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[netCDF #HUH-505770]: Problem installing netCDF-c library

The reason is is still failing is that it is still not getting the proper -L 
and -I flags. The compile test still reads:
  configure:16955: gcc -o conftest    conftest.c -lm -lz  >&5
So I am baffled.

One side comment. It is not a good idea to build in /usr/local
(e.g. /usr/local/netcdf-4.6.1). I think it should work,
so this probably not the problem. Still, you might as an
experiment try to build netcdf in, say you home directory
instead of in /usr/local, just to make sure.

> 
> I followed your suggestion as follows:
> 
> gss@gsslap2:~$ export CPPFLAGS="-I/usr/local/szip/include 
> -I/usr/local/hdf5/include"
> gss@gsslap2:~$ export LDFLAGS="-L/usr/local/szip/lib -L/usr/local/hdf5/lib"
> gss@gsslap2:~$ cd /usr/local
> gss@gsslap2:/usr/local$ cd netcdf-4.6.1/
> gss@gsslap2:/usr/local/netcdf-4.6.1$ printenv CPPFLAGS
> -I/usr/local/szip/include -I/usr/local/hdf5/include
> gss@gsslap2:/usr/local/netcdf-4.6.1$ printenv LDFLAGS
> -L/usr/local/szip/lib -L/usr/local/hdf5/lib
> 
> Then the ./configure etc.
> 
> Then the same result. New config.log in attachment.
> 
> Thanks a lot for your answer.
> Best wishes,
> Gabriela Sousa Santos
> 
> 
> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden]
> Sent: 06 July 2018 20:11
> To: Gabriela Sousa Santos <address@hidden>
> Cc: address@hidden
> Subject: [netCDF #HUH-505770]: Problem installing netCDF-c library
> 
> I looked at the config.log you sent.
> The problem is in these lines:
> > configure:16924: checking for library containing H5Fflush
> > configure:16955: gcc -o conftest    conftest.c -lm -lz  >&5
> > /tmp/ccT4Rx2z.o: In function `main':
> > conftest.c:(.text+0xa): undefined reference to `H5Fflush'
> 
> For some reason, the gcc command is not using the values of CPPFLAGS and 
> LDFLAGS so it is not finding hdf5.
> We need to find out why. Let me suggest the following to start.
> 1. Just before you do the ./configure command, do these commands.
> printenv CPPFLAGS
> printenv LDFLAGS
> 2. then execute your ./configure command.
> 
> This way we can be sure that at the point that you execute ./configure your 
> CPPFLAGS and LDFLAGS are correct.
> 
> 
> >
> > I hope you can help me.
> >
> > I am working in a Ubuntu linux 64 bit laptop and my end point is to install 
> > netCDF to work with fortran.
> >
> > At the point of my problem I had installed successfully in my /usr/local/:
> > zlib-1.2.11
> > szip-2.1
> > hdf5-1.10.1
> >
> > I was on the way of installing netcdf-4.6.1 when at configure I got the 
> > following on the terminal:
> > >checking for library containing H5Flush ... no
> > >configure: error: Can't find or link to the hdf5 library.
> >
> > The config.log is in attachment.
> >
> > The commands I used in /usr/local/netcdf-4.6.1 were
> > >export CPPFLAGS="-I/usr/local/szip/include -I/usr/local/hdf5/include"
> > >export LDFLAGS="-L/usr/local/szip/lib -L/usr/local/hdf5/lib"
> > > ./configure --prefix=/usr/local/netcdf4 --enable-netcdf-4
> > >--enable-shared -disable-dap
> >
> > While trying to solve the problem I inserted those above exports in my
> > .bashrc Then also:
> > export LD_LIBRARY_PATH="/usr/local/lib:/usr/local/hdf5/lib$LD_LIBRARY_PATH"
> > When I echo $CPPFLAGS and $LDFLAGS and $LD_LIBRARY_PATH it gives the 
> > expected answer.
> >
> > I looked for libdll libraries:
> > locate libdl
> > /lib/x86_64-linux-gnu/libdl-2.23.so<https://hes32-ctp.trendmicro.com:4
> > 43/wis/clicktime/v1/query?url=http%3a%2f%2flibdl%2d2.23.so&umid=aa8758
> > 65-e83d-4ad9-8791-e80d6006373e&auth=e546e52f10731554f25104dd08f6a3f4f6
> > ef6894-48b8dffb4e38e5b821497603a696bb70cdce557c>
> > /lib/x86_64-linux-gnu/libdl.so.2
> > /usr/lib/debug/lib/x86_64-linux-gnu/libdl-2.23.so<https://hes32-ctp.tr
> > endmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2flibdl%2d2.23.
> > so&umid=aa875865-e83d-4ad9-8791-e80d6006373e&auth=e546e52f10731554f251
> > 04dd08f6a3f4f6ef6894-48b8dffb4e38e5b821497603a696bb70cdce557c>
> > /usr/lib/libreoffice/program/libdlgprovlo.so
> > /usr/lib/x86_64-linux-gnu/libdl.a
> > /usr/lib/x86_64-linux-gnu/libdl.so
> >
> > I looked if H5Fflush is defined:
> > gss@gsslap2:/usr/local/hdf5/lib$ nm libhdf5.so |fgrep H5Fflush
> > 00000000000e9b50 T H5Fflush
> >
> >
> > So now I am without direction. Could you please help me?
> > Best wishes,
> >
> > Gabriela Sousa Santos
> >
> > Department of Urban Environment and Industry
> >
> > ________________________________
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> >
> >
> >
> > P Please consider the environment before printing this email and
> > attachments
> >
> >
> 
> =Dennis Heimbigner
> Unidata
> 
> 
> Ticket Details
> ===================
> Ticket ID: HUH-505770
> Department: Support netCDF
> Priority: Normal
> Status: Open
> ===================
> NOTE: All email exchanges with Unidata User Support are recorded in the 
> Unidata inquiry tracking system and then made publicly available through the 
> web.  If you do not want to have your interactions made available in this 
> way, you must let us know in each email you send to us.
> 
> 
> P Please consider the environment before printing this email and attachments
> 

=Dennis Heimbigner
  Unidata


Ticket Details
===================
Ticket ID: HUH-505770
Department: Support netCDF
Priority: Normal
Status: Closed
===================
NOTE: All email exchanges with Unidata User Support are recorded in the Unidata 
inquiry tracking system and then made publicly available through the web.  If 
you do not want to have your interactions made available in this way, you must 
let us know in each email you send to us.