[mpich-discuss] Compile error with "undefined reference"

[tetsuro_kikuchi at jesc.or.jp]

Thank you for you advice, Mr. Chan.

I used mpif90 as compiler instead of ifort in the build scripts of the
program and its pre-processors. Then it worked well!!

Thank you again for your consideration and support.

Kind regards,

Tetsuro






The libraries seem to be built OK (compiled by mpif90). But your program is
still
linked by ifort (from bldit.cctm_errorlog_whole110617.txt), the link
command that
caused unresolved symbols is

/opt/intel/composerxe-2011.4.191/bin/intel64/ifort -liomp5 -lpthread
VGRD_DEFN.o CGRID_SPCS.o HGRD_DEFN.o GRID_CONF.o PCGRID_DEFN.o STD_CONC.o
AVG_CONC.o WVEL_DEFN.o PMEM_DEFN.o BIOG_EMIS.o BEIS_DEFN.o DEPVVARS.o
DEPV_DEFN.o UDTYPES.o STK_EMIS.o STK_PRMS.o PTMAP.o PTBILIN.o PTMET.o
PT3D_DEFN.o AERO_EMIS.o EMIS_DEFN.o VDIFF_MAP.o hrdata_mod.o AERO_INFO.o
SOA_NEWT.o PAGRD_DEFN.o advstep.o driver.o hcontvel.o hveloc.o sciproc.o
wr_aconc.o wr_cgrid.o wr_conc.o distr_env.o par_init.o par_term.o diffmsg.o
flcheck.o grdcheck.o initscen.o load_cgrid.o opconc.o setup_logdev.o
couple.o ppmv_msmr.o advbc_map.o hadvyppm.o hppm.o rdbcon.o x_ppm.o
x_yamo.o y_ppm.o y_yamo.o zfdbc.o vppm.o zadvyppm.o deform.o hcdiff3d.o
hdiff.o rho_j.o beis3.o cgrid_depv.o checkmem.o chkgrid.o conv_cgrid.o
czangle.o delta_zs.o eddyx.o fire_plmris.o gas_depv_map.o getfline.o
getparb.o hrno.o m3dry.o matrix.o opddep.o opdepv_diag.o opemis.o
openlayout.o opmet.o oppt3d_diag.o opssemis.o parsline.o plmris.o plsp
 rd.o preplm.o rddepv.o rdmet.o ssemis.o tmpbeis.o tri.o ungridb2.o
vdiffacm2.o wrdaymsg.o write3_distr.o phot.o hrcalcks.o hrdriver.o hrg1.o
hrg2.o hrg3.o hrg4.o hrinit.o hrprodloss.o hrrates.o hrsolver.o
aero_driver.o aero_subs.o hetchem.o isocom.o isofwd.o isorev.o opdiam.o
opvis.o orgaer5.o aero_depv.o acmcld.o aq_map.o aqchem.o cldproc_acm.o
convcld_acm.o getalpha.o hlconst.o indexn.o rescld.o scavwdep.o
set_aeconcmin.o pa_init.o pa_irr.o pa_irr_ctl.o pa_mkhdr.o pa_output.o
pa_update.o cksummer.o findex.o get_envlist.o lstepf.o subhdomain.o
subhfile.o  -L/home/jesc/cmaqv4.7.1/lib/stenex/Linux2_x86_64 -lse_snl
-L/home/jesc/cmaqv4.7.1/lib/pario/Linux2_x86_64 -lpario
-L/usr/local/mpich2-1.4/lib -lmpich
-L/home/jesc/cmaqv4.7.1/lib/ioapi/Linux2_x86ifc -lioapi
-L/home/jesc/cmaqv4.7.1/lib/netCDF/Linux2_x86_64ifort -lnetcdf -o
CCTM_e1a_Linux2_x86_64intel

Notice that you only linked with -lmpich with ifort.  You need to use
mpif90 instead.

A.Chan


----- Original Message -----
> Thank you very much for your consideration, Mr. Chan.
>
> I attach below the whole log file generated when the build script of
> my
> program was run ("bldit.cctm_errorlog_whole110617.txt"), as well as
> the log
> files of the required libraries ("bldit.se.log.txt" and
> "bldit.pario.log.txt"). If you need any other information, please ask
> me.
>
> Kind regards,
>
> Tetsuro
>
> (See attached file: bldit.cctm_errorlog_whole110617.txt)(See attached
> file:
> bldit.se.log.txt)(See attached file: bldit.pario.log.txt)
>
>
>
>
>
> Since we don't have your source code, so looking your build scripts
> isn't
> easy for us to spot the errors. Given you are still getting unresolved
> reference
> of MPICH2's internal symbols, my guess is that your linking is still
> wrong.
> Could you send us the output of your Makefiles (as seen on your
> terminal)
> which
> could be easier for us to spot the errors.
>
> A.Chan
>
> ----- Original Message -----
> > Thank you very much for your advice, Mr. Dave Goodell.
> >
> > I have tried again to build my program. I used the latest version of
> > MPICH2
> > (mpich2-1.4) this time. I have configured it as follows to let the
> > compiler
> > flags being included in the wrappers (the configure log
> > ("c_mpich2-1.4.txt") is attached below):
> >
> > ./configure --disable-fast CFLAGS=-O2 FFLAGS=-O2 CXXFLAGS=-O2
> > FCFLAGS=-O2
> >
> > My program, called "CCTM", uses two kinds of library for parallel
> > processing (named "STENEX" and "PARIO"). These libraries are
> > compiled
> > using
> > the wrapper of MPICH (mpif90). (Please refer to the part "#> Set
> > full
> > path
> > of Fortran 90 compiler" in "User Input Section" of the attached
> > compile
> > scripts for these libraries ("bldit.se_script.txt" and
> > "bldit.pario_script.txt").)
> > I run the build script of CCTM after recompiling the two
> > above-mentioned
> > libraries using the new MPICH wrapper. However, it failed again with
> > messages "undefined reference to '...'". The C source codes for
> > which
> > "undefined reference" errors were annouced were a little bit
> > different
> > from
> > the previous ones. The error part of the build log
> > ("bldit.cctm_errorlog110617.txt") is attached below.
> > Then, I assembled the working compile line of the build script by
> > using
> > "mpif90 -show". (Please refer to "mpif90 -show.txt" attached below.)
> > The
> > modified build script ("bldit.cctm_script_modified110617.txt") is
> > also
> > attached below. The modifications in the build script I made were as
> > follows (all in "User Input Section"):
> >
> > 1. "-lopa -lmpl -lrt" was added to "LINK_FLAGS".
> > 2. "-O2" was added to "C_FLAGS".
> > 3. The line "set FC_FLAGS = "-O2"" was added.
> >
> > This build script could not also build the executable of CCTM with
> > the
> > same
> > error messages as the first trial this time.
> >
> > Could you provide the suggestion for solving this problem?
> >
> > Kind regards,
> >
> > Tetsuro
> >
> > (See attached file: c_mpich2-1.4.txt) (See attached file:
> > bldit.se_script.txt)(See attached file: bldit.pario_script.txt)(See
> > attached file: bldit.cctm_errorlog110617.txt)(See attached file:
> > mpif90
> > -show.txt)(See attached file: bldit.cctm_script_modified110617.txt)
> >
> >
> >
> >
> >
> >
> > How are you building your application? Based on skimming the error
> > messages it looks like you are not using the compiler wrappers
> > ("mpicc" and
> > friends) and are instead attempting to link with the libmpich
> > directly.
> >
> > If this is the case, that will not work unless you are very careful.
> > MPICH2 uses several libraries internally and they must all be
> > present
> > and
> > listed on the link line in the correct order. My recommendation is
> > to
> > use
> > the compiler wrappers. If you can't or won't do that for some
> > reason,
> > you
> > can try to assemble a working compile line for yourself by using
> > "mpicc
> > -show" to show the compile/link flags that you will need to use.
> >
> > -Dave
> >
> > On Jun 16, 2011, at 2:26 AM CDT, tetsuro_kikuchi at jesc.or.jp wrote:
> >
> > > Hello.
> > >
> > > I'm trying to compile an executable of a program using MPICH2
> > > (version:
> > > 1.3.2p1). However, it failed with messages "undefined reference to
> > '...'".
> > > The error part of the compile log
> > > ("bldit.cctm_errorlog110616.txt")
> > > is
> > > attached below. Could anyone teach me what is wrong and how to
> > > solve
> > > this
> > > problem?
> > > My system uses Ubuntu Linux (version 11.04 (64-bit)) as OS and
> > > Intel
> > > Fortran Composer XE 2011 for Linux as compiler. I also attach the
> > configure
> > > log of MPICH2 ("c.txt") and a set of the related C source codes to
> > > this
> > > error ("initthread.c", "param_vals.c", "mpid_vc.c", "init.c" and
> > > "tcp_init.c") below.
> > >
> > > Tetsuro
> > >
> > > (See attached file: bldit.cctm_errorlog110616.txt)(See attached
> > > file:
> > > c.txt)(See attached file:
> > > initthread.c(mpich2-1.3.2p1&src&mpi&init).txt)
> > > (See attached file:
> > > param_vals.c(mpich2-1.3.2p1&src&util&param).txt)(See
> > > attached file: mpid_vc.c(mpich2-1.3.2p1&src&mpid&ch3&src).txt)(See
> > attached
> > > file: init.c(mpich2-1.3.2p1&src&mpi&init).txt)(See attached file:
> > >
> >
>
tcp_init.c(mpich2-1.3.2p1&src&mpid&ch3&channels&nemesis&nemesis&netmod&tcp).txt)

>
> >
> > >
> >
>
<bldit.cctm_errorlog110616.txt><c.txt><initthread.c(mpich2-1.3.2p1&src&mpi&init).txt><param_vals.c(mpich2-1.3.2p1&src&util&param).txt><mpid_vc.c(mpich2-1.3.2p1&src&mpid&ch3&src).txt><init.c(mpich2-1.3.2p1&src&mpi&init).txt><tcp_init.c(mpich2-1.3.2p1&src&mpid&ch3&channels&nemesis&nemesis&netmod&tcp

>
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