[gmx-users] follow up Re: install problems on HP-UX Itanium system
Christopher Daub
cdaub at vcu.edu
Fri Sep 5 19:46:36 CEST 2008
Hi again!
I'm still working on compiling gromacs for our HP-UX system. I got
around the aforementioned problems with xutils.c by renaming all
instances of fmax to fmaxx in xutils.c, ffscan.c and xmdrun.h, but
that just delays the compiler crash to a few steps later:
---------------------------------------------------
source='xutils.c' object='xutils.o' libtool=no \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/
home/snoop/gmacs/share/top\" -I/home/snoop/fftw-3.1.2s/include/ -Ae
+O2 -c xutils.c
source='md.c' object='md.o' libtool=no \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/
home/snoop/gmacs/share/top\" -I/home/snoop/fftw-3.1.2s/include/ -Ae
+O2 -c md.c
source='mdrun.c' object='mdrun.o' libtool=no \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/
home/snoop/gmacs/share/top\" -I/home/snoop/fftw-3.1.2s/include/ -Ae
+O2 -c mdrun.c
source='genalg.c' object='genalg.o' libtool=no \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/
home/snoop/gmacs/share/top\" -I/home/snoop/fftw-3.1.2s/include/ -Ae
+O2 -c genalg.c
/bin/sh ../../libtool --tag=CC --mode=link cc -Ae +O2 -L/home/
snoop/fftw-3.1.2s/lib -o mdrun glaasje.o gctio.o init_sh.o ionize.o
do_gct.o relax_sh.o repl_ex.o xutils.o compute_io.o md.o mdrun.o
genalg.o ../mdlib/libmd.la ../gmxlib/libgmx.la -lnsl -lfftw3f -lm -
lXm -lXt -lSM -lICE -lXext -lXp -lX11
cc -Ae +O2 -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o
relax_sh.o repl_ex.o xutils.o compute_io.o md.o mdrun.o genalg.o -L/
home/snoop/fftw-3.1.2s/lib ../mdlib/.libs/libmd.a ../gmxlib/.libs/
libgmx.a -lnsl /home/snoop/fftw-3.1.2s/lib/libfftw3f.a -lm -lXm -lXt -
lSM -lICE -lXext -lXp -lX11
ld: Unsatisfied symbol "finite" in file ../mdlib/.libs/libmd.a[edsam.o]
ld: Unsatisfied symbol "__divdi3" in file /home/snoop/fftw-3.1.2s/lib/
libfftw3f.a[primes.o]
ld: Unsatisfied symbol "__divdf3" in file /home/snoop/fftw-3.1.2s/lib/
libfftw3f.a[mapflags.o]
ld: Unsatisfied symbol "__divsf3" in file /home/snoop/fftw-3.1.2s/lib/
libfftw3f.a[bluestein.o]
ld: Unsatisfied symbol "__moddi3" in file /home/snoop/fftw-3.1.2s/lib/
libfftw3f.a[primes.o]
ld: Unsatisfied symbol "__umoddi3" in file /home/snoop/fftw-3.1.2s/
lib/libfftw3f.a[planner.o]
6 errors.
gmake[3]: *** [mdrun] Error 1
gmake[3]: Leaving directory `/home/snoop/gromacs-3.3.3/src/kernel'
gmake[2]: *** [all-recursive] Error 1
gmake[2]: Leaving directory `/home/snoop/gromacs-3.3.3/src'
gmake[1]: *** [all] Error 2
gmake[1]: Leaving directory `/home/snoop/gromacs-3.3.3/src'
gmake: *** [all-recursive] Error 1
-----------------------------------------------------
Blah! Looks like a FFTW issue, but that install went smoothly as far
as I can tell. Anybody have any clue as to what's going on? There's
probably not too many HP-UX experts around here... maybe I need to go
to an HP-UX list for clues.
I'm sorry to be so impatient with this, but my boss is on my back to
get this running...
Thanks again,
Chris.
------------------------------------------------
Here's my screen output from ./configure, if it helps... I don't see
anything unusual there, other than this line:
./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found.
The complete command line was:
./configure CC=cc CFLAGS="-Ae +O2" --prefix=/home/snoop/gmacs --
disable-ia64-asm > clog.txt
The rest of the output (clog.txt):
checking build system type... ia64-hp-hpux11.23
checking host system type... ia64-hp-hpux11.23
checking for a BSD-compatible install... config/install-sh -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... plaintar
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... none
checking dependency style of cc... none
checking how to run the C preprocessor... cc -E
******************************************
* Using CFLAGS from environment variable *
******************************************
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... yes
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 4
checking for long long int... yes
checking size of long long int... 8
checking that size_t can hold pointers... yes
checking floating-point format... IEEE754 (big-endian byte and word
order)
checking for a BSD-compatible install... config/install-sh -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -p
checking how to recognise dependent libraries... file_magic (s[0-9]
[0-9][0-9]|ELF-[0-9][0-9]) sh
ared object file - IA64
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking the maximum length of command line arguments... 262144
checking command to parse /usr/bin/nm -p output from cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking for cc option to produce PIC...
checking if cc static flag -Wl,-a -Wl,archive works... no
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/usr/bin/ld) supports shared
libraries... yes
checking dynamic linker characteristics... hpux11.23 dld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
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 g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/usr/bin/ld) supports shared
libraries... yes
checking for g++ option to produce PIC...
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld) supports shared
libraries... yes
checking dynamic linker characteristics... hpux11.23 dld.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... 64
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3f... 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 for working memcmp... yes
checking return type of signal handlers... void
checking for vprintf... yes
checking for _doprnt... yes
checking if malloc debugging is wanted... no
checking for strcasecmp... yes
checking for strdup... yes
checking for bool... no
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 for Motif... libraries in default path, headers in default path
checking for libXext and libXp... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for unistd.h... (cached) 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 uid_t in sys/types.h... yes
checking for inline... __inline
checking whether byte ordering is bigendian... (cached) 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/gmx_blas/Makefile
config.status: creating src/gmxlib/gmx_lapack/Makefile
config.status: creating src/gmxlib/nonbonded/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/
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 include/Makefile
config.status: creating include/types/Makefile
config.status: creating src/mdlib/Makefile
config.status: creating src/kernel/Makefile
config.status: creating src/tools/Makefile
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/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 src/config.h
config.status: executing depfiles commands
On Sep 4, 2008, at 5:46 PM, Christopher Daub wrote:
> Hello list,
>
> I was pretty easily able to compile gromacs on a Linux cluster, but
> now I'm having some problems installing gromacs 3.3.3 on an Itanium
> computer running HP-UX 11.23. I'm compiling without MPI for now;
> maybe later once I get it working without!
>
> I ran ./configure after telling it where to find my FFTW, and there
> was nothing odd there except that the HP-UX C compiler doesn't like
> "+Oall" as a compiler flag, so I ran make as:
>
> make CFLAGS="-Ae +Ofast"
>
> or, when that didn't work, CFLAGS="-Ae +O2"; didn't seem to make
> much difference.
(snip)
> I also tried with --disable-ia64-asm, thinking I'd at least avoid
> these issues. And yes, the compilation gets a fair bit further
> along, but it crashes on xutils.c:
>
> source='xutils.c' object='xutils.o' libtool=no \
> DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
> cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/
> home/snoop/gmacs/share/top\" -I/home/snoop/fftw-3.1.2s/include -Ae
> +O2 -c xutils.c
> Error 187: "xutils.c", line 447 # Referenced object '_Fmax' is not
> a member of struct
> t_ffscan ["xmdrun.h", line 190].
> if ((ff.fmax == 0) || (msf1 < sqr(ff.fmax)))
> ^^^^
> gmake[3]: *** [xutils.o] Error 2
>
> I've tried with a variety of compiler options, both make and gmake,
> etc. but so far am stumped. These problems do not resemble any
> other problems I saw in the archive with HP-UX installations; maybe
> my setup is a bit broken? I've managed to compile other large C
> codes (eg. FFTW) with no major trouble though.
>
> Any help would be greatly appreciated! I can send any other info
> required as requested.
>
> Cheers,
> Chris Daub
> Virginia Commonwealth University
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