AMBER Archive (2006)

Subject: Re: AMBER: Installation amber 9 on IBM SP4

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Aug 24 2006 - 14:00:04 CDT

I don't have vtanh.

Would you send me the patch?

Thank you and have a nice day.

On 8/24/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> 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_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 Myunggi Yi
> > Sent: Thursday, August 24, 2006 09:06
> > To: amber_at_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
> > --------------------------------------------------------------
> > ---------
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> >
>
>
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-- 
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
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