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

[Miah Wadud Dr (ITCS)]

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":

/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

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Wadud Miah
High Performance Computing Systems Developer
Research Computing Services, University of East Anglia
Telephone: 01603 593856

Information Services
----------