Update circular dep warnings branch

configuration/scripts/cice.build

@@ -126,18 +126,21 @@ endif
 if !(-d ${ICE_LOGDIR}) mkdir -p ${ICE_LOGDIR}
 cp -p ${ICE_BLDLOG_FILE} ${ICE_LOGDIR}/
 
-grep -q "make: Circular" ${ICE_BLDLOG_FILE}
-set circularstat = ${status}
+echo " "
 
-if (${bldstat} != 0) then
-  if (${circularstat} == 0) then
-    echo ""
-    echo "ERROR: Circular dependencies :"
-    grep "make: Circular" ${ICE_BLDLOG_FILE}
-    echo ""
-    echo "${0}: ERROR : Make detected circular module dependencies !"
-    echo ""
+# special effort to trap and highlight circular dependency errors
+set circularstat = `grep "make: Circular" ${ICE_BLDLOG_FILE} | wc -l`
+if (${circularstat} > 0) then
+  echo "${0}: ERROR: Circular Dependence found"
+  grep "make: Circular" ${ICE_BLDLOG_FILE}
+  if (-e ${ICE_RUNDIR}/cice) then
+    echo "${0}: Deleting cice executable"
+    rm ${ICE_RUNDIR}/cice
   endif
+  set bldstat = 55
+endif
+
+if (${bldstat} != 0) then
   echo "${0}: COMPILE FAILED, see"
   echo "  cat ${ICE_OBJDIR}/${ICE_BLDLOG_FILE}"
   if (${quiet} == "true") then
@@ -160,14 +163,3 @@ if ( ${ICE_TEST} != ${ICE_SPVAL} ) then
   echo "PEND ${ICE_TESTNAME} run" >> ${ICE_CASEDIR}/test_output
 endif
 
-if (${circularstat} == 0) then
-  echo ""
-  echo "WARNING: Circular dependencies :"
-  grep "make: Circular" ${ICE_BLDLOG_FILE}
-  echo ""
-  echo "${0}: WARNING : Make detected circular module dependencies !"
-  echo "${0}: WARNING : The build is most probably broken !"
-  echo "${0}: WARNING : A clean build will fail !"
-  echo ""
-endif
-

doc/source/developer_guide/dg_scripts.rst

@@ -78,6 +78,18 @@ 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 gmake 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 gmake.
+There is a special trap for circular dependencies in the cice.build script to
+highlight this error when it occurs.
+
 .. _dev_machines:
 
 Machines

doc/source/intro/quickstart.rst

@@ -14,6 +14,8 @@ found in the `CICE Git and Workflow Guide <https://github.com/CICE-Consortium/Ab
 
 You will probably have to download some inputdata, see the `CICE wiki <https://github.com/cice-consortium/CICE/wiki>`_ or :ref:`force`.
 
+Software requirements are noted in this :ref:`software` section.
+
 From your main CICE directory, execute::
 
   ./cice.setup -c ~/mycase1 -g gx3 -m testmachine -s diag1,thread -p 8x1

doc/source/user_guide/ug_running.rst

@@ -7,6 +7,71 @@ Running CICE
 
 Quick-start instructions are provided in the :ref:`quickstart` section.
 
+.. _software:
+
+Software Requirements
+-------
+
+To run stand-alone, CICE requires
+
+- gmake
+- Fortran and C	compilers (intel, pgi, gnu, cray, and nag have been tested)
+- netcdf
+- MPI (this is actually	optional but without it	you can	only run on 1 processor)
+
+Below are lists of software versions that the consortium has tested at some point.  There is no
+guarantee that all compiler versions work with all CICE model versions.  At any given
+point, the consortium is regularly testing on several different compilers, but not 
+necessarily on all possible versions or combinations.  A CICE goal is to be relatively portable
+across different hardware, compilers, and other software.  As a result, the coding
+implementation tends to be on the conservative side at times.  If there are problems 
+porting to a particular system, please let the consortium know.
+
+The consortium has tested the following compilers at some point,
+
+- intel 15.0.3.187
+- intel 16.0.1.150
+- intel 17.0.1.132
+- intel 17.0.2.174
+- intel 17.0.5.239
+- intel 18.0.1.163
+- intel 19.0.2
+- intel 19.0.3.199
+- pgi 16.10.0
+- gnu 6.3.0
+- gnu 7.2.0
+- gnu 7.3.0
+- cray 8.5.8
+- cray 8.6.4
+- nag 6.2
+
+The consortium has tested the following mpi versions,
+
+- mpich 7.3.2
+- mpich 7.5.3
+- mpich 7.6.2
+- mpich 7.6.3
+- mpich 7.7.6
+- intel mpi 18.0.1
+- mpt 2.14
+- mpt 2.17
+- mpt 2.18
+- mpt 2.19
+- openmpi 1.6.5
+
+The netcdf implementation is relatively general and should work with any version of netcdf 3 or 4.  The consortium has tested
+
+- netcdf 4.3.0
+- netcdf 4.3.2
+- netcdf 4.4.0
+- netcdf 4.4.1.1.32
+- netcdf 4.4.1.1
+- netcdf 4.4.2
+- netcdf 4.5.0
+- netcdf 4.6.1.3
+
+Please email the consortium if this list can be extended.
+
 .. _scripts:
 
 Scripts
@@ -82,7 +147,7 @@ Some hints:
 - To change batch settings, manually edit the top of the **cice.run** or **cice.test** (if running a test) file
 - To turn on the debug compiler flags, set ``ICE_BLDDEBUG`` in **cice.setttings** to true.  It is also possible to use the ``debug`` option  (``-s debug``) when creating the case with **cice.setup** to set this option automatically.
 - To change compiler options, manually edit the Macros file
-- To clean the build before each compile, set ``ICE_CLEANBUILD`` in **cice.settings** to true (this is the default value), or use the ``buildclean`` option (``-s buildclean``)  when creating the case with **cice.setup**.  To not clean before the build, set ``ICE_CLEANBUILD`` in **cice.settings** to false, or use the ``buildincremental`` option  (``-s buildincremental``) when creating the case with **cice.setup**.
+- To clean the build before each compile, set ``ICE_CLEANBUILD`` in **cice.settings** to true (this is the default value), or use the ``buildclean`` option (``-s buildclean``)  when creating the case with **cice.setup**.  To not clean before the build, set ``ICE_CLEANBUILD`` in **cice.settings** to false, or use the ``buildincremental`` option  (``-s buildincremental``) when creating the case with **cice.setup**.  It is recommended that the ``ICE_CLEANBUILD`` be set to true if there are any questions about whether the build is proceeding properly.
 
 To build and run::
 
@@ -153,8 +218,8 @@ by doing ``cice.setup --help``.
 
 The default CICE namelist and CICE settings are specified in the 
 files **configuration/scripts/ice_in** and 
-**configuration/scripts/cice.settings** respectively.  When picking a 
-preset setting (option), the set_env.setting and set_nml.setting will be used to 
+**configuration/scripts/cice.settings** respectively.  When picking
+settings (options), the set_env.setting and set_nml.setting will be used to 
 change the defaults.  This is done as part of the ``cice.setup`` and the
 modifications are resolved in the **cice.settings** and **ice_in** file placed in 
 the case directory.  If multiple options are chosen and then conflict, then the last

doc/source/user_guide/ug_troubleshooting.rst

@@ -190,6 +190,9 @@ Known bugs
 -  Latitude and longitude fields in the history output may be wrong when
    using padding.
 
+-  History and restart files will not be written on the first timestep in
+   some cases.
+
 
 Interpretation of albedos
 ----------------------------------------