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HiI had the same problem a few days ago. A quick fix was to simply search for the string "-l -l" in the libtool file generated after running ./configure, and remove it. After saving the file, I was able to proceed with make and install.
Regards, Even Haug On 11/07/2011 12:00 PM, Traian Popeea wrote:
Hello, I have been trying for several days to compile the netcdf-4 library with parallel support through hdf5 and mpich2. I do not have root credentials on the system where I must install the library. I am using mpich2-1.4.1p1, zlib-1.2.5, hdf5-1.8.7 and netcdf-4.1.3 and I require both C and Fortran for netcdf. Mpich2, zlib and hdf5 pass make check and install properly. However, netcdf-4 fails at make with a libtool error, where an extra "-l" appears "out of the blue". The following are the configure scripts that I am using, and the error that I am receiving. I sincerely have no idea why this isn't working and any help is most welcome. Sincerely, Traian Popeea PATH: [traian.popeea@fep-53-1 ~]$ echo $PATH /opt/gnu-gcc/gcc-4.6.0/bin:/opt/tools/qt/qt4.7/bin:/opt/tools/qt/pyqt4.8/bin:/bin:/srv/ncit-cluster/scripts:/usr/kerberos/bin:/opt/n1sge6/sge-6.2u5/bin/lx24-amd64:/usr/local/bin:/bin:/usr/bin:/export/home/ncit-cluster/stud/t/traian.popeea/bin LD_LIBRARY_PATH [traian.popeea@fep-53-1 ~]$ echo $LD_LIBRARY_PATH /opt/gnu-gcc/gcc-4.6.0/lib64:/opt/gnu-gcc/gcc-4.6.0/lib:/opt/libs/gmp-5.0.2/lib:/opt/libs/mpc-0.9/lib:/opt/libs/mpfr-3.0.1/lib:/opt/tools/qt/qt4.7/lib:/opt/n1sge6/sge-6.2u5/lib/lx24-amd64 mpich configure script [traian.popeea@fep-53-1 ~]$ cat hw1/mpich2-1.4.1p1/mpiv3.sh #!/bin/bash export FFLAGS=-fPIC export CFLAGS=-fPIC export FC=gfortran export F77=gfortran ./configure --prefix=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi --enable-fc --enable-f77 zlib configure script [traian.popeea@fep-53-1 ~]$ cat hw1/zlib-1.2.5/zlib.sh #!/bin/bash export CC=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpicc export F9X=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif90 export FC=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif77 export CFLAGS=-fPIC export FFLAGS=-fPIC export LDFLAGS=-L/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib export CPPFLAGS=-I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include export FCFLAGS=-I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include export PATH=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin:$PATH export LD_LIBRARY_PATH=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib:$LD_LIBRARY_PATH ./configure --prefix=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi hdf configure script [traian.popeea@fep-53-1 ~]$ cat hw1/hdf5-1.8.7/hdfv3.sh #!/bin/bash export CC=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpicc export F9X=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif90 export FC=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif77 export CFLAGS=-fPIC export FFLAGS=-fPIC export LDFLAGS=-L/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib export CPPFLAGS=-I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include export FCFLAGS=-I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include export PATH=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin:$PATH export LD_LIBRARY_PATH=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib:$LD_LIBRARY_PATH ./configure --prefix=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi --disable-cxx --enable-fortran --enable-parallel --with-zlib=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include,/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib netcdf configure script [traian.popeea@fep-53-1 ~]$ cat hw1/netcdf-4.1.3/netcdfv3.sh #!/bin/bash export CC=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpicc export F77=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif77 export FC=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif90 export LDFLAGS="-L/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib -lmpich" export CPPFLAGS=-I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include export CFLAGS=-fPIC export FCFLAGS=-I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include export FFLAGS=-fPIC export PATH=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin:$PATH export LD_LIBRARY_PATH=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib:$LD_LIBRARY_PATH ./configure --prefix=/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi --disable-cxx The error [traian.popeea@fep-53-1 netcdf-4.1.3]$ make <snip> make[3]: Entering directory `/export/home/ncit-cluster/stud/t/traian.popeea/hw1/netcdf-4.1.3/fortran' /bin/sh ../libtool --tag=FC --mode=link /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif90 -I/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/include -version-number 5:1:0 -L/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib -lmpich -o libnetcdff.la -rpath /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib fort-attio.lo fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo fort-lib.lo fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo fort-varaio.lo fort-varmio.lo fort-varsio.lo fort-nc4.lo ../liblib/libnetcdf.la ../f90/libnetcdff90.la -lhdf5_hl -lhdf5 -lm -lcurl libtool: link: /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/bin/mpif90 -shared -fPIC .libs/fort-attio.o .libs/fort-control.o .libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o .libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o .libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o .libs/fort-nc4.o -Wl,--whole-archive ../f90/.libs/libnetcdff90.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/export/home/ncit-cluster/stud/t/traian.popeea/hw1/netcdf-4.1.3/liblib/.libs -Wl,-rpath -Wl,/opt/gnu-gcc/gcc-4.6.0/lib/../lib64 -Wl,-rpath -Wl,/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib -Wl,-rpath -Wl,/opt/gnu-gcc/gcc-4.6.0/lib/../lib64 -L/export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib ../liblib/.libs/libnetcdf.so /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib/libhdf5_hl.a /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib/libhdf5.a -lz -lcurl -l -L/opt/gnu-gcc/gcc-4.6.0/lib64/../lib64 -L/opt/gnu-gcc/gcc-4.6.0/lib/../lib64 -L/opt/gnu-gcc/gcc-4.6.0/lib/gcc/x86_64-unknown-linux-gnu/4.6.0 -L/opt/gnu-gcc/gcc-4.6.0/lib/gcc/x86_64-unknown-linux-gnu/4.6.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/gnu-gcc/gcc-4.6.0/lib64 -L/opt/gnu-gcc/gcc-4.6.0/lib -L/opt/libs/gmp-5.0.2/lib -L/opt/libs/mpc-0.9/lib -L/opt/libs/mpfr-3.0.1/lib -L/opt/libs/openmpi/openmpi-1.5.3_gcc-4.6.0/lib -L/opt/libs/openmpi/openmpi-1.5.3_gcc-4.6.0/lib/openmpi -L/opt/gnu-gcc/gcc-4.6.0/lib/gcc/x86_64-unknown-linux-gnu/4.6.0/../../.. -lmpichf90 -lmpich /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib/libopa.a /export/home/ncit-cluster/stud/t/traian.popeea/opt/netcdf-4_mpi/lib/libmpl.a -lrt -lpthread /opt/gnu-gcc/gcc-4.6.0/lib/../lib64/libgfortran.so /opt/gnu-gcc/gcc-4.6.0/lib/../lib64/libquadmath.so -lm -lc -lgcc_s -Wl,-soname -Wl,libnetcdff.so.5 -o .libs/libnetcdff.so.5.1.0 /usr/bin/ld: cannot find -l-L/opt/gnu-gcc/gcc-4.6.0/lib64/../lib64 collect2: ld returned 1 exit status make[3]: *** [libnetcdff.la] Error 1 make[3]: Leaving directory `/export/home/ncit-cluster/stud/t/traian.popeea/hw1/netcdf-4.1.3/fortran' make[2]: *** [all] Error 2 make[2]: Leaving directory `/export/home/ncit-cluster/stud/t/traian.popeea/hw1/netcdf-4.1.3/fortran' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/export/home/ncit-cluster/stud/t/traian.popeea/hw1/netcdf-4.1.3' make: *** [all] Error 2 [traian.popeea@fep-53-1 netcdf-4.1.3]$ _______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/
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