Greetings Christina, Your command: ifort -O2 -parallel -lnetcdf is missing a link flag that is needed for compiling FORTRAN programs. Try: ifort -02 -parallel -lnetcdff -lnetcdf Also, you may find the nc-config command to be helpful. For example, give the following command a try: nc-config --flibs Cheers! Sean > Hi, > > I am a brand new system administrator and have very little > experience with netcdf. I support a team of scientists on Mac systems > and Linux clusters. The system in question is a new system and netcdf > has not worked yet. I came into this situation after the software had > been loaded and parts of the system had been cloned using the Mac > migration tool. The original problem was a sigsegv from ifort > -parallel I have re-installed fortran and netcdf. I would appreciate > any advice, guidance, moral support, etc... > > This was the original problem > > [dhcp101:~/bering_bio/code_0608_bio_2_artificial2] hu% ./0609bio_2_a > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > This is what happened after I re-installed fortran > > > [dhcp101:~/bering_bio/code_0608_bio_2_artificial2] hu% make > > ifort -O2 -parallel -lnetcdf -o 0609bio_2_a ecomodel.o bcond.o > > bcdata.o cz.o dens.o datefun.o depth.o rundata.o oceaninit.o pom.o > > profu.o profv.o proft.o profq.o slpmin.o timefun.o topography.o > > vertvl.o ztosig.o out_nc_z_sigm.o pts.o updateocean.o initialize.o > > sigtosig.o sig2sig.o ncep.o updateice.o vapp.o vappw.o advect.o > > dfcond.o dflat.o dfsens.o diffus.o dlwave.o dsphum.o dvappi.o dvappw.o > > fcond.o felld.o fellip.o flat.o fluxi.o form.o frazil.o fsens.o > > grow2d.o heatflux.o iceadv.o iceinit.o lwave.o plast.o redist.o > > relaxi.o sphum.o stress.o tfreez.o tsflux.o uv_es.o bdadjust.o ninep.o > > callferret.o callferretw.o ncep0608.o bioinit.o environment.o > > biosource_3d.o transport_3d.o changestep.o adv_trans.o fun_assimz.o > > fun_deathp.o fun_deathz.o fun_excretz.o fun_growmp.o fun_respp.o > > fun_rlightp.o icealgae.o fun_rnutrip.o fun_uptakep.o pro_trans.o > > pro_trans2.o sunlight.o ncep.o pro_trans_detr.o > > ld: warning: in /usr/local/lib/libnetcdf.a, file was built for > > unsupported file format which is not the architecture being linked (i386) > > ld: warning: in > > /usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64//libgcc.a, file was > > built for unsupported file format which is not the architecture being > > linked (i386) > > Undefined symbols: > > "_nf_create_", referenced from: > > _out_nc_z_ in out_nc_z_sigm.o > > "_nf_put_att_text_", referenced from: > > _out_nc_z_ in out_nc_z_sigm.o > > _out_nc_z_ in out_nc_z_sigm.o > > _out_nc_z_ in out_nc_z_sigm.o > > "_nf_enddef_", referenced from: > > _out_nc_z_ in out_nc_z_sigm.o > > "_nf_put_var1_real_", referenced from: > > _out_nc_z_ in out_nc_z_sigm.o > > ld: symbol(s) not found > > make: *** [0609bio_2_a] Error 1 > I then re-installed netcdf (in /usr/local), actually I upgraded to > version 4.1.3, using these steps: > > > > cd netcdf-4.1.3 > > > > tcsh > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv CC gcc > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv CXX g++ > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv CFLAGS '-m64 -02' > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv CXXFLAGS 'm64 -02' > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv F77 ifort > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv F90 ifort > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% setenv FC ifort > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% sudo ./configure > > --prefix=/usr/local --disable-netcdf-4 > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% sudo make check install > > > > [dhcp117:/usr/local/netcdf-4.1.3] cis-admin% sudo make install > > > > Congratulations! You have successfully installed netCDF!| > > > > || > > > > | You can use script "nc-config" to find out the relevant| > > > > | compiler options to build your application. Enter| > > > > || > > > We then lost the references to i386, but are still having problems linking: > > ifort -O2 -parallel -lnetcdf -o 0609bio_2_a ecomodel.o bcond.o > > bcdata.o cz.o dens.o datefun.o depth.o rundata.o oceaninit.o pom.o > > profu.o profv.o proft.o profq.o slpmin.o timefun.o topography.o > > vertvl.o ztosig.o out_nc_z_sigm.o pts.o updateocean.o initialize.o > > sigtosig.o sig2sig.o ncep.o updateice.o vapp.o vappw.o advect.o > > dfcond.o dflat.o dfsens.o diffus.o dlwave.o dsphum.o dvappi.o dvappw.o > > fcond.o felld.o fellip.o flat.o fluxi.o form.o frazil.o fsens.o > > grow2d.o heatflux.o iceadv.o iceinit.o lwave.o plast.o redist.o > > relaxi.o sphum.o stress.o tfreez.o tsflux.o uv_es.o bdadjust.o ninep.o > > callferret.o callferretw.o ncep0608.o bioinit.o environment.o > > biosource_3d.o transport_3d.o changestep.o adv_trans.o fun_assimz.o > > fun_deathp.o fun_deathz.o fun_excretz.o fun_growmp.o fun_respp.o > > fun_rlightp.o icealgae.o fun_rnutrip.o fun_uptakep.o pro_trans.o > > pro_trans2.o sunlight.o ncep.o pro_trans_detr.o > > Undefined symbols: > > "_nf_create_", referenced from: > > _out_nc_z_ in out_nc_z_sigm.o > > "_nf_put_var1_real_", referenced from: > > _out_nc_z_ in out_nc_z_sigm.o > > ld: symbol(s) not found > > make: *** [0609bio_2_a] Error 1 > > [dhcp101:~/bering_bio/code_0608_bio_2_artificial2] hu% > > > > > Please excuse my lack of knowledge. I am trying to get up to speed as > quickly as possible. Any input would be appreciated. > > Thanks in advance, > > Christina > > > -- > Christina Salls > GLERL Computer Group > help desk (734)741-2127 > voicemail (734)741-2446 > > > Ticket Details =================== Ticket ID: KDF-410412 Department: Support netCDF Priority: Normal Status: Open
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