[gmx-users] Gromacs build error

[Miah Wadud Dr (ITCS)]

Hello,

I am trying to build Gromacs 4.5 from source using the Portland Group compiler:

[root at master1 gromacs-4.5]# echo $CPPFLAGS
-I/cvos/shared/apps/fftw/pgi/64/3.1.2/include
[root at master1 gromacs-4.5]# echo $LDFLAGS
-L/cvos/shared/apps/fftw/pgi/64/3.1.2/lib
[root at master1 gromacs-4.5]# echo $CC
/cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/bin/pgcc
[root at master1 gromacs-4.5]#

[root at master1 gromacs-4.5]# ./configure --enable-shared --enable-double --enable-mpi --prefix=/cvos/apps/gromacs-4.5 
--program-suffix=_mpi_d
[ see output below ]

However, when I try to build Gromacs, I get the following error which looks to be a syntax error in the code:

[root at master1 gromacs-4.5]# make
[ ... lots of output ... ]
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 -fast -pc 32 -c nb_kernel400_x86_64_sse2.c  -DPIC -o .libs/nb_kernel400_x86_64_sse2.o
PGC-S-0080-Missing braces for array, structure, or union initialization (../../../../include/gmx_sse2_double.h: 457)
PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 514)
PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 515)
PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 516)
PGC-S-0094-Illegal type conversion required (../../../../include/gmx_sse2_double.h: 517)
PGC/x86-64 Linux 7.0-7: compilation completed with severe errors
make[5]: *** [nb_kernel400_x86_64_sse2.lo] Error 1
make[5]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib/nonbonded/nb_kernel_x86_64_sse2'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/gpfs/ueasystem/escluster/gromacs-4.5/src/gmxlib/nonbonded'
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]#

Any help will be greatly appreciated.

-------------------------------------------------------

configure output

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/7.0.7/linux86-64/7.0/bin/pgcc accepts -g... yes
checking for /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/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/7.0.7/linux86-64/7.0/bin/pgcc... none
checking dependency style of /cvos/shared/apps/pgi/7.0.7/linux86-64/7.0/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
checking whether mpicc accepts  -fast -pc 32... 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 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

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

Information Services
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