Have you tried using the suggested -fPIC? I think it is enough to set also
CFLAGS=-fPIC among the whole lot of options you already use in netcdf's
./configure line.
From: Svancara, Randall
Sent: Sunday, July 24, 2011 8:31 PM
To: netcdfgroup@xxxxxxxxxxxxxxxx
Subject: [netcdfgroup] Problems compiling netcdf
Hi,
I am experiencing difficulty compiling netcdf. Here is how I have compiled the
software:
1. Compile zlib 1.2.5
1184 CC=gcc ./configure --prefix=/home/software/zlib-1.2.5_gcc
1185 make
1186 make install
2. Compile szip 2.1
1200 ./configure --prefix=/home/software/szip-2.1_gcc
1201 make
1203 make install
3. Compile HD5
1224 CC=/home/software/mpi/gcc/openmpi-1.4.3/bin/mpicc ./configure
--prefix=/home/software/hd5-1.8.7_gcc_openmpi --enable-parallel
--enable-production --with-szlib=/home/software/szip-2.1_gcc/lib
--with-zlib=/home/software/zlib-1.2.5_gcc --disable-shared
1225 make
1226 make install
3. Compile NetCDF
fc=mpif90 cxx=mpicxx CC=mpicc
CPPFLAGS="-I/home/software/hd5-1.8.7_gcc_openmpi/include
-I/home/software/szip-2.1_gcc/include -I/home/software/zlib-1.2.5_gcc/include"
LDFLAGS="-L/home/software/hd5-1.8.7_gcc_openmpi/lib
-L/home/software/szip-2.1_gcc -L/home/software/zlib-1.2.5_gcc" ./configure
--prefix=/home/software/netcdf-4.1.3
make
I receive the following error during the build:
Making all in liblib
make[2]: Entering directory
`/home/admins/rsvancara/SOFTWARE/NetCDF/netcdf-4.1.3/liblib'
/bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I..
-I../fortran -I../include -I../libsrc4
-I/home/software/hd5-1.8.7_gcc_openmpi/include
-I/home/software/szip-2.1_gcc/include -I/home/software/zlib-1.2.5_gcc/include
-g -O2 -MT libnetcdf_la-stub.lo -MD -MP -MF .deps/libnetcdf_la-stub.Tpo -c -o
libnetcdf_la-stub.lo `test -f 'stub.c' || echo './'`stub.c
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../include
-I../libsrc4 -I/home/software/hd5-1.8.7_gcc_openmpi/include
-I/home/software/szip-2.1_gcc/include -I/home/software/zlib-1.2.5_gcc/include
-g -O2 -MT libnetcdf_la-stub.lo -MD -MP -MF .deps/libnetcdf_la-stub.Tpo -c
stub.c -fPIC -DPIC -o .libs/libnetcdf_la-stub.o
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../include
-I../libsrc4 -I/home/software/hd5-1.8.7_gcc_openmpi/include
-I/home/software/szip-2.1_gcc/include -I/home/software/zlib-1.2.5_gcc/include
-g -O2 -MT libnetcdf_la-stub.lo -MD -MP -MF .deps/libnetcdf_la-stub.Tpo -c
stub.c -o libnetcdf_la-stub.o >/dev/null 2>&1
mv -f .deps/libnetcdf_la-stub.Tpo .deps/libnetcdf_la-stub.Plo
/bin/sh ../libtool --tag=CC --mode=link mpicc -g -O2 -version-number 7:1:1
-L/home/software/hd5-1.8.7_gcc_openmpi/lib -L/home/software/szip-2.1_gcc
-L/home/software/zlib-1.2.5_gcc -o libnetcdf.la -rpath
/home/software/netcdf-4.1.3/lib libnetcdf_la-stub.lo
../libdispatch/libnetcdf2.la ../libdispatch/libdispatch.la
../libsrc/libnetcdf3.la ../libsrc4/libnetcdf4.la -lhdf5_hl -lhdf5 -lm -lz
libtool: link: mpicc -shared -fPIC -DPIC .libs/libnetcdf_la-stub.o
-Wl,--whole-archive ../libdispatch/.libs/libnetcdf2.a
../libdispatch/.libs/libdispatch.a ../libsrc/.libs/libnetcdf3.a
../libsrc4/.libs/libnetcdf4.a -Wl,--no-whole-archive
-L/home/software/hd5-1.8.7_gcc_openmpi/lib -L/home/software/szip-2.1_gcc
-L/home/software/zlib-1.2.5_gcc -L/home/software/zlib-1.2.5_gcc/lib
/home/software/hd5-1.8.7_gcc_openmpi/lib/libhdf5_hl.a
/home/software/hd5-1.8.7_gcc_openmpi/lib/libhdf5.a -lm -lz -O2 -Wl,-soname
-Wl,libnetcdf.so.7 -o .libs/libnetcdf.so.7.1.1
/usr/bin/ld: /home/software/hd5-1.8.7_gcc_openmpi/lib/libhdf5_hl.a(H5DS.o):
relocation R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/home/software/hd5-1.8.7_gcc_openmpi/lib/libhdf5_hl.a: could not read symbols:
Bad value
collect2: ld returned 1 exit status
make[2]: *** [libnetcdf.la] Error 1
make[2]: Leaving directory
`/home/admins/rsvancara/SOFTWARE/NetCDF/netcdf-4.1.3/liblib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/admins/rsvancara/SOFTWARE/NetCDF/netcdf-4.1.3'
make: *** [all] Error 2
Spefically:
/usr/bin/ld: /home/software/hd5-1.8.7_gcc_openmpi/lib/libhdf5_hl.a(H5DS.o):
relocation R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
I am not sure why I am receiving this error from HD5. Anyone have a good build
recipe for this software they care to share?
Thanks,
Randall
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