[Trilinos-Users] decomp ***HDF5 library version mismatched error***

Martin.Raedel at dlr.de Martin.Raedel at dlr.de
Tue Apr 19 04:54:21 EDT 2016


Hello,

I built HDF5-1.8.16 and Trilinos 12.4.2. Everything works fine with one exception. When I use decomp I get the following warning:


Executing:
    /usr/local/bin/trilinos-12.4.2/bin/nem_slice -e -S -l inertial -c -o disk_impact.g.nem -m mesh=2 disk_impact.g
   ...see disk_impact.g.decomp.out for nem_slice status
(B
Beginning nem_slice execution.
Input Mesh File = 'disk_impact.g'
Using 32-bit integer mode for decomposition...
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 1.8.16, library is 1.8.15
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.15
		  Configured on: Sun Oct 25 12:32:44 UTC 2015
		  Configured by: abuild at cloud127
		 Configure mode: production
		    Host system: x86_64-suse-linux-gnu
	      Uname information: Linux cloud127 4.1.10-1-default #1 SMP PREEMPT Mon Oct 12 11:24:48 UTC 2015 (67a24e6) x86_64 x86_64 x86_64 GNU/Linux
		       Byte sex: little-endian
		      Libraries: static, shared
	     Installation point: /usr

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc
                         CFLAGS: -fmessage-length=0 -grecord-gcc-switches -O0 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g
                      H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 -fomit-frame-pointer -finline-functions
                      AM_CFLAGS: 
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_DEFAULT_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
               Shared C Library: yes
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
 	 	Extra libraries: -lpthread -lz -ldl -lm 
 		       Archiver: ar
 		 	 Ranlib: ranlib
 	      Debugged Packages: 
		    API Tracing: no

Languages:
----------
                        Fortran: yes
               Fortran Compiler: /usr/bin/gfortran
          Fortran 2003 Compiler: yes
                  Fortran Flags: 
               H5 Fortran Flags:  
               AM Fortran Flags: 
         Shared Fortran Library: yes
         Static Fortran Library: yes

                            C++: yes
                   C++ Compiler: /usr/bin/g++
                      C++ Flags: -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: yes

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: yes
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib)
                            MPE: no
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
Bye...
[linux-f050:00403] *** Process received signal ***
[linux-f050:00403] Signal: Aborted (6)
[linux-f050:00403] Signal code:  (-6)
[linux-f050:00403] [ 0] /lib64/libpthread.so.0(+0xf870)[0x7f02dd740870]
[linux-f050:00403] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f02dd3be0a7]
[linux-f050:00403] [ 2] /lib64/libc.so.6(abort+0x118)[0x7f02dd3bf458]
[linux-f050:00403] [ 3] /usr/lib64/libhdf5.so.10(H5check_version+0x1c3)[0x7f02e26624eb]
[linux-f050:00403] [ 4] /usr/lib64/libnetcdf.so.11(NC4_create+0x1dd)[0x7f02df14614d]
[linux-f050:00403] [ 5] /usr/lib64/libnetcdf.so.11(NC_create+0x100)[0x7f02df0e81c0]
[linux-f050:00403] [ 6] /usr/lib64/libnetcdf.so.11(nc__create+0x1e)[0x7f02df0e832e]
[linux-f050:00403] [ 7] /usr/local/bin/trilinos-12.4.2/bin/nem_slice(ex_create_int+0xf8)[0x4d0038]
[linux-f050:00403] [ 8] /usr/local/bin/trilinos-12.4.2/bin/nem_slice(_Z13write_nemesisIiEiRSsP19Machine_DescriptionP19Problem_DescriptionP16Mesh_DescriptionIT_EP14LB_DescriptionIS6_EP11Sphere_Info+0x88)[0x437898]
[linux-f050:00403] [ 9] /usr/local/bin/trilinos-12.4.2/bin/nem_slice(_Z13internal_mainIiEiiPPcT_+0xe83)[0x42cf93]
[linux-f050:00403] [10] /usr/local/bin/trilinos-12.4.2/bin/nem_slice(main+0x154)[0x41f9c4]
[linux-f050:00403] [11] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f02dd3aab05]
[linux-f050:00403] [12] /usr/local/bin/trilinos-12.4.2/bin/nem_slice[0x41fc0f]
[linux-f050:00403] *** End of error message ***
/usr/local/bin/trilinos-12.4.2/bin/decomp: line 155:   403 Aborted                 ( $LAUNCH $NEM_SLICE -e $spheres $decomp_method $nem_slice_flag -o $nemesis -m mesh=$processors $genesis >> $output )

ERROR:******************************************************************
ERROR:
ERROR     During nem_slice execution. Check error output above and rerun
ERROR:
ERROR:******************************************************************
(B

The problem seems to be, that I have octave-forge-netcdf installed on my system which writes its one hdf5-library based on hdf5-1.8.15 in /usr/lib64 and decomp seems to use this version.

I build Trilinos with the following cmake-file:

cmake -D CMAKE_INSTALL_PREFIX:PATH=/usr/local/bin/trilinos-12.4.2/ \
-D MPI_BASE_DIR:PATH="/usr/local/lib/openmpi-1.10.2/" \
-D CMAKE_CXX_FLAGS:STRING="-O2 -std=c++11 -pedantic -ftrapv -Wall -Wno-long-long" \
-D CMAKE_BUILD_TYPE:STRING=RELEASE \
-D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
-D Trilinos_ENABLE_Teuchos:BOOL=ON \
-D Trilinos_ENABLE_Shards:BOOL=ON \
-D Trilinos_ENABLE_Sacado:BOOL=ON \
-D Trilinos_ENABLE_Epetra:BOOL=ON \
-D Trilinos_ENABLE_EpetraExt:BOOL=ON \
-D Trilinos_ENABLE_Ifpack:BOOL=ON \
-D Trilinos_ENABLE_AztecOO:BOOL=ON \
-D Trilinos_ENABLE_Amesos:BOOL=ON \
-D Trilinos_ENABLE_Anasazi:BOOL=ON \
-D Trilinos_ENABLE_Belos:BOOL=ON \
-D Trilinos_ENABLE_ML:BOOL=ON \
-D Trilinos_ENABLE_Phalanx:BOOL=ON \
-D Trilinos_ENABLE_Intrepid:BOOL=ON \
-D Trilinos_ENABLE_NOX:BOOL=ON \
-D Trilinos_ENABLE_Stratimikos:BOOL=ON \
-D Trilinos_ENABLE_Thyra:BOOL=ON \
-D Trilinos_ENABLE_Rythmos:BOOL=ON \
-D Trilinos_ENABLE_MOOCHO:BOOL=ON \
-D Trilinos_ENABLE_TriKota:BOOL=OFF \
-D Trilinos_ENABLE_Stokhos:BOOL=ON \
-D Trilinos_ENABLE_Zoltan:BOOL=ON \
-D Trilinos_ENABLE_Piro:BOOL=ON \
-D Trilinos_ENABLE_Teko:BOOL=ON \
-D Trilinos_ENABLE_SEACASIoss:BOOL=ON \
-D Trilinos_ENABLE_SEACAS:BOOL=ON \
-D Trilinos_ENABLE_SEACASBlot:BOOL=ON \
-D Trilinos_ENABLE_Pamgen:BOOL=ON \
-D Trilinos_ENABLE_EXAMPLES:BOOL=OFF \
-D Trilinos_ENABLE_TESTS:BOOL=ON \
-D TPL_ENABLE_Matio:BOOL=OFF \
-D TPL_ENABLE_HDF5:BOOL=ON \
-D HDF5_INCLUDE_DIRS:PATH="/usr/local/bin/hdf5-1.8.16/include" \
-D HDF5_LIBRARY_DIRS:PATH="/usr/local/bin/hdf5-1.8.16/lib" \
-D TPL_ENABLE_Netcdf:BOOL=ON \
-D Netcdf_INCLUDE_DIRS:PATH="/usr/local/bin/netcdf-4.4.0_with_hdf5-1.8.16/include" \
-D Netcdf_LIBRARY_DIRS:PATH="/usr/local/bin/netcdf-4.4.0_with_hdf5-1.8.16/lib64" \
-D TPL_ENABLE_MPI:BOOL=ON \
-D TPL_ENABLE_BLAS:BOOL=ON \
-D TPL_ENABLE_LAPACK:BOOL=ON \
-D TPL_ENABLE_Boost:BOOL=ON \
-D Boost_INCLUDE_DIRS:PATH="/usr/local/lib/boost-1.55.0/include" \
-D Boost_LIBRARY_DIRS:PATH="/usr/local/lib/boost-1.55.0/lib" \
-D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
-D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \
/usr/local/src/trilinos-12.4.2-Source/

I checked all path. Is decomp not build by the hdf5-version specified in the cmake-file? How can I tell decomp which hdf5-version to use. Both libhdf5 are in the LD_LIBRARY_PATH variable (version 1.8.15 under /usr/lib64 and 1.8.16 under /usr/local/bin/netcdf-4.4.0_with_hdf5-1.8.16/lib64)

Best regards
Martin




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