Minor updates for modsurface and modbulkmicro3

config/cheops_2018.cmake

@@ -0,0 +1,26 @@
+# CHEOPS GCC - v. 2018
+# use with: 
+# module load gnu/4.8.2 netcdf/4.1.3-gcc-4.8.2 intelmpi/2018
+# module load hdf5/1.8.11 szlib
+# module load cmake
+
+set(CMAKE_Fortran_COMPILER "gfortran" ) # "ifort") #"gfortran")
+set(Fortran_COMPILER_WRAPPER mpif90 ) # mpiifort)
+
+set(USER_Fortran_FLAGS "-fbacktrace -finit-real=nan -fdefault-real-8  -fno-f2c -ffree-line-length-none")
+set(USER_Fortran_FLAGS_RELEASE "-funroll-all-loops -O3")
+set(USER_Fortran_FLAGS_DEBUG "-W -Wall -Wuninitialized -fcheck=all -fbacktrace -O0 -g -ffpe-trap=invalid,zero,overflow")
+
+set(NETCDF_INCLUDE_DIR "/opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/include") # set(NETCDF_INCLUDE_DIR "/opt/rrzk/lib/netcdf/4.1.3/include")
+set(NETCDF_LIB_1       "/opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/lib/libnetcdff.so") # set(NETCDF_LIB_1       "/opt/rrzk/lib/netcdf/4.1.3/lib/libnetcdff.so")
+set(NETCDF_LIB_2       "/opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/lib/libnetcdf.so") # set(NETCDF_LIB_2       "/opt/rrzk/lib/netcdf/4.1.3/lib/libnetcdf.so")
+# set(NETCDF_LIB_3       "/opt/rrzk/lib/netcdf/netcdf-4.1.3/f90/netcdf.mod")
+set(HDF5_LIB_1         "/opt/rrzk/lib/hdf5/1.8.11/lib/libhdf5_hl.so")  # set(HDF5_LIB_1         "/opt/rrzk/lib/hdf5/1.8.11/lib/libhdf5_hl.so")
+set(HDF5_LIB_2         "/opt/rrzk/lib/hdf5/1.8.11/lib/libhdf5.so") # set(HDF5_LIB_2         "/opt/rrzk/lib/hdf5/1.8.11/lib/libhdf5.so")
+set(SZIP_LIB           "/opt/rrzk/lib/szip/szip-2.1/lib/libsz.so")
+set(LIBS ${NETCDF_LIB_1} ${NETCDF_LIB_2}  ${HDF5_LIB_1} ${HDF5_LIB_2} ${SZIP_LIB} m z curl)
+# set(LIBS ${NETCDF_LIB_1} ${NETCDF_LIB_2} ${NETCDF_LIB_3} ${HDF5_LIB_1} ${HDF5_LIB_2} ${SZIP_LIB} m z curl)  
+#
+
+
+

config/cheops_CMakeLists.txt

@@ -0,0 +1,131 @@
+### Choose CMAKE Type
+if(NOT CMAKE_BUILD_TYPE)
+  set (CMAKE_BUILD_TYPE RELEASE CACHE STRING
+      "Choose the type of build, options are: None Debug Release."
+      FORCE)
+endif()
+
+### Set compiler flags
+if("$ENV{SYST}" STREQUAL "HUYGENS")
+  set(CMAKE_Fortran_COMPILER "mpfort")
+  set(CMAKE_Fortran_FLAGS "-qfree=F90 -qrealsize=8  -qwarn64 -qflttrap=en:ov:zero:inv:imp -qflag=w:e" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O4 -qnoipa -qstrict=none:exceptions" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O2 -g -qfullpath -C -qflttrp=enable:nanq:overflow:zerodivide -qsigtrap -qinitauto=ff" CACHE STRING "")
+elseif("$ENV{SYST}" STREQUAL "CARTESIUS")
+  set(CMAKE_Fortran_COMPILER "mpiifort")
+  set(CMAKE_Fortran_FLAGS "-r8 -ftz -extend_source" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-traceback -fpe1 -O0 -g -check all" CACHE STRING "")
+elseif("$ENV{SYST}" STREQUAL "localpc_ifort")
+  set(CMAKE_Fortran_COMPILER "mpif90")
+  set(CMAKE_Fortran_FLAGS "-r8 -ftz -extend_source" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-traceback -fpe1 -O0 -g -check all" CACHE STRING "")
+elseif("$ENV{SYST}" STREQUAL "HYDRA")
+  set(CMAKE_Fortran_COMPILER "mpiifort")
+  set(CMAKE_Fortran_FLAGS "-r8 -ftz -extend_source" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE STRING "")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-traceback -fpe1 -O0 -g -check all" CACHE STRING "")
+else()
+  set(CMAKE_Fortran_COMPILER "mpif90")
+  set(CMAKE_Fortran_FLAGS "-finit-real=nan -W -Wall -fdefault-real-8 -ffree-line-length-none" CACHE STRING "")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O3" CACHE STRING "")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-fbounds-check -fbacktrace -fno-f2c -O0 -g -ffpe-trap=invalid,zero,overflow" CACHE STRING "")
+endif()
+
+## Project parameters
+PROJECT(DALES Fortran)
+cmake_minimum_required(VERSION 2.6)
+set(VERSION_MAJOR "4")
+set(VERSION_MINOR "1")
+set(VERSION_PATCH "0")
+
+### If necessary, resort to BASH-methods to find netcdf-directory
+EXEC_PROGRAM(${CMAKE_CURRENT_SOURCE_DIR}/findnetcdf OUTPUT_VARIABLE ADDMODULEPATH)
+
+### Find NetCDF files
+FIND_PATH(NETCDF_INCLUDE_DIR netcdf.mod NETCDF.mod
+  PATHS
+  $ENV{SARA_NETCDF_INCLUDE}
+  $ENV{SURFSARA_NETCDF_INCLUDE}
+  $ENV{NETCDF_INCLUDE}
+  ${ADDMODULEPATH}/include
+  /usr/include
+  $ENV{HOME}/include
+  /usr/lib64/gfortran/modules
+  /opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/f90/
+  DOC "NetCDF include directory (must contain netcdf.mod)"
+)
+
+FIND_LIBRARY(NETCDF_C_LIB netcdf
+  PATHS
+  $ENV{SARA_NETCDF_LIB}
+  $ENV{SURFSARA_NETCDF_LIB}
+  $ENV{NETCDF_LIB}
+  ${ADDMODULEPATH}/lib
+  ${ADDMODULEPATH}/lib64
+  /usr/lib
+  /usr/lib64
+  $ENV{HOME}/lib
+  $ENV{HOME}/lib64
+  /opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/lib/
+  DOC "NetCDF C library"
+)
+
+FIND_LIBRARY(NETCDF_FORTRAN_LIB netcdff
+  PATHS
+  $ENV{SARA_NETCDF_LIB}
+  $ENV{SURFSARA_NETCDF_LIB}
+  $ENV{NETCDF_LIB}
+  ${ADDMODULEPATH}/lib
+  ${ADDMODULEPATH}/lib64
+  /usr/lib
+  /usr/lib64
+  $ENV{HOME}/lib
+  $ENV{HOME}/lib64
+  /opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/lib/
+  DOC "NetCDF Fortran library"
+)
+
+if(NETCDF_INCLUDE_DIR)
+  include_directories(${NETCDF_INCLUDE_DIR})
+else(NETCDF_INCLUDE_DIR)
+  MESSAGE(STATUS "WARNING: No NETCDF bindings are found.")
+endif(NETCDF_INCLUDE_DIR)
+
+if(NETCDF_C_LIB)
+  set(NETCDF_LIBS ${NETCDF_C_LIB})
+else(NETCDF_C_LIB)
+  MESSAGE(STATUS "WARNING: No NETCDF bindings are found.")
+endif(NETCDF_C_LIB)
+
+if(NETCDF_FORTRAN_LIB)
+  set(NETCDF_LIBS ${NETCDF_LIBS} ${NETCDF_FORTRAN_LIB})
+else(NETCDF_FORTRAN_LIB)
+  MESSAGE(STATUS "WARNING: No Fortran NETCDF bindings are found.")
+endif(NETCDF_FORTRAN_LIB)
+
+### Documentation
+INCLUDE(FindDoxygen)
+if(DOXYGEN)
+    ADD_SUBDIRECTORY(utils/doc)
+else()
+    MESSAGE(STATUS "WARNING: Doxygen not found - Reference manual will not be created")
+endif()
+
+### Set case
+if(NOT CASE)
+  set (CASE standard CACHE STRING
+      "Set the case."
+      FORCE)
+endif()
+
+### Add case specific file 
+FILE(GLOB usrfile "${CMAKE_CURRENT_SOURCE_DIR}/cases/${CASE}/moduser.f90")
+if(usrfile STREQUAL "")
+  set(usrfile "${CMAKE_CURRENT_SOURCE_DIR}/cases/standard/moduser.f90")
+endif()
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${usrfile} ${CMAKE_CURRENT_SOURCE_DIR}/src/moduser.f90)
+MESSAGE(STATUS "Case " ${CASE} " uses " ${usrfile})
+
+ADD_SUBDIRECTORY(src)

config/modversion.f90

@@ -0,0 +1,12 @@
+! This file is used on Cheops and Juwels
+! to supplement missing Git/Cmake functionalities
+! Variables in this file are filled in by CMake at build time,
+! used to record the git version and hash.
+
+module modversion
+
+  implicit none
+
+  character(80) :: git_version='2.17' ! "@GIT_VERSION@"
+
+end module modversion

rundales/runDALES_parallel_16_cheops_master.sh

@@ -0,0 +1,27 @@
+#!/bin/bash -l
+#SBATCH --ntasks=16
+#SBATCH --mem-per-cpu=20gb
+#SBATCH --time=120:00:00
+#SBATCH --account=UniKoeln
+
+# number of nodes in $SLURM_NNODES (default: 1)
+# number of tasks in $SLURM_NTASKS (default: 1)
+# number of tasks per node in $SLURM_NTASKS_PER_NODE (default: 1)
+# number of threads per task in $SLURM_CPUS_PER_TASK (default: 1)
+
+
+#module avail
+#module load intelmpi/4.1.0 netcdf/4.1.3
+ module load gnu/4.8.2 netcdf/4.1.3-gcc-4.8.2 intelmpi/2018
+ module load hdf5/1.8.11 szlib
+# module load cmake
+
+#echo $PATH
+
+echo "# of nodes, tasks:" $SLURM_NNODES $SLURM_NTASKS
+
+#LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/rneggers/bin/netcdf-4.3.0_ifort/lib"
+#LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/rrzk/lib/netcdf/4.1.3/lib"
+LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/rrzk/lib/netcdf/4.1.3-gcc-4.8.2/lib"
+
+srun -n $SLURM_NTASKS ./dales4