Dear Myunggi
I would completely avoid trying to build a parallel version of the code
until you have the serial version fully working and tested.
I suspect that the error you see comes from the fact that your massv library
does not have the vtanh function in it. This is probably a very old version
of massv. You can check it using 'nm'
nm /usr/lib/libmassv.a | less
Then search for vtanh. You should see something like this:
libmassv.a[vtanh_p4.32.o]:
.vtanh T 0
.vtanh_ T 0
TOC d 3852
vtanh D 3840 12
vtanh t 0 3439
vtanh t 3456 380
vtanh_p4.32s f -
If you don't then that is the problem. You then have three options. Firstly
you can upgrade the massv library to one that supports vtanh. Secondly you
can modify the config script to not use the massv library. This option is
probably the easiest but will lead to a big performance hit. Finally you can
edit part of the amber code to use a scalar approach to doing tanh.
Let me know if you don't find vtanh in your libmassv and I will send you a
quick patch to not use the vectored mass library for tanh.
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 Myunggi Yi
> Sent: Thursday, August 24, 2006 09:06
> To: amber.scripps.edu
> Subject: AMBER: Installation amber 9 on IBM SP4
>
> I'm installing serial version of amber 9 on IBM SP4 first,
> then parrellel.
> However I've got the error message from the screen, and only
> the following
> execute files have been made.
>
> addles lmodprmtop new2oldparm
>
>
>
> I used the following command.
>
> > ./configure xlf90_aix
> > make serial
>
>
> The following is the end of the screen output.
> ===================================
> ../lmod/lmod.a ../dcqtp/src/qmmm/libdivcon.a ../lapack/lapack.a
> ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a -L/usr/lib -lmassv
> -L/usr/lib -lblas
> ld: 0711-317 ERROR: Undefined symbol: .vtanh
> 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.
> ===================================
>
> And I "make clean" then,
>
> > ./configure -mpi xlf90_aix
> > make parallel
>
> Then the following error message
>
> ==============================
> Starting installation of Amber9 (parallel) at Thu Aug 24
> 12:00:48 EDT 2006.
> cd sander; make parallel
> ./checkparconf
> /lib/cpp -P -DMPI -DMASSLIB -DNMLEQ -DCLINK_PLAIN -DXLF90
> -DPOE evb_vars.f > _evb_vars.f
> mpxlf90_r -bmaxdata:0x80000000 -c -qfixed -c -qfree=f90 -o
> evb_vars.o _evb_vars.f
> ** evb_nml === End of Compilation 1 ===
> ** evb_amber === End of Compilation 2 ===
> ** evb_parm === End of Compilation 3 ===
> ** evb_xchff === End of Compilation 4 ===
> ** evb_xdat === End of Compilation 5 ===
> ** evb_mv === End of Compilation 6 ===
> ** evb_data === End of Compilation 7 ===
> "_evb_vars.f", line 496.36: 1514-129 (E) Previous specified type does
> not agree with the actual type of the INTRINSIC function. Type is
> ignored.
> "_evb_vars.f", line 496.63: 1514-129 (E) Previous specified type does
> not agree with the actual type of the INTRINSIC function. Type is
> ignored.
> ** evb_check === End of Compilation 8 ===
> ** evb_math === End of Compilation 9 ===
> 1501-510 Compilation successful for file _evb_vars.f.
> /lib/cpp -P -DMPI -DMASSLIB -DNMLEQ -DCLINK_PLAIN -DXLF90
> -DPOE evb_input.f > _evb_input.f
> mpxlf90_r -bmaxdata:0x80000000 -c -qfixed -c -qfree=f90 -o
> evb_input.o _evb_input.f
> ** evb_input === End of Compilation 1 ===
> ** evb_input_alloc === End of Compilation 2 ===
> ** evb_input_dealloc === End of Compilation 3 ===
> 1501-510 Compilation successful for file _evb_input.f.
> /lib/cpp -P -DMPI -DMASSLIB -DNMLEQ -DCLINK_PLAIN -DXLF90
> -DPOE evb_init.f > _evb_init.f
> "evb_init.f", line 18.12: 1506-296 (S) #include file "mpif.h"
> not found.
> 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.
>
>
> =======================
>
>
> I followed the same process for amber 8 installation on the
> same machine,
> and it was successful.
>
> Please give me some idea.
>
> Have a nice day.
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
> --------------------------------------------------------------
> ---------
> 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 Sun Aug 27 2006 - 06:07:15 PDT
