[CPMD-list] IFC: "undefined reference"
Dr. Balasubramanian Sundaram
bala at jncasr.ac.in
Thu Feb 26 10:37:31 CET 2004
Dear All,
Just an update. I downloaded Intel MKL's more recent version, v6.1.
With this version, the -lg2c LFLAG is not necessary, and cpmd compiled
fine without it also (the newer libmkl_lapack.a does not depend on
s_copy).
Yet, I am getting the following error for a parallel job, run on 1
processor,
through lam.
=============================
mpirun -np 1 ../CPMD-3.7.2/SOURCE/cpmd.x system.in
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).
mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
There is no SIGSEGV violation now. But, the job does not start. Your
help is
most appreciated. Thanks.
Regards,
Bala
--------------Current Makefile that produced a cpmd.x---------------
FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7
LFLAGS = \
-L/opt/intel/mkl61/lib/32 -lmkl_lapack \
-lmkl_ia32 -lguide \
-static-libcxa -Xlinker -Bstatic -lsvml \
-Vaxlib -Xlinker -Bdynamic -static
CFLAGS = -c -O2 -Wall
CPP = /lib/cpp -P -C -traditional
CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \
-DMP_LIBRARY=__MPI -DMYRINET -DLINUX_IFC
NOOPT_FLAG =
CC = mpicc
FC = mpif77
LD = mpif77
"Dr. Balasubramanian Sundaram" wrote:
>
> Dear Axel,
> Thanks for your help. I was not doing a "make install" earlier (for
> lam),
> as I wanted the original rpm-loaded binaries to be intact. Anyway, after
> your advice, I did the full installation, and cpmd compiled fine. (Also,
> the "-us" flag was not necessary). So, as you pointed out, it appears to
> have been an issue of misdirected library searches or something of that
> sort.
> Thanks!
>
> Currently, my Makefile (which created a cpmd.x successfully) looks
> like:
> --------------------------------------
> FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7
> LFLAGS = \
> -L/opt/intel/mkl60/lib/32 -lmkl_lapack \
> -lmkl_ia32 -lmkl_p4 -lguide \
> -static-libcxa -Xlinker -Bstatic -lsvml \
> /usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.1/libg2c.a \
> -Vaxlib -Xlinker -Bdynamic
> CFLAGS = -c -O2 -Wall
> CPP = /lib/cpp -P -C -traditional
> CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \
> -DMP_LIBRARY=__MPI -DMYRINET -DLINUX_IFC
> NOOPT_FLAG =
> CC = mpicc
> FC = mpif77
> LD = mpif77
> -----------------------------------
>
> NOTE: The -lg2c seems to be required by libmkl_lapack; If I remove it
> from
> LFLAGS, I get an undefined reference for s_copy. The following is the
> error message.
> ====================
> /opt/intel/mkl60/lib/32/libmkl_lapack.a(ilaenv.o)(.text+0x52a): In
> function `__MKL_SERV_ilaenv':
> : undefined reference to `s_copy'
> ===================
>
> Strangely, cpmd.x give a runtime error. I have lambooted 2 nodes
> properly, and actually tried to run a job only on one node. This job
> runs fine for a serial cpmd executable that was compiled with IFC and
> MKL.
> So, the input file seems to be fine.
> I get the following runtime error.
> -----------------------------
> PROGRAM CPMD STARTED AT: Thu Feb 26 12:31:44 2004
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> cpmd.x 08677134 Unknown Unknown Unknown
> cpmd.x 08243965 Unknown Unknown Unknown
> cpmd.x 00000000 Unknown Unknown Unknown
> -----------------------------------------------------------------------------
> It seems that [at least] one of the processes that was started with
> mpirun did not invoke MPI_INIT before quitting (it is possible that
> more than one process did not invoke MPI_INIT -- mpirun was only
> notified of the first one, which was on node n0).
>
> mpirun can *only* be used with MPI programs (i.e., programs that
> invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
> to run non-MPI programs over the lambooted nodes.
> -----------------------------------------------------------------------------
>
> Thanks again for your considerable help,
>
> Best Regards,
> Bala
>
> Axel Kohlmeyer wrote:
> >
> > On Wed, 25 Feb 2004, Dr. Balasubramanian Sundaram wrote:
> >
> > BS> Dear All,
> > BS>
> > BS> I have been having this trivial, yet nagging problem, and thought
> > BS> I should seek help to preserve my sanity!
> > BS>
> > BS> Details: CPMD 3.7.2, IFORT (IFC's new name): version 8.0,
> > BS> P4 at 3.0 GHz (with HT), Mandrake Linux 9.2 (kernel 2.4.22), with
> > BS> Intel's MKL version 6.0, gcc, lam-mpi version 7.0.4
> > BS>
> > BS> I compiled lam-mpi using ifort compiler, using "FFLAGS=-us" option
> > BS> (i.e., equivalent of "-assume underscore"). lam-mpi compiled fine,
> > BS> and I could compile and run their examples/pi/fpi code properly
> > BS> on two nodes.
> >
> > dear bala,
> >
> > stupid question: why are you messing with the underscoring, when
> > you are compiling cpmd _and_ lam with the intel compiler anyway?
> >
> > BS>
> > BS> I have problems at the link stage for CPMD. I provide at the end of this
> > BS> mail, my Makefile. Here, I give the output of the command,
> > BS>
> > BS> /home/bala/lam-7.0.4/tools/wrappers/mpif77 -showme
> > BS>
> > BS> OUTPUT:
> > BS> ifort -I/usr/include -llammpio -llamf77mpi -lmpi -llam -lutil
> >
> > hmm. you seem to be running lam from the compilation directory.
> > most likely you are not picking up the new libraries, but
> > an old set, that is installed in the default library search
> > path. if my assertion is correct, than you would have to run
> > 'make install' first. alternatively, you may be able to get
> > away with telling the linker via -L/home/bala/lam-7.0.4/and/so/on...
> > where to pick up the new libraries. but then again, you will
> > run into trouble when you start the lam daemons, since lamboot
> > will not find the matching executables.
> >
> > BS>
> > BS> All CPMD routines compile fine, but at the linker stage, I get the
> > BS> error message,
> > BS> =================
> > BS> my_para.o(.text+0x6): In function `my_start_':
> > BS> : undefined reference to `mpi_init_'
> > BS> my_para.o(.text+0xbe5): In function `my_end_':
> > BS> : undefined reference to `mpi_finalize_'
> > BS> =================
> > BS>
> > BS> I appreciate your help,
> > BS>
> > BS> Thanks,
> > BS>
> > BS> Regards,
> > BS> Bala
> > BS> -------------------------MAKEFILE HEADER--------------------------
> > BS>
> > BS> FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7 -us
> > BS>
> > BS> LFLAGS = \
> > BS> -L/opt/intel/mkl60/lib/32 -lmkl_lapack \
> > BS> -lmkl_ia32 -lmkl_p4 -lguide \
> > BS> -static-libcxa -Xlinker -Bstatic -lsvml \
> > BS> /usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.1/libg2c.a \
> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> >
> > you should not need this. this is the g77 runtime. in fact it
> > may collide with the intel fortran runtime.
> >
> > hope this helps,
> > axel kohlmeyer.
> >
> > BS> -Vaxlib -Xlinker -Bdynamic
> > BS> CFLAGS = -c -O2 -Wall
> > BS> CPP = /lib/cpp -P -C -traditional
> > BS>
> > BS> CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT \
> > BS> -DMP_LIBRARY=__MPI -DMYRINET -DLINUX_IFC
> > BS> NOOPT_FLAG =
> > BS>
> > BS> CC = /home/bala/lam-7.0.4/tools/wrappers/mpicc
> > BS> FC = /home/bala/lam-7.0.4/tools/wrappers/mpif77
> > BS> LD = /home/bala/lam-7.0.4/tools/wrappers/mpif77
> > BS> ---------------------------------------------------------------------
> > BS> _______________________________________________
> > BS> CPMD-list mailing list
> > BS> CPMD-list at cpmd.org
> > BS> http://www.cpmd.org/mailman/listinfo/cpmd-list
> > BS>
> > BS>
> >
> > --
> >
> > =======================================================================
> > Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de
> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > =======================================================================
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