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Created by Mehmet Cüneyd Demirel@cuneyd🏇🏿Developer

Cygwin - Warning! ***HDF5 library version mismatched error***

Hello,

Cygwin users get this error: HDF version mismatch.

In my knowledge the two ways to omit this warning and continue running are (stackoverflow tricks):

  1. export HDF5_DISABLE_VERSION_CHECK=1 (in cygwin terminal)
  2. Adding this to Environmental variables > system variables (if they run mhm from command prompt/cmd).

It would be great if we (@ottor and @thober) can add something to the makefile (like we did once for the memory issues in windows machines EXTRA_LDFLAGS += #-Wl,--stack,12485760 and EXTRA_CFLAGS += #-Wl,--stack,12485760)

I think HDF5 warnings can be avoided with good "Linking Options" during compiling.

Kind Regards, Cüneyd

mhm_HDF

Details of the error message:

D:\mhm-5.10_fixed>start /B /WAIT mhm.exe /k

          mHM-UFZ

MULTISCALE HYDROLOGIC MODEL
       Version 5.10
       June 2019

Originally by L. Samaniego & R. Kumar

Start at 14.02.2020 09:36:08. Using main file mhm_driver.f90 and namelists: mhm.nml mhm_parameter.nml mhm_outputs.nml

Run with OpenMP with 16 threads.

Read namelist file: mhm.nml Read namelist file: mhm_parameter.nml Read namelist file: mhm_outputs.nml INFO: Process (10, neutrons) is deactivated, so output will be suppressed.

Basin 1: resolution Hydrology (basin 1) = 24000. resolution Routing (basin 1) = 24000.

Resolution of routing and hydrological modeling are equal!

Basin 2: resolution Hydrology (basin 2) = 24000. resolution Routing (basin 2) = 24000.

Resolution of routing and hydrological modeling are equal!

Following output will be written: STATES: interceptional storage (L1_inter) [mm] height of snowpack (L1_snowpack) [mm] soil water content in the single layers (L1_soilMoist) [mm] volumetric soil moisture in the single layers [mm/mm] mean volum. soil moisture averaged over all soil layers [mm/mm] waterdepth in reservoir of sealed areas (L1_sealSTW) [mm] waterdepth in reservoir of unsat. soil zone (L1_unsatSTW) [mm] waterdepth in reservoir of sat. soil zone (L1_satSTW) [mm] FLUXES: actual evapotranspiration aET (L1_pet) [mm/T] total discharge generated per cell (L1_total_runoff) [mm/T] direct runoff generated per cell (L1_runoffSeal) [mm/T] fast interflow generated per cell (L1_fastRunoff) [mm/T] slow interflow generated per cell (L1_slowRunoff) [mm/T] baseflow generated per cell (L1_baseflow) [mm/T] groundwater recharge (L1_percol) [mm/T] infiltration (L1_infilSoil) [mm/T]

FINISHED reading config

of basins: 2

Input data directories:

  BASIN                     1
Morphological directory:    test_basin/input/morph/
Land cover directory:       test_basin/input/luse/
Precipitation directory:    test_basin/input/meteo/pre/
Temperature directory:      test_basin/input/meteo/tavg/
PET directory:              test_basin/input/meteo/pet/
Output directory:           test_basin/output_b1/
  BASIN                     2
Morphological directory:    test_basin_2/input/morph/
Land cover directory:       test_basin_2/input/luse/
Precipitation directory:    test_basin_2/input/meteo/pre/
Temperature directory:      test_basin_2/input/meteo/tavg/
PET directory:              test_basin_2/input/meteo/pet/
Output directory:           test_basin_2/output/

Read data ... Reading data ... Reading dem and lcover ... Reading dem for basin: 1 ... Reading dem for basin: 2 ... Reading lcover for basin: 1 ... Reading lcover for basin: 2 ... Reading data for basin: 1 ... Reading slope ... Reading aspect ... Reading soil ids ... Reading LAI ... Reading latitude/logitude ... Warning! HDF5 library version mismatched error The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.10.5, library is 1.10.6 SUMMARY OF THE HDF5 CONFIGURATION =================================

General Information:

               HDF5 Version: 1.10.6
              Configured on: Sat Jan 18 22:29:58 CET 2020
              Configured by: Marco@LAPTOP-82F08ILC
                Host system: x86_64-pc-cygwin
          Uname information: CYGWIN_NT-10.0 LAPTOP-82F08ILC 3.1.2(0.340/5/3) 2020-01-12 11:00 x86_64 Cygwin
                   Byte sex: little-endian
         Installation point: /usr

Compiling Options:

                 Build Mode: production
          Debugging Symbols: no
                    Asserts: no
                  Profiling: no
         Optimization Level: high

Linking Options:

                  Libraries: shared

Statically Linked Executables: LDFLAGS: H5_LDFLAGS: -no-undefined AM_LDFLAGS: Extra libraries: -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib

Languages:

                          C: yes
                 C Compiler: /usr/bin/gcc ( gcc (GCC) 7.4.0)
                   CPPFLAGS:
                H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS:
                    C Flags: -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/hdf5/hdf5-1.10.6-1.x86_64/build=/usr/src/debug/hdf5-1.10.6-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/hdf5/hdf5-1.10.6-1.x86_64/src/hdf5-1.10.6=/usr/src/debug/hdf5-1.10.6-1
                 H5 C Flags:   -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-cond -Whsa -Wnormalized -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2 -Wimplicit-fallthrough=5 -Wrestrict -fstdarg-opt -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3
                 AM C Flags:
           Shared C Library: yes
           Static C Library: no


                    Fortran: no

                        C++: yes
               C++ Compiler: /usr/bin/g++ ( g++ (GCC) 7.4.0)
                  C++ Flags: -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/hdf5/hdf5-1.10.6-1.x86_64/build=/usr/src/debug/hdf5-1.10.6-1 -fdebug-prefix-map=/cygdrive/d/cyg_pub/devel/hdf5/hdf5-1.10.6-1.x86_64/src/hdf5-1.10.6=/usr/src/debug/hdf5-1.10.6-1
               H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
               AM C++ Flags:
         Shared C++ Library: yes
         Static C++ Library: no

                       Java: no

Features:

               Parallel HDF5: no

Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Build HDF5 Tests: yes Build HDF5 Tools: yes Threadsafety: no Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib) MPE: no Direct VFD: no (Read-Only) S3 VFD: no (Read-Only) HDFS VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Strict file format checks: no Optimization instrumentation: no Bye...

Program received signal SIGABRT: Process abort signal.

Backtrace for this error: #0 0xffffffffffffffff in ??? #1 (closed) 0xffffffffffffffff in ??? #2 (closed) 0xffffffffffffffff in ??? #3 0xffffffffffffffff in ??? #4 0xffffffffffffffff in ??? #5 0xffffffffffffffff in ??? #6 0xffffffffffffffff in ??? #7 0xffffffffffffffff in ??? #8 (closed) 0xffffffffffffffff in ??? #9 (closed) 0xffffffffffffffff in ??? #10 (closed) 0xffffffffffffffff in ??? #11 (closed) 0xffffffffffffffff in ??? #12 (closed) 0xffffffffffffffff in ??? #13 (closed) 0xffffffffffffffff in ??? #14 (closed) 0xffffffffffffffff in ??? #15 0xffffffffffffffff in ??? #16 0xffffffffffffffff in ??? #17 0xffffffffffffffff in ??? #18 0xffffffffffffffff in ??? #19 0xffffffffffffffff in ??? #20 (closed) 0xffffffffffffffff in ??? #21 (closed) 0xffffffffffffffff in ??? 0 [main] mhm 10 cygwin_exception::open_stackdumpfile: Dumping stack trace to mhm.exe.stackdump

D:\mhm-5.10_fixed>pause Press any key to continue . . .

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