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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi, <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>thanks for the advice. You were spot on: the FFTW library was compiled using PGI and Gromacs using Intel, so I have re-compiled FFTW using Intel and it all works now. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks ever so much people! <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Mark Abraham<br><b>Sent:</b> Monday, December 13, 2010 1:20 PM<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> Re: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><br><br>On 12/13/10, <b>"Miah Wadud Dr (ITCS)" </b><W.Miah@uea.ac.uk> wrote:<o:p></o:p></p><div><p class=MsoNormal>Hello,<br><br>I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type "make":<o:p></o:p></p></div><p class=MsoNormal><br>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.<br><br>Mark<br><br><o:p></o:p></p><div><p class=MsoNormal><br>/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<br>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<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function `timelimit_to_flags':<br>/gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog'<br>/gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed':<br>/gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk'<br>/gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply':<br>/gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_r2hc':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_hc2r':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function `transpose_toms513':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined reference to `__c_mzero1'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp':<br>/gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to `__fmth_i_dsincos'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference to `__c_mzero8'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference to `__c_mzero8'<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference to `__c_mcopy8_bwd'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function `apply_buf':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf':<br>/gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf':<br>/gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference to `__builtin_alloca'<br>/gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function `apply_buf':<br>/gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined reference to `__builtin_alloca'<br>make[3]: *** [grompp] Error 1<br>make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel'<br>make[2]: *** [all-recursive] Error 1<br>make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src'<br>make[1]: *** [all] Error 2<br>make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src'<br>make: *** [all-recursive] Error 1<br>[root@head00 gromacs-4.5.3]#<br><br>Any help will be greatly appreciated. The configure command prints the following:<br><br>[root@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3<br>checking build system type... x86_64-unknown-linux-gnu<br>checking host system type... x86_64-unknown-linux-gnu<br>checking for a BSD-compatible install... /usr/bin/install -c<br>checking whether build environment is sane... yes<br>checking for a thread-safe mkdir -p... /bin/mkdir -p<br>checking for gawk... gawk<br>checking whether make sets $(MAKE)... yes<br>checking how to create a ustar tar archive... gnutar<br>checking for C compiler default output file name... a.out<br>checking whether the C compiler works... yes<br>checking whether we are cross compiling... no<br>checking for suffix of executables...<br>checking for suffix of object files... o<br>checking whether we are using the GNU C compiler... yes<br>checking whether /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc accepts -g... yes<br>checking for /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc option to accept ISO C89... none needed<br>checking for style of include used by make... GNU<br>checking dependency style of /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc... gcc3<br>checking dependency style of /gpfs/grace/intel/Compiler/11.1/073/bin/intel64/icc... gcc3<br>checking for mpxlc... no<br>checking for mpicc... mpicc<br>checking whether the MPI cc command works... yes<br>checking for MPI_IN_PLACE in collective operations... yes<br>checking for catamount... no<br>checking how to run the C preprocessor... mpicc -E<br>checking for grep that handles long lines and -e... /bin/grep<br>checking for egrep... /bin/grep -E<br>checking whether ln -s works... yes<br>checking whether mpicc accepts -msse2... yes<br>checking whether mpicc accepts -funroll-all-loops... yes<br>checking whether mpicc accepts -std=gnu99... yes<br>checking whether mpicc accepts -fexcess-precision=fast... no<br>checking whether mpicc accepts -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99... yes<br>checking whether byte ordering is bigendian... no<br>checking that size_t can hold pointers... yes<br>checking for SIGUSR1... yes<br>checking for pipes... yes<br>checking floating-point format... IEEE754 (little-endian byte and word order)<br>checking whether ln -s works... yes<br>checking whether make sets $(MAKE)... (cached) yes<br>checking for a sed that does not truncate output... /bin/sed<br>checking for ld used by mpicc... /usr/bin/ld<br>checking if the linker (/usr/bin/ld) is GNU ld... yes<br>checking for /usr/bin/ld option to reload object files... -r<br>checking for BSD-compatible nm... /usr/bin/nm -B<br>checking how to recognise dependent libraries... pass_all<br>checking dlfcn.h usability... yes<br>checking dlfcn.h presence... yes<br>checking for dlfcn.h... yes<br>checking whether we are using the GNU C++ compiler... yes<br>checking whether mpicc accepts -g... yes<br>checking dependency style of mpicc... gcc3<br>checking how to run the C++ preprocessor... mpicc -E<br>checking the maximum length of command line arguments... 32768<br>checking command to parse /usr/bin/nm -B output from mpicc object... ok<br>checking for objdir... .libs<br>checking for ar... ar<br>checking for ranlib... ranlib<br>checking for strip... strip<br>checking if mpicc supports -fno-rtti -fno-exceptions... yes<br>checking for mpicc option to produce PIC... -fPIC<br>checking if mpicc PIC flag -fPIC works... yes<br>checking if mpicc static flag -static works... no<br>checking if mpicc supports -c -o file.o... yes<br>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes<br>checking dynamic linker characteristics... GNU/Linux ld.so<br>checking how to hardcode library paths into programs... immediate<br>checking whether stripping libraries is possible... yes<br>checking for shl_load... no<br>checking for shl_load in -ldld... no<br>checking for dlopen... yes<br>checking whether a program can dlopen itself... yes<br>checking whether a statically linked program can dlopen itself... yes<br>checking if libtool supports shared libraries... yes<br>checking whether to build shared libraries... no<br>checking whether to build static libraries... yes<br>configure: creating libtool<br>appending configuration tag "CXX" to libtool<br>checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64<br>checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes<br>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes<br>checking for mpicc option to produce PIC... -fPIC<br>checking if mpicc PIC flag -fPIC works... yes<br>checking if mpicc static flag -static works... no<br>checking if mpicc supports -c -o file.o... yes<br>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes<br>checking dynamic linker characteristics... GNU/Linux ld.so<br>checking how to hardcode library paths into programs... immediate<br>appending configuration tag "F77" to libtool<br>checking for special C compiler options needed for large files... no<br>checking for _FILE_OFFSET_BITS value needed for large files... no<br>checking for _LARGEFILE_SOURCE value needed for large files... no<br>configure: Using built-in math library with intel compiler<br>checking for fftw3.h... yes<br>checking for main in -lfftw3... yes<br>checking rpc/rpc.h usability... yes<br>checking rpc/rpc.h presence... yes<br>checking for rpc/rpc.h... yes<br>checking for rpc/xdr.h... yes<br>checking for xdr_float in -lnsl... yes<br>checking limits.h usability... yes<br>checking limits.h presence... yes<br>checking for limits.h... yes<br>checking unistd.h usability... yes<br>checking unistd.h presence... yes<br>checking for unistd.h... yes<br>checking for unistd.h... (cached) yes<br>checking sys/types.h usability... yes<br>checking sys/types.h presence... yes<br>checking for sys/types.h... yes<br>checking sys/time.h usability... yes<br>checking sys/time.h presence... yes<br>checking for sys/time.h... yes<br>checking dirent.h usability... yes<br>checking dirent.h presence... yes<br>checking for dirent.h... yes<br>checking regex.h usability... yes<br>checking regex.h presence... yes<br>checking for regex.h... yes<br>checking for working memcmp... yes<br>checking return type of signal handlers... void<br>checking for off_t... yes<br>checking for vprintf... yes<br>checking for _doprnt... no<br>checking if malloc debugging is wanted... no<br>checking for strcasecmp... yes<br>checking for strdup... yes<br>checking for gettimeofday... yes<br>checking for cbrt... yes<br>checking for isnan... yes<br>checking for _isnan... no<br>checking for isfinite... yes<br>checking for _isfinite... no<br>checking for fsync... yes<br>checking for fileno... yes<br>checking for bool... no<br>checking for library containing posix_memalign... none required<br>checking for library containing memalign... none required<br>checking for _aligned_malloc... no<br>checking size of int... 4<br>checking size of long int... 8<br>checking size of long long int... 8<br>checking size of off_t... 8<br>checking size of void*... 8<br>checking for X... libraries , headers<br>checking for gethostbyname... yes<br>checking for connect... yes<br>checking for remove... yes<br>checking for shmat... yes<br>checking for IceConnectionNumber in -lICE... yes<br>checking libxml/parser.h usability... no<br>checking libxml/parser.h presence... no<br>checking for libxml/parser.h... no<br>checking for an ANSI C-conforming const... yes<br>checking for size_t... yes<br>checking whether struct tm is in sys/time.h or time.h... time.h<br>checking for inline... inline<br>checking for C/C++ restrict keyword... __restrict<br>checking for uid_t... yes<br>checking for gid_t... yes<br>checking for sig_atomic_t... yes<br>checking whether your compiler can handle assembly files (*.s)... yes<br>checking whether as fully supports X86_64 SSE2... yes<br>checking whether byte ordering is bigendian... (cached) no<br>checking if dlopen supported... yes<br>configure: creating ./config.status<br>config.status: creating Makefile<br>config.status: creating src/Makefile<br>config.status: creating src/gmxlib/Makefile<br>config.status: creating src/gmxlib/libgmx_mpi_d.pc<br>config.status: creating src/gmxlib/gmx_blas/Makefile<br>config.status: creating src/gmxlib/gmx_lapack/Makefile<br>config.status: creating src/gmxlib/selection/Makefile<br>config.status: creating src/gmxlib/statistics/Makefile<br>config.status: creating src/gmxlib/trajana/Makefile<br>config.status: creating src/gmxlib/thread_mpi/Makefile<br>config.status: creating src/gmxlib/nonbonded/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_c/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_power6/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile<br>config.status: creating include/Makefile<br>config.status: creating include/types/Makefile<br>config.status: creating include/thread_mpi/Makefile<br>config.status: creating include/thread_mpi/atomic/Makefile<br>config.status: creating src/mdlib/Makefile<br>config.status: creating src/mdlib/libmd_mpi_d.pc<br>config.status: creating src/kernel/Makefile<br>config.status: creating src/kernel/libgmxpreprocess_mpi_d.pc<br>config.status: creating src/tools/Makefile<br>config.status: creating src/tools/libgmxana_mpi_d.pc<br>config.status: creating src/ngmx/Makefile<br>config.status: creating src/contrib/Makefile<br>config.status: creating scripts/Makefile<br>config.status: creating admin/Makefile<br>config.status: creating share/Makefile<br>config.status: creating share/tutor/Makefile<br>config.status: creating share/tutor/gmxdemo/Makefile<br>config.status: creating share/tutor/nmr1/Makefile<br>config.status: creating share/tutor/nmr2/Makefile<br>config.status: creating share/tutor/water/Makefile<br>config.status: creating share/tutor/mixed/Makefile<br>config.status: creating share/tutor/methanol/Makefile<br>config.status: creating share/tutor/speptide/Makefile<br>config.status: creating share/template/Makefile<br>config.status: creating share/top/Makefile<br>config.status: creating share/top/gmx.ff/Makefile<br>config.status: creating share/top/gmx2.ff/Makefile<br>config.status: creating share/top/encadv.ff/Makefile<br>config.status: creating share/top/encads.ff/Makefile<br>config.status: creating share/top/oplsaa.ff/Makefile<br>config.status: creating share/top/gromos43a1.ff/Makefile<br>config.status: creating share/top/gromos43a2.ff/Makefile<br>config.status: creating share/top/gromos45a3.ff/Makefile<br>config.status: creating share/top/gromos53a5.ff/Makefile<br>config.status: creating share/top/gromos53a6.ff/Makefile<br>config.status: creating share/top/charmm27.ff/Makefile<br>config.status: creating share/top/amber94.ff/Makefile<br>config.status: creating share/top/amber96.ff/Makefile<br>config.status: creating share/top/amberGS.ff/Makefile<br>config.status: creating share/top/amber99.ff/Makefile<br>config.status: creating share/top/amber99sb.ff/Makefile<br>config.status: creating share/top/amber99sb-ildn.ff/Makefile<br>config.status: creating share/top/amber03.ff/Makefile<br>config.status: creating share/html/Makefile<br>config.status: creating share/html/images/Makefile<br>config.status: creating share/html/online/Makefile<br>config.status: creating man/Makefile<br>config.status: creating man/man1/Makefile<br>config.status: creating man/man7/Makefile<br>config.status: creating Doxyfile<br>config.status: creating src/config.h<br>config.status: executing depfiles commands<br><br>* On most platforms you can save 10X space with dynamic libraries, although<br> the binaries might be less portable. Why not try --enable-shared ?<br>[root@head00 gromacs-4.5<br><br>----------<br>Wadud Miah<br>High Performance Computing Systems Developer<br>Research Computing Services, University of East Anglia<br>Telephone: 01603 593856<br><br>Information Services<br>----------<br><br><br>-- <br>gmx-users mailing list gmx-users@gromacs.org<br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=l>http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=l>http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target=l>http://www.gromacs.org/Support/Mailing_Lists</a><o:p></o:p></p></div></div></div></body></html>