I am tring to link with libtool using the compiler
wrappers on a Cray and with pgi.
At final link, libtool inserts the flag, -pthread, which
causes the compiler to fail. This is shown below.
Is there some way around this?
Also, while the original link line contains
-L/opt/fftw/3.2.2/lib -lfftw3 -lfftw3f
-L/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64 -lpmi
libtool converts the -l flags to full paths,
/opt/fftw/3.2.2/lib/libfftw3.so /opt/fftw/3.2.2/lib/libfftw3f.so \
/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64/libpmi.so
and then the linker complains with
/usr/bin/ld: attempted static link of dynamic object
`/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64/libpmi.so'
Again - is there some way around this?
Thx....John Cary
/bin/sh ../../libtool --tag=CXX --tag=FC --mode=link CC
-I/project/projectdirs/facets/cary/facetsall/fmcfm/interfaces/cppwrap/
-I../../interfaces/wrap/ -I../../interfaces/wrap -I../../interfaces/src
-I/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/include
-I/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/include
-I/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/include
-I/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/include
-fast -Munroll -silent --no_using_std -DMPICH_IGNORE_CXX_SEEK -fPIC -o
testKapisncxx -L.libs -lfmcfmcxx -lfmcfm -L/opt/fftw/3.2.2/lib
-L/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64
-L/opt/cray/mpt/5.1.0/xt/seastar/mpich2-pgi/lib
-L/opt/cray/mpt/5.1.0/xt/seastar/sma/lib64
-L/opt/xt-libsci/10.4.8/pgi/lib -L/opt/xt-xcpe/2.2.48B/lib
-L/opt/xt-pe/default/lib -L/opt/xt-xcpe/2.2.48B/lib/snos64
-L/opt/xt-pe/default/lib/snos64
-L/opt/cray/xt-sysroot/2.2.20091207/usr/lib64
-L/opt/cray/xt-sysroot/2.2.20091207/lib64
-L/opt/cray/xt-sysroot/2.2.20091207/usr/lib/alps -L/usr/lib/alps
-L/opt/pgi/10.8.0/linux86-64/10.8/libso
-L/opt/pgi/10.8.0/linux86-64/10.8/lib
-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -lfftw3 -lfftw3f
-lsci_quadcore_mp -lmpichf90 -lmpich -lrt -lsma -lportals -lpmi
-lalpslli -lalpsutil -lpthread -lm -lpgmp -lpgbind -lpgf90 -lpgf90_rpm1
-lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc
-L/opt/cray/mpt/5.1.0/xt/seastar/mpich2-pgi/lib
-L/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf
-lglf23mpi -lmmm95 -lifspppl -lnclass -lkapisn
-L/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/lib/pgf
-lGYRO -lNEO -lTGLF
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/netlib_lite-1.0.9-r47-ser/lib
-llsode -lnlother -lr8slatec
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/fftw-2.1.5-ser/lib
-lrfftw -lfftw /opt/acml/default/pgi64/lib/libacml.a
/opt/acml/default/pgi64/lib/libacml.a
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/lib
-lezcdf -lvshdf5
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/netcdf-4.1.1-ser/lib
-lnetcdf -L/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/lib
-lhdf5_fortran -lhdf5_hl -lhdf5 -lz testKapisncxx.o -L.libs -lfmcfmcxx
-lfmcfm -L/opt/fftw/3.2.2/lib
-L/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64
-L/opt/cray/mpt/5.1.0/xt/seastar/mpich2-pgi/lib
-L/opt/cray/mpt/5.1.0/xt/seastar/sma/lib64
-L/opt/xt-libsci/10.4.8/pgi/lib -L/opt/xt-xcpe/2.2.48B/lib
-L/opt/xt-pe/default/lib -L/opt/xt-xcpe/2.2.48B/lib/snos64
-L/opt/xt-pe/default/lib/snos64
-L/opt/cray/xt-sysroot/2.2.20091207/usr/lib64
-L/opt/cray/xt-sysroot/2.2.20091207/lib64
-L/opt/cray/xt-sysroot/2.2.20091207/usr/lib/alps -L/usr/lib/alps
-L/opt/pgi/10.8.0/linux86-64/10.8/libso
-L/opt/pgi/10.8.0/linux86-64/10.8/lib
-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -lfftw3 -lfftw3f
-lsci_quadcore_mp -lmpichf90 -lmpich -lrt -lsma -lportals -lpmi
-lalpslli -lalpsutil -lpthread -lm -lpgmp -lpgbind -lpgf90 -lpgf90_rpm1
-lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc
-L/opt/cray/mpt/5.1.0/xt/seastar/mpich2-pgi/lib
-L/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf
-lglf23mpi -lmmm95 -lifspppl -lnclass -lkapisn
-L/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/lib/pgf
-lGYRO -lNEO -lTGLF
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/netlib_lite-1.0.9-r47-ser/lib
-llsode -lnlother -lr8slatec
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/fftw-2.1.5-ser/lib
-lrfftw -lfftw /opt/acml/default/pgi64/lib/libacml.a
/opt/acml/default/pgi64/lib/libacml.a
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/lib
-lezcdf -lvshdf5
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/netcdf-4.1.1-ser/lib
-lnetcdf -L/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/lib
-lhdf5_fortran -lhdf5_hl -lhdf5 -lz
libtool: link: CC
-I/project/projectdirs/facets/cary/facetsall/fmcfm/interfaces/cppwrap/
-I../../interfaces/wrap/ -I../../interfaces/wrap -I../../interfaces/src
-I/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/include
-I/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/include
-I/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/include
-I/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/include
-fast -Munroll -silent --no_using_std -DMPICH_IGNORE_CXX_SEEK -fPIC -o
testKapisncxx testKapisncxx.o -L.libs -L/opt/fftw/3.2.2/lib
-L/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64
-L/opt/cray/mpt/5.1.0/xt/seastar/mpich2-pgi/lib
-L/opt/cray/mpt/5.1.0/xt/seastar/sma/lib64
-L/opt/xt-libsci/10.4.8/pgi/lib -L/opt/xt-xcpe/2.2.48B/lib
-L/opt/xt-pe/default/lib -L/opt/xt-xcpe/2.2.48B/lib/snos64
-L/opt/xt-pe/default/lib/snos64
-L/opt/cray/xt-sysroot/2.2.20091207/usr/lib64
-L/opt/cray/xt-sysroot/2.2.20091207/lib64
-L/opt/cray/xt-sysroot/2.2.20091207/usr/lib/alps -L/usr/lib/alps
-L/opt/pgi/10.8.0/linux86-64/10.8/libso
-L/opt/pgi/10.8.0/linux86-64/10.8/lib
-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2
-L/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf
-L/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/lib/pgf
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/netlib_lite-1.0.9-r47-ser/lib
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/fftw-2.1.5-ser/lib
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/lib
-L/project/projectdirs/facets/franklin/contrib-pgi-10.8/netcdf-4.1.1-ser/lib
-L/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/lib -L/usr/lib64/lib
/scratch/scratchdirs/cary/builds-freedom-pgi/facetsall/fmcfm/par/interfaces/test/.libs/libfmcfmcxx.a
/scratch/scratchdirs/cary/builds-freedom-pgi/facetsall/fmcfm/par/interfaces/test/.libs/libfmcfm.a
/opt/fftw/3.2.2/lib/libfftw3.so /opt/fftw/3.2.2/lib/libfftw3f.so
-lsci_quadcore_mp -lmpichf90 -lmpich -lrt -lsma -lportals
/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64/libpmi.so -ldl -lalpslli
-lalpsutil -lpthread -lpgmp -lpgbind -lpgf90 -lpgf90_rpm1 -lpgf902
-lpgf90rtl -lpgftnrtl -lnspgc -lpgc
/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf/libglf23mpi.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf/libmmm95.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf/libifspppl.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf/libnclass.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ntcc_transport-r1339-par/lib/pgf/libkapisn.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/lib/pgf/libGYRO.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/lib/pgf/libNEO.a
/project/projectdirs/facets/franklin/internal-pgi-10.8/ga_transport-r192-par/lib/pgf/libTGLF.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/netlib_lite-1.0.9-r47-ser/lib/liblsode.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/netlib_lite-1.0.9-r47-ser/lib/libnlother.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/netlib_lite-1.0.9-r47-ser/lib/libr8slatec.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/fftw-2.1.5-ser/lib/librfftw.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/fftw-2.1.5-ser/lib/libfftw.a
/opt/acml/default/pgi64/lib/libacml.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/lib/libezcdf.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/fciowrappers-1.0.44-r107-par/lib/libvshdf5.a
/project/projectdirs/facets/franklin/contrib-pgi-10.8/netcdf-4.1.1-ser/lib/libnetcdf.a
/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/lib/libhdf5_fortran.a
/opt/fftw/3.1.1/cnos/lib/libfftw3.a /opt/fftw/3.1.1/cnos/lib/libfftw3f.a
/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/lib/libhdf5_hl.a
/opt/cray/hdf5-parallel/1.8.2/hdf5-parallel-pgi/lib/libhdf5.a -lm -lz
-pthread -rpath /opt/fftw/3.2.2/lib -rpath
/opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64 -rpath /opt/fftw/3.2.2/lib
-rpath /opt/cray/pmi/1.0-1.0000.7901.22.1.ss/lib64
pgCC-Error-Unknown switch: -pthread
make: *** [testKapisncxx] Error 1
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