Re: [netcdfgroup] linking netcdf to serial code on yellowstone

• To: Ben Foster <foster@xxxxxxxx>
• Subject: Re: [netcdfgroup] linking netcdf to serial code on yellowstone
• From: Jim Edwards <jedwards@xxxxxxxx>
• Date: Tue, 15 Apr 2014 09:37:07 -0600

Hi Ben,

I think that either the ncl or esmf module are causing this - can you try
removing them one at a time to identify which one.   I think it's ncl, but
wouldn't be surprised if esmf does the same thing.


On Tue, Apr 15, 2014 at 9:30 AM, Ben Foster <foster@xxxxxxxx> wrote:

>
> Hi,
>
> I am having trouble linking netcdf to a *serial* post-processor
> since the yellowstone upgrade last week. The symptoms appear to
> be a conflict with libhdf5 and libnetcdf_c++4 leading to undefined
> references to gfortran functions. I am building with Intel/ifort.
> Below is a clip from the failed build. Note I am *not* specifying a
> -L path to netcdf, just link -lnetcdf, so am assuming it is linking
> default lib 4.3.0 according to my module settings - here's my module list:
>
> [foster@yslogin3 tgcmproc_f90]$ module list
> Currently Loaded Modules:
>   1) ncarenv/1.0        4) ncarcompilers/1.0    7) idl/8.2.3 10)
> esmf-6.3.0r-ncdfio-mpi-O
>   2) ncarbinlibs/1.1    5) netcdf/4.3.0         8) job_memusage/1.0
>   3) intel/12.1.5       6) ncl/6.2.0            9) esmf
>
> And here is module avail netcdf:
>
> [foster@yslogin3 tgcmproc_f90]$ module avail netcdf
>
> ----------------------------------- /glade/apps/opt/modulefiles/ys/cdep/intel
> ------------------------------------
>    netcdf-mpi/4.2            netcdf/4.2            pnetcdf/1.3.0
>    netcdf-mpi/4.3.0  (D)     netcdf/4.3.0  (D)     pnetcdf/1.4.1  (D)
>
>
> Thanks for any help on this. Here's the last few compilations, and
> the link error from the build:
>
>
> ifort -O2 -DLINUX   -c -o pltmaps.o pltmaps.F
> ifort -O2 -DLINUX   -c -o getflds.o getflds.F
> ifort -O2 -DLINUX   -c -o mksatut.o mksatut.F
> ifort -O2 -DLINUX   -c -o tgcmproc.o tgcmproc.F
> OBJS=allocf.o ampha.o conrec.o denconv.o doppler.o egadb.o epflux.o
> fields.o fixnamelist.o flist.o fset_known.o getfile.o getflds.o gethist.o
> getna.o getoh.o gettime.o gfac.o hdr3rec.o hist.o htint.o input.o mapeod.o
> mkauxflds.o mkcdf.o mkcon.o mkderived.o mkdrifts.o mkemiss.o mkhvols.o
> mklats.o mklons.o mkmaps.o mksatcdf.o mksatut.o mkutlat.o mkutlon.o
> mkutvert.o mkv5d.o mkxyloc.o mkxyut.o mkzmslt.o napart.o nchist_mod.o
> ohrad.o opnwrk.o plt.o pltmaps.o pltxy.o proc.o proclat.o proclat_old.o
> qadglb.o qbary.o rfft.o scrub_hvols.o setloctype.o setvert.o solred.o
> tgcmproc.o util.o wrlab6.o
> ifort -o tgcmproc_f90 allocf.o ampha.o conrec.o denconv.o doppler.o
> egadb.o epflux.o fields.o fixnamelist.o flist.o fset_known.o getfile.o
> getflds.o gethist.o getna.o getoh.o gettime.o gfac.o hdr3rec.o hist.o
> htint.o input.o mapeod.o mkauxflds.o mkcdf.o mkcon.o mkderived.o mkdrifts.o
> mkemiss.o mkhvols.o mklats.o mklons.o mkmaps.o mksatcdf.o mksatut.o
> mkutlat.o mkutlon.o mkutvert.o mkv5d.o mkxyloc.o mkxyut.o mkzmslt.o
> napart.o nchist_mod.o ohrad.o opnwrk.o plt.o pltmaps.o pltxy.o proc.o
> proclat.o proclat_old.o qadglb.o qbary.o rfft.o scrub_hvols.o setloctype.o
> setvert.o solred.o tgcmproc.o util.o wrlab6.o wrxdrc.o v5d.o binio.o  -lhlu
> -lncarg -lncarg_gks -lncarg_c -lX11 -lXext  -lcairo -lfontconfig -lpixman-1
> -lfreetype -lexpat -lpng -lz -lpthread -lbz2 -lXrender -lgfortran -lnetcdf
> ld: warning: libhdf5_hl.so.7, needed by /glade/apps/opt/netcdf/4.2/
> gnu/4.7.2/lib/libnetcdf_c++4.so.1, may conflict with libhdf5_hl.so.8
> ld: warning: libhdf5.so.7, needed by /glade/apps/opt/netcdf/4.2/
> gnu/4.7.2/lib/libnetcdf_c++4.so.1, may conflict with libhdf5.so.8
> /glade/apps/opt/ncl/6.2.0/gnu/4.7.2/lib/libhlu.a(ERRORF.o): In function
> `nhlpfprnmes_':
> ERRORF.f:(.text+0x61): undefined reference to
> `_gfortran_transfer_character_write'
> ERRORF.f:(.text+0xee): undefined reference to
> `_gfortran_transfer_character_write'
> /glade/apps/opt/ncl/6.2.0/gnu/4.7.2/lib/libhlu.a(CnTriMeshRenderer.o): In
> function `RasterFillRender._omp_fn.1':
> CnTriMeshRenderer.c:(.text+0x30e2): undefined reference to
> `omp_get_num_threads'
> CnTriMeshRenderer.c:(.text+0x3102): undefined reference to
> `omp_get_thread_num'
> CnTriMeshRenderer.c:(.text+0x3208): undefined reference to `GOMP_barrier'
> CnTriMeshRenderer.c:(.text+0x3211): undefined reference to `GOMP_barrier'
> /glade/apps/opt/ncl/6.2.0/gnu/4.7.2/lib/libhlu.a(CnTriMeshRenderer.o): In
> function `BuildDelaunayMesh._omp_fn.0':
> CnTriMeshRenderer.c:(.text+0x3247): undefined reference to
> `omp_get_thread_num'
> CnTriMeshRenderer.c:(.text+0x3250): undefined reference to
> `omp_get_num_threads'
> CnTriMeshRenderer.c:(.text+0x326c): undefined reference to `GOMP_barrier'
> CnTriMeshRenderer.c:(.text+0x3975): undefined reference to `GOMP_barrier'
> /glade/apps/opt/ncl/6.2.0/gnu/4.7.2/lib/libhlu.a(CnTriMeshRenderer.o): In
> function `InitMesh':
> CnTriMeshRenderer.c:(.text+0x428e): undefined reference to
> `GOMP_parallel_start'
> CnTriMeshRenderer.c:(.text+0x42a0): undefined reference to
> `GOMP_parallel_end'
> /glade/apps/opt/ncl/6.2.0/gnu/4.7.2/lib/libhlu.a(CnTriMeshRenderer.o): In
> function `CnTriMeshRender':
> CnTriMeshRenderer.c:(.text+0xabba): undefined reference to
> `GOMP_parallel_start'
> CnTriMeshRenderer.c:(.text+0xabcc): undefined reference to
> `GOMP_parallel_end'
> /glade/apps/opt/ncl/6.2.0/gnu/4.7.2/lib/libncarg.a(cpgiws.o): In function
> `cpgiws_':
> cpgiws.f:(.text+0x153): undefined reference to `_gfortran_transfer_integer_
> write'
> cpgiws.f:(.text+0x167): undefined reference to `_gfortran_transfer_integer_
> write'
>
>
> --Ben
>
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• Follow-Ups:
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    • From: Mary Haley

• References:
  • [netcdfgroup] linking netcdf to serial code on yellowstone
    • From: Ben Foster