AMBER Archive (2007)

Subject: Re: AMBER: Installing amber9 in IBM P5?

From: Du, Shiyu (shiyu.du_at_pnl.gov)
Date: Wed Jun 13 2007 - 16:20:37 CDT

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_at_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_at_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_at_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_at_scripps.edu
>>> [mailto:owner-amber_at_scripps.edu] On Behalf Of Du, Shiyu
>>> Sent: Tuesday, June 12, 2007 22:02
>>> To: amber_at_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_at_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_at_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_at_scripps.edu
>>>>> [mailto:owner-amber_at_scripps.edu] On Behalf Of Du, Shiyu
>>>>> Sent: Tuesday, June 12, 2007 19:10
>>>>> To: amber_at_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
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