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cdo-1.8.0 netcdf configure error

Added by namgu yeo over 8 years ago

To configure,

./configure --with-netcdf=/usr/local/netcdf/363_pgi128 -prefix /home/yeong

but following error occured.

checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking for library containing nc_open... no
configure: error: Could not link to NetCDF library

I attached config.log
please help me ..

config.log (18.7 KB) config.log

Replies (4)

RE: cdo-1.8.0 netcdf configure error - Added by Ralf Mueller over 8 years ago

I'm not sure, this is the right config.log file. the stdout of the configure run does not fit to it. Essentially there is not netcdf-test performed in the config.log

RE: cdo-1.8.0 netcdf configure error - Added by namgu yeo over 8 years ago

I updated config.log file..
please recheck the error.

RE: cdo-1.8.0 netcdf configure error - Added by Ralf Mueller over 8 years ago

here is the interesting part

configure:19035: gcc -std=gnu99 -o conftest -g -O2 -fopenmp  -I/usr/local/netcdf/363_pgi128/include  -L/usr/local/netcdf/363_pgi128/lib  conftest.c -lnetcdf   -lm  >&5
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o): In function `nc_put_vara_text':
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5056: undefined reference to `__builtin_alloca'
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5056: undefined reference to `__builtin_alloca'
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o): In function `nc_put_vara_uchar':
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5163: undefined reference to `__builtin_alloca'
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5163: undefined reference to `__builtin_alloca'
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o): In function `nc_put_vara_schar':
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5269: undefined reference to `__builtin_alloca'
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o):/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5269: more undefined references to `__builtin_alloca' follow
collect2: ld returned 1 exit status

although your netcdf installation may be under /usr/local/netcdf/363_pgi128/ it seems to be build somewhere under /etc/.setup. do you build software as root?

I cannot recommend using such an old netcdf installation. if you insist to do so, use a dynamic version. AFAIK __builtin_alloca should have something to do with gcc, which brings to my last point: you use gcc-4.4.7. it was releases 4.5 years ago, so please update or use a different vendor with a newer release. It's not possible to maintain CDO wrt. such old environments. same is true for netcdf-3.6.3 from June 2008.

if updating is not possible, then conda might a way to go: see Anaconda.

hth
ralf

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