RE: AMBER: Installing amber9 in IBM P5?

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 12 Jun 2007 20:34:33 -0700

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

Received on Wed Jun 13 2007 - 06:07:39 PDT
Custom Search