[netCDF #PDX-714093]: netcdf

From what I can gather this is an issue with If95. When you run the configure 
script, try to add the following:

LIBS=-lfst ./configure .....(whatever options you specified)

Some compilers seems to need to load extra libraries to find things like 
__divdi3 (no idea why).

Make sure to to do `make distclean` before you reconfigure and rebuild / 
install netCDF.

Let me know how this turns out,

Sean

> It seems as if the install went well. However, I think the following error 
> maybe related to gcc, would this be correct?
> 
> -bash-3.2# ./fvcom.bathy.n.sh.lev
> + ulimit -s unlimited
> + lf95 ../interp_bathy_topo.f90 -o interp_fill 
> -L/usr/lib/gcc/i386-redhat-linux/4.1.1 -lgcc -L/usr/X11R6/lib/ -lX11 
> -I/usr/local/net_cdf/include -L/usr/local/net_cdf/lib -lnetcdf
> Encountered 0 errors, 0 warnings in file ../interp_bathy_topo.f90.
> /usr/local/net_cdf/lib/libnetcdf.a(nc.o): In function `NC_begins':
> /opt/netcdf-4.1.1/libsrc/nc.c:246: undefined reference to `__divdi3'
> /opt/netcdf-4.1.1/libsrc/nc.c:250: undefined reference to `__divdi3'
> /opt/netcdf-4.1.1/libsrc/nc.c:253: undefined reference to `__divdi3'
> /opt/netcdf-4.1.1/libsrc/nc.c:284: undefined reference to `__divdi3'
> /opt/netcdf-4.1.1/libsrc/nc.c:281: undefined reference to `__divdi3'
> /usr/local/net_cdf/lib/libnetcdf.a(nc.o):/opt/netcdf-4.1.1/libsrc/nc.c:287: 
> more undefined references to `__divdi3' follow
> /usr/local/net_cdf/lib/libnetcdf.a(posixio.o): In function `px_get':
> /opt/netcdf-4.1.1/libsrc/posixio.c:425: undefined reference to `__moddi3'
> 
> 
> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden]
> Sent: Tuesday, July 05, 2011 2:52 PM
> To: address@hidden
> Cc: address@hidden
> Subject: [netCDF #PDX-714093]: netcdf
> 
> Greetings Carl,
> 
> The way you are setting up your environmental variables is not quite 
> achieving the goal that you want. The output from configure shows that FC is 
> set to '' (the configure scripts picks up ifort as your fortran compiler, 
> which appears to be located at /opt/intel/fc/9.0/bin/ifort - this 
> auto-detection is built in for cases where FC is not defined).  I tried to 
> repeat what you listed as having in your bash_profile, and I too come up with 
> a blank FC environmental variable. Essentially you have set the shell 
> variable FC to $f95, which is not defined at the moment you set the variable, 
> and thus FC is set to ''. Once you export the shell variable, it becomes an 
> environmental variable (which was already set to '' when you declared the 
> shell variable). I would suggest two things:
> 
> 1) Change your bash_profile to export the variables individually and in order:
> 
> export 
> PATH=$PATH:$HOME/bin:$NCARG_ROOT:$GCC:$FC:/opt/jrel.6.0_21/bin:/usr/local/lib:/usr/lib:/usr/local/lf9562/bin:/opt/intel/fc/9.0/bin:
> export f95=/usr/local/lf9560/bin
> export FC=$f95
> export NCARG_ROOT=/usr/local
> export LD_LIBRARY_PATH=/usr/lib
> 
> (Note: most bash shells on Linux distros can do the export and declaration on 
> the same line - however, some will barf. If this does not work, try setting 
> the variable first, then exporting it on the line immediately following the 
> declaration.)
> 
> 2) Is the executable for if95 called bin? If not, make sure you use the 
> complete path to the compiler. For example, it could be something like:
> 
> f95=/usr/local/lf9560/bin/if95
> 
> 
> Let me know if rebuilding in the new environment helps.
> 
> Cheers!
> 
> Sean
> 
> 
> > Attached is the output from ./configure
> >
> > Carl.
> >
> > -----Original Message-----
> > From: Unidata netCDF Support [mailto:address@hidden]
> > Sent: Tuesday, July 05, 2011 1:20 PM
> > To: address@hidden
> > Cc: address@hidden
> > Subject: [netCDF #PDX-714093]: netcdf
> >
> > Greetings Carl,
> >
> > Would you mind sending me a log of the output from configure?
> >
> > Thanks!
> >
> > Sean
> >
> > > Sean,
> > >
> > > Here is the information requested... Linux leviathan.ncd-tcn.noaa.gov 
> > > 2.6.18-238.12.1.el5PAE #1 SMP Sat May 7 20:37:06 EDT 2011 i686 athlon 
> > > i386 GNU/Linux
> > >
> > >
> > > The compiler I would like to use is lf95
> > >
> > > PATH=$PATH:$HOME/bin:$NCARG_ROOT:$GCC:$FC:/opt/jrel.6.0_21/bin:/usr/local/lib:/usr/lib:/usr/local/lf9562/bin:/opt/intel/fc/9.0/bin:
> > > #NETCDF_F90=/disks/NASWORK/NETCDF_Fortran90
> > > #GCC=/usr/bin/gcc
> > > FC=$f95
> > > f95=/usr/local/lf9560/bin
> > > #F90=/opt/intel/Compiler/11.1/072/bin/ia32
> > > #f90=/opt/intel/Compiler/11.1/072/bin/ia32
> > > NCARG_ROOT=/usr/local
> > > LD_LIBRARY_PATH=/usr/lib
> > > #NCARG_ROOT=/disks/NASUSER/NCL_Binaries
> > >
> > > export PATH  NCARG_ROOT FC F90 GCC LD_LIBRARY_PATH
> > > unset USERNAME
> > >
> > > I reconfigured netcdf-4.1.1 into a different directory and attempted to 
> > > run a script and received the following error:
> > >
> > > -bash-3.2# ./fvcom.bathy.n.sh.lev
> > > + ulimit -s unlimited
> > > + lf95 ../interp_bathy_topo.f90 -o interp_fill 
> > > -L/usr/lib/gcc/i386-redhat-linux/4.1.1 -lgcc -L/usr/X11R6/lib/ -lX11 
> > > -I/usr/local/net_cdf/include -L/usr/local/net_cdf/lib -lnetcdf
> > > 1431-S: "../interp_bathy_topo.f90", line 729: Filename specified in 
> > > INCLUDE line not available.
> > > 2005-W: "../interp_bathy_topo.f90", line 741: 'NF_NOERR' is used but 
> > > never set.
> > > 1431-S: "../interp_bathy_topo.f90", line 850: Filename specified in 
> > > INCLUDE line not available.
> > > 2005-W: "../interp_bathy_topo.f90", line 863: 'NF_NOERR' is used but 
> > > never set.
> > > 1431-S: "../interp_bathy_topo.f90", line 1044: Filename specified in 
> > > INCLUDE line not available.
> > > 2005-W: "../interp_bathy_topo.f90", line 1045: 'NF_NOERR' is used but 
> > > never set.
> > > Encountered 3 errors, 3 warnings in file ../interp_bathy_topo.f90.
> > >
> > >
> > > The include directory does not have netcdf.inc
> > >
> > >
> > > /usr/local/net_cdf/include
> > > -bash-3.2# ll
> > > total 68
> > > -rw-r--r-- 1 root root 10123 Jul  5 11:44 ncvalues.h
> > > -rw-r--r-- 1 root root 18918 Jul  5 11:44 netcdfcpp.h
> > > -rw-r--r-- 1 root root 30285 Jul  5 11:43 netcdf.h
> > > -rw-r--r-- 1 root root    23 Jul  5 11:44 netcdf.hh
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: Unidata netCDF Support [mailto:address@hidden]
> > > Sent: Friday, July 01, 2011 1:01 PM
> > > To: address@hidden
> > > Cc: address@hidden
> > > Subject: [netCDF #PDX-714093]: netcdf
> > >
> > > Greetings!
> > >
> > > The configure script will try to use whatever compiler you have set in 
> > > the environmental variable FC. It looks like you have FC pointed to F95. 
> > > On my system, I have f95, but not F95 (case sensitive). Try `which F95` 
> > > at the command line and see what comes out. If it can't be found in your 
> > > path, then that is likely why configure is failing. Also, I see you have 
> > > a few compilers defined in your profile (gcc, intel, f95(?)) - which are 
> > > you wishing to use as your fortran compiler?
> > >
> > > If you wouldn't mind, please let me know which OS you are using (the 
> > > output of `uname -a` would be great), and a complete log of the output 
> > > from your configure script.
> > >
> > > Thanks!
> > >
> > > Sean Arms
> > >
> > > > When running the .configure command, I received the following error:
> > > > configure: error: Fortran could not compile .f90 files
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > -bash-3.2# make check
> > > >
> > > > make: *** No rule to make target `check'.  Stop.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Bash_profile looks as such:
> > > >
> > > >
> > > >
> > > > GCC=/usr/bin/gcc
> > > >
> > > > FC=F95
> > > >
> > > > F95=/opt/lf9560
> > > >
> > > > F90=/opt/intel/Compiler/11.1/072/bin/ia32
> > > >
> > > > #f90=/opt/intel/Compiler/11.1/072/bin/ia32
> > > >
> > > > NCARG_ROOT=/usr/local
> > > >
> > > > LD_LIBRARY_PATH=/usr/lib
> > > >
> > > > #NCARG_ROOT=/disks/NASUSER/NCL_Binaries
> > > >
> > > >
> > > >
> > > > export PATH  NCARG_ROOT FC F90 GCC LD_LIBRARY_PATH
> > > >
> > > > unset USERNAME
> > > >
> > > >
> > > >
> > >
> > >
> > > Ticket Details
> > > ===================
> > > Ticket ID: PDX-714093
> > > Department: Support netCDF
> > > Priority: Normal
> > > Status: Open
> > >
> > >
> > >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: PDX-714093
> > Department: Support netCDF
> > Priority: Normal
> > Status: Open
> >
> >
> >
> 
> 
> Ticket Details
> ===================
> Ticket ID: PDX-714093
> Department: Support netCDF
> Priority: Normal
> Status: Open
> 
> 
> 


Ticket Details
===================
Ticket ID: PDX-714093
Department: Support netCDF
Priority: Normal
Status: Open