Dear Du,
This looks to me like your c compiler is not configured properly. Perhaps
something is corrupting the LD_LIBRARY_PATH variable. Can you check if you
can compile a simple hello world program with it and see if that works. If
that then works try adding a calculation of a cosine to that code so that
you have to use -lm and see if that works. If that doesn't then it is
definately a problem with the way your c compiler or environment is set up.
If this all works then we can try some more debugging.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Du, Shiyu
> Sent: Tuesday, June 12, 2007 22:02
> To: amber.scripps.edu
> Subject: Re: AMBER: Installing amber9 in IBM P5?
>
> Hi, Ross,
>
> Thank you for replying me. This is very helpful.
>
> But I found some new error appears:
>
> When the program shows the command line :
> "xlc bondtype.o -lm -o bondtype"
>
> Error messges comes with it:
> ld: 0711-317 ERROR: Undefined symbol: .__dl__FPv
> ld: 0711-317 ERROR: Undefined symbol: __vn__FUl
> ld: 0711-317 ERROR: Undefined symbol: __vd__FPv
> ld: 0711-317 ERROR: Undefined symbol: .__vec__new2
> ld: 0711-317 ERROR: Undefined symbol: .__ReThrowV6
> ld: 0711-317 ERROR: Undefined symbol:
> .__setUncaughtExceptionFlag__3stdFb
> ld: 0711-317 ERROR: Undefined symbol: .__CleanupCatchV6a
> ld: 0711-317 ERROR: Undefined symbol: .__nw__FUlPv
> ld: 0711-317 ERROR: Undefined symbol: .__nw__FUl
> ld: 0711-317 ERROR: Undefined symbol: .__ThrowV6
> ld: 0711-317 ERROR: Undefined symbol: .unexpected__3stdFv
> ld: 0711-317 ERROR: Undefined symbol: .terminate__3stdFv
> ld: 0711-317 ERROR: Undefined symbol: ._Xran__Q2_3std12_String_baseCFv
> ld: 0711-317 ERROR: Undefined symbol: ._Xlen__Q2_3std12_String_baseCFv
> ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
> information.
> make: 1254-004 The error code from the last command is 8.
>
> Stop.
> make: 1254-004 The error code from the last command is 2.
>
> Stop.
>
> It is again some problem with C compiling (especially when
> there is an "-lm"
> flag). I wonder if it is caused by unoptimized input in config.h or C
> complier's problem?
>
>
> I did try the config.h files you sent me. But it seems still
> shows such
> errors.
>
>
>
>
>
>
> On 6/12/07 8:34 PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>
> > Hi Du,
> >
> > I assume you are running AIX here - AIX 5.3? I have not
> explicitly tried
> > Amber 9 on an SP5 but I have successfully built it on a
> power 4 machine
> > using xlf90 v10.1.
> >
> > The issue you are seeing is coming from the c compiler and
> not the fortran
> > compiler. It is failing on one of the utilities called
> elsize which you
> > likely won't need so as a quick work around you could try editing
> > $AMBERHOME/src/etc/Makefile and remove elsize$(SFX) from
> the PROGS= line.
> >
> > Then try continuing to build. I attach the config.h files I
> used for serial,
> > mpi.
> >
> > Note for actual production runs on an SP5 you should
> consider building and
> > using pmemd (see $AMBERHOME/src/pmemd). If your calculation
> fits within what
> > is supported by pmemd the performance on a power 5 will be awesome.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of
> delivery, may not
> > be read every day, and should not be used for urgent or
> sensitive issues.
> >
> >> -----Original Message-----
> >> From: owner-amber.scripps.edu
> >> [mailto:owner-amber.scripps.edu] On Behalf Of Du, Shiyu
> >> Sent: Tuesday, June 12, 2007 19:10
> >> To: amber.scripps.edu
> >> Subject: AMBER: Installing amber9 in IBM P5?
> >>
> >> Hi, did anyone stall amber 9 in IBM P5 machine?
> >>
> >> What is the correct command to configure?
> >>
> >> I used configure -nopar -xlf90_aix, but error message
> appears at last.
> >> What's going on? I deeply appreciate if some one can help.
> >>
> >>
> >> ** nucgen === End of Compilation 1 ===
> >> ** gennuc === End of Compilation 2 ===
> >> ** setseq === End of Compilation 3 ===
> >> 1501-510 Compilation successful for file _nucgen.f.
> >> /lib/cpp -P -DMASSLIB -DNMLEQ -DCLINK_PLAIN
> -DXLF90 ngfil.f >
> >> _ngfil.f
> >> xlf90 -c -qfixed -c -o ngfil.o _ngfil.f
> >> ** ngfil === End of Compilation 1 ===
> >> 1501-510 Compilation successful for file _ngfil.f.
> >> xlf90 -o nucgen nucgen.o ngfil.o ../lib/amopen.o
> >> ../lib/mexit.o
> >> ../lib/nxtsec.o -L/usr/lib -lmassv -L/usr/lib -lblas
> >> xlc -c -DCLINK_PLAIN -o elsize.o elsize.cc
> >> xlc -DCLINK_PLAIN -o elsize elsize.o -lm
> >> ld: 0711-317 ERROR: Undefined symbol: __dl__FPv
> >> ld: 0711-317 ERROR: Undefined symbol: .__ReThrowV6
> >> ld: 0711-317 ERROR: Undefined symbol:
> >> .__setUncaughtExceptionFlag__3stdFb
> >> ld: 0711-317 ERROR: Undefined symbol: .__CleanupCatchV6a
> >> ld: 0711-317 ERROR: Undefined symbol: .__dl__FPv
> >> ld: 0711-317 ERROR: Undefined symbol: id__Q2_3std8numpunctXTc_
> >> ld: 0711-317 ERROR: Undefined symbol: _Fpz__3std
> >> ld: 0711-317 ERROR: Undefined symbol: ._Getnumpunct__FPCc
> >> ld: 0711-317 ERROR: Undefined symbol: .__vn__FUl
> >> ld: 0711-317 ERROR: Undefined symbol: .__vd__FPv
> >> ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
> >> information.
> >> make: 1254-004 The error code from the last command is 8.
> >>
> >>
> >> Stop.
> >> make: 1254-004 The error code from the last command is 2.
> >>
> >>
> >> Stop.
> >> --------------------------------------------------------------
> >> ---------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>
> --------------------------------------------------------------
> ---------
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Received on Sun Jun 17 2007 - 06:07:09 PDT
