[petsc-users] petsc-3.1-p8 configure error
Yudong Sun
Yudong.Sun at nag.co.uk
Fri Jul 8 09:15:56 CDT 2011
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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