[Beowulf] p4_error: interrupt SIGSEGV: 11 Killed by signal 2.

cjoung at tpg.com.au cjoung at tpg.com.au
Fri Oct 22 02:02:17 EDT 2004


Firstly,
Thank you to Mark H, Anthony S and in particular Henry G for your helpful
comments on my 
MPI/scaLAPACK problem. After reading your comments, I removed MPICH2, installed 
mpich1.2.6 and this did indeed fix the "Null Comm Pointer" error!

> Date: Tue, 19 Oct 2004 14:21:31 -0700 
> From: "Gabb, Henry" <henry.gabb at intel.com>
> Subject: Re: [Beowulf] MPI & ScaLAPACK: 
>              error in MPI_Comm_size: Invalid communicator
> The "Null Comm pointer" error that you're seeing is almost always due to
> a header mismatch. I don't think Intel Cluster MKL 7.0 supports MPICH2 yet. 
>
> > Error message:
> > aborting job: Fatal error in MPI_Comm_size: Invalid communicator, error stack:
> > MPI_Comm_size(82): MPI_Comm_size(comm=0x5b, size=0x80d807c) failed
> > MPI_Comm_size(66): Null Comm pointer
**********************************************************

Current Problem:
I have another problem now, also related to MPI/scaLAPACK.
I tried to compile and run the example1.f program - It uses the
scalapack PDGESV subroutine to solve the equation [A]x=b
(from the netlib/scalapack website - I did NOT modify it)
(see end of email for copy of example1.f)

It seems to compile ok, but on execution it gives this 
error message:
****************************************
[tony at carmine clint]$ mpif77 -o ex1 example1.f 
                             -L/opt/intel/mkl70cluster/lib/32 
                             -lmkl_scalapack 
                             -lmkl_blacsF77init 
                             -lmkl_blacs 
                             -lmkl_blacsF77init 
                             -lmkl_lapack 
                             -lmkl_ia32 
                             -lguide 
                             -lpthread 
                             -static-libcxa
[tony at carmine clint]$ mpirun -np 6 ./ex1 
p0_24505:  p4_error: interrupt SIGSEGV: 11 
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
[tony at carmine clint]$
****************************************
(there are also comments about "broken pipes", but
I didn't include that part above)

..as far as I can discover on the web, SIGSEGV 
represents a "segmentation fault", beyond this,
I don't know what to do for a fix.

Some people have suggested fixes such as:

* increasing memory sizes: i.e. type in:
> >export P4_GLOBMEMSIZE=536870912
> >
> >(=512MB). 

..but this didn't do anything for me.
Generally, I have not seen any other solutions which 
have had a positive response.
They say, a problem like this is normally attributed
to a bug in the source code, but seeing as the 
netlib/scalapack developers give this source code out 
as the beginners basic 'hello world' program, I doubt 
this program would carry a bug in it!
I would have to guess that there's something ELSE wrong.
(In any case, I tried another program out of a book that
does basically the same thing - same problem)

I was hoping a reader in this forum has seen this problem
before, and knows of a solution.

Any suggestions, even speculative, would be most appreciated,
(Please use simple language - I am quite a novice at all of this...)

with many thanks,

Clint Joung

Postdoctoral Research Associate
Department of Chemical Engineering
University of Sydney, NSW 2006
Australia

ps: My system details and the source code 'example1.f':

OS: Linux Redhat Fedora Core 2
FC: Intel Fortran Compiler V8.0 (ifort) 
(I've also tried building MPI libraries using GNU g77 - same problem)
CC: GNU gcc
(for some reason, MPI libraries don't 'make' properly using intel icpc)
Scalapack et al: Intel Cluster Maths Kernel Library for Linux v7.0
MPI: mpich-1.2.6 (I've also tried mpich1.2.5.2 - same problem)

The example1.f program. It runs ok as far as the actual call to
PDGESV, then it falls over.....
**EXAMPLE1.F***************************************
      PROGRAM EXAMPLE1
*
*     Example Program solving Ax=b via ScaLAPACK routine PDGESV
*
*     .. Parameters ..
      INTEGER            DLEN_, IA, JA, IB, JB, M, N, MB, NB, RSRC,
     $                   CSRC, MXLLDA, MXLLDB, NRHS, NBRHS, NOUT,
     $                   MXLOCR, MXLOCC, MXRHSC
      PARAMETER          ( DLEN_ = 9, IA = 1, JA = 1, IB = 1, JB = 1,
     $                   M = 9, N = 9, MB = 2, NB = 2, RSRC = 0,
     $                   CSRC = 0, MXLLDA = 5, MXLLDB = 5, NRHS = 1,
     $                   NBRHS = 1, NOUT = 6, MXLOCR = 5, MXLOCC = 4,
     $                   MXRHSC = 1 )
      DOUBLE PRECISION   ONE
      PARAMETER          ( ONE = 1.0D+0 )
*     ..
*     .. Local Scalars ..
      INTEGER            ICTXT, INFO, MYCOL, MYROW, NPCOL, NPROW
      DOUBLE PRECISION   ANORM, BNORM, EPS, RESID, XNORM
*     ..
*     .. Local Arrays ..
      INTEGER            DESCA( DLEN_ ), DESCB( DLEN_ ),
     $                   IPIV( MXLOCR+NB )
      DOUBLE PRECISION   A( MXLLDA, MXLOCC ), A0( MXLLDA, MXLOCC ),
     $                   B( MXLLDB, MXRHSC ), B0( MXLLDB, MXRHSC ),
     $                   WORK( MXLOCR )
*     ..
*     .. External Functions ..
      DOUBLE PRECISION   PDLAMCH, PDLANGE
      EXTERNAL           PDLAMCH, PDLANGE
*     ..
*     .. External Subroutines ..
      EXTERNAL           BLACS_EXIT, BLACS_GRIDEXIT, BLACS_GRIDINFO,
     $                   DESCINIT, MATINIT, PDGEMM, PDGESV, PDLACPY,
     $                   SL_INIT
*     ..
*     .. Intrinsic Functions ..
      INTRINSIC          DBLE
*     ..
*     .. Data statements ..
      DATA               NPROW / 2 / , NPCOL / 3 /
*     ..
*     .. Executable Statements ..
*
*     INITIALIZE THE PROCESS GRID
*
      CALL SL_INIT( ICTXT, NPROW, NPCOL )
      CALL BLACS_GRIDINFO( ICTXT, NPROW, NPCOL, MYROW, MYCOL )
*
*     If I'm not in the process grid, go to the end of the program
*
      IF( MYROW.EQ.-1 )
     $   GO TO 10
*
*     DISTRIBUTE THE MATRIX ON THE PROCESS GRID
*     Initialize the array descriptors for the matrices A and B
*
      CALL DESCINIT( DESCA, M, N, MB, NB, RSRC, CSRC, ICTXT, MXLLDA,
     $               INFO )
      CALL DESCINIT( DESCB, N, NRHS, NB, NBRHS, RSRC, CSRC, ICTXT,
     $               MXLLDB, INFO )
*
*     Generate matrices A and B and distribute to the process grid
*
      CALL MATINIT( A, DESCA, B, DESCB )
*
*     Make a copy of A and B for checking purposes
*
      CALL PDLACPY( 'All', N, N, A, 1, 1, DESCA, A0, 1, 1, DESCA )
      CALL PDLACPY( 'All', N, NRHS, B, 1, 1, DESCB, B0, 1, 1, DESCB )
*
*     CALL THE SCALAPACK ROUTINE
*     Solve the linear system A * X = B
*
      CALL PDGESV( N, NRHS, A, IA, JA, DESCA, IPIV, B, IB, JB, DESCB,
     $             INFO )
*
      IF( MYROW.EQ.0 .AND. MYCOL.EQ.0 ) THEN
         WRITE( NOUT, FMT = 9999 )
         WRITE( NOUT, FMT = 9998 )M, N, NB
         WRITE( NOUT, FMT = 9997 )NPROW*NPCOL, NPROW, NPCOL
         WRITE( NOUT, FMT = 9996 )INFO
      END IF
*
*     Compute residual ||A * X  - B|| / ( ||X|| * ||A|| * eps * N )
*
      EPS = PDLAMCH( ICTXT, 'Epsilon' )
      ANORM = PDLANGE( 'I', N, N, A, 1, 1, DESCA, WORK )
      BNORM = PDLANGE( 'I', N, NRHS, B, 1, 1, DESCB, WORK )
      CALL PDGEMM( 'N', 'N', N, NRHS, N, ONE, A0, 1, 1, DESCA, B, 1, 1,
     $             DESCB, -ONE, B0, 1, 1, DESCB )
      XNORM = PDLANGE( 'I', N, NRHS, B0, 1, 1, DESCB, WORK )
      RESID = XNORM / ( ANORM*BNORM*EPS*DBLE( N ) )
*
      IF( MYROW.EQ.0 .AND. MYCOL.EQ.0 ) THEN
         IF( RESID.LT.10.0D+0 ) THEN
            WRITE( NOUT, FMT = 9995 )
            WRITE( NOUT, FMT = 9993 )RESID
         ELSE
            WRITE( NOUT, FMT = 9994 )
            WRITE( NOUT, FMT = 9993 )RESID
         END IF
      END IF
*
*     RELEASE THE PROCESS GRID
*     Free the BLACS context
*
      CALL BLACS_GRIDEXIT( ICTXT )
   10 CONTINUE
*
*     Exit the BLACS
*
      CALL BLACS_EXIT( 0 )
*
 9999 FORMAT( / 'ScaLAPACK Example Program #1 -- May 1, 1997' )
 9998 FORMAT( / 'Solving Ax=b where A is a ', I3, ' by ', I3,
     $      ' matrix with a block size of ', I3 )
 9997 FORMAT( 'Running on ', I3, ' processes, where the process grid',
     $      ' is ', I3, ' by ', I3 )
 9996 FORMAT( / 'INFO code returned by PDGESV = ', I3 )
 9995 FORMAT( /
     $   'According to the normalized residual the solution is correct.'
     $       )
 9994 FORMAT( /
     $ 'According to the normalized residual the solution is incorrect.'
     $       )
 9993 FORMAT( / '||A*x - b|| / ( ||x||*||A||*eps*N ) = ', 1P, E16.8 )
      STOP
      END
      SUBROUTINE MATINIT( AA, DESCA, B, DESCB )
*
*     MATINIT generates and distributes matrices A and B (depicted in
*     Figures 2.5 and 2.6) to a 2 x 3 process grid
*
*     .. Array Arguments ..
      INTEGER            DESCA( * ), DESCB( * )
      DOUBLE PRECISION   AA( * ), B( * )
*     ..
*     .. Parameters ..
      INTEGER            CTXT_, LLD_
      PARAMETER          ( CTXT_ = 2, LLD_ = 9 )
*     ..
*     .. Local Scalars ..
      INTEGER            ICTXT, MXLLDA, MYCOL, MYROW, NPCOL, NPROW
      DOUBLE PRECISION   A, C, K, L, P, S
*     ..
*     .. External Subroutines ..
      EXTERNAL           BLACS_GRIDINFO
*     ..
*     .. Executable Statements ..
*
      ICTXT = DESCA( CTXT_ )
      CALL BLACS_GRIDINFO( ICTXT, NPROW, NPCOL, MYROW, MYCOL )
*
      S = 19.0D0
      C = 3.0D0
      A = 1.0D0
      L = 12.0D0
      P = 16.0D0
      K = 11.0D0
*
      MXLLDA = DESCA( LLD_ )
*
      IF( MYROW.EQ.0 .AND. MYCOL.EQ.0 ) THEN
         AA( 1 ) = S
         AA( 2 ) = -S
         AA( 3 ) = -S
         AA( 4 ) = -S
         AA( 5 ) = -S
         AA( 1+MXLLDA ) = C
         AA( 2+MXLLDA ) = C
         AA( 3+MXLLDA ) = -C
         AA( 4+MXLLDA ) = -C
         AA( 5+MXLLDA ) = -C
         AA( 1+2*MXLLDA ) = A
         AA( 2+2*MXLLDA ) = A
         AA( 3+2*MXLLDA ) = A
         AA( 4+2*MXLLDA ) = A
         AA( 5+2*MXLLDA ) = -A
         AA( 1+3*MXLLDA ) = C
         AA( 2+3*MXLLDA ) = C
         AA( 3+3*MXLLDA ) = C
         AA( 4+3*MXLLDA ) = C
         AA( 5+3*MXLLDA ) = -C
         B( 1 ) = 0.0D0
         B( 2 ) = 0.0D0
         B( 3 ) = 0.0D0
         B( 4 ) = 0.0D0
         B( 5 ) = 0.0D0
      ELSE IF( MYROW.EQ.0 .AND. MYCOL.EQ.1 ) THEN
         AA( 1 ) = A
         AA( 2 ) = A
         AA( 3 ) = -A
         AA( 4 ) = -A
         AA( 5 ) = -A
         AA( 1+MXLLDA ) = L
         AA( 2+MXLLDA ) = L
         AA( 3+MXLLDA ) = -L
         AA( 4+MXLLDA ) = -L
         AA( 5+MXLLDA ) = -L
         AA( 1+2*MXLLDA ) = K
         AA( 2+2*MXLLDA ) = K
         AA( 3+2*MXLLDA ) = K
         AA( 4+2*MXLLDA ) = K
         AA( 5+2*MXLLDA ) = K
      ELSE IF( MYROW.EQ.0 .AND. MYCOL.EQ.2 ) THEN
         AA( 1 ) = A
         AA( 2 ) = A
         AA( 3 ) = A
         AA( 4 ) = -A
         AA( 5 ) = -A
         AA( 1+MXLLDA ) = P
         AA( 2+MXLLDA ) = P
         AA( 3+MXLLDA ) = P
         AA( 4+MXLLDA ) = P
         AA( 5+MXLLDA ) = -P
      ELSE IF( MYROW.EQ.1 .AND. MYCOL.EQ.0 ) THEN
         AA( 1 ) = -S
         AA( 2 ) = -S
         AA( 3 ) = -S
         AA( 4 ) = -S
         AA( 1+MXLLDA ) = -C
         AA( 2+MXLLDA ) = -C
         AA( 3+MXLLDA ) = -C
         AA( 4+MXLLDA ) = C
         AA( 1+2*MXLLDA ) = A
         AA( 2+2*MXLLDA ) = A
         AA( 3+2*MXLLDA ) = A
         AA( 4+2*MXLLDA ) = -A
         AA( 1+3*MXLLDA ) = C
         AA( 2+3*MXLLDA ) = C
         AA( 3+3*MXLLDA ) = C
         AA( 4+3*MXLLDA ) = C
         B( 1 ) = 1.0D0
         B( 2 ) = 0.0D0
         B( 3 ) = 0.0D0
         B( 4 ) = 0.0D0
      ELSE IF( MYROW.EQ.1 .AND. MYCOL.EQ.1 ) THEN
         AA( 1 ) = A
         AA( 2 ) = -A
         AA( 3 ) = -A
         AA( 4 ) = -A
         AA( 1+MXLLDA ) = L
         AA( 2+MXLLDA ) = L
         AA( 3+MXLLDA ) = -L
         AA( 4+MXLLDA ) = -L
         AA( 1+2*MXLLDA ) = K
         AA( 2+2*MXLLDA ) = K
         AA( 3+2*MXLLDA ) = K
         AA( 4+2*MXLLDA ) = K
      ELSE IF( MYROW.EQ.1 .AND. MYCOL.EQ.2 ) THEN
         AA( 1 ) = A
         AA( 2 ) = A
         AA( 3 ) = -A
         AA( 4 ) = -A
         AA( 1+MXLLDA ) = P
         AA( 2+MXLLDA ) = P
         AA( 3+MXLLDA ) = -P
         AA( 4+MXLLDA ) = -P
      END IF
      RETURN
      END
      SUBROUTINE SL_INIT( ICTXT, NPROW, NPCOL )
*
*     .. Scalar Arguments ..
      INTEGER            ICTXT, NPCOL, NPROW
*     ..
*
*  Purpose
*  =======
*
*  SL_INIT initializes an NPROW x NPCOL process grid using a row-major
*  ordering  of  the  processes. This routine retrieves a default system
*  context  which  will  include all available processes. In addition it
*  spawns the processes if needed.
*
*  Arguments
*  =========
*
*  ICTXT   (global output) INTEGER
*          ICTXT specifies the BLACS context handle identifying the
*          created process grid.  The context itself is global.
*
*  NPROW   (global input) INTEGER
*          NPROW specifies the number of process rows in the grid
*          to be created.
*
*  NPCOL   (global input) INTEGER
*          NPCOL specifies the number of process columns in the grid
*          to be created.
*
*  =====================================================================
*
*     .. Local Scalars ..
      INTEGER            IAM, NPROCS
*     ..
*     .. External Subroutines ..
      EXTERNAL           BLACS_GET, BLACS_GRIDINIT, BLACS_PINFO,
     $                   BLACS_SETUP
*     ..
*     .. Executable Statements ..
*
*     Get starting information
*
      CALL BLACS_PINFO( IAM, NPROCS )
*
*     If machine needs additional set up, do it now
*
      IF( NPROCS.LT.1 ) THEN
         IF( IAM.EQ.0 )
     $      NPROCS = NPROW*NPCOL
         CALL BLACS_SETUP( IAM, NPROCS )
      END IF
*
*     Define process grid
*
      CALL BLACS_GET( -1, 0, ICTXT )
      CALL BLACS_GRIDINIT( ICTXT, 'Row-major', NPROW, NPCOL )
*
      RETURN
*
*     End of SL_INIT
*
      END
***************************************************


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