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No problem. Congratulations on getting it up and running! Cheers, Sean > Hello again, > > It turns out that it's located in mpi_f77. When I add that flag it compiles > and even runs. > > I wonder whether this will cause problems in the future but it doesn't seem > to be a netcdf problem. > > I suppose that adding those libraries wasn't necessary. I just needed to add > this library. I've never seen that before. > > Thanks a lot for your help. > > Francis > > On 2011-07-28, at 4:04 PM, Unidata netCDF Support wrote: > > > 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 > > Ticket Details =================== Ticket ID: XPO-276613 Department: Support netCDF Priority: High Status: Open