Hi Du,
It is part of the system. Actually part of the X11 development packages.
Your SP5 may not have any X11 stuff installed depending on how it was setup
so you may need to ask you administrator to install it including the
development packages. Note this is only needed for xleap which is the last
thing to be compiled anyway. So if you don't plan to interactively use xleap
on this machine (tleap should still work) then don't worry about it.
Typically I'd use a linux desktop to prepare everything and then copy the
prmtop and inpcrd files over to the power 5 machine to run production MD. In
this 'mode of operation' there is no need to have xleap built on the power 5
machine.
So it is your choice whether you want to go to the trouble of installing the
X11 stuff. Everything else should work fine as is.
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: Wednesday, June 13, 2007 14:21
> To: amber.scripps.edu
> Subject: Re: AMBER: Installing amber9 in IBM P5?
>
>
> Hi,
>
> Is the shape.h file in amber or it should be preinstalled in
> the system?
>
> <X11/extensions/shape.h> ?
>
>
> On 6/13/07 10:52 AM, "Du, Shiyu" <shiyu.du.pnl.gov> wrote:
>
> >
> > Thanks, Ross, and Jed,
> >
> > I just fixed the problem in C++ compiler. It seems working
> for the .C files.
> >
> > But it comes out a new error message:
> "<X11/extensions/shape.h>" cannot be
> > found.
> >
> > Is it a file inside Amber Package or should be preinstalled
> in the server?
> >
> > Shiyu
> >
> >
> > "ShapeWidg.c", line 27.10: 1506-296 (S) #include file
> > <X11/extensions/shape.h> not found.
> > "ShapeWidg.c", line 84.21: 1506-045 (S) Undeclared
> identifier ShapeBounding.
> > "ShapeWidg.c", line 84.48: 1506-045 (S) Undeclared
> identifier ShapeSet.
> > "ShapeWidg.c", line 86.21: 1506-045 (S) Undeclared
> identifier ShapeClip.
> > "ShapeWidg.c", line 141.41: 1506-045 (S) Undeclared identifier
> > ShapeBounding.
> > "ShapeWidg.c", line 143.26: 1506-045 (S) Undeclared
> identifier ShapeSet.
> > "ShapeWidg.c", line 161.45: 1506-045 (S) Undeclared
> identifier ShapeClip.
> > "ShapeWidg.c", line 221.39: 1506-045 (S) Undeclared identifier
> > ShapeBounding.
> > "ShapeWidg.c", line 223.24: 1506-045 (S) Undeclared
> identifier ShapeSet.
> > "ShapeWidg.c", line 236.43: 1506-045 (S) Undeclared
> identifier ShapeClip.
> > make: 1254-004 The error code from the last command is 1.
> >
> >
> > Stop.
> > make: 1254-004 The error code from the last command is 2.
> >
> >
> > Stop.
> > make: 1254-004 The error code from the last command is 2.
> >
> >
> > Stop.
> >
> >
> >
> >
> >
> > On 6/13/07 8:17 AM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
> >
> >> 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
> >>>>>
> >>> --------------------------------------------------------------
> >>> ---------
> >>> 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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> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
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>
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Received on Sun Jun 17 2007 - 06:07:14 PDT
