[ncl-install] addfile and HDF5 library version mismatch
Madeline Miller
madeline at caltech.edu
Thu Jun 9 20:03:45 MDT 2011
Hi Mary,
Thanks for your reply. I tried the test you sent, and it fails with the same
error message I sent previously, at the line:
fout = addfile(filename,"c").
I also discovered that our system administrators had installed an older
version of NCL (5.1.1) on the computer (in a different folder, as part of a
package of programs). I unset all the NC environment variables in hopes
that there was just a search path issue, but it did not change anything.
Besides environment variables, is there any other problem with multiple
installations that might be causing this?
Best,
Madeline
2011/6/9 Mary Haley <haley at ucar.edu>
> Madeline,
>
> Can you try this simple test on your RedHat system and let me know what
> happens? This test creates a small NetCDF-4 file and then tries to read it
> back in:
>
> begin
> x = random_uniform(-100,100,(/5,10/))
>
> ;---Write to netCDF-4 file
> filename = "test_nc4.nc"
> setfileoption("nc","format","netcdf4classic")
> system("/bin/rm -f " + filename)
>
> print("Writing to NC-4 file...")
> fout = addfile(filename,"c")
> fout->x = x
> delete(fout) ; Close the file
>
> fin = addfile(filename,"r")
> print("Reading from NC-4 file...")
> x2 = fin->x
> print("min/max x-x2 = " + min(x-x2) + "/" + max(x-x2))
>
> ; system("/bin/rm -f " + filename)
> end
>
>
> After you run this file, if you type:
>
> file test_nc4.nc
>
> It should say something like:
>
> test_nc4.nc: Hierarchical Data Format (version 5) data
>
> --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
>
>
>
--
Madeline Miller
Ph.D. Candidate - Mechanical Engineering
California Institute of Technology
1200 E. California Blvd., MC 100-23
Pasadena, CA 91125
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.ucar.edu/pipermail/ncl-install/attachments/20110609/6283acb7/attachment.html
More information about the ncl-install
mailing list