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]$
