NOAA machine pass of base_suite #155

cice.setup

@@ -377,7 +377,6 @@ else
     exit -1
   endif
   cp -f ${ICE_SCRIPTS}/tests/report_results.csh ${tsdir}
-  cp -f ${ICE_SCRIPTS}/tests/timeseries.csh ${tsdir}
   cp -f ${ICE_SCRIPTS}/tests/poll_queue.csh ${tsdir}
 
   foreach file (${tsdir}/suite.run ${tsdir}/suite.submit)
@@ -433,6 +432,7 @@ if (${doabort} == true) then
   exit -1
 endif
 
+# Create a new sets_base variable to store sets passed to cice.setup
 set sets_base = "${sets}"
 set bfbcomp_base = "$bfbcomp"
 foreach compiler ( $ncompilers )
@@ -458,13 +458,14 @@ EOF
       continue
     endif
 
+    source ${ICE_SCRIPTS}/machines/env.${machcomp} -nomodules || exit 2
+
     # Obtain the test name, sets, grid, and PE information from .ts file
     set test = `echo $line | cut -d' ' -f1`
     set grid = `echo $line | cut -d' ' -f2`
     set pesx = `echo $line | cut -d' ' -f3`
     set sets_tmp = `echo $line | cut -d' ' -f4`
     set bfbcomp_tmp = `echo $line | cut -d' ' -f5`
-    # Create a new sets_base variable to store sets passed to cice.setup
 
     # Append sets from .ts file to the $sets variable
     set sets = "$sets_base,$sets_tmp"
@@ -482,6 +483,107 @@ EOF
       set fbfbcomp = ${machcomp}_${bfbcomp}
     endif
 
+    #------------------------------------------------------------
+    # Parse pesx with strict checking, limit pes for machine
+
+    set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*$/OK/'`
+    if (${chck} == OK) then
+      set task  = `echo ${pesx} | cut -d x -f 1`
+      set thrd  = `echo ${pesx} | cut -d x -f 2`
+      set blckx = `echo ${pesx} | cut -d x -f 3`
+      set blcky = `echo ${pesx} | cut -d x -f 4`
+      set mblck = `echo ${pesx} | cut -d x -f 5`
+      if (${task} == 0 || ${thrd} == 0 || ${blckx} == 0 || ${blcky} == 0 || ${mblck} == 0) then
+        echo "${0}: ERROR in -p argument, cannot have zeros"
+        exit -1
+      endif
+    else
+      set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*$/OK/'`
+      if (${chck} == OK) then
+        set task  = `echo ${pesx} | cut -d x -f 1`
+        set thrd  = `echo ${pesx} | cut -d x -f 2`
+        set blckx = `echo ${pesx} | cut -d x -f 3`
+        set blcky = `echo ${pesx} | cut -d x -f 4`
+        set mblck = 0
+        if (${task} == 0 || ${thrd} == 0 || ${blckx} == 0 || ${blcky} == 0) then
+          echo "${0}: ERROR in -p argument, cannot have zeros"
+          exit -1
+        endif
+      else
+        set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*x[0-9][0-9]*$/OK/'`
+        if (${chck} == OK) then
+          set task = `echo ${pesx} | cut -d x -f 1`
+          set thrd = `echo ${pesx} | cut -d x -f 2`
+          set blckx = 0
+          set blcky = 0
+          set mblck = 0
+          if (${task} == 0 || ${thrd} == 0) then
+            echo "${0}: ERROR in -p argument, cannot have zeros"
+            exit -1
+          endif
+        else
+          set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*$/OK/'`
+          if (${chck} == OK) then
+            set task = `echo ${pesx} | cut -d x -f 1`
+            set thrd = 1
+            set blckx = 0
+            set blcky = 0
+            set mblck = 0
+            if (${task} == 0) then
+              echo "${0}: ERROR in -p argument, cannot have zeros"
+              exit -1
+            endif
+          else
+            echo "${0}: ERROR in -p argument, ${pesx}, must be [m], [m]x[n], [m]x[n]x[bx]x[by], or [m]x[n]x[bx]x[by]x[mb] "
+            exit -1
+          endif
+        endif
+      endif
+    endif
+
+    @ blkreq = ${task} * ${mblck}
+    # check max threads, reduce threads, increase tasks
+    if ($?ICE_MACHINE_MAXTHREADS) then
+      if (${thrd} > ${ICE_MACHINE_MAXTHREADS}) then
+        @ pesreq = ${task} * ${thrd}
+        @ task = ${pesreq} / ${ICE_MACHINE_MAXTHREADS}
+        @ thrd = ${ICE_MACHINE_MAXTHREADS}
+        @ peschk = ${task} * ${thrd}
+        if (${pesreq} > ${peschk}) then
+          @ task = ${task} + 1
+        endif
+#        echo "tcx1 reset to $task $thrd $mblck"
+      endif
+    endif
+
+    # check max pes, reduce tasks
+    if ($?ICE_MACHINE_MAXPES) then
+      @ pesreq = ${task} * ${thrd}
+      if (${pesreq} > ${ICE_MACHINE_MAXPES}) then
+        @ task = ${ICE_MACHINE_MAXPES} / ${thrd}
+#        echo "tcx2 reset to $task $thrd $mblck"
+      endif
+    endif
+
+    # check max blocks and adjust as needed
+    if ($mblck > 0) then
+      @ mblck = ${blkreq} / ${task}
+      @ blkchk = ${task} * ${mblck}
+      if (${blkreq} > ${blkchk}) then
+        @ mblck = $mblck + 1
+      endif
+#      echo "tcx3 reset to $task $thrd $mblck"
+    endif
+
+    # update pesx based on use defined settings and machine limits to reflect actual value
+    set pesx = ${task}x${thrd}x${blckx}x${blcky}x${mblck}
+    if (${mblck} == 0) then
+      set pesx = ${task}x${thrd}x${blckx}x${blcky}
+    endif
+    if (${blckx} == 0 || ${blcky} == 0) then
+      set pesx = ${task}x${thrd}
+    endif
+
     set testname_noid = ${spval}
     # create case for test cases
     if (${docase} == 0) then
@@ -533,7 +635,7 @@ EOF
     endif
 
     # from basic script dir to case
-    foreach file (cice.build cice.settings Makefile ice_in makdep.c setup_run_dirs.csh)
+    foreach file (cice.build cice.settings Makefile ice_in makdep.c setup_run_dirs.csh timeseries.csh timeseries.py)
       if !(-e ${ICE_SCRIPTS}/$file) then
         echo "${0}: ERROR, ${ICE_SCRIPTS}/$file not found"
         exit -1
@@ -560,7 +662,6 @@ EOF
     end
 
     cd ${casedir}
-    source ./env.${machcomp} -nomodules || exit 2
 
     set quietmode = false
     if ($?ICE_MACHINE_QUIETMODE) then
@@ -586,36 +687,6 @@ EOF
     #------------------------------------------------------------
     # Compute a default blocksize
 
-    set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*$/OK/'`
-    if (${chck} == OK) then
-      set task  = `echo ${pesx} | cut -d x -f 1`
-      set thrd  = `echo ${pesx} | cut -d x -f 2`
-      set blckx = `echo ${pesx} | cut -d x -f 3`
-      set blcky = `echo ${pesx} | cut -d x -f 4`
-      set mblck = `echo ${pesx} | cut -d x -f 5`
-    else
-      set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*x[0-9][0-9]*$/OK/'`
-      if (${chck} == OK) then
-        set task  = `echo ${pesx} | cut -d x -f 1`
-        set thrd  = `echo ${pesx} | cut -d x -f 2`
-        set blckx = `echo ${pesx} | cut -d x -f 3`
-        set blcky = `echo ${pesx} | cut -d x -f 4`
-        set mblck = 0
-      else
-        set chck = `echo ${pesx} | sed  's/^[0-9][0-9]*x[0-9][0-9]*$/OK/'`
-        if (${chck} == OK) then
-          set task = `echo ${pesx} | cut -d x -f 1`
-          set thrd = `echo ${pesx} | cut -d x -f 2`
-          set blckx = 0
-          set blcky = 0
-          set mblck = 0
-        else
-          echo "${0}: ERROR in -p argument, ${pesx}, must be [m]x[n], [m]x[n]x[bx]x[by], or [m]x[n]x[bx]x[by]x[mb] "
-          exit -1
-        endif
-      endif
-    endif
-
     setenv ICE_DECOMP_GRID  ${grid}
     setenv ICE_DECOMP_NTASK ${task}
     setenv ICE_DECOMP_NTHRD ${thrd}
@@ -847,7 +918,7 @@ echo "${testname_base}"
 cd ${testname_base}
 source ./cice.settings
 set ciceexe = "../ciceexe.\${ICE_COMPILER}.\${ICE_COMMDIR}.\${ICE_BLDDEBUG}.\${ICE_THREADED}.\${ICE_IOTYPE}"
-./cice.build \${ciceexe}
+./cice.build --exe \${ciceexe}
 if !(-e \${ciceexe}) cp -p \${ICE_RUNDIR}/cice \${ciceexe}
 EOF
   end

doc/source/conf.py

@@ -54,17 +54,17 @@
 
 # General information about the project.
 project = u'CICE'
-copyright = u'2018, Triad National Security, LLC (code) and National Center for Atmospheric Research (documentation)'
+copyright = u'2019, Triad National Security, LLC (code) and National Center for Atmospheric Research (documentation)'
 author = u'CICE-Consortium'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'6.0.0' 
+version = u'6.0.2' 
 # The full version, including alpha/beta/rc tags.
-version = u'6.0.0' 
+version = u'6.0.2' 
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/developer_guide/dg_about.rst

@@ -16,3 +16,14 @@ Guiding principles for the creation of CICE include the following:
     on individual gridcells, and contain no underlying infrastructure.  CICE must call
     into Icepack using interfaces and approaches specified by Icepack.
 
+
+Git workflow and Pull Requests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+There is extensive Information for Developers documentation available.
+See https://github.com/CICE-Consortium/About-Us/wiki/Resource-Index#information-for-developers
+for information on:
+  - Contributing to model development
+  - Software development practices guide
+  - git Workflow Guide - including extensive information about the Pull Request process and requirements
+  - Documentation Workflow Guide

doc/source/developer_guide/dg_dynamics.rst

@@ -37,8 +37,18 @@ The dynamics solvers are found in **cicecore/cicedynB/dynamics/**.  A couple of
 available including EVP, revised EVP, and EAP.  The dynamics solver is specified in namelist with the
 ``kdyn`` variable.  ``kdyn=1`` is evp, ``kdyn=2`` is eap, and revised evp requires the ``revised_evp``
 namelist flag be set to true.
-A vectorized version of EVP is available through the namelist flag ``evp_kernel_ver``. Default is "normal"
-EVP as usual ``evp_kernel_ver=0``, whereas an vectorized version (ver.2) is available ``evp_kernel_ver=2``.
+
+Multiple evp solvers are supported thru the namelist flag ``kevp_kernel``.  The standard implementation
+and current default is ``kevp_kernel=0``.  In this case, the stress is solved on the regular decomposition
+via subcycling and calls to subroutine stress and subroutine stepu with MPI global sums required in each
+subcycling call.  With ``kevp_kernel=2``, the data required to compute the stress is gathered to the root
+MPI process and the stress calculation is performed on the root task without any MPI global sums.  OpenMP
+parallelism is supported in ``kevp_kernel=2``.  The solutions with ``kevp_kernel`` set to 0 or 2 will 
+not be bit-for-bit
+identical but should be the same to roundoff and produce the same climate.  ``kevp_kernel=2`` may perform
+better for some configurations, some machines, and some pe counts.  ``kevp_kernel=2`` is not supported
+with the tripole grid and is still being validated.  Until ``kevp_kernel=2`` is fully validated, it will
+abort if set.  To override the abort, use value 102 for testing.
 
 
 Transport

doc/source/developer_guide/dg_other.rst

@@ -160,57 +160,57 @@ Additional information about tracers can be found in the
 To add a tracer, follow these steps using one of the existing tracers as
 a pattern.
 
-#. **icepack\_tracers.F90** and **icepack\_[tracer].F90**: declare tracers,
-add flags and indices, and create physics routines as described in the
-`Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/developer_guide/dg_adding_tracers.html>`_
+  1)  **icepack\_tracers.F90** and **icepack\_[tracer].F90**: declare tracers,
+      add flags and indices, and create physics routines as described in the
+      `Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/developer_guide/dg_adding_tracers.html>`_
 
-#. **ice_arrays_column.F90**: declare arrays
+  2)  **ice_arrays_column.F90**: declare arrays
 
-#. **ice_init_column.F90**: initialize arrays
+  3)  **ice_init_column.F90**: initialize arrays
 
-#. **ice\_init.F90**: (some of this may be done in **icepack\_[tracer].F90**
-   instead)
+  4)  **ice\_init.F90**: (some of this may be done in **icepack\_[tracer].F90**
+      instead)
 
-   -  declare ``tr_[tracer]``  and ``nt_[tracer]`` as needed
+     -  declare ``tr_[tracer]``  and ``nt_[tracer]`` as needed
 
-   -  add logical namelist variables ``tr_[tracer]``, ``restart_[tracer]``
+     -  add logical namelist variables ``tr_[tracer]``, ``restart_[tracer]``
 
-   -  initialize and broadcast namelist variables
+     -  initialize and broadcast namelist variables
 
-   -  check for potential conflicts, aborting if any occur
+     -  check for potential conflicts, aborting if any occur
 
-   -  print namelist variables to diagnostic output file
+     -  print namelist variables to diagnostic output file
 
-   -  initialize tracer flags etc in icepack (call *icepack_init_tracer_flags* etc)
+     -  initialize tracer flags etc in icepack (call *icepack_init_tracer_flags* etc)
 
-   -  increment number of tracers in use based on namelist input (``ntrcr``)
+     -  increment number of tracers in use based on namelist input (``ntrcr``)
 
-   -  define tracer dependencies
+     -  define tracer dependencies
 
-#.  **CICE\_InitMod.F90**: initialize tracer (includes reading restart file)
+  5)  **CICE\_InitMod.F90**: initialize tracer (includes reading restart file)
 
-#.  **CICE\_RunMod.F90**, **ice\_step\_mod.F90** (and elsewhere as needed):
+  6)  **CICE\_RunMod.F90**, **ice\_step\_mod.F90** (and elsewhere as needed):
 
-   -  call routine to write tracer restart data
+     -  call routine to write tracer restart data
 
-   -  call Icepack or other routines to update tracer value 
-      (often called from **ice\_step\_mod.F90**)
+     -  call Icepack or other routines to update tracer value 
+        (often called from **ice\_step\_mod.F90**)
 
-#.  **ice\_restart.F90**: define restart variables (for binary, netCDF and PIO)
+  7)  **ice\_restart.F90**: define restart variables (for binary, netCDF and PIO)
 
-#.  **ice\_restart\_column.F90**: create routines to read, write tracer restart data
+  8)  **ice\_restart\_column.F90**: create routines to read, write tracer restart data
 
-#.  **ice\_fileunits.F90**: add new dump and restart file units
+  9)  **ice\_fileunits.F90**: add new dump and restart file units
 
-#.  **ice\_history\_[tracer].F90**: add history variables
-   (Section :ref:`addhist`)
+  10)  **ice\_history\_[tracer].F90**: add history variables
+       (Section :ref:`addhist`)
 
-#.  **ice\_in**: add namelist variables to *tracer\_nml* and
-   *icefields\_nml*. Best practice is to set the namelist values so that the 
-   new capability is turned off, and create an option file with your preferred
-   configuration in **configuration/scripts/options**.
+  11)  **ice\_in**: add namelist variables to *tracer\_nml* and
+       *icefields\_nml*. Best practice is to set the namelist values so that the 
+       new capability is turned off, and create an option file with your preferred
+       configuration in **configuration/scripts/options**.
 
-#.  If strict conservation is necessary, add diagnostics as noted for
-   topo ponds in the `Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/science_guide/index.html>`_.
+  12)  If strict conservation is necessary, add diagnostics as noted for
+       topo ponds in the `Icepack documentation <https://cice-consortium-icepack.readthedocs.io/en/master/science_guide/index.html>`_.
 
-#. Update documentation, including **cice_index.rst** and **ug_case_settings.rst**
+  13)  Update documentation, including **cice_index.rst** and **ug_case_settings.rst**

doc/source/developer_guide/dg_scripts.rst

@@ -31,6 +31,8 @@ The directory structure under configure/scripts is as follows.
 |        **parse_settings.sh**     replaces settings with command-line configuration
 |        **setup_run_dirs.csh**    creates the case run directories
 |        **set_version_number.csh** updates the model version number from the **cice.setup** command line
+|        **timeseries.csh**        generates PNG timeseries plots from output files, using GNUPLOT
+|        **timeseries.py**         generates PNG timeseries plots from output files, using Python
 |        **tests/**                scripts for configuring and running basic tests
 
 .. _dev_strategy:
@@ -78,6 +80,25 @@ with appropriate names and syntax.  The set_nml file syntax is the same as namel
 syntax and the set_env files are consistent with csh setenv syntax.  See other files for
 examples of the syntax.
 
+.. _build:
+
+Build Scripts
+--------------
+
+CICE uses GNU Make to build the model.  There is a common **Makefile** for all machines.  
+Each machine provides a Macros file to define some Makefile variables
+and and an env file to specify the modules/software stack for each compiler.
+The machine is built by the cice.build script which invokes Make.
+There is a special trap for circular dependencies in the cice.build script to
+highlight this error when it occurs.
+
+The **cice.build** script has some additional features including the ability to 
+pass a Makefile target.  This is documented in :ref:`cicebuild`.  In addition, there
+is a hidden feature in the **cice.build** script that allows for reuse of 
+executables.  This is used by the test suites to significantly reduce cost of
+building the model.  It is invoked with the ``--exe`` argument to **cice.build**
+and should not be invoked by users interactively.
+
 .. _dev_machines:
 
 Machines
@@ -122,9 +143,8 @@ setup the various tests, such as smoke and restart tests (**test_smoke.script**,
 and the files that describe with options files are needed for each test (ie. **test_smoke.files**, **test_restart.files**).
 A baseline test script (**baseline.script**) is also there to setup the general regression
 and comparison testing.  That directory also contains the preset test suites 
-(ie. **base_suite.ts**) and a file that supports post-processing on the model
-output (**timeseries.csh**).  There is also a script **report_results.csh** that pushes results 
-from test suites back to the CICE-Consortium test results wiki page.
+(ie. **base_suite.ts**) and a script (**report_results.csh**) that pushes results from 
+test suites back to the CICE-Consortium test results wiki page.
 
 To add a new test (for example newtest), several files may be needed,