AMBER Archive (2007)

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

From: Du, Shiyu (shiyu.du_at_pnl.gov)
Date: Wed Jun 13 2007 - 00:01:56 CDT

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.
>> --------------------------------------------------------------
>> ---------
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