feat(fpm): Add new fpm subproject, icar-trainer

Add new fpm subproject, icar-trainer, which removes dependencies from inference-engine. This commit contains a working solution for an fpm build of inference-engine. The icar-trainer fpm toml file and associated setup script are not yet complete, and need to be edited to be buildable.
BerkeleyLab · Jan 6, 2024 · 6493423 · 6493423
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diff --git a/fpm.toml b/fpm.toml
@@ -1,10 +1,9 @@
 name = "inference-engine"
 version = "0.5.0"
 license = "license"
-author = "Damian Rouson, Tan Nguyen, Jordan Welsman, David Torres, Brad Richardson"
+author = "Damian Rouson, Tan Nguyen, Jordan Welsman, David Torres, Brad Richardson, Katherine Rasmussen"
 maintainer = "rouson@lbl.gov"
 
 [dependencies]
 assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.5.0"}
 sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.5.0"}
-netcdf-interfaces = {git = "https://github.com/LKedward/netcdf-interfaces.git", rev = "d2bbb71ac52b4e346b62572b1ca1620134481096"}
diff --git a/app/train-cloud-microphysics.f90 → ...-trainer/app/train-cloud-microphysics.f90 b/app/train-cloud-microphysics.f90 → ...-trainer/app/train-cloud-microphysics.f90
diff --git a/icar-trainer/fpm.toml b/icar-trainer/fpm.toml
@@ -0,0 +1,10 @@
+name = "icar-trainer"
+version = "0.0.0"
+license = "license"
+author = "Damian Rouson, Tan Nguyen, Jordan Welsman, David Torres, Brad Richardson, Katherine Rasmussen"
+maintainer = "rouson@lbl.gov"
+
+[dependencies]
+assert = {git = "https://github.com/sourceryinstitute/assert", tag = "1.5.0"}
+sourcery = {git = "https://github.com/sourceryinstitute/sourcery", tag = "4.5.0"}
+netcdf-interfaces = {git = "https://github.com/LKedward/netcdf-interfaces.git", rev = "d2bbb71ac52b4e346b62572b1ca1620134481096"}
diff --git a/icar-trainer/setup.sh b/icar-trainer/setup.sh
@@ -0,0 +1,138 @@
+#!/bin/sh
+
+set -e # exit on error
+
+usage()
+{
+  echo "Inference Engine Setup Script"
+  echo ""
+  echo "USAGE:"
+  echo "./setup.sh [--help|-h] | [-p|--prefix=PREFIX]"
+  echo ""
+  echo " --help             Display this help text"
+  echo " --prefix=PREFIX    Install binary in 'PREFIX/bin'"
+  echo "                    Default prefix='\$HOME/.local/bin'"
+  echo ""
+}
+
+PREFIX="$HOME/.local"
+
+while [ "$1" != "" ]; do
+  PARAM=$(echo "$1" | awk -F= '{print $1}')
+  VALUE=$(echo "$1" | awk -F= '{print $2}')
+  case $PARAM in
+    -h | --help)
+      usage
+      exit
+      ;;
+    -p | --prefix)
+      PREFIX=$VALUE
+      ;;
+    *)
+      echo "ERROR: unknown parameter \"$PARAM\""
+      usage
+      exit 1
+      ;;
+  esac
+  shift
+done
+
+set -u # error on use of undefined variable
+
+if ! command -v brew > /dev/null ; then
+  if ! command -v curl > /dev/null ; then
+    echo "Please install curl and then rerun ./setup.sh"
+    exit 1
+  fi
+  /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+  if [ $(uname) = "Linux" ]; then
+    if [ -z "$PATH" ]; then
+      PATH=/home/linuxbrew/.linuxbrew/bin/
+    else
+      PATH=/home/linuxbrew/.linuxbrew/bin/:"$PATH"
+    fi
+  fi
+fi
+
+
+brew tap fortran-lang/fortran # required for building fpm
+brew install fpm netcdf netcdf-fortran pkg-config coreutils # coreutils supports `realpath` below
+
+PREFIX=`realpath $PREFIX`
+
+NETCDF_LIB_PATH="`brew --prefix netcdf`/lib"
+HDF5_LIB_PATH="`brew --prefix hdf5`/lib"
+NETCDFF_LIB_PATH="`brew --prefix netcdf-fortran`/lib"
+
+FPM_LD_FLAG=" -L$NETCDF_LIB_PATH -L$HDF5_LIB_PATH -L$NETCDFF_LIB_PATH"
+FPM_FLAG="-fcoarray=single -O3 -fallow-argument-mismatch -ffree-line-length-none -L$NETCDF_LIB_PATH -L$HDF5_LIB_PATH"
+FPM_FC=${FC:-"gfortran-13"}
+FPM_CC=${CC:-"gcc-13"}
+
+mkdir -p build
+
+CI=${CI:-"false"} # GitHub Actions workflows set CI=true
+
+if [ $CI = true ]; then
+  PKG_CONFIG_PATH=`realpath ./build/pkgconfig`
+  echo "---------------"
+  echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH"
+  echo "---------------"
+else
+  PKG_CONFIG_PATH=`realpath "$PREFIX"/lib/pkgconfig`
+fi
+
+if [ ! -d $PKG_CONFIG_PATH ]; then
+  mkdir -p $PKG_CONFIG_PATH 
+fi
+
+INFERENCE_ENGINE_PC="$PKG_CONFIG_PATH/inference-engine.pc"
+echo "INFERENCE_ENGINE_FPM_CC=\"$FPM_CC\""                  >  $INFERENCE_ENGINE_PC
+echo "INFERENCE_ENGINE_FPM_FC=\"$FPM_FC\""                  >> $INFERENCE_ENGINE_PC
+echo "INFERENCE_ENGINE_FPM_LD_FLAG=\"$FPM_LD_FLAG\""        >> $INFERENCE_ENGINE_PC
+echo "INFERENCE_ENGINE_FPM_FLAG=\"$FPM_FLAG\""              >> $INFERENCE_ENGINE_PC
+echo "Name: inference-engine"                               >> $INFERENCE_ENGINE_PC
+echo "Description: Inference Engine"                        >> $INFERENCE_ENGINE_PC
+echo "URL: https://github.com/berkeleylab/inference-engine" >> $INFERENCE_ENGINE_PC
+echo "Version: 0.1.2"                                       >> $INFERENCE_ENGINE_PC
+if [ $CI = true ]; then
+  echo "---------------"
+  echo "cat $INFERENCE_ENGINE_PC"
+  cat $INFERENCE_ENGINE_PC
+  echo "---------------"
+fi
+
+export PKG_CONFIG_PATH
+cp scripts/run-fpm.sh-header build/run-fpm.sh
+RUN_FPM_SH="`realpath ./build/run-fpm.sh`"
+echo "`which fpm` \$fpm_arguments \\" >>  $RUN_FPM_SH
+echo "--profile release \\" >> $RUN_FPM_SH
+echo "--c-compiler \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_CC`\" \\" >> $RUN_FPM_SH
+echo "--compiler \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_FC`\" \\" >> $RUN_FPM_SH
+echo "--flag \"-cpp `pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_FLAG`\" \\"  >> $RUN_FPM_SH
+echo "--link-flag \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_LD_FLAG`\" \\" >> $RUN_FPM_SH
+echo "\$program_arguments" >> $RUN_FPM_SH
+chmod u+x $RUN_FPM_SH
+if [ $CI = true ]; then
+  echo "---------------"
+  echo "cat $RUN_FPM_SH"
+  cat $RUN_FPM_SH
+  echo "---------------"
+fi
+
+if command -v fpm > /dev/null 2>&1; then
+  brew tap fortran-lang/fortran
+  brew install fpm
+fi
+
+echo "$RUN_FPM_SH test"
+$RUN_FPM_SH test
+
+echo ""
+echo "____________________ Inference-Engine has been set up! _______________________" 
+echo ""
+echo "To run one of the programs in the example subdirectory, enter a command of the"
+echo "following form at a shell command prompt after replacing <example-base-name>"
+echo "with the base name of a file in the example/ subdirectory:"
+echo ""
+echo "./build/run-fpm.sh run --example <example-base-name>"
diff --git a/src/inference_engine/NetCDF_file_m.f90 → icar-trainer/src/NetCDF_file_m.f90 b/src/inference_engine/NetCDF_file_m.f90 → icar-trainer/src/NetCDF_file_m.f90
diff --git a/src/inference_engine/NetCDF_file_s.f90 → icar-trainer/src/NetCDF_file_s.f90 b/src/inference_engine/NetCDF_file_s.f90 → icar-trainer/src/NetCDF_file_s.f90
diff --git a/icar-trainer/test/main.f90 b/icar-trainer/test/main.f90
@@ -0,0 +1,27 @@
+! Copyright (c), The Regents of the University of California
+! Terms of use are as specified in LICENSE.txt
+program main
+  implicit none
+
+  real t_start, t_finish
+
+  integer :: passes=0, tests=0
+
+  call cpu_time(t_start)
+#ifndef __INTEL_FORTRAN
+  block 
+    use netCDF_file_test_m, only : netCDF_file_test_t
+    type(netCDF_file_test_t) netCDF_file_test
+    call netCDF_file_test%report(passes, tests)
+  end block
+#endif // __INTEL_FORTRAN
+  call cpu_time(t_finish)
+
+  print *
+  print *,"Test suite execution time: ",t_finish - t_start
+  print *
+  print '(*(a,:,g0))',"_________ In total, ",passes," of ",tests, " tests pass. _________"
+  sync all
+  print *
+  if (passes/=tests) error stop "-------- One or more tests failed. See the above report. ---------"
+end program
diff --git a/test/netCDF_file_test_m.f90 → icar-trainer/test/netCDF_file_test_m.f90 b/test/netCDF_file_test_m.f90 → icar-trainer/test/netCDF_file_test_m.f90
diff --git a/setup.sh b/setup.sh
@@ -7,11 +7,9 @@ usage()
   echo "Inference Engine Setup Script"
   echo ""
   echo "USAGE:"
-  echo "./setup.sh [--help|-h] | [-p|--prefix=PREFIX]"
+  echo "./setup.sh [--help|-h]"
   echo ""
   echo " --help             Display this help text"
-  echo " --prefix=PREFIX    Install binary in 'PREFIX/bin'"
-  echo "                    Default prefix='\$HOME/.local/bin'"
   echo ""
 }
 
@@ -56,77 +54,15 @@ fi
 
 
 brew tap fortran-lang/fortran # required for building fpm
-brew install fpm netcdf netcdf-fortran pkg-config coreutils # coreutils supports `realpath` below
+brew install fortran-lang/fortran/fpm
 
-PREFIX=`realpath $PREFIX`
-
-NETCDF_LIB_PATH="`brew --prefix netcdf`/lib"
-HDF5_LIB_PATH="`brew --prefix hdf5`/lib"
-NETCDFF_LIB_PATH="`brew --prefix netcdf-fortran`/lib"
-
-FPM_LD_FLAG=" -L$NETCDF_LIB_PATH -L$HDF5_LIB_PATH -L$NETCDFF_LIB_PATH"
-FPM_FLAG="-fcoarray=single -O3 -fallow-argument-mismatch -ffree-line-length-none -L$NETCDF_LIB_PATH -L$HDF5_LIB_PATH"
+FPM_FLAG="-fcoarray=single -O3"
 FPM_FC=${FC:-"gfortran-13"}
 FPM_CC=${CC:-"gcc-13"}
 
 mkdir -p build
 
-CI=${CI:-"false"} # GitHub Actions workflows set CI=true
-
-if [ $CI = true ]; then
-  PKG_CONFIG_PATH=`realpath ./build/pkgconfig`
-  echo "---------------"
-  echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH"
-  echo "---------------"
-else
-  PKG_CONFIG_PATH=`realpath "$PREFIX"/lib/pkgconfig`
-fi
-
-if [ ! -d $PKG_CONFIG_PATH ]; then
-  mkdir -p $PKG_CONFIG_PATH 
-fi
-
-INFERENCE_ENGINE_PC="$PKG_CONFIG_PATH/inference-engine.pc"
-echo "INFERENCE_ENGINE_FPM_CC=\"$FPM_CC\""                  >  $INFERENCE_ENGINE_PC
-echo "INFERENCE_ENGINE_FPM_FC=\"$FPM_FC\""                  >> $INFERENCE_ENGINE_PC
-echo "INFERENCE_ENGINE_FPM_LD_FLAG=\"$FPM_LD_FLAG\""        >> $INFERENCE_ENGINE_PC
-echo "INFERENCE_ENGINE_FPM_FLAG=\"$FPM_FLAG\""              >> $INFERENCE_ENGINE_PC
-echo "Name: inference-engine"                               >> $INFERENCE_ENGINE_PC
-echo "Description: Inference Engine"                        >> $INFERENCE_ENGINE_PC
-echo "URL: https://github.com/berkeleylab/inference-engine" >> $INFERENCE_ENGINE_PC
-echo "Version: 0.1.2"                                       >> $INFERENCE_ENGINE_PC
-if [ $CI = true ]; then
-  echo "---------------"
-  echo "cat $INFERENCE_ENGINE_PC"
-  cat $INFERENCE_ENGINE_PC
-  echo "---------------"
-fi
-
-export PKG_CONFIG_PATH
-cp scripts/run-fpm.sh-header build/run-fpm.sh
-RUN_FPM_SH="`realpath ./build/run-fpm.sh`"
-echo "`which fpm` \$fpm_arguments \\" >>  $RUN_FPM_SH
-echo "--profile release \\" >> $RUN_FPM_SH
-echo "--c-compiler \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_CC`\" \\" >> $RUN_FPM_SH
-echo "--compiler \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_FC`\" \\" >> $RUN_FPM_SH
-echo "--flag \"-cpp `pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_FLAG`\" \\"  >> $RUN_FPM_SH
-echo "--link-flag \"`pkg-config inference-engine --variable=INFERENCE_ENGINE_FPM_LD_FLAG`\" \\" >> $RUN_FPM_SH
-echo "\$program_arguments" >> $RUN_FPM_SH
-chmod u+x $RUN_FPM_SH
-if [ $CI = true ]; then
-  echo "---------------"
-  echo "cat $RUN_FPM_SH"
-  cat $RUN_FPM_SH
-  echo "---------------"
-fi
-
-if command -v fpm > /dev/null 2>&1; then
-  brew tap fortran-lang/fortran
-  brew install fpm
-fi
-
-echo "$RUN_FPM_SH test"
-$RUN_FPM_SH test
+fpm build --flag ${FPM_FLAG}
 
 echo ""
 echo "____________________ Inference-Engine has been set up! _______________________" 
@@ -135,4 +71,4 @@ echo "To run one of the programs in the example subdirectory, enter a command of
 echo "following form at a shell command prompt after replacing <example-base-name>"
 echo "with the base name of a file in the example/ subdirectory:"
 echo ""
-echo "./build/run-fpm.sh run --example <example-base-name>"
+echo "fpm run --example <example-base-name>"
diff --git a/src/inference_engine/trainable_engine_s.f90 b/src/inference_engine/trainable_engine_s.f90
@@ -35,7 +35,8 @@
         class is(differentiable_activation_strategy_t)
            trainable_engine%differentiable_activation_strategy_ = activation
         class default
-           error stop "trainable_engine_s(from_inference_engine): activation strategy must be a differentiable_activation_stragegy_t"
+           error stop &
+           "trainable_engine_s(from_inference_engine): activation strategy must be a differentiable_activation_stragegy_t"
       end select
     end associate
 

diff --git a/src/inference_engine_m.f90 b/src/inference_engine_m.f90
@@ -9,7 +9,6 @@ module inference_engine_m
  use inference_engine_m_, only : inference_engine_t, difference_t
  use kind_parameters_m, only : rkind
  use mini_batch_m, only : mini_batch_t
- use NetCDF_file_m, only : NetCDF_file_t 
  use network_configuration_m, only : network_configuration_t
  use relu_m, only : relu_t
  use sigmoid_m, only : sigmoid_t

diff --git a/test/main.f90 b/test/main.f90
@@ -27,13 +27,6 @@ program main
   call hyperparameters_test%report(passes, tests)
   call network_configuration_test%report(passes, tests)
   call training_configuration_test%report(passes, tests)
-#ifndef __INTEL_FORTRAN
-  block 
-    use netCDF_file_test_m, only : netCDF_file_test_t
-    type(netCDF_file_test_t) netCDF_file_test
-    call netCDF_file_test%report(passes, tests)
-  end block
-#endif // __INTEL_FORTRAN
   call cpu_time(t_finish)
 
   print *

diff --git a/test/network_configuration_test_m.f90 b/test/network_configuration_test_m.f90
@@ -44,7 +44,8 @@ function results() result(test_results)
         [ write_then_read_network_configuration() & 
         ] & 
     )
-      call assert(size(descriptions) == size(outcomes),"network_configuration_test_m(results): size(descriptions) == size(outcomes)")
+      call assert(size(descriptions) == size(outcomes), &
+        "network_configuration_test_m(results): size(descriptions) == size(outcomes)")
       test_results = test_result_t(descriptions, outcomes)
     end associate
 
@@ -62,4 +63,4 @@ function write_then_read_network_configuration() result(test_passes)
 
   end function
 
-end module network_configuration_test_m
+end module network_configuration_test_m