compile problem with mvapich

Axel akoh... at gmail.com
Wed Aug 27 04:10:11 CEST 2008



On Aug 26, 9:45 pm, shanghui <shangh... at gmail.com> wrote:
>  Hello Everyone:
>
> I 've been trying to compile cp2k for a few days on our clusters, I have
> compiled the sopt version ,and it works well . But when I began to compile
> the popt version, I used the intel  10.1.015, mkl 10.0.1.014 and mpif90 in
> mvapich-1.0.0  ( the CPU is Xeon E5420) , I have compiled with  'make
> ARCH=Linux-x86-64-intel VERSION=popt' ,and it give me a exe---cp2k.popt. The
> problem is: when I run it with :mpirun -np 2  -machinefile mech
> /share/apps/cp2k_parallel  H2O.inp ,it give me the error message as follows
> :
>
> "
>  Number of independent orbital functions:        57
>
>   Extrapolation method: initial_guess
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC                Routine            Line
> Source
>
> Stack trace terminated abnormally.
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image              PC                Routine            Line
> Source
> libintlc.so.5      00002AAAAB880FDA  Unknown               Unknown  Unknown
> libintlc.so.5      00002AAAAB8801DA  Unknown               Unknown  Unknown
> libifcore.so.5     00002AAAAB14455A  Unknown               Unknown  Unknown
> libifcore.so.5     00002AAAAB0CF978  Unknown               Unknown  Unknown
> libifcore.so.5     00002AAAAB0DA69C  Unknown               Unknown  Unknown
> libpthread.so.0    00000038DC60DE70  Unknown               Unknown  Unknown
> libc.so.6          00000038DBE67274  Unknown               Unknown  Unknown
> libc.so.6          00000038DBE4BF03  Unknown               Unknown  Unknown
> libintlc.so.5      00002AAAAB880006  Unknown               Unknown  Unknown
> libintlc.so.5      00002AAAAB8810CC  Unknown               Unknown  Unknown
>
> Stack trace terminated abnormally.
> mpispawn.c:303 Unexpected exit status
>
> Child exited abnormally!
> Killing remote processes...forrtl: error (69): process interrupted (SIGINT)
> Image              PC                Routine            Line
> Source
> libpthread.so.0    0000003D1F20DD4D  Unknown               Unknown  Unknown
> cp2k_parallel      000000000170C542  Unknown               Unknown  Unknown
> libpthread.so.0    0000003D1F2062F7  Unknown               Unknown  Unknown
> libc.so.6          0000003D1EACE85D  Unknown               Unknown  Unknown
> DONE
>
> "
>
> I have used this mkl'lib and mvapich-1.0.0 to compiled siesta_parallel ,and
> it works well. I do not know why they can not work for cp2k_popt.

there are a number of potential problems.

- cp2k is much more demanding in standard compliance than
  other codes.
- cp2k requires more "automatic" storage, than other codes.
  make sure that your stack is large enough or use -head-arrays 64
  (read the intel compiler documentation for details).
- not sure how compatible the scalapack/blacs in intel mkl
  are with MVAPICH. i have had good success with openmpi.

please note that you link with a threaded MKL and thus
you should make sure that OMP_NUM_THREADS is set to 1 or
else you may have unwanted cpu overloading as MKL 10 and beyond
by default multi-threads across all available cores and thus
collides with potential MPI tasks.

cheers,
   axel.
>
> and this is my popt arch file:
> "CC       = cc
> CPP      = cpp
> FC       = mpif90  -FR
> LD       = mpif90
> AR       = ar -r
> DFLAGS   = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK
> -D__FFTW3  -D__LIBINT
> CPPFLAGS = -traditional -C $(DFLAGS) -P
> FCFLAGS  = $(DFLAGS)  -O1
> LDFLAGS  = $(FCFLAGS)
> -L/opt/intel/mkl/10.0.1.014/lib/em64t-L/opt/intel/fce/10.1.015/lib \
>            -L/usr/mpi/intel/mvapich-1.0.0/lib/
> LIBS     = /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_scalapack_lp64.a  \
>            /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_blacs_lp64.a  \
>            /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.a  \
>            /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a  \
>           /opt/intel/fce/10.1.015/lib/libguide.a -lpthread -lsvml \
>           /usr/local/lib/libfftw3.a \
>           /home/shanghui/cp2k/libint_tools/libint_cpp_wrapper.o\
>           /home/shanghui/libint-1.1.2/lib/libderiv.a \
>            /home/shanghui/libint-1.1.2/lib/libint.a \
>           -lstdc++
>
> OBJECTS_ARCHITECTURE = machine_intel.o
> "
>
> Can you give me some suggestions? Thank you so much.
>
>                    shanghui


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