Merge pull request #2 from ESMCI/maint-5.6

Maint 5.6
ESMCI · Oct 5, 2018 · 4be92b8 · 4be92b8
2 parents 1d4385a + fcf60c8
commit 4be92b8
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diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,65 @@
 ======================================================================
 
+Originator: Chris Fischer 
+Date: 10-2-2018
+Tag: cime_cesm2_0_rel_06
+Answer Changes: None
+Tests: scripts_regression_tests
+Dependencies:
+
+Brief Summary:
+    - Archive_metadata updates for CMIP6 experiments.
+    - OS is not generic env var.
+    - New machines at ETH and CSCS.
+    - Update ESMF library on cheyenne.
+    - Fix documentation for histaux_r2x namelist variable.
+    - Dont allow zero ntasks nthrds.
+    - Add lapack and blas libraries to pgi compile on cheyenne.
+    - Updates for compatibility with XML to html tools.
+    - Remove additional rad->deg conversion to radians when creating ocean
+      domain files.
+    - ESMF logging fix.
+
+User interface changes: 
+
+PR summary: git log --oneline --first-parent [previous_tag]..master 
+12e1c4d41 (HEAD -> maint-5.6, origin/maint-5.6) Merge pull request #2815 from bertinia/maint-5.6_archive_metadata
+767511a79 OS is not generic env var
+bec49f0c2 Merge pull request #2807 from beyerle/euler_daint
+9e74b8ab3 Merge pull request #2806 from ESMCI/fischer/ESMF_710r
+0f20ab46e Merge pull request #2774 from billsacks/fix_histaux_r2x_docs
+1c10e58e8 Merge pull request #2768 from jedwards4b/dont_allow_zero_ntasks_nthrds
+6a1069ce3 Merge pull request #2753 from jedwards4b/pgi_lapack
+5a0a56721 Merge pull request #2742 from bertinia/maint-5.6-component-return-values
+cbf8f2216 Merge pull request #2736 from jtruesdal/domainfix
+2e34a0305 Merge pull request #2733 from gold2718/esmf_log_fix
+
+
+Modified files: git diff --name-status [previous_tag]
+M       config/cesm/config_grids.xml
+M       config/cesm/machines/config_batch.xml
+M       config/cesm/machines/config_compilers.xml
+M       config/cesm/machines/config_machines.xml
+M       scripts/Tools/archive_metadata
+M       scripts/lib/CIME/XML/component.py
+M       scripts/lib/CIME/XML/compsets.py
+M       scripts/lib/CIME/XML/env_mach_pes.py
+M       scripts/lib/CIME/XML/machines.py
+M       scripts/lib/CIME/utils.py
+M       src/components/data_comps/docn/cime_config/config_component.xml
+M       src/drivers/mct/cime_config/config_component.xml
+M       src/drivers/mct/cime_config/namelist_definition_drv.xml
+M       src/drivers/mct/main/cime_comp_mod.F90
+M       src/drivers/mct/main/cime_driver.F90
+M       src/drivers/mct/shr/seq_comm_mct.F90
+M       src/drivers/mct/shr/seq_infodata_mod.F90
+M       src/share/esmf_wrf_timemgr/ESMF_Stubs.F90
+M       tools/mapping/gen_domain_files/src/gen_domain.F90
+
+======================================================================
+
+======================================================================
+
 Originator: Chris Fischer 
 Date: 7-24-2018
 Tag: cime_cesm2_0_rel_05

diff --git a/config/cesm/machines/config_batch.xml b/config/cesm/machines/config_batch.xml
@@ -96,7 +96,7 @@
     </submit_args>
   </batch_system>
 
-  <batch_system type="lsf" version="9.1">
+  <batch_system type="lsf">
     <batch_query args=" -w" >bjobs</batch_query>
     <batch_submit>bsub</batch_submit>
     <batch_cancel>bkill</batch_cancel>
@@ -110,19 +110,12 @@
     <batch_mail_flag>-u</batch_mail_flag>
     <batch_mail_type_flag></batch_mail_type_flag>
     <batch_mail_type></batch_mail_type>
-    <submit_args>
-      <arg flag="-q" name="$JOB_QUEUE"/>
-      <arg flag="-W" name="$JOB_WALLCLOCK_TIME"/>
-      <arg flag="-P" name="$PROJECT"/>
-    </submit_args>
     <directives>
+      <directive                       > -J {{ job_id }} </directive>
       <directive                       > -n {{ total_tasks }} </directive>
-      <directive                       > -R "span[ptile={{ tasks_per_node }}]"</directive>
-      <directive                       > -N  </directive>
-      <directive default="poe"         > -a {{ poe }} </directive>
+      <directive                       > -W $JOB_WALLCLOCK_TIME </directive>
       <directive default="cesm.stdout" > -o {{ job_id }}.%J  </directive>
       <directive default="cesm.stderr" > -e {{ job_id }}.%J  </directive>
-      <directive                       > -J {{ job_id }} </directive>
     </directives>
   </batch_system>
 
@@ -189,13 +182,36 @@
     </directives>
   </batch_system>
 
-  <!-- brutus is PBS -->
-  <batch_system type="pbs" MACH="brutus" >
+  <!-- euler2 is LSF -->
+  <batch_system MACH="euler2" type="lsf" >
     <directives>
-      <directive default="/bin/bash" > -S {{ shell }}  </directive>
+      <directive> -R "select[model==XeonE5_2680v3]" </directive>
+    </directives>
+    <queues>
+      <queue walltimemax="23:59:00" default="true">normal.24h</queue>
+      <queue walltimemax="03:59:00" >normal.4h</queue>
+    </queues>
+  </batch_system>
+
+  <!-- euler3 is LSF -->
+  <batch_system MACH="euler3" type="lsf" >
+    <directives>
+      <directive> -R "span[ptile=4] select[model==XeonE3_1585Lv5]" </directive>
     </directives>
     <queues>
-      <queue walltimemax="00:59:00" nodemin="1" nodemax="624" default="true">batch</queue>
+      <queue walltimemax="23:59:00" default="true">normal.24h</queue>
+      <queue walltimemax="03:59:00" >normal.4h</queue>
+    </queues>
+  </batch_system>
+
+  <!-- euler4 is LSF -->
+  <batch_system MACH="euler4" type="lsf" >
+    <directives>
+      <directive> -R "select[model==XeonGold_6150]" </directive>
+    </directives>
+    <queues>
+      <queue walltimemax="23:59:00" default="true">normal.24h</queue>
+      <queue walltimemax="03:59:00" >normal.4h</queue>
     </queues>
   </batch_system>
 
@@ -212,13 +228,6 @@
     </queues>
   </batch_system>
 
-  <!-- brutus is PBS -->
-  <batch_system MACH="brutus" type="pbs">
-    <directives>
-      <directive default="/bin/bash" > -S {{ shell }}  </directive>
-    </directives>
-  </batch_system>
-
   <!-- eos is PBS -->
   <batch_system MACH="eos" type="pbs">
     <jobid_pattern>^(\d+)</jobid_pattern>
@@ -523,7 +532,7 @@
     </queues>
   </batch_system>
 
-  <batch_system MACH="rosa" type="slurm" >
+  <batch_system MACH="daint" type="slurm" >
     <batch_submit>sbatch</batch_submit>
     <submit_args>
       <arg flag="--time" name="$JOB_WALLCLOCK_TIME"/>

diff --git a/config/cesm/machines/config_compilers.xml b/config/cesm/machines/config_compilers.xml
@@ -69,7 +69,6 @@ using a fortran linker.
      compilers -->
 <compiler>
   <CPPDEFS>
-    <append> -D<env>OS</env> </append>
     <append MODEL="pop"> -D_USE_FLOW_CONTROL </append>
   </CPPDEFS>
   <SUPPORTS_CXX>FALSE</SUPPORTS_CXX>
@@ -486,6 +485,124 @@ using a fortran linker.
   <SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
 </compiler>
 
+<compiler MACH="daint" COMPILER="pgi">
+  <FFLAGS>
+    <append> -I/project/s824/edavin/OASIS3-MCT_2.0/build.pgi/build/lib/mct -I/project/s824/edavin/OASIS3-MCT_2.0/build.pgi/build/lib/psmile.MPI1 </append>
+  </FFLAGS>
+  <SLIBS>
+    <append> -llapack -lblas </append>
+    <append> -L/project/s824/edavin/OASIS3-MCT_2.0/build.pgi/lib -lpsmile.MPI1 -lscrip -lmct_oasis -lmpeu_oasis </append>
+  </SLIBS>
+</compiler>
+
+<compiler MACH="daint" COMPILER="cray">
+  <FFLAGS>
+    <append> -I/project/s824/edavin/OASIS3-MCT_2.0/build.cray/build/lib/mct -I/project/s824/edavin/OASIS3-MCT_2.0/build.cray/build/lib/psmile.MPI1 </append>
+  </FFLAGS>
+  <SLIBS>
+    <append> -L/project/s824/edavin/OASIS3-MCT_2.0/build.cray/lib -lpsmile.MPI1 -lscrip -lmct_oasis -lmpeu_oasis </append>
+  </SLIBS>
+</compiler>
+
+<compiler MACH="euler2">
+  <CPPDEFS>
+    <append> -DLINUX </append>
+  </CPPDEFS>
+  <NETCDF_PATH>$ENV{NETCDF}</NETCDF_PATH>
+  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
+  <PNETCDF_PATH>$ENV{PNETCDF}</PNETCDF_PATH>
+  <SLIBS>
+    <base> -L$ENV{NETCDF}/lib -lnetcdf -lnetcdff </base>
+  </SLIBS>
+</compiler>
+
+<compiler MACH="euler2" COMPILER="intel">
+  <CFLAGS>
+    <append DEBUG="FALSE"> -xCORE-AVX2 </append>
+  </CFLAGS>
+  <FFLAGS>
+    <append DEBUG="FALSE"> -xCORE-AVX2 </append>
+  </FFLAGS>
+  <LDFLAGS>
+    <append> -mkl </append>
+  </LDFLAGS>
+</compiler>
+
+<compiler MACH="euler2" COMPILER="pgi">
+  <CFLAGS>
+    <append DEBUG="FALSE"> -O2 </append>
+  </CFLAGS>
+  <FFLAGS>
+    <append DEBUG="FALSE"> -O2 </append>
+  </FFLAGS>
+</compiler>
+
+<compiler MACH="euler3">
+  <CPPDEFS>
+    <append> -DLINUX </append>
+  </CPPDEFS>
+  <NETCDF_PATH>$ENV{NETCDF}</NETCDF_PATH>
+  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
+  <PNETCDF_PATH>$ENV{PNETCDF}</PNETCDF_PATH>
+  <SLIBS>
+    <base> -L$ENV{NETCDF}/lib -lnetcdf -lnetcdff </base>
+  </SLIBS>
+</compiler>
+
+<compiler MACH="euler3" COMPILER="intel">
+  <CFLAGS>
+    <append DEBUG="FALSE"> -xCORE-AVX2 </append>
+  </CFLAGS>
+  <FFLAGS>
+    <append DEBUG="FALSE"> -xCORE-AVX2 </append>
+  </FFLAGS>
+  <LDFLAGS>
+    <append> -mkl </append>
+  </LDFLAGS>
+</compiler>
+
+<compiler MACH="euler3" COMPILER="pgi">
+  <CFLAGS>
+    <append DEBUG="FALSE"> -O2 </append>
+  </CFLAGS>
+  <FFLAGS>
+    <append DEBUG="FALSE"> -O2 </append>
+  </FFLAGS>
+</compiler>
+
+<compiler MACH="euler4">
+  <CPPDEFS>
+    <append> -DLINUX </append>
+  </CPPDEFS>
+  <NETCDF_PATH>$ENV{NETCDF}</NETCDF_PATH>
+  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
+  <PNETCDF_PATH>$ENV{PNETCDF}</PNETCDF_PATH>
+  <SLIBS>
+    <base> -L$ENV{NETCDF}/lib -lnetcdf -lnetcdff </base>
+  </SLIBS>
+</compiler>
+
+<compiler MACH="euler4" COMPILER="intel">
+  <CFLAGS>
+    <append DEBUG="FALSE"> -xCORE-AVX2 </append>
+  </CFLAGS>
+  <FFLAGS>
+    <append DEBUG="FALSE"> -xCORE-AVX2 </append>
+  </FFLAGS>
+  <LDFLAGS>
+    <append> -mkl </append>
+  </LDFLAGS>
+</compiler>
+
+<compiler MACH="euler4" COMPILER="pgi">
+  <CFLAGS>
+    <append DEBUG="FALSE"> -O2 </append>
+  </CFLAGS>
+  <FFLAGS>
+    <append DEBUG="FALSE"> -O2 </append>
+  </FFLAGS>
+</compiler>
+
 <compiler MACH="constance" COMPILER="intel">
   <CFLAGS>
     <append DEBUG="FALSE"> -O2 </append>