Merge pull request #47 from SamuelTrahanNOAA/update-rrfs-dev

merge develop and new ifi support

.github/workflows/gcc.yml

@@ -34,6 +34,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      - name: checkout-upp  # This is for getting spack.yaml
+        uses: actions/checkout@v2
+        with:
+            path: UPP
+
       # Cache spack, compiler and dependencies
       - name: cache-env
         id: cache-env
@@ -42,13 +47,7 @@ jobs:
           path: |
             spack
             ~/.spack
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
-
-      - name: checkout-upp  # This is for getting spack.yaml
-        if: steps.cache-env.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
-        with:
-            path: UPP
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
 
       # Install dependencies using Spack
       - name: install-dependencies-with-spack
@@ -58,11 +57,11 @@ jobs:
           source spack/share/spack/setup-env.sh
           spack env create upp-env UPP/ci/spack.yaml
           spack env activate upp-env
-          spack compiler find
+          sudo apt install cmake
           spack external find
           spack add mpich@3.4.2
           spack concretize
-          spack install --dirty -v
+          spack install -v --fail-fast --dirty
 
   build:
     needs: setup
@@ -81,7 +80,7 @@ jobs:
           path: |
             spack
             ~/.spack
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
 
       - name: build-upp
         run: |

.github/workflows/intel.yml

@@ -36,6 +36,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      - name: checkout-upp  # This is for getting spack.yaml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        uses: actions/checkout@v2
+        with:
+            path: UPP
+
       # Cache spack, compiler and dependencies
       - name: cache-env
         id: cache-env
@@ -45,10 +51,9 @@ jobs:
             spack
             ~/.spack
             /opt/intel
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
 
       - name: install-intel-compilers
-        if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
           wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
@@ -57,25 +62,21 @@ jobs:
           sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
           echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
 
-      - name: checkout-upp  # This is for getting spack.yaml
-        if: steps.cache-env.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
-        with:
-            path: UPP
-
       # Install dependencies using Spack
       - name: install-dependencies-with-spack
         if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
+          sudo mv /usr/local/ /usr_local_mv
           git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
           source spack/share/spack/setup-env.sh
           spack env create upp-env UPP/ci/spack.yaml
           spack env activate upp-env
           spack compiler find
+          sudo apt install cmake
           spack external find
           spack add intel-oneapi-mpi
           spack concretize
-          spack install --dirty -v
+          spack install --dirty -v --fail-fast
 
   build:
     needs: setup
@@ -99,7 +100,7 @@ jobs:
             spack
             ~/.spack
             /opt/intel
-          key: spack-${{ runner.os }}-${{ env.cache_key }}
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('UPP/ci/spack.yaml') }}
 
       - name: build-upp
         run: |

.gitmodules

@@ -2,3 +2,6 @@
   path = sorc/ncep_post.fd/post_gtg.fd
   url = https://github.com/NCAR/UPP_GTG
   update = none
+[submodule "sorc/libIFI.fd"]
+	path = sorc/libIFI.fd
+	url = ssh://git@github.com/NCAR/UPP_IFI

CMakeLists.txt

@@ -54,15 +54,32 @@ if(BUILD_WITH_GTG)
   find_package(ip REQUIRED)
 endif()
 
-if(REQUIRE_IFI)
+if(INTERNAL_IFI)
+  if(BUILD_WITH_IFI)
+    message(SEND_ERROR "Cannot use INTERNAL_IFI with either BUILD_WITH_IFI or REQUIRE_IFI.")
+  endif()
+  if(IFI_DIR)
+    message(SEND_ERROR "When INTERNAL_IFI is specified, do not set IFI_DIR.")
+  endif()
+  set(REQUIRE_IFI ON)
   set(BUILD_WITH_IFI ON)
-endif()
-
-if(BUILD_WITH_IFI)
+  set(IFI_FOUND ON)
+  set(IFI_DIR ${CMAKE_INSTALL_DIR})
+  message(NOTICE "Building IFI inside the post.")
+else()
   if(REQUIRE_IFI)
-    find_package(IFI REQUIRED)
-  else()
-    find_package(IFI)
+    set(BUILD_WITH_IFI ON)
+  endif()
+
+  if(BUILD_WITH_IFI)
+    if(REQUIRE_IFI)
+      find_package(IFI REQUIRED)
+    else()
+      find_package(IFI)
+    endif()
+  endif()
+  if(IFI_FOUND)
+    message(NOTICE "Linking to IFI external to the post.")
   endif()
 endif()
 
@@ -88,7 +105,7 @@ if(BUILD_POSTEXEC)
   endif()
 endif()
 
-if(IFI_FOUND)
+if(IFI_FOUND OR INTERNAL_IFI)
   message(NOTICE "Enabling USE_IFI in the post.")
   add_definitions(-DUSE_IFI=1)
 endif()

README.md

@@ -45,8 +45,7 @@ Examples of UPP products include:
 
 
 ## User Support
-Support for the UFS UPP is provided through the [UFS Forum](https://forums.ufscommunity.org/)
-by the Developmental Testbed Center (DTC). 
+Support for the UFS UPP is provided through [GitHub Discussions](https://github.com/NOAA-EMC/UPP/discussions).
 
 ## Documentation 
 User Guide for latest public release: https://upp.readthedocs.io/en/latest/.

ci/spack.yaml

@@ -2,7 +2,9 @@
 spack:
   packages:
     all:
-      compiler: [intel, gcc]
+      compiler:
+      - intel
+      - gcc@10:10
   specs:
   - netcdf-c@4.7.4
   - netcdf-fortran@4.5.3

docs/AddNewVariable.rst

@@ -20,8 +20,8 @@ NOAA UPP developers who wish to add new variables to the UPP, please follow the
     Hui-Ya Chuang). UPP supports many NOAA operational models and we can not change operational products
     without coordination and advanced notices.
 
-We encourage non NOAA UPP developers to contact the Developmental Testbed Center (DTC) via the UPP
-`forum <https://forums.ufscommunity.org/forum/post-processing>`_ to make them aware of modifications you
+We encourage non NOAA UPP developers to contact EPIC via
+`GitHub Discussions <https://github.com/NOAA-EMC/UPP/discussions>`_ to make them aware of modifications you
 are making. In some cases, if they determine the changes you are making may be relevant for operational
 and/or community purposes, they will be interested in incorporating your changes into the code base for
 support and future release. We would then work with you to make this possible.
@@ -40,20 +40,20 @@ with examples in the sections below.
 
             1.  If no (not available in the NCEP Grib2 Table)
 
-                a.  NOAA users can email Boi.Vuong@noaa.gov with the following information for your new
+                a.  NOAA users can email Andrew.Benjamin@noaa.gov with the following information for your new
                     variable: variable definition, unit, and what Grib2 discipline and category you think this
-                    variable should belong to. Boi will define your new variable in the `NCEP Grib2 Table
+                    variable should belong to. Andrew will define your new variable in the `NCEP Grib2 Table
                     <https://www.nco.ncep.noaa.gov/pmb/docs/grib2/grib2_doc/grib2_table4-2.shtml>`_ and
                     inform you of the Grib2 discipline and category numbers you should use.
 
-                b.  Contact with Boi to update parm/params_grib2_tbl_new.text with your new variable and
+                b.  Contact with Andrew to update parm/params_grib2_tbl_new.text with your new variable and
                     generate a params_grib2_tbl_new which lists in alphabetical order to improve post
                     processing efficiency.
 
                 c.  Save new params_grib2_tbl_new.text and params_grib2_tbl_new under parm/ of your UPP
                     working version.
 
-                d.  Other users please coordinate through the DTC for the above three steps.
+                d.  Other users please coordinate through EPIC for the above three steps.
 
                 e.  Add a new entry in post_avblflds.xml with your new variable, then follow step B), then step 2)
                     and beyond. You should assign a new UPP ID for your new variable.

docs/CodeOverview.rst

@@ -30,4 +30,4 @@ Examples of UPP products include:
 
 A full list of fields that can be generated by the UPP is provided in :doc:`UPP_GRIB2_Table`.
 
-Support for the community UPP is provided through the `UFS Forum <https://forums.ufscommunity.org/>`_.
+Support for the community UPP is provided through `GitHub Discussions <https://github.com/NOAA-EMC/UPP/discussions>`_.

fix/Breadboard/Breadboard1.nsw

@@ -0,0 +1,43 @@
+// Weights saved from breadboard C:\MY DOCUMENTS\BREADBOARD1R.NSB.
+// Saved after epoch 1, exemplar 0.
+
+#NSWeightFileVersion 225
+
+#inputFile File
+7
+1.077844262123108e+000 -1.778443008661270e-001
+2.295625507831574e-001 6.163756549358368e-002
+2.081887423992157e-001 6.210270524024963e-001
+3.646677434444428e-001 1.214343756437302e-001
+2.430133521556854e-001 3.004860281944275e-001
+1.935067623853684e-001 4.185551702976227e-001
+1.962280571460724e-001 -4.804643988609314e-001
+0
+
+#inputAxon Axon
+7 1
+1
+0 
+
+#hidden1Axon TanhAxon
+40 1
+1
+40 -1.150484442710877e+000 -1.461968779563904e+000 1.349107265472412e+000 6.686212420463562e-001 -8.486616015434265e-001 -1.908162593841553e+000 -1.514992356300354e+000 -1.632351636886597e+000 -1.794843912124634e+000 1.354879975318909e+000 1.389558911323547e+000 1.464104652404785e+000 1.896052122116089e+000 1.401677846908569e+000 1.436681509017944e+000 -1.590880393981934e+000 -1.070504426956177e+000 2.047163248062134e+000 1.564107656478882e+000 1.298712372779846e+000 -1.316817998886108e+000 -1.253177642822266e+000 -1.392926216125488e+000 7.356406450271606e-001 1.594561100006104e+000 -1.532955884933472e+000 -1.021214842796326e+000 1.341110348701477e+000 6.124811172485352e-001 1.415654063224793e+000 -8.509962558746338e-001 1.753035664558411e+000 6.275475621223450e-001 1.482843875885010e+000 1.326028347015381e+000 1.641556143760681e+000 1.339018464088440e+000 -1.374068379402161e+000 -1.220067739486694e+000 1.714797854423523e+000 
+
+#outputAxon SoftMaxAxon
+3 1
+1
+3 0.000000000000000e+000 0.000000000000000e+000 0.000000000000000e+000 
+
+#hidden1Synapse FullSynapse
+280 -4.612099826335907e-001 -3.177818655967712e-001 -2.800635099411011e-001 -6.984808295965195e-002 6.583837419748306e-002 -5.769817233085632e-001 3.955098092556000e-001 -1.624705344438553e-001 -2.889076173305512e-001 -9.411631226539612e-001 -5.058886408805847e-001 -3.110982775688171e-001 -3.723000884056091e-001 8.419776558876038e-001 2.598794996738434e-001 -1.364605724811554e-001 9.416468143463135e-001 -4.025689139962196e-002 4.176554381847382e-001 1.196979433298111e-001 -3.846398293972015e-001 -1.414917409420013e-001 -2.344214916229248e+000 -3.556166291236877e-001 -7.762963771820068e-001 -1.243659138679504e+000 4.907984733581543e-001 -1.891903519630432e+000 -5.802390575408936e-001 -5.546363592147827e-001 -4.520095884799957e-001 -2.473797500133514e-001 -7.757837772369385e-001 -5.350160598754883e-001 1.817676275968552e-001 -1.932217180728912e-001 5.944451093673706e-001 -6.568105518817902e-002 -1.562235504388809e-001 4.926294833421707e-002 -6.931540369987488e-001 7.082754969596863e-001 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-4.065496101975441e-002 -1.131931394338608e-001 7.050336003303528e-001 3.453079611063004e-002 5.642467141151428e-001 7.171959280967712e-001 -3.295499980449677e-001 5.192958116531372e-001 7.558688521385193e-001 6.164067387580872e-001 -1.597565859556198e-001 1.512383669614792e-001 5.231227278709412e-001 -2.199545800685883e-001 -3.987313508987427e-001 -9.710572957992554e-001 -4.689137935638428e-001 -4.037811756134033e-001 -4.528387784957886e-001 -4.784810543060303e-001 1.759306043386459e-001 7.449938654899597e-001 1.120681285858154e+000 -5.609570741653442e-001 1.393345594406128e+000 1.374282408505678e-002 -2.458193153142929e-001 1.237058401107788e+000 -4.854794219136238e-002 -6.664386391639710e-001 -8.786886334419251e-001 -3.208510577678680e-001 -4.315690398216248e-001 -5.186472535133362e-001 -2.117208093404770e-001 8.998587727546692e-002 7.763032317161560e-001 1.078992128372192e+000 3.667660653591156e-001 5.805531740188599e-001 1.517073512077332e-001 9.344519972801209e-001 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-6.173372268676758e-001 -8.801369071006775e-001 -1.111719012260437e+000 -3.223371803760529e-001 -6.491173505783081e-001 -3.894545435905457e-001 -2.843862473964691e-001 7.331426739692688e-001 -3.287445753812790e-002 -5.741032306104899e-003 6.212961673736572e-001 3.749484941363335e-002 6.244438700377941e-003 -6.228777766227722e-001 -4.667133837938309e-002 2.016694307327271e+000 2.834755480289459e-001 6.229624748229981e-001 6.552317738533020e-001 -9.771268069744110e-002 7.506207823753357e-001 6.942567825317383e-001 -1.662521809339523e-001 3.003259599208832e-001 -2.531996071338654e-001 2.399661689996719e-001 5.109554529190064e-001 -7.031706571578980e-001 2.836774885654450e-001 4.888223409652710e-001 1.384589523077011e-001 -3.524579405784607e-001 -2.050135582685471e-001 1.160808563232422e+000 -4.008938968181610e-001 1.656456440687180e-001 -5.116114616394043e-001 8.800522685050964e-001 6.836380064487457e-002 -5.902936309576035e-002 5.672354102134705e-001 -7.219299674034119e-001 3.463289514183998e-002 -1.044675827026367e+000 -8.341925591230393e-002 -3.036961853504181e-001 -5.605638027191162e-001 5.722484588623047e-001 -1.604338049888611e+000 -5.696258544921875e-001 -2.531512081623077e-001 -4.675458073616028e-001 -6.486019492149353e-001 -2.437075823545456e-001 -2.898264527320862e-001 3.836293518543243e-001 4.061043560504913e-001 3.909072279930115e-001 -8.113911151885986e-001 1.260317683219910e+000 -3.924282491207123e-001 3.586370870471001e-002 7.703443765640259e-001 6.714462637901306e-001 -4.909946396946907e-002 3.536651730537415e-001 1.900762617588043e-001 3.638494014739990e-001 2.248179465532303e-001 -6.255846619606018e-001 
+
+#outputSynapse FullSynapse
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+
+#activeOutputProbe DataWriter
+3
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+8.999999761581421e-001 5.000000074505806e-002
+