[gmx-users] problem building Gromacs 4.5.3 using the Intel compiler

[Mark Abraham]

On 12/13/10, "Miah Wadud Dr (ITCS)"  <W.Miah at 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
> [root at head00 gromacs-4.5.3]#
> 
> Any help will be greatly appreciated. The configure command prints the following:
> 
> [root at 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 ?
> [root at head00 gromacs-4.5
> 
> ----------
> Wadud Miah
> High Performance Computing Systems Developer
> Research Computing Services, University of East Anglia
> Telephone: 01603 593856
> 
> Information Services
> ----------
> 
> 
> -- 
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