AMBER Archive (2004)

Subject: AMBER: Compiling using pgf90

From: David Lomelin (dlomelin_at_itsa.ucsf.edu)
Date: Tue Oct 05 2004 - 20:33:22 CDT

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu