AMBER Archive (2008)

Subject: Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'"

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Thu Apr 24 2008 - 14:16:50 CDT

The combination of replies got me there. Thanks!

What I needed was "-lfmpi"

The ScaMPI was compiled with an older version of ifort. Will that
cause issues with pmemd? I just ran the tests (pmemd and
pmemd.AMOEBA), and they all passed. Even if you think there might be
issues, I'm not sure I'll be able to do anything about it.

Below, for anyone else who has interest, is my linux_p4.ifort.scali
that works. If "-lfmpi" is added to any line containing "-lmpi" in
the gfortran version (earlier), parallel pmemd also compiles. If
anyone is curious, I could compare benchmarks between them...

===========================================================
>more linux_p4.ifort.scali
DIRFRC_DEFINES = -DDIRFRC_COMTRANS -DDIRFRC_EFS
MPI_DEFINES = -DMPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBS = -L$(MPI_LIBDIR) -lfmpi -lmpi -Wl -lpthread

CPP = /lib/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = ifort
MODULE_SUFFIX = mod
F90FLAGS = -c -auto
F90_OPT_DBG = -g -traceback
F90_OPT_LO = -tpp7 -O0
F90_OPT_MED = -tpp7 -O2
F90_OPT_HI = -tpp7 -xW -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS =

LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH) -lmpi -lfmpi
===========================================================

On Thu, Apr 24, 2008 at 1:51 PM, Gustavo Seabra
<gustavo.seabra_at_gmail.com> wrote:
> Hi,
>
> I did have some problems compiling pmemd in the past, but that was
> actually related to MKL10.0 (the thread starts here:
> http://structbio.vanderbilt.edu/archives/amber-archive/2008/0529.php).
> Unfortunately, I have never used Scali MPI myself. However, this
> question has come up before, and I believe the thread bob was
> referring to was this one:
> http://structbio.vanderbilt.edu/archives/amber-archive/2007/1245.php
>
> HTH,
> Gustavo.
>
>
>
> On Thu, Apr 24, 2008 at 11:04 AM, Robert Duke <rduke_at_email.unc.edu> wrote:
> > Okay, you need to use the same fortran 90 for both compiling scali and
> > pmemd, which I presume you are doing, but since you are mucking with
> > gfortran, and I don't, you are sort of on your own unless you want to use
> > ifort. Then I believe Gustavo Seabra posted some mail to the reflector
> > about compiling pmemd with scali? I did a quick search and did not find it,
> > but I know it is there somewhere; maybe Gustavo will reply. I don't have
> > access to scali myself, so don't support it. I don't touch gfortran because
> > the whole point of pmemd is performance (I know it is getting better; still
> > I would bet on ifort staying ahead of it); all that is probably going on
> > here is that you either are pointing at the wrong libraries, or the linkage
> > convention for "name mangling" in the compiler is not correct - and I don't
> > know what latitude you have on this for gfortran. You can look at the
> > "undefined reference" form and go looking for exported symbols in the scali
> > mpi library, first confirming where you can find an exported symbol with
> > mpi_bcast in it, and then looking at how it is decorated - this can be done
> > with nm and grep pretty easily. I reiterate, gfortran is untested by me for
> > both correctness and performance. It could be bad on either score, easily
> > (or just fine; point is, I don't know, and you are "outside your warranty
> > here" ;-)).
> > Regards - Bob
> > ----- Original Message ----- From: "Lachele Foley (Lists)"
> > <lf.list_at_gmail.com>
> > To: <amber_at_scripps.edu>
> > Sent: Thursday, April 24, 2008 10:22 AM
> > Subject: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'"
> >
> >
> >
> >
> >
> > > I'm trying to compile parallel pmemd for Amber 10. The serial compile
> > > goes fine.
> > >
> > > Short version: At the final stage ("(compiler) -o pmemd
> > > gbl_constants.o (etc.)"), I get lots (>100) of variations on:
> > >
> > > mdin_ctrl_dat.o(.text+0xa456): In function
> > > `__mdin_ctrl_dat_mod__bcast_mdin_ctrl_dat':
> > > : undefined reference to `mpi_bcast_'
> > >
> > > Can this be made to work for us?
> > >
> > > More info:
> > >
> > > We have ScaMPI (Scali MPI). I've tried gfortran and ifort. Gfortran
> > > compiles in serial just fine (and I assume ifort would, too). Both
> > > have the same mpi issues in the parallel compile. I tried setting
> > > -fno-second-underscore because that was indicated in the config.h for
> > > parallel amber, but it didn't change anything. The parallel version
> > > of Amber 10 compiles and tests fine (with some trivial and unrelated
> > > exceptions). $MPI_HOME is set to /opt/scali.
> > >
> > > Here's the config data file I made for gfortran with ScaMPI. I got a
> > > file that works with gfortran by starting with the ifort file and
> > > deleting compiler options until it stopped complaining. I didn't
> > > delete options from the ifort version when I tried ifort, but it
> > > behaved the same WRT the mpi calls. If you need more info, just say.
> > >
> > >
> > > > more linux_p4.gfortran.scali
> > > >
> > > MPI_DEFINES = -DMPI
> > > MPI_INCLUDE = -I$(MPI_HOME)/include
> > > MPI_LIBDIR = $(MPI_HOME)/lib
> > > MPI_LIBS = -L$(MPI_LIBDIR) -lmpi -Wl -lpthread
> > >
> > > DIRFRC_DEFINES = -DDIRFRC_COMTRANS -DDIRFRC_EFS
> > > CPP = /lib/cpp
> > > CPPFLAGS = -traditional -P
> > > F90_DEFINES = -DFFTLOADBAL_2PROC
> > >
> > > F90 = gfortran
> > > MODULE_SUFFIX = mod
> > > F90FLAGS = -c -fno-second-underscore
> > > F90_OPT_DBG = -g -traceback
> > > F90_OPT_LO = -O0
> > > F90_OPT_MED = -O2
> > > F90_OPT_HI = -ip -O3
> > > F90_OPT_DFLT = $(F90_OPT_HI)
> > >
> > > CC = gcc
> > > CFLAGS =
> > >
> > > LOAD = gfortran
> > > LOADFLAGS =
> > > LOADLIBS = -lmpi -Wl
> > >
> > >
> > > Thanks!
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > 2-0263
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
2-0263
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu