@ atmosphere_ens_perturbation:
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}

parm/stage/atmosphere_nest.yaml.j2

@@ -7,7 +7,7 @@ atmosphere_nest:
         {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
@@ -25,7 +25,7 @@ atmosphere_nest:
         {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_INPUT_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}

parm/stage/atmosphere_warm.yaml.j2

@@ -5,7 +5,7 @@ atmosphere_warm:
         {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}

parm/stage/ice.yaml.j2

@@ -13,7 +13,7 @@ ice:
         {% set COMOUT_ICE_ANALYSIS_MEM = COMOUT_ICE_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ICE_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ICE_ANALYSIS_MEM = COMOUT_ICE_ANALYSIS_MEM_list[imem] %}
@@ -26,7 +26,7 @@ ice:
         {% set COMOUT_ICE_RESTART_PREV_MEM = COMOUT_ICE_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_ICE_RESTART_PREV_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ICE_RESTART_PREV_MEM = COMOUT_ICE_RESTART_PREV_MEM_list[imem] %}

parm/stage/master_gefs.yaml.j2

@@ -10,13 +10,17 @@
 #         - "COM directory to create"
 #     copy:
 #         - ["source_file", "destination_file"]
+#     link:
+#         - ["target", "link_name"]
 # key2:
 #     mkdir:
 #         - "COM directory to create"
 #     copy:
 #         - ["source_file", "destination_file"]
+#     link:
+#         - ["target", "link_name"]
 #
-# Any number of keys with nested mkdir and copy are permitted
+# Any number of keys with nested mkdir, and copy/link are permitted
 # Jinja is permitted in this yaml, as long as the keys are:
 # - COMOUT_
 # - DO_ATM, DO_OCN, DO_ICE, etc.

parm/stage/master_gfs.yaml.j2

@@ -1,184 +0,0 @@
-###################################################################
-# This is the master yaml for the GFS
-#
-# Cycle, member, and RUN settings are set before including each
-# component yaml based on DO switches
-#
-# The included yamls are intended to be of the following structure:
-# key1:
-#     mkdir:
-#         - "COM directory to create"
-#     copy:
-#         - ["source_file", "destination_file"]
-# key2:
-#     mkdir:
-#         - "COM directory to create"
-#     copy:
-#         - ["source_file", "destination_file"]
-#
-# Any number of keys with nested mkdir and copy are permitted
-# Jinja is permitted in this yaml, as long as the keys are:
-# - COMOUT_
-# - DO_ATM, DO_OCN, DO_ICE, etc.
-# For a full list see scripts/exglobal_stage_ic.py
-###################################################################
-
-# Set cycle date variables
-# ------------------------
-{% set half_window = assim_freq // 2 %}
-{% set half_window_begin = (-half_window | string + "H") | to_timedelta %}
-{% set half_window_end = (half_window | string + "H") | to_timedelta %}
-{% if DOIAU and MODE == "cycled" %}
-    {% set model_start_date_current_cycle = current_cycle | add_to_datetime(half_window_begin) %}
-{% else %}
-    {% if REPLAY_ICS %}
-        {% set model_start_date_current_cycle = current_cycle | add_to_datetime(half_window_end) %}
-    {% else %}
-        {% set model_start_date_current_cycle = current_cycle %}
-    {% endif %}
-{% endif %}
-
-{% set current_cycle_YMD = current_cycle | to_YMD %}
-{% set current_cycle_HH = current_cycle | strftime("%H") %}
-{% set previous_cycle_YMD = previous_cycle | to_YMD %}
-{% set previous_cycle_HH = previous_cycle | strftime("%H") %}
-{% set p_prefix = previous_cycle | strftime("%Y%m%d.%H0000") %}
-{% set m_prefix = model_start_date_current_cycle | strftime("%Y%m%d.%H0000") %}
-
-# Determine restart RUN
-# ---------------------
-{% set rRUN = RUN %}
-{% if RUN == "gfs" %}
-    {% set rRUN = "gdas" %}
-{% endif %}
-
-# Set first/last mem for loop
-# ---------------------------
-{% if RUN == "enkfgdas" %} # Ensemble RUN
-  {% set first_mem = 1 %}
-  {% set last_mem = NMEM_ENS %}
-{% else %} # Deterministic RUN
-  {% set first_mem = -1 %}
-  {% set last_mem = -1 %}
-{% endif %}
-
-# Declare to-be-filled lists of member COM directories
-# ----------------------------------------------------
-{% set COMOUT_ATMOS_INPUT_MEM_list = [] %}
-{% set COMOUT_ATMOS_RESTART_PREV_MEM_list = [] %}
-{% set COMOUT_ATMOS_ANALYSIS_MEM_list = [] %}
-{% set COMOUT_ICE_ANALYSIS_MEM_list = [] %}
-{% set COMOUT_ICE_RESTART_PREV_MEM_list = [] %}
-{% set COMOUT_OCEAN_RESTART_PREV_MEM_list = [] %}
-{% set COMOUT_OCEAN_ANALYSIS_MEM_list = [] %}
-{% set COMOUT_MED_RESTART_PREV_MEM_list = [] %}
-{% set COMOUT_WAVE_RESTART_PREV_MEM_list = [] %}
-
-# Construct member COM directory lists
-# ------------------------------------
-{% for mem in range(first_mem, last_mem + 1) %}
-
-    {% if mem >= 0 %}
-        {% set mem_char = 'mem%03d' | format(mem) %}
-    {% else %}
-        {% set mem_char = '' %}
-    {% endif %}
-
-    {% set current_cycle_dict = ({ '${ROTDIR}':ROTDIR,
-                                   '${RUN}':RUN,
-                                   '${YMD}':current_cycle_YMD,
-                                   '${HH}':current_cycle_HH,
-                                   '${MEMDIR}': mem_char }) %}
-    {% set previous_cycle_dict = ({ '${ROTDIR}':ROTDIR,
-                                    '${RUN}':rRUN,
-                                    '${YMD}':previous_cycle_YMD,
-                                    '${HH}':previous_cycle_HH,
-                                    '${MEMDIR}': mem_char }) %}
-
-    {% set COMOUT_ATMOS_INPUT_MEM = COM_ATMOS_INPUT_TMPL | replace_tmpl(current_cycle_dict) %}
-    {% set COMOUT_ATMOS_RESTART_PREV_MEM = COM_ATMOS_RESTART_TMPL | replace_tmpl(previous_cycle_dict) %}
-    {% set COMOUT_ATMOS_ANALYSIS_MEM = COM_ATMOS_ANALYSIS_TMPL | replace_tmpl(current_cycle_dict) %}
-    {% set COMOUT_ICE_ANALYSIS_MEM = COM_ICE_ANALYSIS_TMPL | replace_tmpl(current_cycle_dict) %}
-    {% set COMOUT_ICE_RESTART_PREV_MEM = COM_ICE_RESTART_TMPL | replace_tmpl(previous_cycle_dict) %}
-    {% set COMOUT_OCEAN_RESTART_PREV_MEM = COM_OCEAN_RESTART_TMPL | replace_tmpl(previous_cycle_dict) %}
-    {% set COMOUT_OCEAN_ANALYSIS_MEM = COM_OCEAN_ANALYSIS_TMPL | replace_tmpl(current_cycle_dict) %}
-    {% set COMOUT_MED_RESTART_PREV_MEM = COM_MED_RESTART_TMPL | replace_tmpl(previous_cycle_dict) %}
-    {% set COMOUT_WAVE_RESTART_PREV_MEM = COM_WAVE_RESTART_TMPL | replace_tmpl(previous_cycle_dict) %}
-
-    # Append the member COM directories
-    {% do COMOUT_ATMOS_INPUT_MEM_list.append(COMOUT_ATMOS_INPUT_MEM)%}
-    {% do COMOUT_ATMOS_RESTART_PREV_MEM_list.append(COMOUT_ATMOS_RESTART_PREV_MEM)%}
-    {% do COMOUT_ATMOS_ANALYSIS_MEM_list.append(COMOUT_ATMOS_ANALYSIS_MEM)%}
-    {% do COMOUT_ICE_ANALYSIS_MEM_list.append(COMOUT_ICE_ANALYSIS_MEM)%}
-    {% do COMOUT_ICE_RESTART_PREV_MEM_list.append(COMOUT_ICE_RESTART_PREV_MEM)%}
-    {% do COMOUT_OCEAN_RESTART_PREV_MEM_list.append(COMOUT_OCEAN_RESTART_PREV_MEM)%}
-    {% do COMOUT_OCEAN_ANALYSIS_MEM_list.append(COMOUT_OCEAN_ANALYSIS_MEM)%}
-    {% do COMOUT_MED_RESTART_PREV_MEM_list.append(COMOUT_MED_RESTART_PREV_MEM)%}
-    {% do COMOUT_WAVE_RESTART_PREV_MEM_list.append(COMOUT_WAVE_RESTART_PREV_MEM)%}
-
-{% endfor %}
-
-###################################################################
-# Initial condition to stage - include components based on switches
-###################################################################
-
-{% if MODE == "cycled" %}
-{% filter indent(width=4) %}
-{% include "analysis.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-
-{% if EXP_WARM_START %}
-{% filter indent(width=4) %}
-{% include "atmosphere_warm.yaml.j2" %}
-{% endfilter %}
-{% else %} # cold start
-{% filter indent(width=4) %}
-{% include "atmosphere_cold.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-
-{% if DO_NEST %}
-{% filter indent(width=4) %}
-{% include "atmosphere_nest.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-
-{% if REPLAY_ICS %}
-{% filter indent(width=4) %}
-{% include "atmosphere_perturbation.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-
-{% if DO_ICE %}
-{% filter indent(width=4) %}
-{% include "ice.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-
-{% if DO_OCN %}
-{% filter indent(width=4) %}
-{% include "ocean.yaml.j2" %}
-{% endfilter %}
-{% if DO_JEDIOCNVAR %}
-{% filter indent(width=4) %}
-{% include "ocean_rerun.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-{% if REPLAY_ICS %}
-{% filter indent(width=4) %}
-{% include "ocean_replay.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-{% if EXP_WARM_START %}
-{% filter indent(width=4) %}
-{% include "ocean_mediator.yaml.j2" %}
-{% endfilter %}
-{% endif %}
-{% endif %}
-
-{% if DO_WAVE %}
-{% filter indent(width=4) %}
-{% include "wave.yaml.j2" %}
-{% endfilter %}
-{% endif %}

parm/stage/ocean.yaml.j2

@@ -5,7 +5,7 @@ ocean:
         {% set COMOUT_OCEAN_RESTART_PREV_MEM = COMOUT_OCEAN_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_OCEAN_RESTART_PREV_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_RESTART_PREV_MEM = COMOUT_OCEAN_RESTART_PREV_MEM_list[imem] %}

parm/stage/ocean_ens_perturbations.yaml.j2

@@ -5,7 +5,7 @@ ocean_ens_perturbation:
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_OCEAN_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}

parm/stage/ocean_mediator.yaml.j2

@@ -6,7 +6,7 @@ ocean_mediator:
         {% set COMOUT_MED_RESTART_PREV_MEM = COMOUT_MED_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_MED_RESTART_PREV_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_MED_RESTART_PREV_MEM = COMOUT_MED_RESTART_PREV_MEM_list[imem] %}

parm/stage/ocean_rerun.yaml.j2

@@ -5,7 +5,7 @@ ocean_rerun:
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_OCEAN_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}

parm/stage/wave.yaml.j2

@@ -5,7 +5,7 @@ wave:
         {% set COMOUT_WAVE_RESTART_PREV_MEM = COMOUT_WAVE_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_WAVE_RESTART_PREV_MEM }}"
         {% endfor %} # mem loop
-    copy:
+    link:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_WAVE_RESTART_PREV_MEM = COMOUT_WAVE_RESTART_PREV_MEM_list[imem] %}