[ncl-install] addfile and HDF5 library version mismatch
Madeline Miller
madeline at caltech.edu
Mon Jun 13 15:59:31 MDT 2011
Hi Mary,
The test script fails on the line:
fout = addfile(filename,"c")
with error output:
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 1.8.5, library is 1.8.6
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.6
Configured on: Mon May 23 09:21:22 MDT 2011
Configured by: haley at mirage1
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux mirage1 2.6.18-194.17.4.el5 #1 SMP
Wed Oct 20 13:03:08 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /fs/blizzard/contrib/ncl-6.0.0/external
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
CFLAGS: -fPIC
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 -Wno-long-long -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 -Wnonnull -Winit-self -Wmissing-include-dirs
-Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations
-Wc++-compat -Wvolatile-register-var -O3 -fomit-frame-pointer
-finline-functions
AM_CFLAGS:
CPPFLAGS: -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
-I/fs/blizzard/contrib/ncl-6.0.0/external/include
-I/fs/blizzard/contrib/ncl-6.0.0/external/include -D_LARGEFILE_SOURCE
-D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared Libraries: no
Static Libraries: yes
Statically Linked Executables: no
LDFLAGS:
AM_LDFLAGS:
-L/fs/blizzard/contrib/ncl-6.0.0/external/lib
-L/fs/blizzard/contrib/ncl-6.0.0/external/lib
Extra libraries: -lsz -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
Bye...
Aborted
Madeline
2011/6/13 Mary Haley <haley at ucar.edu>
> Hi Madeline,
>
> My sincere apologies. I responded to this on Friday (I think), but either I
> forgot to hit "send", or it just never got sent.
>
> In my response, I asked you to run this sample test script and let me know
> what happens:
>
> filename = "test_nc4.nc" ; name of netcdf 4
> file
> x = random_uniform(-100,100,(/10,64,128/)) ; dummy data
>
> if(isfilepresent(filename)) then
> system("rm " + filename)
> end if
>
> ;---Open netCDF-4 file
> setfileoption("nc","format","netcdf4classic")
> fout = addfile(filename,"c")
>
> ;---Write to netCDF-4 file
> fout->x = x
> delete(fout) ; Close the file
>
> ;---Read variable back in
> fin = addfile(filename,"r")
> xin = fin->x
>
> diffs = xin-x
> print("min/max diffs (should be 0) = " + min(diffs) + "/" + max(diffs))
>
>
> On the UNIX command line, if you type:
>
> file test_nc4.nc
>
> It should say something like:
>
> test_nc4.nc: Hierarchical Data Format (version 5) data
>
> Let me know if you have any luck with this.
>
> --Mary
>
> On Jun 8, 2011, at 4:55 PM, Madeline Miller wrote:
>
> Hello,
>
> I just installed NCL on a Linux Red Hat workstation. I used the
> pre-compiled binary ncl_ncarg-6.0.0.Linux_RedHat_x86_64_nodap_gcc412.tar,
> which matches my architecture and version of gcc.
>
> I ran all the tests under the download instructions and they all worked
> fine. Then, I tried opening a .nc file in NCL using the command
> in=addfile("filename.nc","r").
>
> I created the .nc file using MATLAB on my Linux workstation, and am able to
> read it on my Mac laptop using another version of NCL installed there.
>
> However, on my Linux workstation it returns:
>
>
> 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 1.8.5, library is 1.8.6
> SUMMARY OF THE HDF5 CONFIGURATION
> =================================
>
> General Information:
> -------------------
> HDF5 Version: 1.8.6
> Configured on: Mon May 23 09:21:22 MDT 2011
> Configured by: haley at mirage1
> Configure mode: production
> Host system: x86_64-unknown-linux-gnu
> Uname information: Linux mirage1 2.6.18-194.17.4.el5 #1 SMP
> Wed Oct 20 13:03:08 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
> Byte sex: little-endian
> Libraries:
> Installation point: /fs/blizzard/contrib/ncl-6.0.0/external
>
> Compiling Options:
> ------------------
> Compilation Mode: production
> C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
> CFLAGS: -fPIC
> 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 -Wno-long-long -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 -Wnonnull -Winit-self -Wmissing-include-dirs
> -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations
> -Wc++-compat -Wvolatile-register-var -O3 -fomit-frame-pointer
> -finline-functions
> AM_CFLAGS:
> CPPFLAGS: -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
> H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
> AM_CPPFLAGS:
> -I/fs/blizzard/contrib/ncl-6.0.0/external/include
> -I/fs/blizzard/contrib/ncl-6.0.0/external/include -D_LARGEFILE_SOURCE
> -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
> Shared Libraries: no
> Static Libraries: yes
> Statically Linked Executables: no
> LDFLAGS:
> AM_LDFLAGS:
> -L/fs/blizzard/contrib/ncl-6.0.0/external/lib
> -L/fs/blizzard/contrib/ncl-6.0.0/external/lib
> Extra libraries: -lsz -lz -lm
> Archiver: ar
> Ranlib: ranlib
> Debugged Packages:
> API Tracing: no
>
> Languages:
> ----------
> Fortran: no
> C++: no
>
> Features:
> ---------
> Parallel HDF5: no
> High Level library: yes
> Threadsafety: no
> Default API Mapping: v18
> With Deprecated Public Symbols: yes
> I/O filters (external): deflate(zlib),szip(encoder)
> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
> MPE: no
> Direct VFD: no
> dmalloc: no
> Clear file buffers before write: yes
> Using memory checker: no
> Function Stack Tracing: no
> GPFS: no
> Strict File Format Checks: no
> Optimization Instrumentation: no
> Large File Support (LFS): yes
> H5dump Packed Bits: yes
> Bye...
> Aborted
>
>
> Does anyone know what the problem is and/or what I can do to fix this?
>
> Thanks,
>
> Madeline
> _______________________________________________
> ncl-install mailing list
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-install
>
>
>
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