[netCDF #PDX-714093]: netcdf

Unfortunately I think so too. You could always try a different compiler, but I 
assume you are using the Lahey compiler for a reason.

Best of luck!

Sean

PS: If you get this resolved through Lahey, would you mind sending a message 
letting me know what was going on here?


> I downloaded the patch and got the same errors, I may have to contact lahey 
> with this issue...
> 
> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden]
> Sent: Wednesday, July 06, 2011 12:13 PM
> To: address@hidden
> Cc: address@hidden
> Subject: [netCDF #PDX-714093]: netcdf
> 
> The reason I ask is that there has been a few patch updates to lf95, and one 
> of them was supposed to address this particular issue. If you have not 
> patched your install, check out:
> 
> http://www.lahey.com/lf9562proupdt.htm
> 
> and snag the 6.20e update. Once you have applied that patched, give the 
> configure, install, yada yada, another go and let's see what happens.
> 
> Cheers!
> 
> Sean
> 
> > Which version of lf95 are you running?
> >
> > > Re-installed the nefcdf with the CPPFLAGS=-pgiFortran ./configure 
> > > --prefix=/usr/local/net_cdf --disable-dap
> > >
> > > Ran the script and received the same 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
> > > 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'
> > >
> > > Doesn't seem to like lf95.
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: Unidata netCDF Support [mailto:address@hidden]
> > > Sent: Wednesday, July 06, 2011 11:04 AM
> > > To: address@hidden
> > > Cc: address@hidden
> > > Subject: [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
> > >
> > >
> > >
> >
> 
> 
> 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