Merge pull request #1 from MarkUoLeeds/uol_arc4_complete

Uol arc4 complete
jedwards4b · Feb 22, 2022 · 36adbed · 36adbed
2 parents 3a47fc9 + 5ba36a1
commit 36adbed
Show file tree

Hide file tree

Showing 10 changed files with 169 additions and 22 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,47 @@
 ======================================================================
 
+Originator: Chris Fischer 
+Date: 12-7-2021
+Tag: cime5.6.37
+Answer Changes: None
+Tests:  Build SMS.f19_g17.B1850.cori-haswell_intel and SMS.f19_g17.B1850.cori-knl_intel
+        Tested query_config --compsets by hand
+        scripts_regression_tests
+Dependencies:
+
+Brief Summary:
+    - Update cori modules.
+    - Fix documentation of seq_flux_mct_alb* variables.
+    - Fix issue iterating over compsets.
+    - Fix issue reading streams from user_nl_datm.
+    - Add a check for case_dir.
+    - Update comet port. 
+
+User interface changes: 
+
+PR summary: git log --oneline --first-parent [previous_tag]..master 
+6ee76f234 Merge pull request #4138 from ESMCI/fischer/cori_update
+27b5571ff Merge pull request #4069 from billsacks/fix_albedo_doc
+ba4251401 Merge pull request #4044 from jedwards4b/maint-5.6
+56b8845f5 Merge pull request #3992 from jedwards4b/bugfix/streams_from_user_nl
+ccdea36cd Merge pull request #4004 from jedwards4b/case_dir_check/maint-5.6
+4d507fd33 Merge pull request #3928 from jedwards4b/SDSCcomet_port
+
+Modified files: git diff --name-status [previous_tag]
+M       config/cesm/machines/config_compilers.xml
+M       config/cesm/machines/config_machines.xml
+M       scripts/Tools/xmlchange
+M       scripts/lib/CIME/case/case.py
+M       scripts/lib/CIME/nmlgen.py
+M       scripts/query_config
+M       src/components/data_comps/datm/cime_config/buildnml
+M       src/drivers/mct/cime_config/namelist_definition_drv.xml
+
+
+======================================================================
+
+======================================================================
+
 Originator: Chris Fischer 
 Date: 4-2-2021
 Tag: cime5.6.36

diff --git a/config/cesm/machines/config_batch.xml b/config/cesm/machines/config_batch.xml
@@ -148,6 +148,31 @@
     </directives>
   </batch_system>
 
+  <batch_system type="sge" >
+    <batch_query args="-j">qstat</batch_query>
+    <batch_submit>qsub </batch_submit>
+    <batch_cancel>qdel</batch_cancel>
+    <batch_env>-v</batch_env>
+    <batch_directive>#$ </batch_directive>
+    <jobid_pattern>(\d+)</jobid_pattern>
+    <depend_string> -hold_jid jobid</depend_string>
+    <depend_separator> , </depend_separator>
+    <walltime_format>%H:%M:%S</walltime_format>
+    <batch_mail_flag>-M</batch_mail_flag>
+    <batch_mail_type_flag>-m</batch_mail_type_flag>
+    <batch_mail_type>, bea, b, e, a, n, bes</batch_mail_type>
+    <submit_args>
+      <arg flag="-q" name="$JOB_QUEUE"/>
+      <arg flag="-P" name="$PROJECT"/>
+      <arg flag="-l h_rt=" name="$JOB_WALLCLOCK_TIME"/>
+    </submit_args>
+    <directives>
+      <directive> -N {{ job_id }}</directive>
+      <directive> -V </directive>
+      <directive> -l nodes={{ num_nodes }},ppn={{ tasks_per_node }},tpp={{ thread_count }}</directive>
+    </directives>
+  </batch_system>
+
   <batch_system type="slurm" >
     <batch_query per_job_arg="-j">squeue</batch_query>
     <batch_cancel>scancel</batch_cancel>
@@ -218,6 +243,13 @@
     </queues>
   </batch_system>
 
+  <batch_system MACH="arc4" type="sge">
+    <queues>
+      <queue walltimemax="48:00:00" nodemin="1" nodemax="149" default="true" >40core-192G.q</queue>
+      <queue walltimemax="48:00:00" nodemax="1">planet.q</queue>
+    </queues>
+  </batch_system>
+
   <!-- athena is lsf -->
   <batch_system MACH="athena" type="lsf">
     <batch_env>none</batch_env>

diff --git a/config/cesm/machines/config_compilers.xml b/config/cesm/machines/config_compilers.xml
@@ -481,6 +481,18 @@ using a fortran linker.
   </LDFLAGS>
 </compiler>
 
+<compiler MACH="arc4" COMPILER="intel">
+  <PNETCDF_PATH>$ENV{NETCDF_HOME}</PNETCDF_PATH>
+  <NETCDF_PATH>$ENV{NETCDF_HOME}</NETCDF_PATH>
+  <SLIBS>
+    <append> -L$ENV{NETCDF_HOME}/lib -lnetcdff -lnetcdf -L$ENV{PNETCDF_PATH}/lib -lpnetcdf -mkl</append>
+  </SLIBS>
+  <LDFLAGS>
+    <append>-mkl </append>
+  </LDFLAGS>
+  <ESMF_LIBDIR>$ENV{ESMF_LIBDIR}</ESMF_LIBDIR>
+</compiler>
+
 <compiler MACH="athena">
   <CPPDEFS>
     <!-- these flags enable nano timers -->

diff --git a/config/cesm/machines/config_machines.xml b/config/cesm/machines/config_machines.xml
@@ -116,6 +116,57 @@ This allows using a different mpirun command to launch unit tests
     </environment_variables>
   </machine>
 
+  <machine MACH="arc4">
+    <DESC>A port of CEM to the Leeds ARC4 machine, batch system is sge. CEMAC.</DESC>
+    <NODENAME_REGEX>.*.arc*</NODENAME_REGEX>
+    <OS>LINUX</OS>
+    <COMPILERS>intel</COMPILERS>
+    <MPILIBS>intelmpi,openmpi,mpich</MPILIBS>
+    <CIME_OUTPUT_ROOT>/nobackup/$ENV{USER}/cesm_sims</CIME_OUTPUT_ROOT>
+    <DIN_LOC_ROOT>$ENV{ARC4_CESM2_ROOT}/inputdata</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>$ENV{ARC4_CESM2_ROOT}/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
+    <DOUT_S_ROOT>${CIME_OUTPUT_ROOT}/archive/$CASE</DOUT_S_ROOT>
+    <BASELINE_ROOT>${CIME_OUTPUT_ROOT}/cesm_baselines</BASELINE_ROOT>
+    <CCSM_CPRNC>${CIMEROOT}/tools/cprnc</CCSM_CPRNC>
+    <GMAKE>make</GMAKE>
+    <GMAKE_J>16</GMAKE_J>
+    <BATCH_SYSTEM>sge</BATCH_SYSTEM>
+    <SUPPORTED_BY>cemac-at-leeds.ac.uk</SUPPORTED_BY>
+    <MAX_TASKS_PER_NODE>40</MAX_TASKS_PER_NODE>
+    <MAX_MPITASKS_PER_NODE>40</MAX_MPITASKS_PER_NODE>
+    <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
+    <mpirun mpilib="default">
+      <executable>mpirun</executable>
+      <arguments>
+        <arg name="ntasks"> -np {{ total_tasks }} </arg>
+      </arguments>
+    </mpirun>
+
+    <module_system type="module" allow_error="true">
+      <init_path lang="perl">/apps/Modules/default/init/perl.pm</init_path>
+      <init_path lang="python">/apps/Modules/default/init/python.py</init_path>
+      <init_path lang="sh">/apps/Modules/default/init/sh</init_path>
+      <init_path lang="csh">/apps/Modules/default/init/csh</init_path>
+      <cmd_path lang="perl">module</cmd_path>
+      <cmd_path lang="python">module</cmd_path>
+      <cmd_path lang="sh">module</cmd_path>
+      <cmd_path lang="csh">module</cmd_path>
+      <modules compiler="intel">
+        <command name="unload">openmpi</command>
+        <command name="load">intel/19.0.4</command>
+        <command name="load">intelmpi/2019.4.243</command>
+        <command name="load">netcdf/4.6.3</command>
+        <command name="load">esmf</command>
+      </modules>
+    </module_system>
+    <environment_variables>
+      <env name="OMP_STACKSIZE">64M</env>
+    </environment_variables>
+    <resource_limits>
+      <resource name="RLIMIT_STACK">-1</resource>
+    </resource_limits>
+  </machine>
+
   <machine MACH="athena">
     <DESC> CMCC IBM iDataPlex, os is Linux, 16 pes/node, batch system is LSFd mpich</DESC>
     <NODENAME_REGEX>.*.cluster.net</NODENAME_REGEX>
@@ -762,19 +813,19 @@ This allows using a different mpirun command to launch unit tests
 	<command name="switch">cray-libsci/19.02.1</command>
       </modules>
       <modules>
-	<command name="load">cray-mpich/7.7.8</command>
+	<command name="load">cray-mpich/7.7.10</command>
       </modules>
       <modules mpilib="mpi-serial">
-	<command name="load">cray-hdf5/1.10.5.0</command>
-	<command name="load">cray-netcdf/4.6.3.0</command>
+	<command name="load">cray-hdf5/1.10.5.2</command>
+	<command name="load">cray-netcdf/4.6.3.2</command>
       </modules>
       <modules mpilib="!mpi-serial">
-	<command name="load">cray-netcdf-hdf5parallel/4.6.3.0</command>
-	<command name="load">cray-hdf5-parallel/1.10.5.0</command>
-	<command name="load">cray-parallel-netcdf/1.11.1.0</command>
+	<command name="load">cray-netcdf-hdf5parallel/4.6.3.2</command>
+	<command name="load">cray-hdf5-parallel/1.10.5.2</command>
+	<command name="load">cray-parallel-netcdf/1.11.1.1</command>
       </modules>
       <modules>
-	<command name="load">cmake/3.14.4</command>
+	<command name="load">cmake/3.21.3</command>
       </modules>
     </module_system>
     <environment_variables>
@@ -868,16 +919,16 @@ This allows using a different mpirun command to launch unit tests
 	<command name="switch">cray-libsci/19.02.1</command>
       </modules>
       <modules>
-	<command name="load">cray-mpich/7.7.8</command>
+	<command name="load">cray-mpich/7.7.10</command>
       </modules>
       <modules mpilib="mpi-serial">
-	<command name="load">cray-hdf5/1.10.5.0</command>
-	<command name="load">cray-netcdf/4.6.3.0</command>
+	<command name="load">cray-hdf5/1.10.5.2</command>
+	<command name="load">cray-netcdf/4.6.3.2</command>
       </modules>
       <modules mpilib="!mpi-serial">
-	<command name="load">cray-netcdf-hdf5parallel/4.6.3.0</command>
-	<command name="load">cray-hdf5-parallel/1.10.5.0</command>
-	<command name="load">cray-parallel-netcdf/1.11.1.0</command>
+	<command name="load">cray-netcdf-hdf5parallel/4.6.3.2</command>
+	<command name="load">cray-hdf5-parallel/1.10.5.2</command>
+	<command name="load">cray-parallel-netcdf/1.11.1.1</command>
       </modules>
     </module_system>
     <environment_variables>

diff --git a/scripts/Tools/xmlchange b/scripts/Tools/xmlchange
@@ -161,6 +161,7 @@ def xmlchange(caseroot, listofsettings, xmlfile, xmlid, xmlval, subgroup,
               append, noecho, force, dryrun):
 
     with Case(caseroot, read_only=False) as case:
+        expect(os.path.isdir(caseroot), "Directory {} does not appear to be a valid case directory".format(caseroot))
         comp_classes = case.get_values("COMP_CLASSES")
         if xmlfile:
             case.set_file(xmlfile)

diff --git a/scripts/lib/CIME/case/case.py b/scripts/lib/CIME/case/case.py
@@ -84,6 +84,9 @@ def __init__(self, case_root=None, read_only=True):
 
         if case_root is None:
             case_root = os.getcwd()
+
+        expect(not os.path.isdir(case_root) or os.path.isfile(os.path.join(case_root,"env_case.xml")), "Directory {} does not appear to be a valid case directory".format(case_root))
+
         self._caseroot = case_root
         logger.debug("Initializing Case.")
         self._read_only_mode = True

diff --git a/scripts/lib/CIME/nmlgen.py b/scripts/lib/CIME/nmlgen.py
@@ -286,8 +286,15 @@ def get_default(self, name, config=None, allow_none=False):
         return default
 
     def get_streams(self):
-        """Get a list of all streams used for the current data model  mode."""
-        return self.get_default("streamslist")
+        """Get a list of all streams used for the current data model mode, possibly modified in user_nl_dxxx."""
+        streams = self.get_value("streams")
+        if streams[0]:
+            streams[:] = [text.split(" ",1)[0] for text in streams]
+            streams[:] = [text.split("txt.",1)[1] for text in streams]
+        else:
+            streams = self.get_default("streamslist")
+
+        return streams
 
     def clean_streams(self):
         for variable in self._streams_variables:

diff --git a/scripts/query_config b/scripts/query_config
@@ -59,7 +59,7 @@ def query_compsets(files, name, xml=False):
     query compset definition give a compset name
     """
     # Determine valid component values by checking the value attributes for COMPSETS_SPEC_FILE
-    components = get_compsets()
+    _, components = get_compsets()
     match_found = None
     all_components = False
     if re.search("^all$", name):  # print all compsets
@@ -74,7 +74,6 @@ def query_compsets(files, name, xml=False):
     # If name is not a valid argument - exit with error
     expect(match_found is not None,
            "Invalid input argument {}, valid input arguments are {}".format(name, components))
-
     if all_components:  # print all compsets
         for component in components:
             # the all_components flag will only print available components

diff --git a/src/components/data_comps/datm/cime_config/buildnml b/src/components/data_comps/datm/cime_config/buildnml
@@ -90,13 +90,13 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path
     # may return a string or a list.  See issue #877 in ESMCI/cime
     #
     #pylint: disable=no-member
-    if datm_presaero != "none":
+    if datm_presaero != "none" and not any(x.startswith('presaero') for x in streams):
         streams.append("presaero.{}".format(datm_presaero))
 
-    if datm_topo != "none":
+    if datm_topo != "none" and not any(x.startswith('topo') for x in streams):
         streams.append("topo.{}".format(datm_topo))
 
-    if datm_co2_tseries != "none":
+    if datm_co2_tseries != "none" and not any(x.startswith('co2tseries') for x in streams):
         streams.append("co2tseries.{}".format(datm_co2_tseries))
 
     # Add bias correction stream if given in namelist.

diff --git a/src/drivers/mct/cime_config/namelist_definition_drv.xml b/src/drivers/mct/cime_config/namelist_definition_drv.xml
@@ -4246,7 +4246,7 @@
     <category>seq_flux_mct</category>
     <group>seq_flux_mct_inparm</group>
     <desc>
-       Surface albedo for direct radiation
+       Surface albedo for diffuse radiation
     </desc>
     <values>
       <value>0.06</value>
@@ -4259,7 +4259,7 @@
     <category>seq_flux_mct</category>
     <group>seq_flux_mct_inparm</group>
     <desc>
-       Surface albedo for diffuse radiation
+       Surface albedo for direct radiation
     </desc>
     <values>
       <value>0.07</value>