[gmx-users] follow up Re: install problems on HP-UX Itanium system

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 5 19:53:27 CEST 2008


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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