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[netCDF #PDX-714093]: netcdf

Greetings Carl,

I think I was barking up the wrong tree on this one. Let's forget about the 
FCFLAGS and LIB for a moment. Go ahead and do a `make distclean` and run your 
configure script again, but this time setting the CPPFLAGS variable:

CPPFLAGS=-pgiFortran ./configure ...

I think we were taking the route of brute force to fix the problems, when maybe 
all we needed to do it tell the pre-processor a little info.

Let me know if this works out. I do not think we have a machine here at Unidata 
with lf95 installed, or else I could work on it on this end too.

Cheers,

Sean

> I ran make distclean.....re-installed netcdf with the following command ... 
> FCFLAGS=-no-multibyte-chars LIB=-1fst ./configure --prefix=/usr/local/net_cdf 
> --disable-dap.....in this line, if I run this with LIBS=-1fst I get the same 
> error checking if Fortran "byte" is C "signed char"... configure: error: 
> Could not link conftestf.o and conftest.o, if I run it LIB=-1fst, it run 
> through the ./configure. After running make install, I get this at the tail 
> end of the results.
> 
> See any operating system documentation about shared libraries for
> more information, such as the ld(1) and ld.so(8) manual pages.
> ----------------------------------------------------------------------
> test -z "/usr/local/net_cdf/include" || /bin/mkdir -p 
> "/usr/local/net_cdf/include"
> /usr/bin/install -c -m 644 netcdfcpp.h ncvalues.h netcdf.hh 
> '/usr/local/net_cdf/include'
> make[2]: Leaving directory `/opt/netcdf-4.1.1/cxx'
> make[1]: Leaving directory `/opt/netcdf-4.1.1/cxx'
> Making install in nc_test
> make[1]: Entering directory `/opt/netcdf-4.1.1/nc_test'
> make[2]: Entering directory `/opt/netcdf-4.1.1/nc_test'
> make[2]: Nothing to be done for `install-exec-am'.
> make[2]: Nothing to be done for `install-data-am'.
> make[2]: Leaving directory `/opt/netcdf-4.1.1/nc_test'
> make[1]: Leaving directory `/opt/netcdf-4.1.1/nc_test'
> Making install in man4
> make[1]: Entering directory `/opt/netcdf-4.1.1/man4'
> TEXINPUTS=".:$TEXINPUTS" \
> MAKEINFO='/bin/sh /opt/netcdf-4.1.1/missing --run makeinfo   -I .' \
> texi2dvi -s  --pdf --batch netcdf.texi
> /bin/sh: texi2dvi: command not found
> make[1]: *** [netcdf.pdf] Error 127
> make[1]: Leaving directory `/opt/netcdf-4.1.1/man4'
> make: *** [install-recursive] Error 1
> 
> 
> I still get the error when running the script after make install:
> 
> -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 6:25 PM
> To: address@hidden
> Cc: address@hidden
> Subject: [netCDF #PDX-714093]: netcdf
> 
> Hi Carl,
> 
> Could you add -no-multibyte-chars to your FFLAGS when you run the configure 
> script?
> 
> FCFLAGS=-no-multibyte-chars LIBS=-lfst ./configure .....(whatever options you 
> specified)
> 
> Let's see if that helps,
> 
> Sean
> 
> > The configuration stops with this line... checking if Fortran "byte" is C 
> > "signed char"... configure: error: Could not link conftestf.o and conftest.o
> >
> > Carl.
> >
> > LIBS=-lfst ./configure --prefix=/usr/local/net_cdf
> >
> > -----Original Message-----
> > From: Unidata netCDF Support [mailto:address@hidden]
> > Sent: Tuesday, July 05, 2011 4:43 PM
> > To: address@hidden
> > Cc: address@hidden
> > Subject: [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
> >
> >
> >
> 
> 
> 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