AMBER Archive (2004)

Subject: Re: AMBER: Compiling using pgf90

From: David Lomelin (dlomelin_at_itsa.ucsf.edu)
Date: Wed Oct 06 2004 - 15:30:34 CDT

My path was set correctly, but the make LOCALFLAGS="-fastsse" serial did
the trick. It now compiles and runs without a segmentation fault error
using pgf90.
Thanks a lot!

--David

On Wed, 6 Oct 2004, Craig TOEPFER wrote:

>
> David,
>
> You need to set your PATH to:
>
> /usr/pgi/linux86-64/5.2/bin
>
> such that when you issue the command "which pgf90" you should see:
>
> /usr/pgi/linux86-64/5.2/bin/pgf90
>
> I also recommend for best performance that the "-fastsse" switch be used
> for compilation. This can be done when you invoke make as follows:
>
> make LOCALFLAGS="-fastsse" serial
>
> -craig
>
>
> David Lomelin wrote:
> > Amber users:
> >
> > I have been able to compile and successfully run Amber8 using
> > Intel?s ifort compiler and Math Kernel Library; however, I was told that
> > the Portland Group?s compilers might improve performance, so I have been
> > trying to recompile Amber8 using the Portland Group compilers. I have a
> > dual processor opteron system using Fedora Core 2 ? I have installed
> > MPICH but I have not tried compiling Amber8 using those libraries
> > though. After using ?configure ?opteron pgf90? and running ?make
> > serial?, it successfully compiles but when I try and run a simple
> > minimization, I get a segmentation fault error. I found that the
> > configure script had the directory of the ACML and LAPACK libraries
> > hardcoded and did not point at the correct directory, so I changed it to
> > my local installation:
> >
> > if [ -e $PGI/linux86/5.2/lib/liblapack.a ]; then ?
> >
> > instead of:
> >
> > if [ -e /usr/pgi/lib/liblapack.a ?.
> >
> > This did not fix the problem however.
> >
> > The Portland group?s website offers alternate versions of the configure
> > script that should fix any problems, but I have not been able to get
> > them to work. http://www.pgroup.com/resources/amber/amber8_pgi52.htm
> > When I use their configure script and run ?configure ?nopar ?opteron
> > ?acml ?lapack pgf90? followed by ?make serial?, I get the following
> > error, after which compilation halts:
> >
> > .
> >
> > .
> >
> > .
> >
> > .
> >
> > pgf90 -Mfree -o sander trace.o lmod.o decomp.o icosasurf.o egb.o
> > findmask.o pb_force.o sander.o cshf.o noecalc.o noeread.o caldis.o
> > calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o
> > nmrcal.o nmrred.o restal.o getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o
> > tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o
> > chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.o rdparm.o mdread.o
> > locmem.o runmd.o getcor.o r6ave.o r6drv.o aveint.o degcnt.o corf.o
> > threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.o jnrg.o
> > shake.o ene.o mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o nmlsrc.o
> > ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o ew_direct.o
> > ew_recip.o pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o
> > lsqfit.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
> > ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.o
> > assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o mdm.o pb_init.o
> > constantph.o prn_dipoles.o \
> >
> > ../lmod/lmod.a -lacml -llapack -lblas \
> >
> > ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
> >
> > icosasurf.o(.text+0x1cb4): In function `icosasurf_gen_rot_mat_':
> >
> > : undefined reference to `__mth_i_dcosx'
> >
> > icosasurf.o(.text+0x1ccb): In function `icosasurf_gen_rot_mat_':
> >
> > : undefined reference to `__mth_i_dsinx'
> >
> > egb.o(.text+0x1ba3): In function `genborn_egb_':
> >
> > : undefined reference to `__mth_i_dlogx'
> >
> > egb.o(.text+0x1ef1): In function `genborn_egb_':
> >
> > : undefined reference to `__mth_i_dlogx'
> >
> > .
> >
> > .
> >
> > .
> >
> > .
> >
> > Any help would be appreciated. Thank you.
> >
> > --David
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