Karen, > I decided to switch to netcdf-fortran-4.2. I was able to get it to > compile as below. I was being overly cautious on specifying all the > compilers just to be safe. > > ./configure --enable-parallel-tests FCFLAGS=-fsecond-underscore > CPPFLAGS=-I/pic/people/d39974/exahdf/include > LDFLAGS=-L/pic/people/d39974/exahdf/lib LIBS="-lnetcdf -lhdf5_hl -lhdf5 > -lz -lm" --disable-shared --prefix=/pic/people/d39974/exahdf CC=mpicc > FC=mpif90 CXX=mpiCC F77=mpif77 > > This is essentially what I was trying to do with 4.4-beta. It seems to > work except that the FCFLAGS do not get passed on to the compilation of > test programs so I can't build them without hacking the makefile. At > least not when using the gnu compilers. Thanks for contributing this. The 4.4 approach using he Fortran-2003 C interoperability features is supposed to eliminate the need for options like FCFLAGS=-fsecond-underscore, but I'm not sure if the mpi compilers support that F2003 feature yet ... > Could you let me know if you get a revised 4.4 for me to try? Yes, when there's a new beta release, it will be announced on the netcdfgroup mailing list, and I'll try to include you also, in case you're not on that list. --Russ > On 11/7/12 8:07 PM, "Schuchardt, Karen L" <address@hidden> > wrote: > > >Hi Russ, > > > >hopper is kind of slow at the moment so I decided to move everything to a > >linux cluster. I haven't built there before. hdf189 checked out fine > >including parallel. So do netcdf-c. When I try to build fortran netcdf, > >I'm having trouble with configure again but this time du to > >ISO_C_BINDING. I only know a little about this from googling. I tried > >the --disable-f03 which didn't help with the configure error. So I added > >--disable-f03-compiler-check which got me through configure but then make > >failed. no real surprise. > > > >The basic underlying error is that iso_c_binding.mod can't be found. > >here is the configure error > >... > >checking whether mpif90 accepts -g... yes > >checking whether we are using the GNU Fortran 77 compiler... no > >checking whether mpif77aa accepts -g... no > >checking whether Fortran compiler is checked for ISO_C_BINDING support... > >yes > >checking for Fortran flag to compile .f90 files... none > >checking fortran 90 modules inclusion flag... -I > >checking if Fortran compiler supports Fortran 2003 ISO_C_BINDING... no > >configure: error: in `/pic/people/d39974/netcdf-fortran-4.4-beta1': > >configure: error: Can't use build F03 interfaces and cannot do compiler > >recovery > >See `config.log' for more details > > > >The details: > >configure:5158: checking if Fortran compiler supports Fortran 2003 > >ISO_C_BINDING > >configure:5166: mpif90 -c -g -O2 conftest.f90 > > In file conftest.f90:2 > > > >USE ISO_C_BINDING > > 1 > >Fatal Error: Can't open module file 'iso_c_binding.mod' for reading at > >(1): No such file or directory > >configure:5169: $? = 1 > >configure:5175: result: no > >configure:5184: error: in `/pic/people/d39974/netcdf-fortran-4.4-beta1': > >configure:5186: error: Can't use build F03 interfaces and cannot do > >compiler recovery > >See `config.log' for more details > > > > > > > >For my first attempt, I thought I'd use gnu. Perhaps that was my first > >mistake. Should this work? > >GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-51) > >Copyright (C) 2007 Free Software Foundation, Inc. > > > > > > > >./configure --disable-f03 --disable-f03-compiler-check > >--enable-parallel-tests CPPFLAGS=-I/pic/people/d39974/exahdf/include > >LDFLAGS=-L/pic/people/d39974/exahdf/lib LIBS="-lnetcdf -lhdf5_hl -lhdf5" > >--disable-shared --prefix=/pic/people/d39974/exahdf CC=mpicc FC=mpif90 > >F77=mpif77 > > > >For what its worth, I still don't see the symbols in the .mod file. > > > >address@hidden ~/netcdf-fortran-4.4-beta1]$ grep _mpiio fortran/* > >fortran/netcdf4.inc: integer nf_mpiio > >fortran/netcdf4.inc: parameter (nf_mpiio = 8192) > > > >Here is the make error if I use the f03 disable flags > > > >bin/sh ../libtool --tag=FC --mode=compile mpif90 -DHAVE_CONFIG_H -I. > >-I.. -I../libsrc -I/pic/people/d39974/exahdf/include -g -O2 -c -o > >module_netcdf_nc_data.lo module_netcdf_nc_data.F90 > >libtool: compile: mpif90 -DHAVE_CONFIG_H -I. -I.. -I../libsrc > >-I/pic/people/d39974/exahdf/include -g -O2 -c module_netcdf_nc_data.F90 > >-o module_netcdf_nc_data.o > > In file module_netcdf_nc_data.F90:30 > > > > USE ISO_C_BINDING ! All subsequent USE associations of netcdf_nc_data > > 1 > >Fatal Error: Can't open module file 'iso_c_binding.mod' for reading at > >(1): No such file or directory > >make: *** [module_netcdf_nc_data.lo] Error 1 > >make: Leaving directory > >`/pic/people/d39974/netcdf-fortran-4.4-beta1/fortran' > >make: *** [all] Error 2 > >make: Leaving directory > >`/pic/people/d39974/netcdf-fortran-4.4-beta1/fortran' > >make: *** [all-recursive] Error 1 > >make: Leaving directory `/pic/people/d39974/netcdf-fortran-4.4-beta1' > >make: *** [all] Error 2 > > > > > >I guess I should try 4.2 as well. > >________________________________________ > >From: Unidata netCDF Support address@hidden > >Sent: Wednesday, November 07, 2012 8:41 AM > >To: Schuchardt, Karen L > >Cc: address@hidden > >Subject: [netCDF #AZX-585461]: fortran configure problems > > > >Hi Karen, > > > >> Hi I am struggling to get the fortran build for netcdf4 going on hopper. > >> > >> I'm referring to the docs here > >> https://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-inst> > >> all.html > >> > >> The first issue I encountered is that the configure script did not > >> work correctly unless I separated> the LDFLAGS and LIBS or the > >> parallel io test. This is because th> e contest.c was specified > >> after LDFLAGS. You might want to upd> ate the documentation (which > >> specifies everything in LDFLAGS) > as it took me a bit of time to > >> discover this and track it down. > > > >I think I've corrected this as you suggest, but please let us know if > >this is not what you intended (the second step 3 in this document): > > > > > >http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.ht > >ml > > > >> The second problem I'm having is getting the required symbols > >>nf90_mpiio defined. > >> > >> Here is my configure > >> ./configure --enable-parallel-tests > >> CPPFLAGS="-I/scratch/scratchdirs/karen/hdf5-pre-notrunc/avoid_tr> > >> uncate/install/include -I/scratch/> > >> scratchdirs/karen/netcdf-220.127.116.11/install/include" LDFLAGS="-L/sc> > >> ratch/scratchdirs/karen/hdf5-pre-n> > >> otrunc/avoid_truncate/install/lib -L/scratch/scratchdirs/karen/n> > >> etcdf-18.104.22.168/install/lib" LIBS="-> lnetcdf -lhdf5_hl -lhdf5 -lz" > >> --disable-shared --prefix=`pwd` CC> =cc CXX=CC FC=ftn > >> > >> Configured like this, the nf90_mpiio variable can be found in > >>netcdf.inc but not in netcdf.mod. > >> > >> If I also set F90=ftn, then the symbol doesn't show up in either place . > >> > >> If I run ./nf-config âall, it says I don't have f90 in either case > >> but the examples/F90 programs bui> ld. > >> > >> Asside from these missing symbols, everything else is in order but > >> of course parallel IO aborts if I> don't specify one of the parallel > >>io flags. > >> > >> What am I overlooking? > > > >I don't think you're overlooking anything. This looks like a bug, due > >to inadequate testing of the --enable-parallel-tests and separate > >Fortran distribution. I've entered it into our Jira issue-tracking > >system, where you can monitor it or add comments on the issue: > > > > https://www.unidata.ucar.edu/jira/browse/NCFORTRAN-21 > > > >> Also I'm not sure how to get the parallel tests to build. Including > >> the flag didn't seem to do the trick. > > > >Did you build the C library according to these instructions, with > >--enable-parallel, and also use --enable-parallel when you build the > >HDF5 library? > > > > http://www.unidata.ucar.edu/software/netcdf/docs/build_parallel.html > > > >If you did that, I don't know what's wrong. We'll defintiely look > >into this when we get to that Jira issue ... > > > >--Russ > > > >Russ Rew UCAR Unidata Program > >address@hidden http://www.unidata.ucar.edu > > > > > > > >Ticket Details > >=================== > >Ticket ID: AZX-585461 > >Department: Support netCDF > >Priority: Normal > >Status: Closed > > Russ Rew UCAR Unidata Program address@hidden http://www.unidata.ucar.edu Ticket Details =================== Ticket ID: AZX-585461 Department: Support netCDF Priority: Normal Status: Closed
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