netcdf hdf5 mismatch

[basmac]

When a user runs ncdump on a netCDF4 compressed file, he gets the following HDF5 library error information. We did a selfupdate and outdated upgrade last Friday

bash-3.2# port installed|grep net

netcdf @4.1.1_2+dap+netcdf4 netcdf @4.1.1_3+dap+netcdf4 netcdf @4.1.1_4+dap+netcdf4 (active) netcdf-devel @4.1.1_1 (active) netpbm @10.26.64_0 (active)

bash-3.2# port installed|grep -i hdf

hdf4 @4.2.5_1 (active) hdf5-18 @1.8.5_0 (active) hdfeos @2.16v1.00_0 hdfeos @2.17v1.00_0 (active) hdfeos5 @1.12_1 hdfeos5 @1.13_0 (active)

bash-3.2#

[dmurray@mac16 grids]$ which ncdump /opt/local/bin/ncdump

[dmurray@mac16 grids]$ ncdump filework.nc > ncdump.out 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 1.8.4

SUMMARY OF THE HDF5 CONFIGURATION =================================

General Information:

---

HDF5 Version: 1.8.4-patch1

Configured on: Fri May 28 13:21:14 MDT 2010 Configured by: root@…

Configure mode: production

Host system: i386-apple-darwin10.3.0

Uname information: Darwin mac78.psd.esrl.noaa.gov 10.3.0 Darwin Kernel Version 10.3.0: Fri Feb 26 11:58:09 PST 2010; root:xnu-1504.3.12~1/RELEASE_I386 i386

Byte sex: little-endian

Libraries:

Installation point: /usr/local/ifort

Compiling Options:

---

Compilation Mode: production

C Compiler: /usr/local/bin/gcc (gcc-4.4.4)

CFLAGS:

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 -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O0 -fomit-frame-pointer -finline-functions AM_CFLAGS:

CPPFLAGS:

H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/usr/local/include

Shared Libraries: yes Static Libraries: yes

Statically Linked Executables: no

LDFLAGS:

AM_LDFLAGS: -L/usr/local/lib

Extra libraries: -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) 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

Linux Large File Support (LFS): no

Bye... Abort