[gmx-users] follow up Re: install problems on HP-UX Itanium system
Christopher Daub
cdaub at vcu.edu
Fri Sep 5 20:42:32 CEST 2008
David,
Thanks so much for the reply, this time the compilation worked!
I recall having trouble with FFTW3 previously (even though the test
program seems to work), so I tried compiling with FFTW2 after fixing
the fmax stuff and commenting out the bad coordinate checking bit in
edsam.c, and that finally worked. Whew!
I should try to get it working with either the fast Fortran stuff or
the assembler loops for Itanium as well, but that's enough fighting
with compilers for today...
Thanks again,
Chris.
On Sep 5, 2008, at 1:53 PM, David van der Spoel wrote:
> Christopher Daub wrote:
>> 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...
>
> Have you tried test programs in fftw?
>
> We'll fix the fmax thingie, thanks for pointing that out.
> As regards the finite in edsam, that turns out to be a function in
> the math library that may be missing. Maybe you can comment that
> one out in the edsam.c function. I will also fix that one for the
> new release.
>
>> 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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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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