AMBER Archive (2003)

Subject: Re: Amber7 & mpich

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Tue Feb 04 2003 - 12:07:47 CST

On Tue, 2003-02-04 at 09:27, FyD wrote:
> Dear All,
>
> I still have problems to compile AMBER7 (pgi compilators) with mpich 1.2.4:
>
> 1- I used the following MACHINE file:
> http://www.amber.ucsf.edu/amber/cluster_info/Machine.pgf77_mpich
>
> 2- Setted "setenv SYSDIR Machines/standard" in this file
>
> 3- I put the file "farg.f" in ~src/lib, ~src/lapack and ~src/sander directories
> and compiled 'manually' it using "pgf77 -c Msecond_underscore farg.f"
                                       -----^
I hope this is just a typo in the message (I mean missing dash). Also,
let's make sure we're talking about the same farg.f file. Here is the
contents of ours:
-----------------
      integer function mpir_iargc()
      mpir_iargc = iargc()
      return
      end

      subroutine mpir_getarg( i, s )
      integer i
      character*(*) s
      call getarg(i,s)
      return
      end
------------------

>
> 4- I ran "make install" either in the ~/src/sander or ~/src directories: I get
> always the same error message:
>
> pgf77 -o sander 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 newvel.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 grdmax.o rfree.o
> rgroup.o ddotp.o random.o lsqfit.o amopen.o debug.o ew_recip_reg.o
> ew_handle_dips.
> o ew_dipole_recip.o mexit.o egb.o new_time.o extra_pts.o thermo_int.o
> reorderwat.o matinv.o decomp.o ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o
> /hom
> e/fyd/amber7/src/Machines/standard/sys.a -lm -L/usr/pgi/linux86/lib farg.o -lmpich
                                        ---------^
Hm, how come I don't see the directory (after -L switch) pointing to the
location of your mpich libraries? (it seems unlikely you'd have them
installed under pgi, and it's also unlikely you have added them to
LD_LIBRARY_PATH). Where is your mpich-1.2.4 installed and what are the
following variables in your MACHINE file set to?

setenv MPICH_HOME /usr/lib/mpich
setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPICH_LIB mpich

> sander.o: In function `trajene':
> _sander_.f:1247: undefined reference to `mpi_init__'
> _sander_.f:1248: undefined reference to `mpi_comm_rank__'
> _sander_.f:1249: undefined reference to `mpi_comm_size__'
> _sander_.f:1450: undefined reference to `mpi_bcast__'
> _sander_.f:1451: undefined reference to `mpi_barrier__'
> _sander_.f:1590: undefined reference to `mpi_bcast__'
> nmrcal.o: In function `nmrcal':
> _nmrcal_.f:884: undefined reference to `mpi_bcast__'
> _nmrcal_.f:886: undefined reference to `mpi_bcast__'
>
> etc...
>
> ew_direct.o(.text+0x2394): undefined reference to `mpi_barrier__'
> ew_recip.o: In function `do_pmesh_kspace__':
> ew_recip.o(.text+0xd6a): undefined reference to `mpi_barrier__'
>
> Any idea what is the problem ?
>
> Thanks a lot, regards, Francois
> 

-- 
===================================================================
Viktor Hornak
CSB computational facility   Phone: (631)632-1439
SUNY at Stony Brook          Fax:   (631)632-1555
Stony Brook, NY 11794-5115   E-mail: viktor.hornak_at_sunysb.edu
===================================================================