On 12/13/10, "Miah Wadud Dr (ITCS)" <w.m...@uea.ac.uk> wrote: > Hello, > > I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am > encountering the following problems when I type "make": >
It seems like there's some mismatch between how FFTW was compiled and how you're linking to it. Try a fresh FFTW compilation with this compiler, etc. Mark > > /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w > -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o > grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la > ../gmxlib/libgmx_mpi_d.la -lnsl -lm > mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -o grompp > grompp.o -L/gpfs/grace/fftw-3.2.2/lib ./.libs/libgmxpreprocess_mpi_d.a > /gpfs/ueasystem/grace/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a > ../mdlib/.libs/libmd_mpi_d.a /gpfs/grace/fftw-3.2.2/lib/libfftw3.a > /gpfs/ueasystem/grace/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a > ../gmxlib/.libs/libgmx_mpi_d.a -lnsl -lm > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function > `timelimit_to_flags': > /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to > `__fmth_i_dlog' > /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to > `__fmth_i_dlog' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed': > /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to > `__mth_i_dfloatuk' > /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to > `__mth_i_dfloatuk' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply': > /gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to > `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function > `apply_r2hc': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to > `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function > `apply_hc2r': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to > `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function > `transpose_toms513': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined > reference to `__c_mzero1' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp': > /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to > `__fmth_i_dsincos' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference > to `__c_mzero8' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference > to `__c_mzero8' > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference > to `__c_mcopy8_bwd' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function > `apply_buf': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined > reference to `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf': > /gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference > to `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf': > /gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to > `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference > to `__builtin_alloca' > /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function > `apply_buf': > /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined > reference to `__builtin_alloca' > make[3]: *** [grompp] Error 1 > make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' > make: *** [all-recursive] Error 1 > [r...@head00 gromacs-4.5.3]# > > Any help will be greatly appreciated. The configure command prints the > following: > > [r...@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi > --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3 > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... /bin/mkdir -p > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking how to create a ustar tar archive... gnutar > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc accepts > -g... yes > checking for /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc option to > accept ISO C89... none needed > checking for style of include used by make... GNU > checking dependency style of > /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc... gcc3 > checking dependency style of > /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc... gcc3 > checking for mpxlc... no > checking for mpicc... mpicc > checking whether the MPI cc command works... yes > checking for MPI_IN_PLACE in collective operations... yes > checking for catamount... no > checking how to run the C preprocessor... mpicc -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking whether ln -s works... yes > checking whether mpicc accepts -msse2... yes > checking whether mpicc accepts -funroll-all-loops... yes > checking whether mpicc accepts -std=gnu99... yes > checking whether mpicc accepts -fexcess-precision=fast... no > checking whether mpicc accepts -O3 -tpp7 -axW -ip -w -msse2 > -funroll-all-loops -std=gnu99... yes > checking whether byte ordering is bigendian... no > checking that size_t can hold pointers... yes > checking for SIGUSR1... yes > checking for pipes... yes > checking floating-point format... IEEE754 (little-endian byte and word order) > checking whether ln -s works... yes > checking whether make sets $(MAKE)... (cached) yes > checking for a sed that does not truncate output... /bin/sed > checking for ld used by mpicc... /usr/bin/ld > checking if the linker (/usr/bin/ld) is GNU ld... yes > checking for /usr/bin/ld option to reload object files... -r > checking for BSD-compatible nm... /usr/bin/nm -B > checking how to recognise dependent libraries... pass_all > checking dlfcn.h usability... yes > checking dlfcn.h presence... yes > checking for dlfcn.h... yes > checking whether we are using the GNU C++ compiler... yes > checking whether mpicc accepts -g... yes > checking dependency style of mpicc... gcc3 > checking how to run the C++ preprocessor... mpicc -E > checking the maximum length of command line arguments... 32768 > checking command to parse /usr/bin/nm -B output from mpicc object... ok > checking for objdir... .libs > checking for ar... ar > checking for ranlib... ranlib > checking for strip... strip > checking if mpicc supports -fno-rtti -fno-exceptions... yes > checking for mpicc option to produce PIC... -fPIC > checking if mpicc PIC flag -fPIC works... yes > checking if mpicc static flag -static works... no > checking if mpicc supports -c -o file.o... yes > checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared > libraries... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking for shl_load... no > checking for shl_load in -ldld... no > checking for dlopen... yes > checking whether a program can dlopen itself... yes > checking whether a statically linked program can dlopen itself... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... no > checking whether to build static libraries... yes > configure: creating libtool > appending configuration tag "CXX" to libtool > checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64 > checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes > checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared > libraries... yes > checking for mpicc option to produce PIC... -fPIC > checking if mpicc PIC flag -fPIC works... yes > checking if mpicc static flag -static works... no > checking if mpicc supports -c -o file.o... yes > checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared > libraries... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > appending configuration tag "F77" to libtool > checking for special C compiler options needed for large files... no > checking for _FILE_OFFSET_BITS value needed for large files... no > checking for _LARGEFILE_SOURCE value needed for large files... no > configure: Using built-in math library with intel compiler > checking for fftw3.h... yes > checking for main in -lfftw3... yes > checking rpc/rpc.h usability... yes > checking rpc/rpc.h presence... yes > checking for rpc/rpc.h... yes > checking for rpc/xdr.h... yes > checking for xdr_float in -lnsl... yes > checking limits.h usability... yes > checking limits.h presence... yes > checking for limits.h... yes > checking unistd.h usability... yes > checking unistd.h presence... yes > checking for unistd.h... yes > checking for unistd.h... (cached) yes > checking sys/types.h usability... yes > checking sys/types.h presence... yes > checking for sys/types.h... yes > checking sys/time.h usability... yes > checking sys/time.h presence... yes > checking for sys/time.h... yes > checking dirent.h usability... yes > checking dirent.h presence... yes > checking for dirent.h... yes > checking regex.h usability... yes > checking regex.h presence... yes > checking for regex.h... yes > checking for working memcmp... yes > checking return type of signal handlers... void > checking for off_t... yes > checking for vprintf... yes > checking for _doprnt... no > checking if malloc debugging is wanted... no > checking for strcasecmp... yes > checking for strdup... yes > checking for gettimeofday... yes > checking for cbrt... yes > checking for isnan... yes > checking for _isnan... no > checking for isfinite... yes > checking for _isfinite... no > checking for fsync... yes > checking for fileno... yes > checking for bool... no > checking for library containing posix_memalign... none required > checking for library containing memalign... none required > checking for _aligned_malloc... no > checking size of int... 4 > checking size of long int... 8 > checking size of long long int... 8 > checking size of off_t... 8 > checking size of void*... 8 > checking for X... libraries , headers > checking for gethostbyname... yes > checking for connect... yes > checking for remove... yes > checking for shmat... yes > checking for IceConnectionNumber in -lICE... yes > checking libxml/parser.h usability... no > checking libxml/parser.h presence... no > checking for libxml/parser.h... no > checking for an ANSI C-conforming const... yes > checking for size_t... yes > checking whether struct tm is in sys/time.h or time.h... time.h > checking for inline... inline > checking for C/C++ restrict keyword... __restrict > checking for uid_t... yes > checking for gid_t... yes > checking for sig_atomic_t... yes > checking whether your compiler can handle assembly files (*.s)... yes > checking whether as fully supports X86_64 SSE2... yes > checking whether byte ordering is bigendian... (cached) no > checking if dlopen supported... yes > configure: creating ./config.status > config.status: creating Makefile > config.status: creating src/Makefile > config.status: creating src/gmxlib/Makefile > config.status: creating src/gmxlib/libgmx_mpi_d.pc > config.status: creating src/gmxlib/gmx_blas/Makefile > config.status: creating src/gmxlib/gmx_lapack/Makefile > config.status: creating src/gmxlib/selection/Makefile > config.status: creating src/gmxlib/statistics/Makefile > config.status: creating src/gmxlib/trajana/Makefile > config.status: creating src/gmxlib/thread_mpi/Makefile > config.status: creating src/gmxlib/nonbonded/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_c/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_power6/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile > config.status: creating include/Makefile > config.status: creating include/types/Makefile > config.status: creating include/thread_mpi/Makefile > config.status: creating include/thread_mpi/atomic/Makefile > config.status: creating src/mdlib/Makefile > config.status: creating src/mdlib/libmd_mpi_d.pc > config.status: creating src/kernel/Makefile > config.status: creating src/kernel/libgmxpreprocess_mpi_d.pc > config.status: creating src/tools/Makefile > config.status: creating src/tools/libgmxana_mpi_d.pc > config.status: creating src/ngmx/Makefile > config.status: creating src/contrib/Makefile > config.status: creating scripts/Makefile > config.status: creating admin/Makefile > config.status: creating share/Makefile > config.status: creating share/tutor/Makefile > config.status: creating share/tutor/gmxdemo/Makefile > config.status: creating share/tutor/nmr1/Makefile > config.status: creating share/tutor/nmr2/Makefile > config.status: creating share/tutor/water/Makefile > config.status: creating share/tutor/mixed/Makefile > config.status: creating share/tutor/methanol/Makefile > config.status: creating share/tutor/speptide/Makefile > config.status: creating share/template/Makefile > config.status: creating share/top/Makefile > config.status: creating share/top/gmx.ff/Makefile > config.status: creating share/top/gmx2.ff/Makefile > config.status: creating share/top/encadv.ff/Makefile > config.status: creating share/top/encads.ff/Makefile > config.status: creating share/top/oplsaa.ff/Makefile > config.status: creating share/top/gromos43a1.ff/Makefile > config.status: creating share/top/gromos43a2.ff/Makefile > config.status: creating share/top/gromos45a3.ff/Makefile > config.status: creating share/top/gromos53a5.ff/Makefile > config.status: creating share/top/gromos53a6.ff/Makefile > config.status: creating share/top/charmm27.ff/Makefile > config.status: creating share/top/amber94.ff/Makefile > config.status: creating share/top/amber96.ff/Makefile > config.status: creating share/top/amberGS.ff/Makefile > config.status: creating share/top/amber99.ff/Makefile > config.status: creating share/top/amber99sb.ff/Makefile > config.status: creating share/top/amber99sb-ildn.ff/Makefile > config.status: creating share/top/amber03.ff/Makefile > config.status: creating share/html/Makefile > config.status: creating share/html/images/Makefile > config.status: creating share/html/online/Makefile > config.status: creating man/Makefile > config.status: creating man/man1/Makefile > config.status: creating man/man7/Makefile > config.status: creating Doxyfile > config.status: creating src/config.h > config.status: executing depfiles commands > > * On most platforms you can save 10X space with dynamic libraries, although > the binaries might be less portable. Why not try --enable-shared ? > [r...@head00 gromacs-4.5 > > ---------- > Wadud Miah > High Performance Computing Systems Developer > Research Computing Services, University of East Anglia > Telephone: 01603 593856 > > Information Services > ---------- > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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