Use autotools as build system to find and try to link the libraries

.github/workflows/ci.yml

@@ -1,6 +1,6 @@
 name: CI
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   build:
@@ -11,13 +11,20 @@ jobs:
       run: sudo apt-get install -y --no-install-recommends gfortran libhdf5-openmpi-dev libopenmpi-dev
     - name: Install ED2
       run: |
-        cd ED/build
-        ./install.sh -g -p travisci -k A
+        pushd ED/build/shell
+        bash build_objects.sh
+        popd
+        aclocal
+        automake --add-missing
+        autoconf
+        ./configure
+        make
+        sudo make install
     - name: Upload compiled ED2 binary
       uses: actions/upload-artifact@v1
       with:
         name: ed2-binary
-        path: ED/build/ed_2.2-dbg
+        path: ed2
 
   test-umbs-bg:
     needs: build
@@ -33,8 +40,8 @@ jobs:
     - name: Run ED2
       working-directory: ./EDTS/
       run: |
-        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed_2.2-dbg
-        ./run-test.sh umbs.bg "$GITHUB_WORKSPACE/ed2-binary/ed_2.2-dbg"
+        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed2
+        ./run-test.sh umbs.bg "$GITHUB_WORKSPACE/ed2-binary/ed2"
 
   test-tonzi:
     needs: build
@@ -50,8 +57,8 @@ jobs:
     - name: Run ED2
       working-directory: ./EDTS/
       run: |
-        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed_2.2-dbg
-        ./run-test.sh tonzi "$GITHUB_WORKSPACE/ed2-binary/ed_2.2-dbg"
+        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed2
+        ./run-test.sh tonzi "$GITHUB_WORKSPACE/ed2-binary/ed2"
 
   test-tonzi-harvest:
     needs: build
@@ -67,5 +74,5 @@ jobs:
     - name: Run ED2
       working-directory: ./EDTS/
       run: |
-        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed_2.2-dbg
-        ./run-test.sh tonzi.harvest "$GITHUB_WORKSPACE/ed2-binary/ed_2.2-dbg"
+        chmod +x "$GITHUB_WORKSPACE"/ed2-binary/ed2
+        ./run-test.sh tonzi.harvest "$GITHUB_WORKSPACE/ed2-binary/ed2"

.gitignore

@@ -166,3 +166,34 @@ R-utils/read.q.quick.r
 #Xiangtao Ignores
 ED/build/ed2_gfortran
 ED/build/ed2_ifort
+
+
+# http://www.gnu.org/software/automake
+Makefile.in
+/ar-lib
+/mdate-sh
+/py-compile
+/test-driver
+/ylwrap
+.deps/
+.dirstamp
+
+# http://www.gnu.org/software/autoconf
+autom4te.cache
+/autoscan.log
+/autoscan-*.log
+/aclocal.m4
+/compile
+/config.cache
+/config.guess
+/config.h.in
+/config.log
+/config.status
+/config.sub
+/configure
+/configure.scan
+/depcomp
+/install-sh
+/missing
+/stamp-h1
+/Makefile

ED/build/shell/build_objects.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# Add your build commands here
+SOURCES=$( (cd ../../.. && find ED/src -name "*.[Ff]90" -and -not -path "ED/src/preproc/*"))
+
+# Remove ED/src/driver/edmain.F90 from OBJECTS
+SOURCES=$(echo $SOURCES | sed 's/ED\/src\/driver\/edmain.F90//')
+
+echo SOURCES = $SOURCES ED/src/utils/utils_c.c > sources.mk
+
+rm -f dependency.mk
+
+# Build dependency rules for object files
+for src in $SOURCES; do
+  # Mod depends on the source file building
+  SRC_MOD_NAME=$(echo $(basename "${src%.[Ff]90}.mod"))
+  echo $SRC_MOD_NAME: ${src%.[Ff]90}.o >> dependency.mk
+
+  # Find modules used in the source file and add as dependency for the object file
+  MODS_USED=$(cd ../../.. && grep -i '^\s*use\s\+' $src | awk '{print $2}' | sed 's/,.*//' | sort | uniq)
+
+  # Update MODS_USED to include only modules that has a corresponding
+  # source file with the pattern ED/src/*/$mod.[Ff]90
+  MODS_USED=$(for mod in $MODS_USED; do
+    if [ -f ../../../ED/src/*/$mod.F90 -o -f ../../../ED/src/*/$mod.f90 ]; then
+      echo $mod
+    fi
+  done)
+
+  MODS_USED_MOD=$(for line in $MODS_USED; do echo -n "$line.mod "; done)
+
+  length=$(echo $MODS_USED_MOD | wc -w)
+  if [ $length -gt 0 ]; then
+    echo ${src%.[Ff]90}.o: $MODS_USED_MOD >> dependency.mk
+  fi;
+done

ED/build/shell/sources.mk

@@ -0,0 +1 @@
+SOURCES = ED/src/driver/ed_1st.F90 ED/src/driver/ed_driver.F90 ED/src/driver/ed_met_driver.f90 ED/src/driver/ed_model.F90 ED/src/dynamics/bdf2_solver.f90 ED/src/dynamics/canopy_struct_dynamics.f90 ED/src/dynamics/disturbance.f90 ED/src/dynamics/euler_driver.f90 ED/src/dynamics/events.f90 ED/src/dynamics/farq_katul.f90 ED/src/dynamics/farq_leuning.f90 ED/src/dynamics/fire.f90 ED/src/dynamics/forestry.f90 ED/src/dynamics/growth_balive.f90 ED/src/dynamics/heun_driver.f90 ED/src/dynamics/hybrid_driver.f90 ED/src/dynamics/lsm_hyd.f90 ED/src/dynamics/mortality.f90 ED/src/dynamics/multiple_scatter.f90 ED/src/dynamics/old_twostream_rad.f90 ED/src/dynamics/phenology_aux.f90 ED/src/dynamics/phenology_driv.f90 ED/src/dynamics/photosyn_driv.f90 ED/src/dynamics/plant_hydro.f90 ED/src/dynamics/radiate_driver.f90 ED/src/dynamics/reproduction.f90 ED/src/dynamics/rk4_copy_patch.f90 ED/src/dynamics/rk4_derivs.f90 ED/src/dynamics/rk4_driver.F90 ED/src/dynamics/rk4_integ_utils.f90 ED/src/dynamics/rk4_misc.f90 ED/src/dynamics/soil_respiration.f90 ED/src/dynamics/stem_resp_driv.f90 ED/src/dynamics/structural_growth.f90 ED/src/dynamics/twostream_rad.f90 ED/src/dynamics/vegetation_dynamics.f90 ED/src/init/ed_bigleaf_init.f90 ED/src/init/ed_init.F90 ED/src/init/ed_init_atm.F90 ED/src/init/ed_nbg_init.f90 ED/src/init/ed_params.f90 ED/src/init/ed_type_init.f90 ED/src/init/landuse_init.f90 ED/src/init/phenology_startup.f90 ED/src/io/average_utils.f90 ED/src/io/edio.f90 ED/src/io/ed_init_history.f90 ED/src/io/ed_load_namelist.f90 ED/src/io/ed_opspec.F90 ED/src/io/ed_print.F90 ED/src/io/ed_read_ed10_20_history.f90 ED/src/io/ed_read_ed21_history.f90 ED/src/io/ed_xml_config.f90 ED/src/io/h5_output.F90 ED/src/io/leaf_database.f90 ED/src/memory/c34constants.f90 ED/src/memory/canopy_air_coms.f90 ED/src/memory/canopy_layer_coms.f90 ED/src/memory/canopy_radiation_coms.f90 ED/src/memory/consts_coms.F90 ED/src/memory/decomp_coms.f90 ED/src/memory/detailed_coms.f90 ED/src/memory/disturb_coms.f90 ED/src/memory/ed_max_dims.F90 ED/src/memory/ed_mem_alloc.f90 ED/src/memory/ed_misc_coms.f90 ED/src/memory/ed_state_vars.F90 ED/src/memory/ed_var_tables.f90 ED/src/memory/ed_work_vars.f90 ED/src/memory/ename_coms.f90 ED/src/memory/fusion_fission_coms.f90 ED/src/memory/grid_coms.f90 ED/src/memory/hdf5_coms.f90 ED/src/memory/hydrology_coms.f90 ED/src/memory/hydrology_constants.f90 ED/src/memory/mem_polygons.f90 ED/src/memory/met_driver_coms.f90 ED/src/memory/pft_coms.f90 ED/src/memory/phenology_coms.f90 ED/src/memory/physiology_coms.f90 ED/src/memory/rk4_coms.f90 ED/src/memory/soil_coms.F90 ED/src/mpi/ed_mpass_init.F90 ED/src/mpi/ed_node_coms.f90 ED/src/mpi/ed_para_coms.f90 ED/src/mpi/ed_para_init.f90 ED/src/utils/allometry.f90 ED/src/utils/budget_utils.f90 ED/src/utils/charutils.f90 ED/src/utils/dateutils.f90 ED/src/utils/ed_cn_utils.f90 ED/src/utils/ed_filelist.F90 ED/src/utils/ed_grid.f90 ED/src/utils/ed_therm_lib.f90 ED/src/utils/fatal_error.F90 ED/src/utils/fuse_fiss_utils.f90 ED/src/utils/great_circle.f90 ED/src/utils/hdf5_utils.f90 ED/src/utils/hrzshade_utils.f90 ED/src/utils/invmondays.f90 ED/src/utils/lapse.f90 ED/src/utils/libxml2f90.f90_pp.f90 ED/src/utils/numutils.f90 ED/src/utils/radiate_utils.f90 ED/src/utils/random_utils.F90 ED/src/utils/rsys.F90 ED/src/utils/stable_cohorts.f90 ED/src/utils/therm_lib.f90 ED/src/utils/therm_lib8.f90 ED/src/utils/update_derived_utils.f90 ED/src/utils/utils_f.f90 ED/src/utils/utils_c.c

ED/src/driver/ed_1st.F90

@@ -23,12 +23,12 @@ subroutine ed_1st_master (ipara, nnodestotal,nslaves, headnode_num, max_threads,
    use ed_state_vars, only : allocate_edglobals   & ! subroutine
                            , filltab_alltypes     ! ! subroutine
 
+#if defined(RAMS_MPI)
+  use mpi
+#endif
    implicit none
 
    !----- Pre-compiled variables from MPI. ------------------------------------------------!
-#if defined(RAMS_MPI)
-   include 'mpif.h'
-#endif
    !----- Arguments. ----------------------------------------------------------------------!
    integer         , intent(in) :: ipara        ! 0 if sequential run; 1 if parallel run
    integer         , intent(in) :: nnodestotal  ! total number of nodes on any run
@@ -176,10 +176,12 @@ end subroutine ed_1st_master
 !------------------------------------------------------------------------------------------!
 subroutine ed_1st_node()
    use ed_mem_alloc, only : ed_memory_allocation ! ! subroutine
+#if defined(RAMS_MPI)
+     use mpi
+#endif
    implicit none
    !----- Pre-compiled variables from MPI. ------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h'
    !----- Local variable (MPI only). ------------------------------------------------------!
    integer             :: ierr
 #endif

ED/src/driver/ed_driver.F90

@@ -36,11 +36,12 @@ subroutine ed_driver()
    use hrzshade_utils       , only : init_cci_variables            ! ! subroutine
    use canopy_radiation_coms, only : ihrzrad                       ! ! intent(in)
    use random_utils         , only : init_random_seed              ! ! subroutine
-   implicit none
-   !----- Included variables. -------------------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h' ! MPI commons
+  use mpi ! MPI commons
 #endif
+   implicit none
+
+   !----- Included variables. -------------------------------------------------------------!
    !----- Local variables. ----------------------------------------------------------------!
    character(len=12)           :: c0
    character(len=12)           :: c1

ED/src/driver/ed_model.F90

@@ -94,11 +94,10 @@ subroutine ed_model()
    use vegetation_dynamics , only : veg_dynamics_driver         ! ! sub-routine
    use ed_type_init        , only : ed_init_viable              ! ! sub-routine
    use soil_respiration    , only : zero_litter_inputs          ! ! sub-routine
-   implicit none
-   !----- Common blocks. ------------------------------------------------------------------!
 #if defined(RAMS_MPI)
-   include 'mpif.h'
+   use mpi
 #endif
+   implicit none
    !----- Local variables. ----------------------------------------------------------------!
    type(simtime)      :: daybefore
    character(len=28)  :: fmthead

ED/src/driver/edmain.F90

@@ -14,7 +14,10 @@
 !------------------------------------------------------------------------------------------!
 program main
    !$ use omp_lib
-   implicit none
+#if defined(RAMS_MPI)
+  use mpi
+#endif
+  implicit none
 
    !---------------------------------------------------------------------------------------!
    !      Local constants.                                                                 !
@@ -49,10 +52,7 @@ program main
    integer, dimension(64)                :: thread_use
    integer, dimension(64)                :: cpu_use
    integer, external                     :: findmycpu
-   !------ MPI interface. -----------------------------------------------------------------!
-#if defined(RAMS_MPI)
-   include 'mpif.h'
-#endif
+
    !---------------------------------------------------------------------------------------!