[gmx-users] Gromacs 4.5 build problems

Wed Nov 10 15:45:48 CET 2010

Hi,

compiling with PGI doesn't currently work. It would not be difficult to get
it to compile with PGI but currently it is not supported. Please let us know
if their is a compelling reason why you need to use PGI.

Their should be no performance advantage. Thus I suggest to use Intel or
GNU.

Roland

On Wed, Nov 10, 2010 at 8:26 AM, Miah Wadud Dr (ITCS) <W.Miah at uea.ac.uk>wrote:

> Hello Gromacs users,
>
> I am trying to build Gromacs 4.5 using PGI compiler 10.9 and am getting the
> following error message:
>
> mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
> -I../../include
> -DGMXLIBDIR=\"/cvos/apps/gromacs-4.5/share/top\"
> -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include -Mm128 -c main.c -o main.o
> >/dev/null 2>&1
> source='maths.c' object='maths.lo' libtool=yes \
>        DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
>        /bin/sh ../../libtool --tag=CC   --mode=compile mpicc
> -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
> -I../../include -DGMXLIBDIR=\"/cvos/apps/gromacs-4.5/share/top\"
> -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include  -Mm128 -c -o maths.lo
> maths.c
>  mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
> -I../../include -DGMXLIBDIR=\"/cvos/apps/gromacs-4.5/share/top\"
> -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include -Mm128 -c maths.c  -DPIC -o
> .libs/maths.o
> PGC-F-0249-#error --  ERROR: No 32 bit wide integer type found! (maths.c:
> 99)
> PGC/x86-64 Linux 10.9-0: compilation aborted
> make[4]: *** [maths.lo] Error 1
> make[4]: Leaving directory
> `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src'
> make: *** [all-recursive] Error 1
> [root at master1 gromacs-4.5]#
>
> The configure command typed is:
>
> [root at master1 gromacs-4.5]# ./configure --enable-shared --enable-double
> --enable-mpi --program-suffix=_mpi_d \
> --prefix=/cvos/apps/gromacs-4.5
> 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... no
> checking whether /cvos/shared/apps/pgi/10.9/linux86-64/10.9/bin/pgcc
> accepts
> -g... yes
> checking for /cvos/shared/apps/pgi/10.9/linux86-64/10.9/bin/pgcc option to
> accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of
> /cvos/shared/apps/pgi/10.9/linux86-64/10.9/bin/pgcc... none
> checking dependency style of
> /cvos/shared/apps/pgi/10.9/linux86-64/10.9/bin/pgcc... none
> checking for mpxlc... no
> checking for mpicc... mpicc
> checking whether the MPI cc command works... yes
> checking for MPI_IN_PLACE in collective operations... no
> 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
> ******************************************
> * Using CFLAGS from environment variable *
> ******************************************
> 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 non-GNU ld... /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... no
> checking whether mpicc accepts -g... no
> checking dependency style of mpicc... none
> checking how to run the C++ preprocessor... /lib/cpp
> checking the maximum length of command line arguments... 32768
> checking command to parse /usr/bin/nm -B output from mpicc object... failed
> checking for objdir... .libs
> checking for ar... ar
> checking for ranlib... ranlib
> checking for strip... strip
> checking for mpicc option to produce PIC...
> checking if mpicc static flag  works... yes
> 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 if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> configure: creating libtool
> appending configuration tag "CXX" to libtool
> checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
> shared libraries... yes
> libtool.m4: error: problem compiling CXX test program
> checking for mpicc option to produce PIC...
> checking if mpicc static flag  works... no
> checking if mpicc supports -c -o file.o... no
> 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... unsupported
> 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
> checking for sqrt in -lm... yes
> 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... no
> 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... yes
> checking libxml/parser.h presence... yes
> checking for libxml/parser.h... yes
> checking for main in -lxml2... yes
> 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
>
> Any help will be greatly appreciated.
>
> Thanks in advance
>
> ----------
> Wadud Miah
> High Performance Computing Systems Developer
> Research Computing Group, University of East Anglia
>
> Information Services
> ----------
>
> ----------
> Wadud Miah
> High Performance Computing Systems Developer
> Research Computing Group, University of East Anglia
> Telephone: 01603 593856
>
> Information Services
> ----------
>
>
> --
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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