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[netCDF #XGO-377487]: problem building netcdf-4.3.3.1

Subject: [netCDF #XGO-377487]: problem building netcdf-4.3.3.1
Date: Tue, 23 Jun 2015 11:03:04 -0600
Jae-Min,

> Thank you for your guidance. I am still having trouble with the configure,
> and have attached the config.log.
> HDF5 is built as a static, and thus "setenv LDFLAG -L/..../"

It looks like mpi.h can't be found by the cpp preprocessor, but it's included
in H5public.h, which is included in hdf5.h. I suspect you need to specify the
C compiler as "mpicc" if you are going to support parallel I/O. To do this,
you need to set another environment variable, CC, to "mpicc".

Here's more details on building netCDF-C library for parallel I/O support:

  
http://www.unidata.ucar.edu/netcdf/docs/getting_and_building_netcdf.html#build_parallel

> 
> Extra librariese: -lsz -lz -ldl -lm
> 
> What could these mean?

They are for getting other libraries used by HDF5, for szip compression, zip 
deflation, 
dynamic loader library, and math library.  You shouldn't need to worry about 
those, as
the HDF5 library should know where to find them or what's needed from them is 
already
included in the HDF5 static library.

--Russ

> address@hidden> wrote:
> 
> > > Hello Russ,
> > >
> > > setenv fixed a problem I was stuck on for a while, but now it still can't
> > > find some pieces of hdf5. Are there other variables that needs to be
> > set? I
> > > have set:
> > >
> > > the LD_LIBRARY_PATH to the lib directory,
> > > PATH to bin directory,
> > > INCLUDE to include directory,
> > > CPPFLAGS to -I/.../include directory,
> > > and LDFLAGS -L/.../lib directlry...
> >
> > You don't need to set PATH or INCLUDE for building the netCDF-C library.
> > Again, you'll need to send us the new config.log file to determine the
> > cause of the problem, if configure exits with an error message. If the
> > configure script succeeds, you'll need to send us the output from make
> > or make check to determine what specific problem you're seeing.
> >
> > If you built the HDF5 library as a static library rather than a shared
> > library,
> > you may need to add additional libraries to LDFLAGS. For details about
> > this. See the build documentation:
> >
> >   http://www.unidata.ucar.edu/netcdf/docs/getting_and_building_netcdf.html
> >
> > and look at the lib/libhdf5.settings file where your HDF5 library was
> > installed
> > Check the line in that file labeled "Extra libraries:", which may provide
> > a clue
> > to what needs to be added for the linker to find whatever is still missing.
> >
> > --Russ
> >
> > > Do you know of any other variable that might need to be set?
> > > Thank you.
> > >
> > > Regards,
> > > Jae-Min
> > >
> > > On Mon, Jun 22, 2015 at 9:19 PM, Jae-Min Jo <address@hidden>
> > wrote:
> > >
> > > > Wow!! It did fix some of it!
> > > >
> > > > I had no idea that "set" rather than "setenv" could have caused the
> > > > problem!
> > > > Thank you so much!
> > > > I am still running into some problems right now, but I will work on it
> > > > some more and see if it works!
> > > > Thank you!
> > > >
> > > > Regards,
> > > > Jae-Min
> > > >
> > > > address@hidden> wrote:
> > > >
> > > >> Hi Jae-Min,
> > > >>
> > > >> > I just tried setting the variables with the quotation marks.
> > > >> >
> > > >> > set LDFLAGS="-L/lustre05/vol0/jojchi/Projects/REEMS/mpi/lib"
> > > >> > set CPPFLAGS="-I/lustre05/vol0/jojchi/Projects/REEMS/mpi/include"
> > > >> > set LD_LIBRARY_PATH="/lustre05/vol0/jojchi/Projects/REEMS/mpi/lib"
> > > >> >
> > > >> > rather than
> > > >> >
> > > >> > set LDFLAGS=-L/lustre05...
> > > >> >
> > > >> > I get the same error.
> > > >> >
> > > >> > I have attached the config.log!
> > > >>
> > > >> You have to use setenv instead of set if you are using csh, because
> > csh
> > > >> variables set with the
> > > >> setenv command are automatically exported to subshell, but csh
> > variables
> > > >> set to with set
> > > >> command are NOT automatically exported to subshell. The configure
> > script
> > > >> is run in a subshell.
> > > >>
> > > >> The building instructions specify that CPPFLAGS, LDFLAGS, and
> > > >> LD_LIBRARY_PATH are
> > > >> environment variables rather than merely shell variables:
> > > >>
> > > >>
> > > >>
> > http://www.unidata.ucar.edu/netcdf/docs/getting_and_building_netcdf.html
> > > >>
> > > >> Hope that helps ...
> > > >>
> > > >> --Russ
> > > >>
> > > >> > address@hidden> wrote:
> > > >> >
> > > >> > > Hello Jae-Min,
> > > >> > >
> > > >> > > I’m sorry; yes, when I say libhdf5 I mean hdf5.
> > > >> > >
> > > >> > > What happens if you try to run the following?
> > > >> > >
> > > >> > > $ LDFLAGS="-L/lustre05/vol0/jojchi/Projects/REEMS/mpi/lib"
> > > >> > > CPPFLAGS="-I/lustre05/vol0/jojchi/Projects/REEMS/mpi/include"
> > > >> > > ./configure
> > > >> > >
> > > >> > > If configure exits properly, what happens if you try the
> > following?
> > > >> > >
> > > >> > > $ LD_LIBRARY_PATH="/lustre05/vol0/jojchi/Projects/REEMS/mpi/lib"
> > make
> > > >> check
> > > >> > >
> > > >> > > If these work, great; if not, can you provide the config.log file
> > > >> generated
> > > >> > > when you run configure as above?
> > > >> > >
> > > >> > > Thanks!
> > > >> > >
> > > >> > > -Ward
> > > >> > >
> > > >> > > address@hidden> wrote:
> > > >> > >
> > > >> > > New Client Reply: problem building netcdf-4.3.3.1
> > > >> > > >
> > > >> > > > Hello,
> > > >> > > >
> > > >> > > > I do not have root or sudo access to this machine, and I set my
> > > >> variables
> > > >> > > > like this:
> > > >> > > >
> > > >> > > > set LDFLAGS=-L/lustre05/vol0/jojchi/Projects/REEMS/mpi/lib
> > > >> > > > set CPPFLAGS=-I/lustre05/vol0/jojchi/Projects/REEMS/mpi/include
> > > >> > > > (ran them in csh)
> > > >> > > >
> > > >> > > >
> > > >> > > > HDF5 is built in the /lustre05/vol0/jojchi/Projects/REEMS/mpi
> > > >> > > >
> > > >> > > > By libhdf5, do you mean the hdf5? or is that an additional
> > library
> > > >> that I
> > > >> > > > need to install?
> > > >> > > > Thank you.
> > > >> > > >
> > > >> > > > Regards,
> > > >> > > > Jae-Min
> > > >> > > >
> > > >> > > > address@hidden> wrote:
> > > >> > > >
> > > >> > > > > Hello,
> > > >> > > > >
> > > >> > > > > Thank you for providing the config.log.  If you open it and
> > go to
> > > >> > > > > approximately line 3000, you can see that the development
> > > >> environment
> > > >> > > is
> > > >> > > > > not picking up LDFLAGS, CPPFLAGS, etc.  Is it possible you are
> > > >> running
> > > >> > > > this
> > > >> > > > > as `sudo`? If so, that could explain the behavior.
> > Otherwise, it
> > > >> could
> > > >> > > > be
> > > >> > > > > a matter of how the variables are being set.
> > > >> > > > >
> > > >> > > > > Where is libhdf5 installed on your system?
> > > >> > > > >
> > > >> > > > > Thank you,
> > > >> > > > >
> > > >> > > > > -Ward
> > > >> > > > >
> > > >> address@hidden>
> > > >> > > > > wrote:
> > > >> > > > >
> > > >> > > > > > New Client Reply: problem building netcdf-4.3.3.1
> > > >> > > > > >
> > > >> > > > > > Hello,
> > > >> > > > > >
> > > >> > > > > > Thank you for your reply.
> > > >> > > > > >
> > > >> > > > > > I have tried setting those variables to where hdf5's lib and
> > > >> include
> > > >> > > > were
> > > >> > > > > > located, but it still seems to not work.
> > > >> > > > > > I have attached the config.log
> > > >> > > > > > Thank you.
> > > >> > > > > >
> > > >> > > > > > Regards,
> > > >> > > > > > Jae-Min
> > > >> > > > > >
> > > >> > > > > > address@hidden <javascript:;>> wrote:
> > > >> > > > > >
> > > >> > > > > > > Hello,
> > > >> > > > > > >
> > > >> > > > > > > There are several reasons this may be happening.
> > Depending on
> > > >> > > where
> > > >> > > > > you
> > > >> > > > > > > installed libhdf5, `configure` may not be able to locate
> > it.
> > > >>  You
> > > >> > > > > would
> > > >> > > > > > > correct this using the LDFLAGS and CPPFLAGS environmental
> > > >> > > variables .
> > > >> > > > > For
> > > >> > > > > > > example:
> > > >> > > > > > >
> > > >> > > > > > >     $ LDFLAGS=-L/custom/install/lib
> > > >> > > > CPPFLAGS=-I/custom/install/include
> > > >> > > > > > > ./configure
> > > >> > > > > > >
> > > >> > > > > > > Note that, depending on your system, you may also need to
> > > >> modify
> > > >> > > your
> > > >> > > > > > > LD_LIBRARY_PATH at runtime, or else the program may fail
> > when
> > > >> it
> > > >> > > > cannot
> > > >> > > > > > > find the libraries.
> > > >> > > > > > >
> > > >> > > > > > > If this is not enough information, please let me know.
> > I'll
> > > >> need
> > > >> > > to
> > > >> > > > > know
> > > >> > > > > > > where you installed the hdf5 libraries, and if you can
> > > >> provide the
> > > >> > > > > > > config.log file generated when you configure netcdf, that
> > > >> would
> > > >> > > help
> > > >> > > > > too.
> > > >> > > > > > >
> > > >> > > > > > > Thank you,
> > > >> > > > > > >
> > > >> > > > > > > -Ward
> > > >> > > > > > >
> > > >> > > > > > > > Hello,
> > > >> > > > > > > >
> > > >> > > > > > > > I have already installed the hdf5-1.8.15-patch1 and the
> > > >> > > hdf-4-2.11
> > > >> > > > > > > > successfully.
> > > >> > > > > > > >
> > > >> > > > > > > > I am now trying to install netcdf-4.3.3.1, but the
> > > >> configuration
> > > >> > > > > fails
> > > >> > > > > > > > while checking for library containing H5Fflush. It
> > > >> complains that
> > > >> > > > it
> > > >> > > > > > > can't
> > > >> > > > > > > > find or link to the hdf5 library. The lines look like
> > this:
> > > >> > > > > > > >
> > > >> > > > > > > > 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 need to enable the netcdf-4 feature. How can I get
> > past
> > > >> this
> > > >> > > > > problem?
> > > >> > > > > > > > Thank you.
> > > >> > > > > > > >
> > > >> > > > > > > > Regards,
> > > >> > > > > > > > Jae-Min
> > > >> > > > > > > >
> > > >> > > > > > > >
> > > >> > > > > > >
> > > >> > > > > > >
> > > >> > > > > > > Ticket Details
> > > >> > > > > > > ===================
> > > >> > > > > > > Ticket ID: XGO-377487
> > > >> > > > > > > Department: Support netCDF
> > > >> > > > > > > Priority: Normal
> > > >> > > > > > > Status: Closed
> > > >> > > > > > >
> > > >> > > > > > >
> > > >> > > > > >
> > > >> > > > > >
> > > >> > > > > >
> > > >> > > > > > Ticket Details
> > > >> > > > > > ===================
> > > >> > > > > > Ticket ID: XGO-377487
> > > >> > > > > > Department: Support netCDF
> > > >> > > > > > Priority: Normal
> > > >> > > > > > Status: Open
> > > >> > > > > > Link:
> > > >> > > > > >
> > > >> > > > >
> > > >> > > >
> > > >> > >
> > > >>
> > https://andy.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=25797
> > > >> > > > >
> > > >> > > > >
> > > >> > > > >
> > > >> > > > > Ticket Details
> > > >> > > > > ===================
> > > >> > > > > Ticket ID: XGO-377487
> > > >> > > > > Department: Support netCDF
> > > >> > > > > Priority: Normal
> > > >> > > > > Status: Open
> > > >> > > > >
> > > >> > > > >
> > > >> > > >
> > > >> > > >
> > > >> > > >
> > > >> > > > Ticket Details
> > > >> > > > ===================
> > > >> > > > Ticket ID: XGO-377487
> > > >> > > > Department: Support netCDF
> > > >> > > > Priority: Normal
> > > >> > > > Status: Open
> > > >> > > > Link:
> > > >> > > >
> > > >> > >
> > > >>
> > https://andy.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=25797
> > > >> > > >
> > > >> > > >  ?
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > > Ticket Details
> > > >> > > ===================
> > > >> > > Ticket ID: XGO-377487
> > > >> > > Department: Support netCDF
> > > >> > > Priority: Normal
> > > >> > > Status: Open
> > > >> > >
> > > >> > >
> > > >> >
> > > >> >
> > > >> Russ Rew                                         UCAR Unidata Program
> > > >> address@hidden
> > http://www.unidata.ucar.edu
> > > >>
> > > >>
> > > >>
> > > >> Ticket Details
> > > >> ===================
> > > >> Ticket ID: XGO-377487
> > > >> Department: Support netCDF
> > > >> Priority: Normal
> > > >> Status: Closed
> > > >>
> > > >>
> > > >
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: XGO-377487
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: XGO-377487
Department: Support netCDF
Priority: Normal
Status: Closed
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