<font style="font-family: arial,helvetica,sans-serif;" size="2">Hi Mary,</font><br><br>The test script fails on the line:<br><font face="Courier"> fout = addfile(filename,"c")<br><br style="font-family: tahoma,sans-serif;">
<font style="font-family: arial,helvetica,sans-serif;" size="2"><span style="font-family: arial,helvetica,sans-serif;">with error output:</span><br></font><br>Warning! ***HDF5 library version mismatched error***<br>The HDF5 header files used to compile this application do not match<br>
the version used by the HDF5 library to which this application is linked.<br>Data corruption or segmentation faults may occur if the application continues.<br>This can happen when an application was compiled by one version of HDF5 but<br>
linked with a different version of static or shared HDF5 library.<br>You should recompile the application or check your shared library related<br>settings such as 'LD_LIBRARY_PATH'.<br>You can, at your own risk, disable this warning by setting the environment<br>
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.<br>Setting it to 2 or higher will suppress the warning messages totally.<br>Headers are 1.8.5, library is 1.8.6<br> SUMMARY OF THE HDF5 CONFIGURATION<br>
=================================<br><br>General Information:<br>-------------------<br> HDF5 Version: 1.8.6<br> Configured on: Mon May 23 09:21:22 MDT 2011<br> Configured by: haley@mirage1<br>
Configure mode: production<br> Host system: x86_64-unknown-linux-gnu<br> 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<br>
Byte sex: little-endian<br> Libraries: <br> Installation point: /fs/blizzard/contrib/ncl-6.0.0/external<br><br>Compiling Options:<br>------------------<br> Compilation Mode: production<br>
C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )<br> CFLAGS: -fPIC<br> 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<br>
AM_CFLAGS: <br> CPPFLAGS: -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE<br> H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API<br> 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 <br>
Shared Libraries: no<br> Static Libraries: yes<br> Statically Linked Executables: no<br> LDFLAGS: <br> AM_LDFLAGS: -L/fs/blizzard/contrib/ncl-6.0.0/external/lib -L/fs/blizzard/contrib/ncl-6.0.0/external/lib<br>
Extra libraries: -lsz -lz -lm <br> Archiver: ar<br> Ranlib: ranlib<br> Debugged Packages: <br> API Tracing: no<br><br>Languages:<br>
----------<br> Fortran: no<br> C++: no<br><br>Features:<br>---------<br> Parallel HDF5: no<br> High Level library: yes<br> Threadsafety: no<br>
Default API Mapping: v18<br> With Deprecated Public Symbols: yes<br> I/O filters (external): deflate(zlib),szip(encoder)<br> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset<br> MPE: no<br>
Direct VFD: no<br> dmalloc: no<br>Clear file buffers before write: yes<br> Using memory checker: no<br> Function Stack Tracing: no<br> GPFS: no<br>
Strict File Format Checks: no<br> Optimization Instrumentation: no<br> Large File Support (LFS): yes<br> H5dump Packed Bits: yes<br>Bye...<br>Aborted<br><br><br><font size="2">Madeline</font><br>
</font><br><div class="gmail_quote">2011/6/13 Mary Haley <span dir="ltr"><<a href="mailto:haley@ucar.edu">haley@ucar.edu</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;">Hi Madeline,<div><br></div><div>My sincere apologies. I responded to this on Friday (I think), but either I forgot to hit "send", or it just never got sent.</div><div><br></div>
<div>In my response, I asked you to run this sample test script and let me know what happens:</div><div><br></div><div><div><font face="Courier"> filename = "<a href="http://test_nc4.nc" target="_blank">test_nc4.nc</a>" ; name of netcdf 4 file</font></div>
<div><font face="Courier"> x = random_uniform(-100,100,(/10,64,128/)) ; dummy data</font></div><div><font face="Courier"><br></font></div><div><font face="Courier"> if(isfilepresent(filename)) then</font></div>
<div><font face="Courier"> system("rm " + filename)</font></div><div><font face="Courier"> end if</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">;---Open netCDF-4 file</font></div>
<div><font face="Courier"> setfileoption("nc","format","netcdf4classic")</font></div><div><font face="Courier"> fout = addfile(filename,"c")</font></div><div class="im"><div><font face="Courier"><br>
</font></div><div><font face="Courier">;---Write to netCDF-4 file</font></div></div><div class="im"><div><font face="Courier"> fout->x = x</font></div><div><font face="Courier"> delete(fout) ; Close the file</font></div>
<div><font face="Courier"><br></font></div></div><div><font face="Courier">;---Read variable back in</font></div><div><font face="Courier"> fin = addfile(filename,"r")</font></div><div><font face="Courier"> xin = fin->x</font></div>
<div><font face="Courier"><br></font></div><div><font face="Courier"> diffs = xin-x</font></div><div><font face="Courier"> print("min/max diffs (should be 0) = " + min(diffs) + "/" + max(diffs))</font></div>
<div><font face="Courier"><br></font></div></div><div><br></div><div>On the UNIX command line, if you type:</div><div><br></div><div><div class="im"><div> file <a href="http://test_nc4.nc" target="_blank">test_nc4.nc</a></div>
<div><br></div><div>It should say something like:</div><div><br></div><div><a href="http://test_nc4.nc" target="_blank">test_nc4.nc</a>: Hierarchical Data Format (version 5) data</div><div><br></div></div><div>Let me know if you have any luck with this.</div>
<div><br></div><font color="#888888"><div>--Mary</div><div><br></div></font><div><div class="im"><div>On Jun 8, 2011, at 4:55 PM, Madeline Miller wrote:</div><br></div><blockquote type="cite"><div><div></div><div class="h5">
Hello,<br><br>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. <br><br>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 <br>
in=addfile("<a href="http://filename.nc/" target="_blank">filename.nc</a>","r"). <br><br>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. <br>
<br>However, on my Linux workstation it returns:<br><br><br>Warning! ***HDF5 library version mismatched error***<br>The HDF5 header files used to compile this application do not match<br>the version used by the HDF5 library to which this application is linked.<br>
Data corruption or segmentation faults may occur if the application continues.<br>This can happen when an application was compiled by one version of HDF5 but<br>linked with a different version of static or shared HDF5 library.<br>
You should recompile the application or check your shared library related<br>settings such as 'LD_LIBRARY_PATH'.<br>You can, at your own risk, disable this warning by setting the environment<br>variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.<br>
Setting it to 2 or higher will suppress the warning messages totally.<br>Headers are 1.8.5, library is 1.8.6<br> SUMMARY OF THE HDF5 CONFIGURATION<br> =================================<br><br>General Information:<br>
-------------------<br> HDF5 Version: 1.8.6<br> Configured on: Mon May 23 09:21:22 MDT 2011<br> Configured by: haley@mirage1<br> Configure mode: production<br>
Host system: x86_64-unknown-linux-gnu<br> 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<br> Byte sex: little-endian<br>
Libraries: <br> Installation point: /fs/blizzard/contrib/ncl-6.0.0/external<br><br>Compiling Options:<br>------------------<br> Compilation Mode: production<br> C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )<br>
CFLAGS: -fPIC<br> 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<br>
AM_CFLAGS: <br> CPPFLAGS: -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE<br> H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API<br> 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 <br>
Shared Libraries: no<br> Static Libraries: yes<br> Statically Linked Executables: no<br> LDFLAGS: <br> AM_LDFLAGS: -L/fs/blizzard/contrib/ncl-6.0.0/external/lib -L/fs/blizzard/contrib/ncl-6.0.0/external/lib<br>
Extra libraries: -lsz -lz -lm <br> Archiver: ar<br> Ranlib: ranlib<br> Debugged Packages: <br> API Tracing: no<br><br>Languages:<br>
----------<br> Fortran: no<br> C++: no<br><br>Features:<br>---------<br> Parallel HDF5: no<br> High Level library: yes<br> Threadsafety: no<br>
Default API Mapping: v18<br> With Deprecated Public Symbols: yes<br> I/O filters (external): deflate(zlib),szip(encoder)<br> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset<br> MPE: no<br>
Direct VFD: no<br> dmalloc: no<br>Clear file buffers before write: yes<br> Using memory checker: no<br> Function Stack Tracing: no<br> GPFS: no<br>
Strict File Format Checks: no<br> Optimization Instrumentation: no<br> Large File Support (LFS): yes<br> H5dump Packed Bits: yes<br>Bye...<br>Aborted<br><br><br>Does anyone know what the problem is and/or what I can do to fix this?<br>
<br>Thanks,<br><br>Madeline<br></div></div><div class="im">
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</div></blockquote></div><br></div></div></blockquote></div><br><br><br>