[netCDF #KDF-410412]: failure message

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