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Re: Problem with libtool adding -pthread


From: John R. Cary
Subject: Re: Problem with libtool adding -pthread
Date: Sun, 28 Nov 2010 07:41:10 -0700
User-agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6

System information below

On 11/28/10 7:02 AM, John R. Cary wrote:
I am trying 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?

freedom1.cary$ libtool --version
libtool (GNU libtool) 2.4
freedom1.cary$ uname -a
Linux freedom1 2.6.16.60-0.69.1-smp #1 SMP Fri Sep 17 17:07:54 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux


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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