Arch makefiles

Makefile.global

@@ -16,55 +16,48 @@ ARG_FLAGS         = -DARG_INT1=$(INPUT_INT1) -DARG_INT2=$(INPUT_INT2)
 OBJDIR           := build
 
 ifeq ($(strip $(FF)),)
-	FF = $(F95COMPILER)
+	FF = $(F90COMPILER)
 endif
 
 ifeq ($(NETCDFLIBS),"none")
 	LIB_DIR =
 	INC_DIR =
 	ORM_FLAGS += -Dno_netcdf
-endif
-ifeq ($(NETCDFLIBS),"automatic")
+else ifeq ($(NETCDFLIBS),"automatic")
 	LIB_DIR = $(shell nc-config --flibs)
 	INC_DIR = -I$(shell nc-config --includedir)
-endif
-ifeq ($(NETCDFLIBS),"automatic-44")
+else ifeq ($(NETCDFLIBS),"automatic-44")
 	INC_DIR = $(shell nf-config --cflags)
 	LIB_DIR = $(shell nf-config --flibs)
-endif 
-ifeq ($(NETCDFLIBS),"macports")
-	LIB_DIR          = -L/opt/local/lib
-	INC_DIR          = -I/opt/local/include/
-	LNK_FLAGS        = -lnetcdf -lnetcdff 
-endif
-ifeq ($(NETCDFLIBS),"fink")
-        LIB_DIR          = -L/sw/lib # -L/sw/lib/netcdf-gfortran/lib
-        INC_DIR          = -I/sw/include  #-I/sw/lib/netcdf-gfortran/include
-        LNK_FLAGS        = -lnetcdf -lnetcdff -lsz 
+else 
+	LIB_DIR = -L/usr/local/lib
+	INC_DIR = -I/usr/local/include/
+	LNK_FLAGS = -lnetcdf -lnetcdff 
 endif
 
-ifeq ($(F95COMPILER),"gfortran")
-	FF_FLAGS         = -O3 -c -x f95-cpp-input -g -fbacktrace -fbounds-check 
-#	FF_FLAGS         = -O3 -c -x f95-cpp-input -g -fbacktrace -fbounds-check -ffpe-trap=denormal -static -Wall -pedantic
-  	#FF_FLAGS         = -O3 -c -x f95-cpp-input 	
+ifeq ($(ARCH),"macports")
+        F90COMPILER      = gfortran-mp-8 
+	PROD_FF_FLAGS    = -O3 -c -x f95-cpp-input -g -fbacktrace -fbounds-check 
+	DEV_FF_FLAGS     = -O1 -c -x f95-cpp-input -g -fbacktrace -fbounds-check -ffpe-trap=denormal -static -Wall -pedantic
         F90_FLAGS        = -fno-underscoring 
 	FF              += $(LIB_DIR) $(INC_DIR) $(F90_FLAGS) $(ORM_FLAGS) -J$(OBJDIR) 
 endif
-ifeq ($(F95COMPILER),"g95")
-	FF_FLAGS         = -c -cpp -fendian=big
-	F90_FLAGS        = -O3 -C  -g  -fno-underscoring
-	FF              += $(LIB_DIR) $(INC_DIR) $(F90_FLAGS) $(ORM_FLAGS)
-endif
 
-ifeq ($(F95COMPILER),"ifort")
-        FF_FLAGS         = -O3 -cpp -convert big_endian -xcore-avx512
+ifeq ($(ARCH),"tetralith")
+        F90COMPILER      = ifort
+        PROD_FF_FLAGS    = -O3 -cpp -convert big_endian -xcore-avx512
+        DEV_FF_FLAGS     = -O1 -cpp -convert big_endian -xcore-avx512 -g -traceback -fpe0 
         F90_FLAGS        = -free 
         ARG_FLAGS       += -Tf
         FF              += $(LIB_DIR) $(INC_DIR) $(F90_FLAGS) $(ORM_FLAGS)
 	TT_FLAGS         = -c 
 endif
 
-
+ifeq ($(OPT),"opt")
+        FF_FLAGS         = $(PROD_FF_FLAGS)
+else
+        FF_FLAGS         = $(DEV_FF_FLAGS) 
+endif
 
 
 CC                = gcc -O  $(INC_DIR)
@@ -75,12 +68,12 @@ VPATH = src:projects/$(PROJECT):src/active_particles
 
 all: runfile
 
-objects := $(addprefix $(OBJDIR)/,modules.o interp_general.o $(ACTVEL) calendar.o \
+objects := $(addprefix $(OBJDIR)/,modules.o interp_general.o interp2.o $(ACTVEL) calendar.o \
 	   	    laplacian.o savepsi.o savepsi_new.o loop_pos.o writetrajs.o \
                     sw_stat.o tracer_functions.o \
 	            seed.o init_seed.o getfile.o \
                     vertvel.o coord.o cross.o init_par.o time_subs.o \
-                    pos.o interp2.o sw_seck.o sw_pres.o sw_dens0.o \
+                    pos.o sw_seck.o sw_pres.o sw_dens0.o \
                     writepsi.o writetracer.o printinfo.o loop.o main.o \
 		    setupgrid.o readfield.o diffusion.o)
 

Makefile_tmpl

@@ -2,17 +2,23 @@ PROJECT	          = theoretical
 CASE              = theoretical
 RUNFILE 	  = runtracmass
 
-#F95COMPILER        = "g95"
-F95COMPILER        = "gfortran"
-#F95COMPILER        = "ifort"
-#FF                 = "/sw/bin/gfortran-fsf-4.9" #Alt. compiler location
+# Possible architectures: 
+# tetralith (Swedish HPC with intel)
+# macports (MacPorts for Mac OS)
+# generic (copy this to make your own arch)
+ARCH = "macports"
+#FF = "/sw/bin/gfortran-fsf-4.9" #Alt. compiler location
 
-NETCDFLIBS	   = "none"
-#NETCDFLIBS        = "automatic"  # set using nc-config
-#NETCDFLIBS        = "automatic-44"  # set using nf-config
-#NETCDFLIBS        = "macports"
-#NETCDFLIBS        = "fink"
-#NETCDFLIBS        = "source"
+# Possible netCDF settings
+# automatic (set by nc-config)
+# automatic-44 (set by nf-config, for netCDF version >4.4)
+# generic (set by yourself in Makefile.global)
+# none (no netCDF)
+NETCDFLIBS = "automatic-44"
+
+# Opt = optimise, i.e. dont use so many error checks
+# Else TRACMASS will compile with lots of error check which might slowdown the code
+OPT = "opt"
 
 #================================================================
 

README.md

@@ -13,18 +13,42 @@ It is still in development.
 Quickstart
 ==========
 
-Prerequisites to run on Mac OS X
---------------------------------
+Download the code
+-----------------
 
-Download and install macports (www.macports.org)
-Install the following ports:
+```bash
+git clone https://github.com/TRACMASS/tracmass.git
+```
 
-```sh
-sudo port install openmpi +gcc45 +valgrind
-sudo port install netcdf +openmpi +netcdf4 
-sudo port install netcdf-fortran +gcc45 +openmpi
-sudo port install git-core 
-sudo port install git-extras
+Compile
+-------
+
+Enter the tracmass directory and copy the template Makefile
+
+```bash
+cd tracmass
+cp Makefile_tmpl Makefile
+```
+
+Modify the Makefile to fit your system. 
+You will need to set ARCH, which is the name of your system, i.e. macports, tetralith etc. 
+You will also need to configure how TRACMASS should find the netCDF libraries, if at all. 
+For most systems, we recommend the option automatic-44.
+Then you can run the make command. 
+
+```bash
+make
+```
+
+Running a first test case
+-------------------------
+
+We recommend testing that TRACMASS was properly compiled by letting PROJECT and CASE be "theoretical" in the Makefile (which is the default). 
+In this case, TRACMASS will use a simple oscillating velocity field to trace trajectories. 
+You can run this case by setting
+
+```bash
+./runtracmass
 ```
 
 Download test data
@@ -36,26 +60,43 @@ You can find some input data for testing the code on
 https://www.dropbox.com/sh/b6leim7tb99i3hm/AAA7M0mxuYTwJLKjqmLnoJuca?dl=0
 ```
 
+This test data includes data from NEMO, IFS and ROMS. 
 Before doing any analysis we recommend to download some of the test data and make sure TRACMASS is working properly. 
 
-Compile the code
-----------------
-
-Copy Makefile_tmpl to Makefile. 
-Choose a change PROJECT and CASE in Makefile to your projectname.
-If you are using netCDF version >4.4 you can set NETCDFLIBS to "automatic-44", in which case netCDF paths will be taken from nc-config and nf-config. 
+In order to set up TRACMASS to run trajectories on e.g. NEMO data, you will need to change PROJECT and CASE to NEMO, and then re-compile the code. 
 
-run:
-
-```bash
+```bash 
+make clean
 make
-./runtrm
+./runtracmass
 ```
 
+Run your analysis
+-----------------
+
+If you wish to run TRACMASS using fields from NEMO, ROMS, IFS or CMEMS satellite altimetry, you may use these projects as is (see projects directory). 
+If you wish to run another case or a very specific case of the above models, you may create your own project in the projects directory. 
+To run with e.g. your own NEMO data, you will need to modify the projects/nemo/nemo.in namelist to suit your needs. 
+
 
 Change log
 ==========
 
 
 6.0.0 First public release
-7.0.0_alpha New features for parametrising sub-grid scale motions, tracing water in the atmosphere, simplified set-up for users + code clean–up + bug-fixes.  
+7.0.0_alpha New features for parametrising sub-grid scale motions, tracing water in the atmosphere, simplified set-up for users + code clean–up + bug-fixes.  
+
+
+Prerequisites to run on Mac OS X
+================================
+
+Download and install macports (www.macports.org)
+Install the following ports:
+
+```sh
+sudo port install openmpi +gcc45 +valgrind
+sudo port install netcdf +openmpi +netcdf4 
+sudo port install netcdf-fortran +gcc45 +openmpi
+sudo port install git-core 
+sudo port install git-extras
+```

projects/theoretical/readfield.f95 → projects/theoretical/readfield.F90

@@ -6,7 +6,8 @@ subroutine readfields
   USE mod_grid
   USE mod_name
   USE mod_vel
-  !  USE mod_dens
+  USE mod_dens
+  USE mod_tempsalt
   USE mod_stat
 
   IMPLICIT none
@@ -47,11 +48,9 @@ subroutine readfields
       do i=1,IMT
          im=i-1
          if(im.eq.0) im=IMT
-#ifdef tempsalt 
          tem  (i,j,k,2)=20.*float(k)/float(km)
          sal  (i,j,k,2)=30.
          rho  (i,j,k,2)=(28.-20.)*float(km-k)/float(km) +20.
-#endif
 
 ! time evolving oscilating field
 ! ------------------------------

projects/theoretical/setupgrid.f95 → projects/theoretical/setupgrid.F90

@@ -44,14 +44,14 @@ SUBROUTINE setupgrid
   integer, dimension(2) :: dim2d
   integer, dimension(3) :: dim3d
   real, allocatable, dimension(:,:) :: lon, lat
-  real, allocatable, dimension(:) :: depth
+  real, allocatable, dimension(:) :: depth_1d
   logical :: lwrite_nc, lread_nc
 
 lwrite_nc = .true.
 lread_nc  = .true.
 
 allocate( lon(imt,jmt), lat(imt,jmt) )
-allocate( depth(km) )
+allocate( depth_1d(km) )
 
 kmt=KM ! flat bottom
 
@@ -74,9 +74,9 @@ SUBROUTINE setupgrid
    end do 
 end do
 
-depth(1) = dz(1)/2.
+depth_1d(1) = dz(1)/2.
 do k = 2, km
-   depth(k) = SUM(dz(1:k-1)) + dz(k)/2.
+   depth_1d(k) = SUM(dz(1:k-1)) + dz(k)/2.
 end do
 
 if (lwrite_nc) then 
@@ -98,7 +98,7 @@ SUBROUTINE setupgrid
 
    call check( nf90_put_var(ncid, idlon, lon) )
    call check( nf90_put_var(ncid, idlat, lat) )
-   call check( nf90_put_var(ncid, iddep, depth) )
+   call check( nf90_put_var(ncid, iddep, depth_1d) )
    call check( nf90_put_var(ncid, iddx, dxv(1:jmt,1:imt)) )
    call check( nf90_put_var(ncid, iddy, dyu(1:jmt,1:imt)) )
    call check( nf90_put_var(ncid, iddz, dzt(1:imt,1:jmt,1:km,2)) )
@@ -112,13 +112,16 @@ SUBROUTINE setupgrid
    map3d = [2, 3, 4, 1]
    lon = get2DfieldNC('mesh.nc', 'lon')
    lat = get2DfieldNC('mesh.nc', 'lat')
-   depth = get1DfieldNC('mesh.nc', 'depth')
+   depth_1d = get1DfieldNC('mesh.nc', 'depth')
    dxv(1:imt,1:jmt) = get2DfieldNC('mesh.nc', 'dx')
    dyu(1:imt,1:jmt) = get2DfieldNC('mesh.nc', 'dy')
    dzt(1:imt,1:jmt,1:km,2) = get3DfieldNC('mesh.nc', 'dz')
    dzt(:,:,:,1) = dzt(:,:,:,2)
 end if
 
+depth(:,:) = depth_1d(km)
+
+
 
 ! ===
 

projects/theoretical/theoretical.in

@@ -37,7 +37,8 @@
 /
 &INIT_GRID_TIME
    fieldsperfile =      1,
-            ngcm =      1,
+       ngcm_step =      1,
+       ngcm_unit =      4,
             iter =      1,
           intmax = 146000,
         minveljd =     -1,
@@ -67,7 +68,7 @@
   !                 5 = write at chosen intervals
   !                 6 = write each spatial grid-crossing 
              kriva =      6,
-      outdatadir =   '/proj/bolinc/users/x_sarbe/TRACMASS/projects/theoretical/',
+      outdatadir =   'data_out'
      outdatafile =     'test_k6',
 !     outdatafile =     'analyt_k1',
     ! outdatafile =     'dt1_k1',
@@ -169,3 +170,5 @@
            twave =    8.0,
          critvel =    0.1,
 /
+&INIT_TRACERS
+/

src/cross.F90

@@ -39,8 +39,6 @@ subroutine cross_stat(ijk,ia,ja,ka,r0,sp,sn)
  if(im.eq.0) im=IMT
  uu=(intrpg*uflux(ia,ja,ka,nsp)+intrpr*uflux(ia,ja,ka,nsm))!*ff
  um=(intrpg*uflux(im,ja,ka,nsp)+intrpr*uflux(im,ja,ka,nsm))!*ff
- frac1 = min( abs(upr(1,1)), abs(0.99*uu/upr(1,1)) )
- frac2 = min( abs(upr(2,1)), abs(0.99*um/upr(2,1)) )
  !print*,'cross x',uu,um,upr(1,1),upr(2,1)
 #ifdef turb   
  if(r0.ne.dble(ii)) then
@@ -66,8 +64,6 @@ subroutine cross_stat(ijk,ia,ja,ka,r0,sp,sn)
  ii=ja
  uu=(intrpg*vflux(ia,ja  ,ka,nsp)+intrpr*vflux(ia,ja  ,ka,nsm))!*ff
  um=(intrpg*vflux(ia,ja-1,ka,nsp)+intrpr*vflux(ia,ja-1,ka,nsm))!*ff
- frac1 = min( abs(upr(3,1)), abs(0.99*uu/upr(3,1)) )
- frac2 = min( abs(upr(4,1)), abs(0.99*um/upr(4,1)) )
  !print*,'cross y',uu,um,upr(3,1),upr(4,1)
 #ifdef turb    
  if(r0.ne.dble(ja  )) then

src/init_par.F90

@@ -410,14 +410,12 @@ SUBROUTINE init_params
          seedsubints(1) = 0
       end if
 
-#ifdef tempsalt
       ALLOCATE ( tem(imt,jmt,km,nst) ) 
       ALLOCATE ( sal(imt,jmt,km,nst) )
       ALLOCATE ( rho(imt,jmt,km,nst) )
       tem = 0.
       sal = 0.
       rho = 0.
-#endif
 
       ALLOCATE ( tracers2D(n2Dtracers), tracers3D(n3Dtracers) )
       DO jt=1,n2Dtracers

src/interp2.F90

@@ -1,4 +1,3 @@
-#ifdef tempsalt
 subroutine interp2(i,j,k,temp,salt,dens)
 
   ! === NO interpolation of the temperature, salinity, and density===
@@ -28,5 +27,5 @@ subroutine interp2(i,j,k,temp,salt,dens)
 
   return
 end subroutine interp2
-#endif
+