[petsc-users] petsc-3.1-p8 configure error

Sun Jul 10 12:47:51 CDT 2011

On cray - suggest using --with-clib-autodetect=0 --with-cxxlib-autodetect=0 --with-fortranlib-autodetect=0

Check config/examples/arch-cray-xt5-opt.py

Satish

On Fri, 8 Jul 2011, Yudong Sun wrote:

> I am configuring petsc-3.1-p8 for GNU compilers with the options as follows.
> 
> ./configure --known-mpi-c-double-complex=0 --known-level1-dcache-size=65536
> --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=2
> --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8
> --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8
> --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8
> --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=4
> --known-sizeof-MPI_Fint=8 --known-mpi-long-double=0 --with-x=0 --with-batch
> --with-blas-lib=-lsci --with-lapack-lib=-lsci --with-dynamic=false
> --with-shared=false --CXX=CC --CC=cc --CPP=cpp --with-cpp=cpp --FC=ftn
> --with-fc=ftn --with-mpi-shared=false --with-debugging=0
> --with-fortran-kernels=generic --known-mpi-shared=0 --with-single-library
> --with-mpi-lib=/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/libmpich.a
> --with-mpi-include=/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/include
> --with-debugging=1 --LDFLAGS="-Wl,-z,muldefs" --FFLAGS="-Wl,-z,muldefs"
> 
> 
> 
> The configure fails with the log info as:
> 
> ... ...
> Using built-in specs.
> COLLECT_GCC=/opt/gcc/4.5.2/bin/../snos/bin/gfortran
> COLLECT_LTO_WRAPPER=/opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/4.5.2/lto-wrapper
> Target: x86_64-suse-linux
> Configured with: ../xt-gcc-4.5.2/configure --prefix=/opt/gcc/4.5.2/snos
> --disable-nls --libdir=/opt/gcc/4.5.2/snos/lib
> --enable-languages=c,c++,fortran
> --with-gxx-include-dir=/opt/gcc/4.5.2/snos/include/g++
> --with-slibdir=/opt/gcc/4.5.2/snos/lib --with-system-zlib --enable-shared
> --enable-__cxa_atexit x86_64-suse-linux --with-mpc=/opt/gcc/mpc/0.8.1
> --with-mpfr=/opt/gcc/mpfr/2.4.2 --with-gmp=/opt/gcc/gmp/4.3.2 --with-sysroot=
> Thread model: posix
> gcc version 4.5.2 20101216 (Cray Inc.) (GCC)
> COMPILER_PATH=/opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/4.5.2/:/opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/4.5.2/:/opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/:/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/:/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/
> LIBRARY_PATH=/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/:/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/../../../:/lib/:/usr/lib/
> COLLECT_GCC_OPTIONS='-u' 'pthread_mutex_trylock' '-fno-second-underscore'
> '-static' '-o' 'conftest' '-v' '-g'
> '-L/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/lib64'
> '-L/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/lib64'
> '-L/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/lib64'
> '-L/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/lib64'
> '-L/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/lib64'
> '-L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/45'
> '-L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib'
> '-L/opt/cray/mpt/5.1.4/xt/gemini/sma/lib64'
> '-L/opt/xt-libsci/10.5.0/gnu/lib/45' '-L/opt/xt-libsci/10.5.0/gnu/lib'
> '-L/opt/cray/portals/default/lib64' '-L/usr/lib/alps'
> '-L/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2'
> '-L/opt/gcc/4.5.2/snos/lib64' '-L/opt/gcc/4.5.2/snos/lib'
> '-L/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/lib64'
> '-L/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/lib64'
> '-L/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/lib64'
> '-L/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/lib64'
> '-L/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/lib64'
> '-I/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/include'
> '-I/opt/cray/gni-headers/2.1-1.0301.2792.5.1.gem/include'
> '-I/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/include'
> '-I/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/include'
> '-I/opt/cray/gni-headers/2.1-1.0301.2792.5.1.gem/include'
> '-I/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/include'
> '-I/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/include' '-D__x86_64__' '-D__CRAYXE'
> '-D__CRAYXT_COMPUTE_LINUX_TARGET' '-D__TARGET_LINUX__'
> '-I/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/include/45'
> '-I/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/include'
> '-I/opt/cray/mpt/5.1.4/xt/gemini/sma/include'
> '-I/opt/xt-libsci/10.5.0/gnu/lib/45' '-I/opt/xt-libsci/10.5.0/gnu/lib'
> '-I/opt/xt-libsci/10.5.0/gnu/include' '-I/usr/include/alps'
> '-L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/45'
> '-L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib'
> '-L/opt/cray/mpt/5.1.4/xt/gemini/sma/lib64'
> '-L/opt/xt-libsci/10.5.0/gnu/lib/45' '-L/opt/xt-libsci/10.5.0/gnu/lib'
> '-L/usr/lib/alps' '-mtune=generic' '-march=x86-64'
>  /opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/4.5.2/collect2 --sysroot=
> -m elf_x86_64 -static -o conftest -u pthread_mutex_trylock
> /usr/lib/../lib64/crt1.o /usr/lib/../lib64/crti.o
> /opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/crtbeginT.o
> -L/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/lib64
> -L/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/lib64
> -L/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/lib64
> -L/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/lib64
> -L/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/lib64
> -L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/45
> -L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib
> -L/opt/cray/mpt/5.1.4/xt/gemini/sma/lib64 -L/opt/xt-libsci/10.5.0/gnu/lib/45
> -L/opt/xt-libsci/10.5.0/gnu/lib -L/opt/cray/portals/default/lib64
> -L/usr/lib/alps -L/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2
> -L/opt/gcc/4.5.2/snos/lib64 -L/opt/gcc/4.5.2/snos/lib
> -L/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/lib64
> -L/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/lib64
> -L/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/lib64
> -L/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/lib64
> -L/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/lib64
> -L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/45
> -L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib
> -L/opt/cray/mpt/5.1.4/xt/gemini/sma/lib64 -L/opt/xt-libsci/10.5.0/gnu/lib/45
> -L/opt/xt-libsci/10.5.0/gnu/lib -L/usr/lib/alps
> -L/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2
> -L/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64
> -L/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/../../.. -z muldefs
> conftest.o -ldl -lgfortran -lm -lsci -lmpich -lrt -lsma -lxpmem -ldmapp -lugni
> -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lgomp -lgcc_eh -ldl
> -rpath=/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/lib64
> -rpath=/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/lib64
> -rpath=/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/lib64
> -rpath=/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/lib64
> -rpath=/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/lib64
> -rpath=/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/45
> -rpath=/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib
> -rpath=/opt/cray/mpt/default/xt/gemini/mpich2-gnu/lib/45
> -rpath=/opt/cray/mpt/default/xt/gemini/mpich2-gnu/lib
> -rpath=/opt/cray/mpt/5.1.4/xt/gemini/sma/lib64
> -rpath=/opt/cray/mpt/default/xt/gemini/sma/lib64
> -rpath=/opt/xt-libsci/10.5.0/gnu/lib/45
> -rpath=/opt/xt-libsci/default/gnu/lib/45 -rpath=/opt/xt-libsci/10.5.0/gnu/lib
> -rpath=/opt/xt-libsci/default/gnu/lib/45 -rpath=/usr/lib/alps --start-group
> -lsci -lgfortran -lm -lmpichf90 -lmpich -lrt -lsma -lxpmem -ldmapp -lugni
> -lpmi -lalpslli -lalpsutil -ludreg --whole-archive -lpthread
> --no-whole-archive --end-group -lgomp -lpthread -lgfortran -lm --start-group
> -lgcc -lgcc_eh -lc --end-group
> /opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2/crtend.o
> /usr/lib/../lib64/crtn.o
> /usr/lib/../lib64/libpthread.a(sem_open.o): In function `sem_open':
> /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of
> `mktemp' is dangerous, better use `mkstemp'
> }
>                   Pushing language FC
>                   Popping language FC
>  in ftn  -o conftest  -v  -Wl,-z,muldefs -g   conftest.o
> -L/opt/cray/udreg/2.1-1.0301.2797.5.2.gem/lib64
> -L/opt/cray/ugni/2.1-1.0301.2864.7.44.gem/lib64
> -L/opt/cray/dmapp/2.2-1.0301.2791.5.1.gem/lib64
> -L/opt/cray/xpmem/0.1-2.0301.24575.5.2.gem/lib64
> -L/opt/cray/pmi/1.0-1.0000.8160.39.2.gem/lib64
> -L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib/45
> -L/opt/cray/mpt/5.1.4/xt/gemini/mpich2-gnu/lib
> -L/opt/cray/mpt/5.1.4/xt/gemini/sma/lib64 -L/opt/xt-libsci/10.5.0/gnu/lib/45
> -L/opt/xt-libsci/10.5.0/gnu/lib -L/opt/cray/portals/default/lib64
> -L/usr/lib/alps -L/opt/gcc/4.5.2/snos/lib/gcc/x86_64-suse-linux/4.5.2
> -L/opt/gcc/4.5.2/snos/lib64 -L/opt/gcc/4.5.2/snos/lib -ldl -lgfortran -lsci
> -lmpich -lrt -lsma -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg
> -lpthread -lgomp -lgcc_eh -ldl
> Source:
>       program main
> 
>       end
>         Popping language FC
> *******************************************************************************
>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
> details):
> -------------------------------------------------------------------------------
> Mismatched single quotes in Fortran library string
> *******************************************************************************
>   File "./configure", line 257, in petsc_configure
>     framework.configure(out = sys.stdout)
>   File
> "/esfs2/z03/z03/ydsun/queries/q173396_petsc/petsc-3.1-p8/config/BuildSystem/config/framework.py",
> line 944, in configure
>     child.configure()
>   File
> "/esfs2/z03/z03/ydsun/queries/q173396_petsc/petsc-3.1-p8/config/BuildSystem/config/compilers.py",
> line 1220, in configure
>     self.executeTest(self.checkFortranLibraries)
>   File
> "/esfs2/z03/z03/ydsun/queries/q173396_petsc/petsc-3.1-p8/config/BuildSystem/config/base.py",
> line 97, in executeTest
>     ret = apply(test, args,kargs)
>   File
> "/esfs2/z03/z03/ydsun/queries/q173396_petsc/petsc-3.1-p8/config/BuildSystem/config/compilers.py",
> line 680, in checkFortranLibraries
>     if output.count('\'')%2: raise RuntimeError('Mismatched single quotes in
> Fortran library string')
> 
> 
> I'd like to know what causes the mismatched single quotes error. However the
> same configure options work fine with petsc-3.0.0-p12 without any error.
> 
> Thanks,
> 
> Yudong
> 
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