Merge branch 'develop' into 'master'

Develop

See merge request !61

.VERSION

+0.6.4
\ No newline at end of file

.gitignore

@@ -16,7 +16,6 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
 lib64/
 parts/
 sdist/

CMakeLists.txt

+
+# This cmake file is not meant to be edited for a special setup.
+# For special setups use cache line files or command line options, as described a few
+# lines ahead concerning module INDEPENDENT builds
+cmake_minimum_required(VERSION 3.5)
+
+project(MPR Fortran)
+
+# common (default) options to cmake
+# -DCMAKE_BUILD_TYPE=Release     - compile in debug or release mode
+# -DBUILD_TESTING=ON             - whether to compile tests
+# -DCMAKE_VERBOSE_MAKEFILE=OFF   - see all the commands
+# -DCMAKE_BUILD_MODULE_SYSTEM_INDEPENDENT=OFF   - build the library INDEPENDENT of the module system,
+# -DCMAKE_FIND_LIBRARY_CUSTOM_LIB_SUFFIX=64     - find extra library paths on some systems (eve.nag62)
+#         so the build in the build tree works even after a module purge
+
+# automatically enables testing
+include(CTest)
+
+set(CMAKE_BUILD_MODULE_SYSTEM_INDEPENDENT OFF CACHE STRING "build the module INDEPENDENT of the module system, so the build in the build tree works even after a module purge")
+
+# set compiling flags for debug and relese version
+if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+	# https://www.mankier.com/1/gfortran#Options-Options_to_request_or_suppress_errors_and_warnings
+	# this is super detailed...
+	# set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -Og -g -Wall -Wextra -Warray-temporaries -Wconversion -Wrealloc-lhs-all -fimplicit-none -fbacktrace -fcheck=all -ffpe-trap=zero,overflow,underflow -finit-real=snan")
+	set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -Og -g -Wall -Wextra -fimplicit-none -fbacktrace -fcheck=all -ffpe-trap=zero,overflow,underflow -finit-real=snan")
+	set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -Ofast")
+	set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ffree-line-length-none")
+endif()
+if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
+	set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -warn all -g -debug extended -traceback -fp-stack-check -O0 -check all -fstack-protector-all -fstack-security-check -fpe0")
+	set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -O3 -qoverride-limits")
+	set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -assume byterecl -fp-model=source -m64 -assume realloc_lhs")
+endif()
+if(CMAKE_Fortran_COMPILER_ID MATCHES "NAG")
+	set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -g -nan -O0 -C=all -strict95 -ieee=stop")
+	# set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -pedantic -Wall -W -O -g")
+	set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -O4 -ieee=full")
+	# set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O3")
+	set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fpp -colour -unsharedf95 -ideclient")
+endif()
+if(CMAKE_Fortran_COMPILER_ID MATCHES "PGI")
+	set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -C -c -g -traceback -O0")
+	set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -fast")
+	set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Mfree -mcmodel=medium")
+endif()
+
+# library module specific settings
+add_subdirectory(./src)
+add_subdirectory(./src_python)
+
+# this command is able to create dependencies, compile and add the sources in the right order
+set(EXECUTABLE_NAME "${CMAKE_PROJECT_NAME}_runner")
+add_executable(${EXECUTABLE_NAME} ./src/main.f90)
+target_link_libraries(${EXECUTABLE_NAME} PUBLIC mpr)
+
+# ifort and gfortran need the flag -cpp to interpret definitions like -DMRM2MHM
+# the nag compiler is not able to interpret the flag -cpp but can interpret these definitions anyway
+# so we check whether the compiler is able to use the flag -cpp
+# for that we need the module CheckFortranCompilerFlag
+include(CheckFortranCompilerFlag)
+CHECK_Fortran_COMPILER_FLAG("-cpp" CPP_FLAG)
+# if the flag exists, we add it to the compilation flags
+if (CPP_FLAG)
+	target_compile_options(${EXECUTABLE_NAME} PUBLIC "-cpp")
+endif()
+
+#----------------------------------
+# Get version (semantic versioning)
+# C.F. semver.org
+#----------------------------------
+file ( STRINGS "${CMAKE_SOURCE_DIR}/.VERSION" VERSION )
+string( REPLACE "." ";" VERSION_LIST ${VERSION} )
+list(GET VERSION_LIST 0 VERSION_MAJOR)
+list(GET VERSION_LIST 1 VERSION_MINOR)
+list(GET VERSION_LIST 2 VERSION_PATCH)
+set(PROJECT_VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
+message ( STATUS "CMake build configuration for ${CMAKE_PROJECT_NAME} ${PROJECT_VERSION}" )
+
+set_target_properties ( ${EXECUTABLE_NAME}
+  PROPERTIES
+  COMPILE_FLAGS "${CMAKE_Fortran_FLAGS}"
+  OUTPUT_NAME "${CMAKE_PROJECT_NAME}"
+  SOVERSION "${VERSION_MAJOR}.${VERSION_MINOR}"
+  VERSION "${VERSION}"
+  )
+
+if (CMAKE_BUILD_MODULE_SYSTEM_INDEPENDENT)
+	set_target_properties ( ${EXECUTABLE_NAME}
+	  PROPERTIES
+      INSTALL_RPATH "${CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES}"
+      BUILD_WITH_INSTALL_RPATH ON
+      )
+endif()
+
+
+

COPYRIGHTS.md

 ------------------
 
-Copyright(c) 2018, 
+Copyright(c) 2019, 
 Helmholtz-Zentrum fuer Umweltforschung GmbH - UFZ. 
 All rights reserved.
 
@@ -11,8 +11,8 @@ Registered Office: Leipzig
 Registration Office: Amtsgericht Leipzig
 Trade Register: Nr. B 4703
 Chairman of the Supervisory Board: MinDirig Wilfried Kraus
-Scientific Director: Prof. Dr. Dr. h.c. Georg Teutsch
-Administrative Director: Dr. Heike Grassmann
+Scientific Director: Prof. Dr. Georg Teutsch
+Administrative Director: Prof. Dr. Heike Graßmann
 
 ------------------
 

Makefile

@@ -94,7 +94,7 @@ SHELL = /bin/bash
 #
 
 # . is current directory, .. is parent directory
-SRCPATH    := src/ deps/lib/src # where are the source files; use test_??? to run a test directory
+SRCPATH    := src/ deps/lightweight_fortran_lib/src deps/flogging/src # where are the source files; use test_??? to run a test directory
 PROGPATH   := .                  # where shall be the executable
 CONFIGPATH := make.config        # where are the $(system).$(compiler) files
 MAKEDPATH  := $(CONFIGPATH)      # where is the make.d.sh script
@@ -186,7 +186,7 @@ static   := shared
 EXTRA_FCFLAGS  :=
 EXTRA_F90FLAGS := #-mismatch #-C=undefined
 EXTRA_DEFINES  := -DWRF_HYDRO -DUFZ -DHIDDEN -DHYDRO_D
-EXTRA_INCLUDES := 
+EXTRA_INCLUDES := -Ideps/flogging/include
 EXTRA_LDFLAGS  :=
 EXTRA_LIBS     :=
 EXTRA_CFLAGS   :=

README.md

 # Multiscale parameter regionalization - MPR
 
-- The current release is **[MPR 0.3](https://git.ufz.de/chs/MPR/tags/0.3)**.
+- The current release is **[MPR 0.5](https://git.ufz.de/chs/MPR/tags/0.5)**.
 - General information can be found on the [MPR website](http://www.ufz.de/index.php?en=40126).
 
 **Please note:** The [GitLab repository](https://git.ufz.de/chs/MPR) grants read access to the code.
-If you like to contribute to the code, please contact [mhm-admin@ufz.de](mailto:mhm-admin@ufz.de).
+If you would like to contribute to the code, please contact [robert.schweppe@ufz.de](mailto:robert.schweppe@ufz.de).
 
 ## Cite us in your scientific work
 
-TODO: add citation, once it is published
-The code can be cited as:
+The model code can be cited as:
 
-- **MPR:** 
+* MPR: Schweppe et al. (2019) TODO 
 
-## Installation
+Please see the original publication of the MPR framework in Samaniego et al. (2010) and Kumar et al. (2013):
 
-Please see the file [DEPENDENCIES](docs/src/dependencies.md) for external software required to run MPR.
-All Python libraries needed to run the pre-processor script ([f90nml](https://github.com/marshallward/f90nml)) 
-and the documentation builder ([FORD](https://github.com/Fortran-FOSS-Programmers/ford/wiki/Dependencies))
-are also available on the UFZ Eve Linux-Cluster when loading the module from
-`/global/apps/chspython/virtualenvs/python-3.6.2/`.
+* Samaniego L., R. Kumar, S. Attinger (2010): Multiscale parameter regionalization of a grid-based hydrologic model at the mesoscale. Water Resour. Res., 46,W05523, doi:10.1029/2008WR007327, http://onlinelibrary.wiley.com/doi/10.1029/2008WR007327/abstract
+* Kumar, R., L. Samaniego, and S. Attinger (2013): Implications of distributed hydrologic model parameterization on water fluxes at multiple scales and locations, Water Resour. Res., 49, doi:10.1029/2012WR012195, http://onlinelibrary.wiley.com/doi/10.1029/2012WR012195/abstract
 
-## Compilation
+## Dependencies
 
-The code is based on the Fortran90 standard and also uses many features from 
-the Fortran 2003 and 2008 standards. MPR is routinely tested with the following
-compilers: gfortran versions 6.0, 7.3 and 8.1, nag 6.2 (>build 6214). We
-hope to support ifortran version 18.0 from Intel soon (pending bug report).
-On the UFZ Eve Linux Cluster, currently only the gfortran compiler 7.3 works.
+Please see the file [DEPENDENCIES](docs/src/01_dependencies.md) 
+for external software required to run and compile MPR.
 
 ## Documentation
 
 In the near future, the documentation will be hosted on a gitlab server of the UFZ (gitlab pages),
 once the infrastructure is set up. Until then the documentation needs to be
-built locally by running the tool [FORD](https://github.com/Fortran-FOSS-Programmers/ford):
+built locally by running the Python tool [FORD](https://github.com/Fortran-FOSS-Programmers/ford):
 `ford ./docs/MPR.md` and then view `./doc/index.html` in your browser.
 
 ## License
@@ -53,17 +46,12 @@ with the UFZ CHS MPR preprocessor. The
 complete GNU license text can also be found at 
 <http://www.gnu.org/licenses/>.
 
-## Quick start
+MPR uses a logging library [flogging](https://github.com/Exteris/flogging) that is licensed under a permissive license [MIT](deps/flogging/LICENSE) with: Copyright (c) 2016 Daan van Vugt
 
-1. Compile MPR with the `make` command, which uses settings from [Makefile](Makefile).
-2. Run MPR with our test configuration `./mpr`, which uses settings from [mhm.nml](./predefined_nmls/mpr_default.nml).
-3. Explore the results in the [output file](./default_output.nc), e.g. by using the NetCDF viewer `ncview`.
+MPR uses a remapping library [SCRIP](https://github.com/SCRIP-Project/SCRIP) that is licensed under a permissive license [MIT](deps/SCRIP/SCRIP/source/copyright) with: Copyright (c) 1997, 1998 the Regents of the University of California
 
-@Bugs
+## Quick start
 
-With gFortran compiler:
-- (version 8.0), an error is issued ("Fortran runtime error: Bad repeat count in item * of list input"), if
-to_file keyword is not last in respective data_array block.
-- (version 6.0-8.0), the file mpr_global_paramaters.nml raises an end-of-file-error.
-Strangely, it works when adding another line with a backslash at the end of the file.
+A guide to set up a minimal example can be found
+[here](docs/src/02_configuration/index.md).
 

deps/flogging/.gitignore

+.fuse_hidden*
+*.o
+*.so
+test
+test_mpi
+*.mod

deps/flogging/.gitrepo

+; DO NOT EDIT (unless you know what you are doing)
+;
+; This subdirectory is a git "subrepo", and this file is maintained by the
+; git-subrepo command. See https://github.com/git-commands/git-subrepo#readme
+;
+[subrepo]
+	remote = https://github.com/gitporst/flogging.git
+	branch = mpr_compat
+	commit = 789047189a2e7cedd78272522cfeedc9f1163faa
+	parent = 3ea27226b2ee091e3009ce6002d5e5b31d1792ac
+	method = merge
+	cmdver = 0.4.0

deps/flogging/LICENSE

+Copyright (c) 2016 Daan van Vugt
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

deps/flogging/Makefile

+# Builds flogging as a shared library
+
+F90=.f90
+OBJ=.o
+LIB = libflogging.so
+SRC = src
+BUILD = $(SRC)
+
+
+FC = mpif90
+ifeq ($(FC),nagfor)
+	FLAGS = -fpp -colour -free -Iinclude -DNAG
+	LIB_FLAGS =
+else
+	FLAGS = -fpic -O3 -cpp -ffree-line-length-none -Iinclude
+	LIB_FLAGS = -shared
+endif
+ifeq (USE_MPI,1)
+	FLAGS += -DUSE_MPI
+endif
+
+SOURCES = $(wildcard $(SRC)/*$(F90))
+OBJS = $(patsubst $(SRC)/%$(F90), $(BUILD)/%$(OBJ), $(SOURCES))
+
+$(LIB): $(OBJS)
+	$(FC) $(LIB_FLAGS) -o $(LIB) $(OBJS)
+
+$(BUILD)/%$(OBJ): $(SRC)/%$(F90)
+	$(FC) $(FLAGS) -c $< -o $@
+
+$(BUILD)/flogging.o: $(BUILD)/vt100.o
+
+# Some test executables
+#
+test : src/flogging.f90 src/tests/test_flogging.f90 src/vt100.f90 include/flogging.h
+	$(FC) $(FLAGS) -Iinclude src/vt100.f90 src/flogging.f90 src/tests/test_flogging.f90 -o test
+
+test_mpi : src/flogging.f90 src/tests/test_flogging.f90 src/vt100.f90 include/flogging.h
+	$(FC) $(FLAGS) -DUSE_MPI -Iinclude src/vt100.f90 src/flogging.f90 src/tests/test_flogging.f90 -o test_mpi
+
+.PHONY: clean doc
+clean:
+	@find . -name '*.o' -delete
+	@find . -name '*.mod' -delete
+	@find . -name '*.so' -delete
+	@rm -f test test_mpi
+
+doc:
+	ford flogging.md
+doc_deploy: doc
+	git subtree push --prefix doc origin gh-pages

deps/flogging/README.md

+# Flogging
+This logging system aims to be simple to use, similar to existing write statements and therefore easy to implement in existing codes,
+while providing some convenient extra features not present in fortran by default.
+
+Usage is very simple:
+```fortran
+use flogging
+```
+
+To load the logging module and its utility functions.
+To use the preprovided macros, include the header file and turn on the preprocessor by compiling with `-cpp`
+```C
+#include "flogging.h"
+```
+This macro defines the following functions:
+```fortran
+log_fatal(format)
+log_error(format)
+log_warn(format)
+log_info(format)
+log_debug(format)
+log_trace(format)
+
+log_root_fatal(format)
+log_root_error(format)
+log_root_warn(format)
+log_root_info(format)
+log_root_debug(format)
+log_root_trace(format)
+```
+Where `format` is usually `*`, but can be adjusted to suit your needs. Remember to include a single `A` specifier for the log lead if you set it yourself.
+
+The functions print a log message only if the level is greater than or equal to the current minimum loglevel.
+The second functions include a check to print a log message only from the root MPI process, if compiled
+with `USE_MPI`. If not compiled with `USE_MPI`, it works the same as the log function.
+
+If you do not want to use the preprocessor macros, you can log like this.
+```fortran
+if (logp(LEVEL)) then
+  write(logu,FORMAT) trim(logl(LEVEL))//" ", "this is a log message"
+endif
+```
+Note that it is not possible to use the filename and linenumber features then.
+
+# Installation
+You can compile `flogging.f90` and `vt100.f90` into a library `flogging.so` with `make`.
+To compile with MPI support use 
+```bash
+make USE_MPI=1
+```
+Then, place `libflogging.so` into your `LD_LIBRARY_PATH` and put `flogging.h` into your include path.
+
+## Compilation flags
+Compile your own code with
+```
+-DDISABLE_LOG_DEBUG
+```
+to remove any debug statements from your code. Note that you cannot use `-v` to get these back then.
+By default any `log_trace` messages are not included in the executable. Compile with
+```
+-DENABLE_LOG_TRACE
+```
+to get these back. Note that you still need to use `-vv` (by default) to see the messages.
+This is a good compilation flag to have in your debug build profile.
+
+## Transitioning to flogging
+You can change all of the messages in your application to the `log_info` level by
+```bash
+git sed 's/write ?(\*,\*)/log_info(*)/g'
+```
+You might need to split some lines, as the `__FILE__` and `__LINE__` macros require quite some space.
+This can also be circumvented by compiling with `-ffree-line-length-none` or equivalent.
+
+# Examples
+```fortran
+log_error(*) "this is an error"
+log_warn(*) "this is a warning"
+log_info(*) "here, have some info"
+log_debug(*) "and this is a debug message"
+```
+outputs (without any compilation flags)
+```
+ localhost test.f90:9  ERROR this is an error
+ localhost test.f90:10  WARN this is a warning
+ localhost test.f90:11  INFO here, have some info
+```
+(The leading space is a consequence of using the fortran * format specifier)
+
+## Interface
+The module `flogging` defines some subroutines you can use to alter it's behaviour:
+```fortran
+public :: log_set_output_hostname
+public :: log_set_output_severity
+public :: log_set_output_date
+public :: log_set_time_only
+public :: log_set_output_fileline
+public :: log_set_skip_terminal_check
+public :: log_set_disable_colors
+public :: log_disable_cli_arguments
+```
+
+## Command-line flags
+The logging module allows the following command-line flags, checked at the time of the first log output.
+```
+  -v, --verbose                 Increase the logging verbosity
+  -q, --quiet                   Decrease the logging verbosity
+  --log-output-hostname         Output the hostname in the log lead
+  --log-force-colors            Force colors, even when outputting to a file
+  --log-no-colors               Disable colors (overrides --log-force-colors)
+  --log-output-date             Output the date in the log lead
+  --log-output-time             Output the time in the log lead
+```
+
+### Argument parsing
+By default, flogging parses the command-line arguments above on the first invocation of `log()`.
+If you want to use your own argument parsing you can disable this behaviour by calling `log_disable_cli_arguments` before any output is logged.
+
+## Output to a file
+Logging is to stderr by default. Another output unit can be selected by setting
+```fortran
+  logu = some_unit
+```
+This will probably not work well with MPI.
+
+## Internals
+The latest documentation can be found [here](http://exteris.github.io/flogging/).
+
+The module defines a function defining whether or not to print this log message,
+```fortran
+  logp(level)
+```
+where level is one of `LOG_FATAL`, `LOG_ERROR`, `LOG_WARN`, `LOG_INFO`, `LOG_DEBUG` or `LOG_TRACE`.
+The logp function can also be used with MPI support, using an optional integer parameter `only_n` to return true
+only if the level is sufficient and the MPI rank of the current thread is equal to `only_n`.
+This can be used to print messages only from the root thread, to prevent log messages from being printed N times as shown below.
+```fortran
+  logp(level,0)
+```
+
+## Contributing
+Pull requests and comments are appreciated.
+
+## TODO
+- Argument parsing is quite flaky (try -qqqqqq and see what happens)
+- Time and date output at the same time does not work yet
+- Compilation flag to control argument parsing
+- Log output to a different file per MPI process
+- Multiple logging streams/outputs (this will be tricky)

deps/flogging/flogging.md

+project: flogging
+project_github: https://github.com/exteris/flogging
+summary: FLOGGING -- Fortran logging system with MPI support
+author: Daan van Vugt
+github: https://github.com/exteris
+project_dir: ./src
+output_dir: ./doc
+docmark: <
+docmark_alt: *
+predocmark: >
+predocmark_alt: #
+graph: true
+coloured_edges: true
+
+This library provides a logging framework for Fortran 90 and up, with MPI support, vt100 colors, command-line arguments and more.
+
+License
+---------------
+
+The bspline-fortran source code and related files and documentation are distributed under a permissive [license](https://github.com/exteris/flogging/blob/master/LICENSE) (MIT).

deps/flogging/include/flogging.h

+/* This code is governed by the MIT license. See LICENSE for details. */
+/* The lines below have little spacing to ease the fortran line-length requirements */
+
+/* Log level constants */
+#define LOG_LEVEL_FATAL_DEF 1
+#define LOG_LEVEL_ERROR_DEF 2