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
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>
>
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Received on Sun Jun 17 2007 - 06:07:11 PDT
