AMBER Archive (2006)

Subject: AMBER: Error compiling amber on parallel (MPICH)

From: Muhammad Naim Mohmad Rouyan (m_naim_at_putra.upm.edu.my)
Date: Wed Dec 27 2006 - 00:35:47 CST

Dear Amber users,

I have been attempting to compile a parallel version of amber 8 (Sun HPC
ClusterTools 5) on a Sun Fire V1280 running on Solaris 9 using sparc as my
compiler. The serial version compiles with no problems. Now I'm trying to
use mpich flag for parallel and try compile 'make parallel'. It get an
error like this:

.
.
.
cd lmod; make
/lib/cpp -I/opt/sfw/mpich-1.2.7p1/include -P -I/opt/sfw/amber8/src/include
-DMPI
   lmod.f > _lmod.f
f90 -c -O2 -o lmod.o _lmod.f
ar rv lmod.a xmin/*.o nvib/*.o lmod/*.o
a - xmin/xmin.o
a - nvib/nvib.o
a - lmod/lmod.o
ar: creating lmod.a
ar: writing lmod.a
ranlib lmod.a
f90 -free -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 d
rates.o indexn.o kmat.o pearsn.o plane.o remarc.o nmrcal.o nmrred.o
restal.o g
etnat.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
paralle
l.o jnrg.o shake.o ene.o mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o
nmls
rc.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
amope
n.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 -lm \
        ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
Undefined first referenced
 symbol in file
mpi_allreduce_ egb.o
mpi_comm_free_ sander.o
mpi_init_ sander.o
mpi_recv_ ew_fft.o
mpi_wait_ ew_fft.o
mpi_comm_rank_ sander.o
mpi_barrier_ sander.o
mpi_bcast_ sander.o
mpi_finalize_ mexit.o
mpi_comm_size_ sander.o
mpi_comm_split_ sander.o
mpi_isend_ ew_fft.o
mpi_abort_ mexit.o
mpi_sendrecv_ parallel.o
mpi_reduce_ parallel.o
mpi_send_ new_time.o
ld: fatal: Symbol referencing errors. No output written to sander
*** Error code 1
make: Fatal error: Command failed for target `sander'
Current working directory /opt/sfw/amber8/src/sander
*** Error code 1
make: Fatal error: Command failed for target `parallel'

The config.h was made using the following command.

./configure -mpich sparc

If anyone could advise me i would be most grateful.

Many regards

naim, UPM

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