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[netCDF #MLF-697840]: Parallel NetCDF 4.1.3 compile error finding HDFflush

> Yes, I did a make install.  I set the
> --prefix=/u/home/eylandej/netcdf-4.3.0.  I did find the include directory,
> but no lib.  I thought that was weird because the compile was supposedly
> successful, and the make check passed all tests.

Oops, I suspect you are using the netCDF source directory as the place where
netCDF is to be installed, and that's a mistake we warn against in the last
sentence of the build instructions:

  The installation location specified with the –prefix option must be different 
  from the source directory where the software is being built.

If you have used the source directory as installation directory, it will have
overwritten some of the source files, and won't be fixed by a mere "make clean".

You'll have to start over with a new tarball and make sure you either accept the
default /usr/local installation location by not specifying --prefix=... or
specify an installation location different from where the source is unpacked and
built. 

I assume you know that "make install" must be run *after* "make check", so
"make check" doesn't indicate anything about whether "make install" worked
or not.

For "make install" to have run successfully, it must have created 4 
subdirectories of your installation directory: bin/, lib/, include/,
and share/.  If you don't see those, something went wrong with "make install"
and you should have seen an error message when running it.

Here's what I see in the lib/ directory for the netcdf-4.3.0 installation 
location specified with --prefix=, after running "make install":

  /home/russ/m/nc430/lib:
  total used in directory 8176 available 127666864
  drwxrwxr-x 2 russ ustaff    4096 May 16 09:13 pkgconfig/
  drwxrwxr-x 3 russ ustaff    4096 May 16 09:13 ./
  -rw-r--r-- 1 root root   5120282 May 16 09:13 libnetcdf.a
  -rwxr-xr-x 1 root root      1112 May 16 09:13 libnetcdf.la*
  lrwxrwxrwx 1 root root        18 May 16 09:13 libnetcdf.so -> 
libnetcdf.so.7.2.0*
  lrwxrwxrwx 1 root root        18 May 16 09:13 libnetcdf.so.7 -> 
libnetcdf.so.7.2.0*
  -rwxr-xr-x 1 root root   3228778 May 16 09:13 libnetcdf.so.7.2.0*
  drwxrwxr-x 6 russ ustaff    4096 May 13 15:19 ../

--Russ

> On 7/31/13 10:24 AM, "Unidata netCDF Support"
> <address@hidden> wrote:
> 
> >> Ok...now after running through a complete make check install, I think I
> >> have everything ok; however, there is no netcdf-4.3.0/lib directory.  I
> >> have a bunch of lib directories, (liblib, libsrc, libsrc4, etc), but no
> >> lib directory with the .a files.  Everything in the liblib, libsrc,
> >> libsrc4 directories is a .la file.  Am I missing something?
> >
> >Did you run "make install" (or "sudo make install")?
> >
> >By default that will install netCDF header files and libraries under
> >/user/local
> >directories, unless you've specified a different location with --prefix=
> >on the
> >netCCF configure invocation.
> >
> >The liblib, libsrc4, etc. are all source directories, which aren't needed
> >after
> >you've run "make install".
> >
> >--Russ
> >
> >> John
> >>
> >> --
> >>
> >>
> >> ________________________________________
> >>
> >> John B. Eylander
> >> Cold Regions Research and Engineering Lab
> >> U.S. Army Engineer Research and Development Center
> >> 72 Lyme Road
> >> Hanover, NH  03755
> >>
> >> PH:  603-646-4188    BB:  603-359-9717
> >>
> >> Unclass:  address@hidden
> >> SIPR:  address@hidden
> >> JWICS:  address@hidden
> >> ________________________________________
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On 7/30/13 6:43 PM, "Unidata netCDF Support"
> >> <address@hidden> wrote:
> >>
> >> >OK, let's concentrate on just this failure in config.log:
> >> >
> >> >> /site/intel/impi/4.1.0.024/intel64/bin/mpicc -o conftest
> >> >> -I/u/home/eylandej/hdf5/include -I/u/home/eylandej/zlib-1.2.7/include
> >> >> -I/u/home/eylandej/szip-2.1/include -L /u/home/eylandej/hdf5/lib -L
> >> >> /u/home/eylandej/zlib-1.2.7/lib -
> >> >> L /u/home/eylandej/szip-2.1/lib conftest.c -lsz -ldl -lhdf5 >&5
> >> >> configure:4377: $? = 0
> >> >> configure:4384: ./conftest
> >> >> ./conftest: error while loading shared libraries: libsz.so.2: cannot
> >> >>open
> >> >
> >> >It compiled OK, but couldn't run, because libsz.so.2 couldn't be found
> >>at
> >> >run time.  Does it help to put /u/home/eylandej/szip-2.1/lib in your
> >> >LD_LIBRARY_PATH, so the dynamic loader will look there?
> >> >
> >> >Does the following file exist and is it readable?
> >> >
> >> >  /u/home/eylandej/szip-2.1/lib/libsz.so.2
> >> >
> >> >If you just compile a "hello world" C program using something like
> >> >
> >> >  mpicc -o hello -L/u/home/eylandej/zlib-1.2.7/lib hello.c -lsz
> >> >
> >> >and then try to run the result, does it run OK?
> >> >
> >> >Maybe putting "-lsz" in LIBS is not the right place, perhaps it needs
> >>to
> >> >be
> >> >in LDFLAGS or LDLIBS.  The autoconf-generated configure scripts are
> >> >supposed
> >> >to be able to figure out this kind of thing, but maybe they get it
> >>wrong
> >> >in
> >> >this case.  I'm CC:ing Ward Fisher, who knows more about LDFLAGS vs.
> >>LIBS
> >> >vs.
> >> >LDLIBS than I do, and may be able to figure this out.
> >> >
> >> >--Russ
> >> >
> >> >> If I put -lsz in my LIBS variable, I get the following error during
> >>the
> >> >> compile:
> >> >>
> >> >> checking whether a default cache preemption for HDF5 was specified...
> >> >>0.75
> >> >> checking whether netCDF-4 logging is enabled... no
> >> >> checking whether cdmremote client is to be built... no
> >> >> checking whether DAP client is to be built... yes
> >> >> checking for style of include used by make... GNU
> >> >> checking for gcc... /site/intel/impi/4.1.0.024/intel64/bin/mpicc
> >> >> checking whether the C compiler works... yes
> >> >> checking for C compiler default output file name... a.out
> >> >> checking for suffix of executables...
> >> >> checking whether we are cross compiling... configure: error: in
> >> >> `/u/home/eylandej/netcdf-4.3.0':
> >> >> configure: error: cannot run C compiled programs.
> >> >> If you meant to cross compile, use `--host'.
> >> >> See `config.log' for more details
> >> >> + exit
> >> >>
> >> >>
> >> >>
> >> >> This is what the config.log complains about:
> >> >>
> >> >>
> >> >> /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64/crt1.o: In
> >> >> function `_start':
> >> >> (.text+0x20): undefined reference to `main'
> >> >> collect2: ld returned 1 exit status
> >> >> configure:4205: $? = 1
> >> >> configure:4225: checking whether the C compiler works
> >> >> configure:4247: /site/intel/impi/4.1.0.024/intel64/bin/mpicc
> >> >> -I/u/home/eylandej/hdf5/include -I/u/home/eylandej/zlib-1.2.7/include
> >> >> -I/u/home/eylandej/szip-2.1/include -L /u/home/eylandej/hdf5/lib -L
> >> >> /u/home/eylandej/zlib-1.2.7/lib -L /u/home/ey
> >> >> landej/szip-2.1/lib conftest.c -lsz -ldl -lhdf5 >&5
> >> >> configure:4251: $? = 0
> >> >> configure:4299: result: yes
> >> >> configure:4302: checking for C compiler default output file name
> >> >> configure:4304: result: a.out
> >> >> configure:4310: checking for suffix of executables
> >> >> configure:4317: /site/intel/impi/4.1.0.024/intel64/bin/mpicc -o
> >>conftest
> >> >> -I/u/home/eylandej/hdf5/include -I/u/home/eylandej/zlib-1.2.7/include
> >> >> -I/u/home/eylandej/szip-2.1/include -L /u/home/eylandej/hdf5/lib -L
> >> >> /u/home/eylandej/zlib-1.2.7/lib -
> >> >> L /u/home/eylandej/szip-2.1/lib conftest.c -lsz -ldl -lhdf5 >&5
> >> >> configure:4321: $? = 0
> >> >> configure:4343: result:
> >> >> configure:4365: checking whether we are cross compiling
> >> >> configure:4373: /site/intel/impi/4.1.0.024/intel64/bin/mpicc -o
> >>conftest
> >> >> -I/u/home/eylandej/hdf5/include -I/u/home/eylandej/zlib-1.2.7/include
> >> >> -I/u/home/eylandej/szip-2.1/include -L /u/home/eylandej/hdf5/lib -L
> >> >> /u/home/eylandej/zlib-1.2.7/lib -
> >> >> L /u/home/eylandej/szip-2.1/lib conftest.c -lsz -ldl -lhdf5 >&5
> >> >> configure:4377: $? = 0
> >> >> configure:4384: ./conftest
> >> >> ./conftest: error while loading shared libraries: libsz.so.2: cannot
> >> >>open
> >> >> shared object file: No such file or directory
> >> >> configure:4388: $? = 127
> >> >> configure:4395: error: in `/u/home/eylandej/netcdf-4.3.0':
> >> >> configure:4397: error: cannot run C compiled programs.
> >> >> If you meant to cross compile, use `--host'.
> >> >> See `config.log' for more details
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> I've recompiled szip-2.1 a couple of different times, and that hasn't
> >> >> changed the outcome.  The libsz.so.2 file is in the szip-2.1/lib
> >> >> directory, so I don't know why netcdf can't see the file.
> >> >>
> >> >> John
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >>
> >> >>
> >> >> ________________________________________
> >> >>
> >> >> John B. Eylander
> >> >> Cold Regions Research and Engineering Lab
> >> >> U.S. Army Engineer Research and Development Center
> >> >> 72 Lyme Road
> >> >> Hanover, NH  03755
> >> >>
> >> >> PH:  603-646-4188    BB:  603-359-9717
> >> >>
> >> >> Unclass:  address@hidden
> >> >> SIPR:  address@hidden
> >> >> JWICS:  address@hidden
> >> >> ________________________________________
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> On 7/30/13 5:05 PM, "Unidata netCDF Support"
> >> >> <address@hidden> wrote:
> >> >>
> >> >> >> Ok.  Added the export statements back in, and the resulting output
> >> >>from
> >> >> >> the "configure" script is the same:
> >> >> >>
> >> >> >> Script:
> >> >> >> #!/bin/bash
> >> >> >> # Proper header for a Bash script.
> >> >> >>
> >> >> >> set -x
> >> >> >>
> >> >> >> export H5DIR=/u/home/eylandej/hdf5
> >> >> >> export CC=/site/intel/impi/4.1.0.024/intel64/bin/mpicc
> >> >> >> echo $LD_LIBRARY_PATH
> >> >> >> export LD_LIBRARY_PATH=${H5DIR}/lib:$LD_LIBRARY_PATH
> >> >> >> export CPPFLAGS="-I${H5DIR}/include
> >> >> >>-I/u/home/eylandej/zlib-1.2.7/include
> >> >> >> -I/u/home/eylandej/szip-2.1/include"
> >> >> >> export LDFLAGS="-L${H5DIR}/lib -L/u/home/eylandej/zlib-1.2.7/lib
> >> >> >> -L/u/home/eylandej/szip-2.1/lib"
> >> >> >> export LIBS=-ldl
> >> >> >> ./configure --prefix=/u/home/eylandej/netcdf-4.3.0
> >> >> >>--enable-parallel-tests
> >> >> >> --disable-shared
> >> >> >>
> >> >> >> exit
> >> >> >
> >> >> >From the config.log file you sent,  it looks like you compiled HDF5
> >> >> >with --disable-shared, so all libraries that HDF5 depends on need to
> >> >> >be expicitly specified when linking.  But there's no "-lsz" for the
> >> >> >szip library, so that has to be added to LIBS, which should be:
> >> >> >
> >> >> >  LIBS="-lsz -ldl"
> >> >> >
> >> >> >If that doesn't work, keep sending the config.log and we should be
> >> >>able to
> >> >> >figure out if anything else is needed.
> >> >> >
> >> >> >--Russ
> >> >> >
> >> >> >> Screen output from configure:
> >> >> >>
> >> >> >>
> >> >> >> checking whether isinf is declared... yes
> >> >> >> checking whether isfinite is declared... yes
> >> >> >> checking whether signbit is declared... yes
> >> >> >> checking for struct stat.st_blksize... yes
> >> >> >> checking for IEEE floating point format... yes
> >> >> >> checking for size_t... (cached) yes
> >> >> >> checking for off_t... yes
> >> >> >> checking for ssize_t... yes
> >> >> >> checking for ptrdiff_t... yes
> >> >> >> checking for uchar... no
> >> >> >> checking for longlong... no
> >> >> >> checking whether char is unsigned... no
> >> >> >> checking whether byte ordering is bigendian... no
> >> >> >> checking size of short... 2
> >> >> >> checking size of int... 4
> >> >> >> checking size of long... 8
> >> >> >> checking size of long long... 8
> >> >> >> checking size of float... 4
> >> >> >> checking size of double... 8
> >> >> >> checking size of off_t... 8
> >> >> >> checking size of size_t... 8
> >> >> >> checking for library containing deflate... none required
> >> >> >> checking for floor in -lm... yes
> >> >> >> checking for library containing H5Fflush... no
> >> >> >> configure: error: Can't find or link to the hdf5 library. Use
> >> >> >> --disable-netcdf-4, or see config.log for errors.
> >> >> >> + exit
> >> >> >>
> >> >> >> While the above is identical to all results I've seen from each
> >> >>attempt
> >> >> >>to
> >> >> >> configure, I notice different errors in the config.log (see
> >> >>attached).
> >> >> >> The compile commands do have the hdf5 libs and include files
> >> >>corrected
> >> >> >> referenced, but still can't link to the Hdf5 library:
> >> >> >>
> >> >> >> /* end confdefs.h.  */
> >> >> >> |
> >> >> >> | /* Override any GCC internal prototype to avoid an error.
> >> >> >> |    Use char because int might match the return type of a GCC
> >> >> >> |    builtin and then its argument prototype would still apply.
> >>*/
> >> >> >> | #ifdef __cplusplus
> >> >> >> | extern "C"
> >> >> >> | #endif
> >> >> >> | char H5Fflush ();
> >> >> >> | int
> >> >> >> | main ()
> >> >> >> | {
> >> >> >> | return H5Fflush ();
> >> >> >> |   ;
> >> >> >> |   return 0;
> >> >> >> | }
> >> >> >> configure:16246: result: no
> >> >> >> configure:16253: error: Can't find or link to the hdf5 library.
> >>Use
> >> >> >> --disable-netcdf-4, or see config.log for errors.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> NOTE:  I'm using Intel MPI compiler...just in case you didn't see
> >> >>that.
> >> >> >> I
> >> >> >> tried using OpenMPI, but had the same result as using IntelMPI.
> >> >> >>
> >> >> >> John
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >>
> >> >> >>
> >> >> >> ________________________________________
> >> >> >>
> >> >> >> John B. Eylander
> >> >> >> Cold Regions Research and Engineering Lab
> >> >> >> U.S. Army Engineer Research and Development Center
> >> >> >> 72 Lyme Road
> >> >> >> Hanover, NH  03755
> >> >> >>
> >> >> >> PH:  603-646-4188    BB:  603-359-9717
> >> >> >>
> >> >> >> Unclass:  address@hidden
> >> >> >> SIPR:  address@hidden
> >> >> >> JWICS:  address@hidden
> >> >> >> ________________________________________
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On 7/30/13 3:33 PM, "Unidata netCDF Support"
> >> >> >> <address@hidden> wrote:
> >> >> >>
> >> >> >> >John,
> >> >> >> >
> >> >> >> >> I am not running as root or sudo.  I don't have those
> >>privileges
> >> >>on
> >> >> >>the
> >> >> >> >> system.
> >> >> >> >>
> >> >> >> >> Also understand...the --with statements are ignored; however, I
> >> >>also
> >> >> >> >>have
> >> >> >> >> included the libraries in my LDFLAGS and CPPFLAGS environmental
> >> >> >> >>variables
> >> >> >> >> that I included in the --with statements.  I will clean up my
> >> >> >>configure
> >> >> >> >> script to remove the --with statements though.
> >> >> >> >>
> >> >> >> >> My config.log is attached.
> >> >> >> >
> >> >> >> >Are you exporting the environment variables LDFLAGS and CPPFLAGS?
> >> >>One
> >> >> >> >way of doing this is preceding the invocation of configure but on
> >> >>the
> >> >> >> >same line, or you can also
> >> >> >> >give them as arguments to configure.  However, if you just define
> >> >>them
> >> >> >>in
> >> >> >> >the shell
> >> >> >> >in which configure is invoked, I don't think they get inherited
> >>by
> >> >> >> >configure's
> >> >> >> >subshell.
> >> >> >> >
> >> >> >> >I'm asking, because of these lines in the config.log you sent:
> >> >> >> >
> >> >> >> >  CC='/site/intel/impi/4.1.0.024/intel64/bin/mpicc'
> >> >> >> >   ...
> >> >> >> >  CPPFLAGS=''
> >> >> >> >   ...
> >> >> >> >  LDFLAGS=''
> >> >> >> >
> >> >> >> >and the compile lines that don't have the "-L" or "-I" flags
> >>needed
> >> >>to
> >> >> >> >find the
> >> >> >> >HDF5 libraries:
> >> >> >> >
> >> >> >> >  /site/intel/impi/4.1.0.024/intel64/bin/mpicc -o conftest -g -O2
> >> >> >> >conftest.c -lhdf5  -lm -lcurl  >&5
> >> >> >> >  /usr/bin/ld: cannot find -lhdf5
> >> >> >> >  collect2: ld returned 1 exit status
> >> >> >> >
> >> >> >> >Different shells have different syntax for exporting environment
> >> >> >> >variables, but
> >> >> >> >I think you only need to use
> >> >> >> >
> >> >> >> >  export CPPFLAGS="-I${H5DIR}/include
> >> >> >> >-I/u/home/eylandej/zlib-1.2.7/include
> >> >> >>-I/u/home/eylandej/szip-2.1/include"
> >> >> >> >
> >> >> >> >and similarly for LDFLAGS ...
> >> >> >> >
> >> >> >> >--Russ
> >> >> >> >
> >> >> >> >> On 7/30/13 2:43 PM, "Unidata netCDF Support"
> >> >> >> >> <address@hidden> wrote:
> >> >> >> >>
> >> >> >> >> >> Ok.  Thanks so far. I am now transitioning to go with your
> >> >> >> >>suggestion of
> >> >> >> >> >> compiling netcdf 4.3.0 first then compiling NetCDF 4.2
> >>fortran.
> >> >> >> >> >>
> >> >> >> >> >> However...trying to compile NetCDF4.3.0 I get the exact same
> >> >> >>error as
> >> >> >> >> >>when
> >> >> >> >> >> I was trying to compile netcdf 4.1.3.
> >> >> >> >> >>
> >> >> >> >> >> My configure script (sets up the enviro variables, etc)
> >> >> >> >> >>
> >> >> >> >> >> In directory /u/home/eylandej/netcdf-4.3.0
> >> >> >> >> >>
> >> >> >> >> >> #!/bin/bash
> >> >> >> >> >> # Proper header for a Bash script.
> >> >> >> >> >>
> >> >> >> >> >> set -x
> >> >> >> >> >
> >> >> >> >> >Are you running configure using sudo or as root?  There can be
> >> >> >> >> >problems with inheriting environment variables with sudo, due
> >>to
> >> >> >> >> >security policies.  We recommend running configure and make
> >>check
> >> >> >>as a
> >> >> >> >> >normal user, and only using sudo for "make install".
> >> >> >> >> >
> >> >> >> >> >If that's not it, can you attach or otherwise make available
> >>the
> >> >> >>whole
> >> >> >> >> >config.log file created by the configure script.  Also, note
> >>that
> >> >> >>the
> >> >> >> >> >"--with-zlib=" and "--with-szip=" option syntax hasn't been
> >> >> >>supported
> >> >> >> >> >by the netCDF configure script for a while.  Instead, all the
> >> >> >> >> >information about libraries and header file locations is
> >> >>supposed to
> >> >> >> >> >be conveyed in the LDFLAGS and CPPFLAGS, and LD_LIBRARY_PATH
> >> >> >> >>environment
> >> >> >> >> >variables.  The configure script just ignores flags it doesn't
> >> >> >> >> >process, such as --with-zlib= ...  It also ignores CXX, as the
> >> >> >> >> >netcdf-4.3.0 distribution is only for the C libraries and
> >> >>utilities.
> >> >> >> >> >
> >> >> >> >> >--Russ
> >> >> >> >> >
> >> >> >> >> >> export H5DIR=/u/home/eylandej/hdf5
> >> >> >> >> >> CC=/site/intel/impi/4.1.0.024/intel64/bin/mpicc
> >> >> >> >> >> CXX=/site/intel/impi/4.1.0.024/intel64/bin/mpicxx
> >> >> >> >> >> echo $LD_LIBRARY_PATH
> >> >> >> >> >> LD_LIBRARY_PATH=${H5DIR}/lib:$LD_LIBRARY_PATH
> >> >> >> >> >> CPPFLAGS="-I${H5DIR}/include
> >> >>-I/u/home/eylandej/zlib-1.2.7/include
> >> >> >> >> >> -I/u/home/eylandej/szip-2.1/include"
> >> >> >> >> >> LDFLAGS="-L${H5DIR}/lib -L/u/home/eylandej/zlib-1.2.7/lib
> >> >> >> >> >> -L/u/home/eylandej/szip-2.1/lib"
> >> >> >> >> >> LIBS=-ldl
> >> >> >> >> >> ./configure --prefix=/u/home/eylandej/netcdf-4.3.0
> >> >> >> >> >> --with-zlib=/u/home/eylandej/zlib-1.2.7
> >> >> >> >> >> --with-szip=/u/home/eylandej/szip-2.1 \
> >> >> >> >> >> --enable-parallel-tests --disable-shared
> >> >> >> >> >>
> >> >> >> >> >> exit
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> Here is the output of the ./configure script:
> >> >> >> >> >>
> >> >> >> >> >> checking for ssize_t... yes
> >> >> >> >> >> checking for ptrdiff_t... yes
> >> >> >> >> >> checking for uchar... no
> >> >> >> >> >> checking for longlong... no
> >> >> >> >> >> checking whether char is unsigned... no
> >> >> >> >> >> checking whether byte ordering is bigendian... no
> >> >> >> >> >> checking size of short... 2
> >> >> >> >> >> checking size of int... 4
> >> >> >> >> >> checking size of long... 8
> >> >> >> >> >> checking size of long long... 8
> >> >> >> >> >> checking size of float... 4
> >> >> >> >> >> checking size of double... 8
> >> >> >> >> >> checking size of off_t... 8
> >> >> >> >> >> checking size of size_t... 8
> >> >> >> >> >> checking for library containing deflate... none required
> >> >> >> >> >> checking for floor in -lm... yes
> >> >> >> >> >> checking for library containing H5Fflush... no
> >> >> >> >> >> configure: error: Can't find or link to the hdf5 library.
> >>Use
> >> >> >> >> >> --disable-netcdf-4, or see config.log for errors.
> >> >> >> >> >>
> >> >> >> >> >> I looked through the config.log file, but nothing seems
> >> >>obvious.
> >> >> >> >> >>
> >> >> >> >> >> I KNOW that H5Fflush is in the HDF libraries.  I ran a nm on
> >> >>the
> >> >> >>HDF5
> >> >> >> >> >> libs, and H5Fflush is in there.  I don't know why netcdf
> >>won't
> >> >>see
> >> >> >> >>that.
> >> >> >> >> >>
> >> >> >> >> >> John
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> ________________________________________
> >> >> >> >> >>
> >> >> >> >> >> John B. Eylander
> >> >> >> >> >> Cold Regions Research and Engineering Lab
> >> >> >> >> >> U.S. Army Engineer Research and Development Center
> >> >> >> >> >> 72 Lyme Road
> >> >> >> >> >> Hanover, NH  03755
> >> >> >> >> >>
> >> >> >> >> >> PH:  603-646-4188    BB:  603-359-9717
> >> >> >> >> >>
> >> >> >> >> >> Unclass:  address@hidden
> >> >> >> >> >> SIPR:  address@hidden
> >> >> >> >> >> JWICS:  address@hidden
> >> >> >> >> >> ________________________________________
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> On 7/30/13 1:28 PM, "Unidata netCDF Support"
> >> >> >> >> >> <address@hidden> wrote:
> >> >> >> >> >>
> >> >> >> >> >> >Hi John,
> >> >> >> >> >> >
> >> >> >> >> >> >We recommend this way to build with parallel I/O support:
> >> >> >> >> >> >
> >> >> >> >> >> >
> >>http://www.unidata.ucar.edu/netcdf/docs/build_parallel.html
> >> >> >> >> >> >
> >> >> >> >> >> >This works for netCDF version 4.3.0, but I don't know for
> >>sure
> >> >> >> >> >> >whether it works for the older 4.1.3 release.  Is there
> >>some
> >> >> >>reason
> >> >> >> >> >> >you have to use version 4.1.3?  I notice you're building a
> >> >> >>separate
> >> >> >> >> >> >netCDF-Fortran library anyway, which is what you would do
> >>if
> >> >>you
> >> >> >> >> >> >first build and install netCDF-C library version 4.3.0,
> >>then
> >> >> >>build
> >> >> >> >> >> >and install netCDF-Fortran version 4.2 according to these
> >> >> >> >>instructions:
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >>
> >>>>http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html
> >> >> >> >> >> >
> >> >> >> >> >> >paying attention to the parallel I/O instructions in step
> >>4,
> >> >> >>under
> >> >> >> >>the
> >> >> >> >> >> >"Using Static Libraries" section, if that's what you want
> >>to
> >> >> >> >>install.
> >> >> >> >> >> >
> >> >> >> >> >> >--Russ
> >> >> >> >> >> >
> >> >> >> >> >> >> Full Name: John Eylander
> >> >> >> >> >> >> Email Address: address@hidden
> >> >> >> >> >> >> Organization: Army Cold Regions Research & Eng. Lab
> >> >> >> >> >> >> Package Version: 4.1.3
> >> >> >> >> >> >> Operating System: RHEL 6.2 64-bit OS
> >> >> >> >> >> >> Hardware: 64-Bit
> >> >> >> >> >> >> Description of problem: I'm having extreme troubles
> >> >>compiling
> >> >> >> >>NetCDF
> >> >> >> >> >> >>4.1.3 (with parallel I/O support enabled).  I have HDF5
> >>1.8.6
> >> >> >> >> >>installed
> >> >> >> >> >> >>and successfully compiled and installed.  I have searched
> >>all
> >> >> >>the
> >> >> >> >> >>google
> >> >> >> >> >> >>sources I know to try to find the right flag or option to
> >> >>turn
> >> >> >> >>off/on
> >> >> >> >> >> >>with no luck.  Here is my NetCDF compile script:
> >> >> >> >> >> >>
> >> >> >> >> >> >> HDF_DIR=/u/home/eylandej/hdf5
> >> >> >> >> >> >> export CC=/site/intel/impi/4.1.0.024/intel64/bin/mpicc
> >> >> >> >> >> >> export F77=/site/intel/impi/4.1.0.024/intel64/bin/mpif77
> >> >> >> >> >> >> export CXX=/site/intel/impi/4.1.0.024/intel64/bin/mpicxx
> >> >> >> >> >> >> export FC=/site/intel/impi/4.1.0.024/intel64/bin/mpif90
> >> >> >> >> >> >> echo $LD_LIBRARY_PATH
> >> >> >> >> >> >> export
> >> >> >> >>
> >>>>LD_LIBRARY_PATH=/u/home/eylandej/hdf5-1.8.6/lib:$LD_LIBRARY_PATH
> >> >> >> >> >> >> export FCFLAGS="-I/u/home/eylandej/hdf5/include
> >> >> >> >> >> >>-I/u/home/eylandej/zlib-1.2.7/include
> >> >> >> >> >> >>-I/u/home/eylandej/szip-2.1/include -m64"
> >> >> >> >> >> >> export CPPFLAGS="-I/u/home/eylandej/hdf5/include
> >> >> >> >> >> >>-I/u/home/eylandej/zlib-1.2.7/include
> >> >> >> >> >> >>-I/u/home/eylandej/szip-2.1/include -DpgiFortran"
> >> >> >> >> >> >> export FFLAGS="-I/u/home/eylandej/hdf5/include
> >> >> >> >> >> >>-I/u/home/eylandej/zlib-1.2.7/include
> >> >> >> >> >> >>-I/u/home/eylandej/szip-2.1/include -m64"
> >> >> >> >> >> >> export LDFLAGS="-L${HDF_DIR}/lib
> >> >> >>-L/u/home/eylandej/zlib-1.2.7/lib
> >> >> >> >> >> >>-L/u/home/eylandej/szip-2.1/lib"
> >> >> >> >> >> >> LIBS="-ldl -lz -lm -lhdf5 -lhdf5_hl -lhdf5_fortran
> >> >> >> >>-lhdf5hl_fortran"
> >> >> >> >> >> >> ./configure --prefix=/u/home/eylandej/netcdf-4.1.3
> >> >> >> >> >> >>--with-zlib=/u/home/eylandej/zlib-1.2.7
> >> >> >> >> >> >>--with-szip=/u/home/eylandej/szip-2.1 \
> >> >> >> >> >> >> --enable-netcdf-4 --enable-pnetcdf4 --disable-dap
> >> >> >>--disable-shared
> >> >> >> >> >> >>--enable-static \
> >> >> >> >> >> >> --enable-separate-fortran  --enable-f90 --with-udunits
> >> >> >> >>--with-libcf
> >> >> >> >> >> >>--enable-large-file-tests --enable-parallel-tests
> >> >> >> >> >> >>
> >> >> >> >> >> >> This is the error I get during the "configure" stage of
> >> >> >>compiling
> >> >> >> >> >> >>NetCDF:
> >> >> >> >> >> >>
> >> >> >> >> >> >> checking for ptrdiff_t... yes
> >> >> >> >> >> >> checking for uchar... no
> >> >> >> >> >> >> checking for longlong... no
> >> >> >> >> >> >> checking whether char is unsigned... no
> >> >> >> >> >> >> checking whether byte ordering is bigendian... no
> >> >> >> >> >> >> checking size of short... 2
> >> >> >> >> >> >> checking size of int... 4
> >> >> >> >> >> >> checking size of long... 8
> >> >> >> >> >> >> checking size of float... 4
> >> >> >> >> >> >> checking size of double... 8
> >> >> >> >> >> >> checking size of off_t... 8
> >> >> >> >> >> >> checking size of size_t... 8
> >> >> >> >> >> >> checking for library containing deflate... none required
> >> >> >> >> >> >> checking for floor in -lm... yes
> >> >> >> >> >> >> checking for library containing H5Fflush... no
> >> >> >> >> >> >> configure: error: Can't find or link to the hdf5 library.
> >> >>Use
> >> >> >> >> >> >>--disable-netcdf-4, or see config.log for errors.
> >> >> >> >> >> >> + exit
> >> >> >> >> >> >>
> >> >> >> >> >> >> I need to compile NetCDF 4 with parallel I/O support for
> >>WRF
> >> >> >> >>version
> >> >> >> >> >> >>3.4.1. Any ideas on what I have done wrong with my
> >> >> >>flags/options?
> >> >> >> >> >>I've
> >> >> >> >> >> >>been struggling with this for a couple of weeks...
> >>Thanks in
> >> >> >> >>adance!
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >Russ Rew                                         UCAR
> >>Unidata
> >> >> >> >>Program
> >> >> >> >> >> >address@hidden
> >> >> >> >>http://www.unidata.ucar.edu
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> >Ticket Details
> >> >> >> >> >> >===================
> >> >> >> >> >> >Ticket ID: MLF-697840
> >> >> >> >> >> >Department: Support netCDF
> >> >> >> >> >> >Priority: Normal
> >> >> >> >> >> >Status: Closed
> >> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >
> >> >> >> >> >Russ Rew                                         UCAR Unidata
> >> >> >>Program
> >> >> >> >> >address@hidden
> >> >> >>http://www.unidata.ucar.edu
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >Ticket Details
> >> >> >> >> >===================
> >> >> >> >> >Ticket ID: MLF-697840
> >> >> >> >> >Department: Support netCDF
> >> >> >> >> >Priority: Normal
> >> >> >> >> >Status: Closed
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >Russ Rew                                         UCAR Unidata
> >> >>Program
> >> >> >> >address@hidden
> >> >>http://www.unidata.ucar.edu
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >Ticket Details
> >> >> >> >===================
> >> >> >> >Ticket ID: MLF-697840
> >> >> >> >Department: Support netCDF
> >> >> >> >Priority: Normal
> >> >> >> >Status: Closed
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >Russ Rew                                         UCAR Unidata
> >>Program
> >> >> >address@hidden
> >>http://www.unidata.ucar.edu
> >> >> >
> >> >> >
> >> >> >
> >> >> >Ticket Details
> >> >> >===================
> >> >> >Ticket ID: MLF-697840
> >> >> >Department: Support netCDF
> >> >> >Priority: Normal
> >> >> >Status: Closed
> >> >> >
> >> >>
> >> >>
> >> >Russ Rew                                         UCAR Unidata Program
> >> >address@hidden                      http://www.unidata.ucar.edu
> >> >
> >> >
> >> >
> >> >Ticket Details
> >> >===================
> >> >Ticket ID: MLF-697840
> >> >Department: Support netCDF
> >> >Priority: Normal
> >> >Status: Closed
> >> >
> >>
> >>
> >
> >Russ Rew                                         UCAR Unidata Program
> >address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> >Ticket Details
> >===================
> >Ticket ID: MLF-697840
> >Department: Support netCDF
> >Priority: Normal
> >Status: Closed
> >
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: MLF-697840
Department: Support netCDF
Priority: Normal
Status: Closed