[netCDF #XPO-276613]: compiling f90 and including netcdf

What is the output of

nm /usr/local/lib/libmpi.dylib | grep mpi_sendrecv

give  you?

> There's a lot there,
> 
> /usr/local/lib/libmpi.0.dylib         /usr/local/lib/libmpi_cxx.0.dylib       
> /usr/local/lib/libmpi_f77.0.dylib       /usr/local/lib/libmpi_f90.a
> /usr/local/lib/libmpi.dylib           /usr/local/lib/libmpi_cxx.dylib         
> /usr/local/lib/libmpi_f77.dylib         /usr/local/lib/libmpi_f90.la
> /usr/local/lib/libmpi.la              /usr/local/lib/libmpi_cxx.la            
> /usr/local/lib/libmpi_f77.la
> 
> I tried adding -lmpi_f90 into the path but with no success.
> 
> Any advice?
> 
> Francis
> 
> On 2011-07-28, at 3:38 PM, Unidata netCDF Support wrote:
> 
> > This is an error with the mpi lib. Do these symbols show up in your libmpi 
> > in /usr/local/lib? I don't know the full name of libmpi on your system, but 
> > you could do the following:
> >
> > nm /usr/local/lib/libmpi(.dylib .a .la - not sure what it looks like) | 
> > grep mpi_sendrecv
> >
> > What does that give you?
> >
> > Sean
> >
> >> I copied the files over and got a bunch of error messages because it 
> >> cannot find my mpif.h even thought it's in /usr/local/include, that is 
> >> indicated in the path.
> >>
> >> Undefined symbols:
> >> "_mpi_sendrecv_", referenced from:
> >> ___fourier_MOD_ffty in fourier.o
> >> ___fourier_MOD_iffty in fourier.o
> >> "_mpi_bcast_", referenced from:
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> _params_ in params.o
> >> "_mpi_comm_size_", referenced from:
> >> _MAIN__ in rsw_nl_forced.o
> >> "_mpi_allreduce_", referenced from:
> >> _rk4_time_step_ in rk4.o
> >> "_mpi_finalize_", referenced from:
> >> _MAIN__ in rsw_nl_forced.o
> >> "_mpi_barrier_", referenced from:
> >> _MAIN__ in rsw_nl_forced.o
> >> _save_ncdata_double_ in save_fields.o
> >> _save_ncdata_ in save_fields.o
> >> _checkpoint_ in save_fields.o
> >> _save_mean_state_ in save_fields.o
> >> _save_fields_ in save_fields.o
> >> _save_fields_ in save_fields.o
> >> _init_mean_ in init_u.o
> >> _init_u_ in init_u.o
> >> "_mpi_init_", referenced from:
> >> _MAIN__ in rsw_nl_forced.o
> >> "_mpi_gather_", referenced from:
> >> _save_ncdata_double_ in save_fields.o
> >> _save_ncdata_ in save_fields.o
> >> "_mpi_comm_rank_", referenced from:
> >> _MAIN__ in rsw_nl_forced.o
> >> "_mpi_reduce_", referenced from:
> >> _save_fields_ in save_fields.o
> >> ld: symbol(s) not found
> >> collect2: ld returned 1 exit status
> >> make: *** [rsw] Error 1
> >>
> >> On 2011-07-28, at 3:07 PM, Unidata netCDF Support wrote:
> >>
> >>> You can give it a try, although I am not sure why they didn't get 
> >>> installed in the first place. The output from `make check` shows that the 
> >>> tests passed just fine with the libnetcdff lib, so you should be in good 
> >>> shape to copy them to /usr/local/lib.
> >>>
> >>> Let me know how that goes,
> >>>
> >>> Sean
> >>>
> >>>> Yes.  Should I just copy them over manually?
> >>>>
> >>>> Francis
> >>>>
> >>>> On 2011-07-28, at 3:01 PM, Unidata netCDF Support wrote:
> >>>>
> >>>>> Interesting. What libnetcdf* files do you have in /usr/local/lib? Do 
> >>>>> you see libnetcdff within your netcdf build directory 
> >>>>> (<build-dir>/fortran/.libs/)?
> >>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> I decided to do the make install and it seemed to work.
> >>>>>>
> >>>>>> The serial code still works.  So I haven't lost that.
> >>>>>>
> >>>>>
> >>>>>
> >>>>>> My make file has the line that you suggested.  However, when I try and 
> >>>>>> make all I get that each file compiles ok (better than before) but it 
> >>>>>> cannot find -lnetcdff.  Indeed, it's not in my /usr/local/lib.
> >>>>>>
> >>>>>> ld: library not found for -lnetcdff
> >>>>>> collect2: ld returned 1 exit status
> >>>>>> make: *** [rsw] Error 1
> >>>>>>
> >>>>>> When I configured netcdfi I told it to use a fortran compiler and it 
> >>>>>> seems to know that.  Any ideas why it didn't build the library?
> >>>>>>
> >>>>>> Francis
> >>>>>>
> >>>>>> On 2011-07-28, at 2:19 PM, Unidata netCDF Support wrote:
> >>>>>>
> >>>>>>> Greetings Francis,
> >>>>>>>
> >>>>>>> I looked through your logs and everything looks ok. You could always 
> >>>>>>> do a `make clean` and start from the beginning, but this time set the 
> >>>>>>> --prefix=/where/ever/you/want when running netcdf config to install 
> >>>>>>> the libs in a different directory. Just be sure to update
> >>>>>>>
> >>>>>>> NETCDF = -L/usr/local/lib -lnetcdff -lnetcdf -L/sw/lib -lcurl
> >>>>>>>
> >>>>>>> to point to the custom install directory rather than /usr/local/lib.
> >>>>>>>
> >>>>>>> Let me know how it goes,
> >>>>>>>
> >>>>>>> Sean
> >>>>>>>
> >>>>>>>
> >>>>>>>> Hello Sean,
> >>>>>>>>
> >>>>>>>> I am a bit hesitate to make install the netcdf for fear that it 
> >>>>>>>> won't work serially anymore.  I thought I could compile some netcdf 
> >>>>>>>> code using these libraries but 1) I'm not sure where they are and 2) 
> >>>>>>>> because I'm using fftw3 that is in /usr/local/lib, there's the old 
> >>>>>>>> netcdf that is also there and I'm not sure how to tell it to use one 
> >>>>>>>> or the other.
> >>>>>>>>
> >>>>>>>> Any advice?
> >>>>>>>>
> >>>>>>>> Francis
> >>>>>>>>
> >>>>>>>> On 2011-07-27, at 2:41 PM, Unidata netCDF Support wrote:
> >>>>>>>>
> >>>>>>>>> Francis,
> >>>>>>>>>
> >>>>>>>>> Try re-running config, but add lt_cv_ld_force_load=no like this:
> >>>>>>>>>
> >>>>>>>>> lt_cv_ld_force_load=no ./configure <whatever options you added>
> >>>>>>>>>
> >>>>>>>>> To log make and make check, do the following:
> >>>>>>>>>
> >>>>>>>>> make >& make.out&
> >>>>>>>>>
> >>>>>>>>> Then, to watch things progress, you can do:
> >>>>>>>>>
> >>>>>>>>> tail -f make.out
> >>>>>>>>>
> >>>>>>>>> You can do the exact same thing for make check (just be sure to 
> >>>>>>>>> rename make.out to make_check.out or something like that).
> >>>>>>>>>
> >>>>>>>>> Make sure to do a `make clean` before trying the above steps.
> >>>>>>>>>
> >>>>>>>>> Cheers!
> >>>>>>>>>
> >>>>>>>>> Sean
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> Hello Sean,
> >>>>>>>>>>
> >>>>>>>>>> Here is a copy of my config.log.  I don't see where the make and 
> >>>>>>>>>> make check were stored.  If you tell me I'll send them.  
> >>>>>>>>>> Otherwise, I'll redo the make and make check and send you the 
> >>>>>>>>>> output.
> >>>>>>>>>>
> >>>>>>>>>> Thanks,
> >>>>>>>>>> Francis
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On 2011-07-27, at 1:15 PM, Unidata netCDF Support wrote:
> >>>>>>>>>>
> >>>>>>>>>>> Francis,
> >>>>>>>>>>>
> >>>>>>>>>>> Would you mind sending me the configure, make, and make check 
> >>>>>>>>>>> logs from your desktop build?
> >>>>>>>>>>>
> >>>>>>>>>>> Thanks!
> >>>>>>>>>>>
> >>>>>>>>>>> Sean
> >>>>>>>>>>>
> >>>>>>>>>>>> Hello Sean,
> >>>>>>>>>>>>
> >>>>>>>>>>>> Thanks for the advice.  I'm testing this out on a MacPro and  
> >>>>>>>>>>>> MacBook Pro.
> >>>>>>>>>>>>
> >>>>>>>>>>>> On my laptop it compiles fine, thanks!   The nc-config didn't 
> >>>>>>>>>>>> say that but now I know better.
> >>>>>>>>>>>>
> >>>>>>>>>>>> On my desktop it no longer complains about not finding 
> >>>>>>>>>>>> netcdf.mod (that's progress) but now it doesn't find netcdff.  
> >>>>>>>>>>>> When I look in usr/local/lib I see netcdf and netcdf_c++ but no 
> >>>>>>>>>>>> netcdff.  Maybe I needed to do something to include it when I 
> >>>>>>>>>>>> built netcdf 4.1.1?
> >>>>>>>>>>>>
> >>>>>>>>>>>> Cheers,
> >>>>>>>>>>>> Francis
> >>>>>>>>>>>>
> >>>>>>>>>>>> On 2011-07-27, at 11:48 AM, Unidata netCDF Support wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Greetings Francis!
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> You seem to be missing the netcdf fortran library (-lnetcdff) 
> >>>>>>>>>>>>> in your NETCDF variable. It should be something like:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> NETCDF = -L/usr/local/lib -lnetcdff -lnetcdf -L/sw/lib -lcurl
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> If you need to see what lib flags you should use, check out the 
> >>>>>>>>>>>>> program nc-config:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> nc-config --flibs
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> There are all kinds of goodies that can be found using 
> >>>>>>>>>>>>> nc-config...check out
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> nc-config --help
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> for more info.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Please let me know if adding -lnetcdff works for you.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Cheers!
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Sean
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> Hello,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Since my first email I've made some progress, but I'm still 
> >>>>>>>>>>>>>> having some difficulty.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Since last I wrote I have figured out that netcdf does seem to 
> >>>>>>>>>>>>>> be installed correctly because I can run some f90 programs 
> >>>>>>>>>>>>>> that call netcdf.  At least in serial.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> For my serial problem my makefile looks like
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> FC      = /sw/bin/gfortran
> >>>>>>>>>>>>>> FFLAGS  = -g -O2 -I/usr/local/include
> >>>>>>>>>>>>>> MATH    = -lm
> >>>>>>>>>>>>>> NETCDF  = -L/usr/local/lib -lnetcdf -L/sw/lib -lcurl
> >>>>>>>>>>>>>> FFT     = -L/usr/local/lib -lfftw3
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> all:rsw
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> %.o: %.f90
> >>>>>>>>>>>>>> $(FC) $(FFLAGS) -c $<
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> rsw: $(OBJ)
> >>>>>>>>>>>>>> $(FC) $(FFLAGS) -o rsw_nl.out $(OBJ) $(MATH) $(FFT) $(NETCDF)
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> My MPI version is very similar and looks like this,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> FC      = /usr/local/bin/mpif90
> >>>>>>>>>>>>>> FFLAGS  = -g -O2 -I/usr/local/include
> >>>>>>>>>>>>>> MATH    = -lm
> >>>>>>>>>>>>>> NETCDF  = -L/usr/local/lib -lnetcdf -L/sw/lib -lcurl
> >>>>>>>>>>>>>> FFT     = -L/usr/local/lib -lfftw3
> >>>>>>>>>>>>>> MPI     = -L/usr/local/lib -lmpi
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> all:rsw
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> %.o: %.f90
> >>>>>>>>>>>>>> $(FC) $(FFLAGS) $(NETCDF) -c $<
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> rsw: $(OBJ)
> >>>>>>>>>>>>>> $(FC) $(FFLAGS) -o rsw_nl.out $(OBJ) $(MATH) $(FFT) $(MPI) 
> >>>>>>>>>>>>>> $(NETCDF)
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Unfortunately in this case it cannot find netcdf.mod
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> /usr/local/bin/mpif90 -g -O2 -I/usr/local/include 
> >>>>>>>>>>>>>> -L/usr/local/lib -lnetcdf -L/sw/lib -lcurl -c save_fields.f90
> >>>>>>>>>>>>>> save_fields.f90:6.12:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> USE netcdf
> >>>>>>>>>>>>>> 1
> >>>>>>>>>>>>>> Fatal Error: Wrong module version '0' (expected '6') for file 
> >>>>>>>>>>>>>> 'netcdf.mod' opened at (1)
> >>>>>>>>>>>>>> make: *** [save_fields.o] Error 1
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> even though there is a local copy of it in the directory,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Do you have any ideas why I can use netcdf in serial but not 
> >>>>>>>>>>>>>> in parallel? I've tried restructuring my makefile but to no 
> >>>>>>>>>>>>>> avail.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Thanks,
> >>>>>>>>>>>>>> Francis
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> On 2011-07-20, at 10:54 AM, Unidata netCDF Support wrote:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Francis Poulin,
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Your Ticket has been received, and a Unidata staff member 
> >>>>>>>>>>>>>>> will review it and reply accordingly. Listed below are 
> >>>>>>>>>>>>>>> details of this new Ticket. Please make sure the Ticket ID 
> >>>>>>>>>>>>>>> remains in the Subject: line on all correspondence related to 
> >>>>>>>>>>>>>>> this Ticket.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Ticket ID: XPO-276613
> >>>>>>>>>>>>>>> Subject: compiling f90 and including netcdf
> >>>>>>>>>>>>>>> Department: Support netCDF
> >>>>>>>>>>>>>>> Priority: Normal
> >>>>>>>>>>>>>>> Status: Open
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> The NetCDF libraries are developed at the Unidata Program 
> >>>>>>>>>>>>>>> Center/UCAR,
> >>>>>>>>>>>>>>> in Boulder, Colorado; we are funded primarily by the U.S. 
> >>>>>>>>>>>>>>> National
> >>>>>>>>>>>>>>> Science Foundation.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> All support requests are handled by the development team; no
> >>>>>>>>>>>>>>> dedicated support staff are funded at this time. For this 
> >>>>>>>>>>>>>>> reason
> >>>>>>>>>>>>>>> we cannot guarantee response times, nor can we resolve every 
> >>>>>>>>>>>>>>> support
> >>>>>>>>>>>>>>> issue, although we do our best to respond within 72 hours.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> It is in the nature of support requests that the same 
> >>>>>>>>>>>>>>> question is
> >>>>>>>>>>>>>>> asked many times. We urge you to search the support archives 
> >>>>>>>>>>>>>>> for
> >>>>>>>>>>>>>>> material relating to your support inquiry:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> http://www.unidata.ucar.edu/search.jsp?support&netcdf
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> If you are having trouble building netCDF, please take a look 
> >>>>>>>>>>>>>>> at the
> >>>>>>>>>>>>>>> "Build Troubleshooter" section of the netCDF home page:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> http://www.unidata.ucar.edu/software/netcdf/
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Windows users should see the FAQ list:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#windows_netcdf4
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Complete documentation (including a tutorial, and sample 
> >>>>>>>>>>>>>>> programs in
> >>>>>>>>>>>>>>> C, Fortran, Java, and other programming languages) can be 
> >>>>>>>>>>>>>>> found on the
> >>>>>>>>>>>>>>> netCDF Documentation page:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> http://www.unidata.ucar.edu/software/netcdf/docs/
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> If you resolve your issue through one of these methods, 
> >>>>>>>>>>>>>>> please send a
> >>>>>>>>>>>>>>> reply to this email letting us know that you no longer require
> >>>>>>>>>>>>>>> assistance. This will help us spend more time on netCDF 
> >>>>>>>>>>>>>>> development.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Best regards,
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Unidata User Support
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Ticket Details
> >>>>>>>>>>>>> ===================
> >>>>>>>>>>>>> Ticket ID: XPO-276613
> >>>>>>>>>>>>> Department: Support netCDF
> >>>>>>>>>>>>> Priority: High
> >>>>>>>>>>>>> Status: Open
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> Ticket Details
> >>>>>>>>>>> ===================
> >>>>>>>>>>> Ticket ID: XPO-276613
> >>>>>>>>>>> Department: Support netCDF
> >>>>>>>>>>> Priority: High
> >>>>>>>>>>> Status: Open
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Ticket Details
> >>>>>>>>> ===================
> >>>>>>>>> Ticket ID: XPO-276613
> >>>>>>>>> Department: Support netCDF
> >>>>>>>>> Priority: High
> >>>>>>>>> Status: Open
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Ticket Details
> >>>>>>> ===================
> >>>>>>> Ticket ID: XPO-276613
> >>>>>>> Department: Support netCDF
> >>>>>>> Priority: High
> >>>>>>> Status: Open
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>> Ticket Details
> >>>>> ===================
> >>>>> Ticket ID: XPO-276613
> >>>>> Department: Support netCDF
> >>>>> Priority: High
> >>>>> Status: Open
> >>>>
> >>>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: XPO-276613
> >>> Department: Support netCDF
> >>> Priority: High
> >>> Status: Open
> >>
> >>
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: XPO-276613
> > Department: Support netCDF
> > Priority: High
> > Status: Open
> 
> 


Ticket Details
===================
Ticket ID: XPO-276613
Department: Support netCDF
Priority: High
Status: Open