scalapack installer error

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scalapack installer error

Postby karthikn234 » Tue Jul 26, 2011 2:17 pm

Dear friends,
I am trying to compile scalapack on SGI ALTIX ICE 8400. I used scalapack installer as adviced by many. I need to compile with sgi mpi. I have placed mpiblacs.tgz and scalapack.tgz in the build directory. My script code is:

./setup.py --mpicc=gcc --mpif77=ifort --mpiincdir=/opt/sgi/mpt/mpt-2.01/include --blaslib=/lustre/home/murugan/sgiopt/GotoBLAS2/libgoto2_nehalem-r1.13.a --lapacklib=/lustre/home/murugan/sgiopt/lapack-3.3.1/libreflapack.a --ldflags_c=-nofor_main --f90=ifort --ccflags=-lmpi --fcflags=-lmpi

And the output i get is:

========================================
Setting up the framework

mpicc is gcc
mpif77 is ifort
MPI include dir is /opt/sgi/mpt/mpt-2.01/include
The Fortran 90/95 compiler is ifort
C flags are -lmpi
Fortran 77 flags are -lmpi
Setting Fortran mangling.../lustre/home/murugan/sgiopt/scalapack_installer_0.96/script/utils.py:39: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
import popen2
-DAdd_
Setting download command...
Checking availability of urllib... available
Testing urllib... not working
Checking availablility of wget... available
Testing wget... not working.
Setting ranlib command... /usr/bin/ranlib
Detecting Fortran 77 compiler... unknown
Detecting C compiler... unknown
Selected C compiler flags: -lmpi
Selected Fortran77 compiler flags: -lmpi
Selected loader flags (C main): -nofor_main
Selected loader flags (F77 main):
Selected NOOPT flags:
Checking loader... works

========================================
BLAS installation/verification
========================================
Checking if provided BLAS works... yes

========================================
Lapack installation/verification
========================================
Checking if provided LAPACK works... yes

========================================
BLACS installation/verification
========================================
Unzip and untar BLACS... done
Setting TRANSCOMM... -DCSameF77

Writing Bmake.inc... done.
Compiling BLACS... done.
(log is in /lustre/home/murugan/sgiopt/scalapack_installer_0.96/log/blacslog )

========================================
ScaLAPACK installer is starting now. Buckle up!
========================================
Installing scalapack-1.8.0 ...
Writing SLmake.inc... done.
Compiling ScaLAPACK... Installation of ScaLAPACK successful..
(log is in /lustre/home/murugan/sgiopt/scalapack_installer_0.96/log/scalog )
Compiling test routines...


ScaLAPACK: error building ScaLAPACK test routines
stderr:
****************************************
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacsF77.a(blacs_pinfo_.o): In function `blacs_pinfo_':
blacs_pinfo_.c:(.text+0x21): undefined reference to `MPI_Initialized'
blacs_pinfo_.c:(.text+0x75): undefined reference to `MPI_Comm_size'
blacs_pinfo_.c:(.text+0x87): undefined reference to `MPI_Comm_rank'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(bi_f77_init.o): In function `bi_f77_init_':
bi_f77_init.f:(.text+0x8): undefined reference to `mpi_init_'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgesd2d_.o): In function `sgesd2d_':
sgesd2d_.c:(.text+0xfe): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgerv2d_.o): In function `sgerv2d_':
sgerv2d_.c:(.text+0xde): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(igebs2d_.o): In function `igebs2d_':
igebs2d_.c:(.text+0x18a): undefined reference to `MPI_Bcast'
igebs2d_.c:(.text+0x196): undefined reference to `MPI_Type_free'
igebs2d_.c:(.text+0x317): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgebs2d_.o): In function `sgebs2d_':
sgebs2d_.c:(.text+0x18a): undefined reference to `MPI_Bcast'
sgebs2d_.c:(.text+0x196): undefined reference to `MPI_Type_free'
sgebs2d_.c:(.text+0x317): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(igebr2d_.o): In function `igebr2d_':
igebr2d_.c:(.text+0x1c1): undefined reference to `MPI_Bcast'
igebr2d_.c:(.text+0x1cd): undefined reference to `MPI_Type_free'
igebr2d_.c:(.text+0x376): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgebr2d_.o): In function `sgebr2d_':
sgebr2d_.c:(.text+0x1c1): undefined reference to `MPI_Bcast'
sgebr2d_.c:(.text+0x1cd): undefined reference to `MPI_Type_free'
sgebr2d_.c:(.text+0x376): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(igsum2d_.o): In function `igsum2d_':
igsum2d_.c:(.text+0x307): undefined reference to `MPI_Reduce'
igsum2d_.c:(.text+0x387): undefined reference to `MPI_Allreduce'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(igamx2d_.o): In function `igamx2d_':
igamx2d_.c:(.text+0x440): undefined reference to `MPI_Type_struct'
igamx2d_.c:(.text+0x44f): undefined reference to `MPI_Type_commit'
igamx2d_.c:(.text+0x5c1): undefined reference to `MPI_Op_create'
igamx2d_.c:(.text+0x5da): undefined reference to `MPI_Op_create'
igamx2d_.c:(.text+0x62f): undefined reference to `MPI_Reduce'
igamx2d_.c:(.text+0x73d): undefined reference to `MPI_Allreduce'
igamx2d_.c:(.text+0x7f9): undefined reference to `MPI_Op_free'
igamx2d_.c:(.text+0x813): undefined reference to `MPI_Type_free'
igamx2d_.c:(.text+0xa5f): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgamx2d_.o): In function `sgamx2d_':
sgamx2d_.c:(.text+0x44b): undefined reference to `MPI_Type_struct'
sgamx2d_.c:(.text+0x45a): undefined reference to `MPI_Type_commit'
sgamx2d_.c:(.text+0x5cc): undefined reference to `MPI_Op_create'
sgamx2d_.c:(.text+0x5e5): undefined reference to `MPI_Op_create'
sgamx2d_.c:(.text+0x63a): undefined reference to `MPI_Reduce'
sgamx2d_.c:(.text+0x748): undefined reference to `MPI_Allreduce'
sgamx2d_.c:(.text+0x804): undefined reference to `MPI_Op_free'
sgamx2d_.c:(.text+0x81e): undefined reference to `MPI_Type_free'
sgamx2d_.c:(.text+0xa6a): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgamn2d_.o): In function `sgamn2d_':
sgamn2d_.c:(.text+0x44b): undefined reference to `MPI_Type_struct'
sgamn2d_.c:(.text+0x45a): undefined reference to `MPI_Type_commit'
sgamn2d_.c:(.text+0x5cc): undefined reference to `MPI_Op_create'
sgamn2d_.c:(.text+0x5e5): undefined reference to `MPI_Op_create'
sgamn2d_.c:(.text+0x63a): undefined reference to `MPI_Reduce'
sgamn2d_.c:(.text+0x748): undefined reference to `MPI_Allreduce'
sgamn2d_.c:(.text+0x804): undefined reference to `MPI_Op_free'
sgamn2d_.c:(.text+0x81e): undefined reference to `MPI_Type_free'
sgamn2d_.c:(.text+0xa6a): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(blacs_get_.o): In function `blacs_get_':
blacs_get_.c:(.text+0xa7): undefined reference to `MPI_Attr_get'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(blacs_exit_.o): In function `blacs_exit_':
blacs_exit_.c:(.text+0xdc): undefined reference to `MPI_Type_free'
blacs_exit_.c:(.text+0xe9): undefined reference to `MPI_Type_free'
blacs_exit_.c:(.text+0xfb): undefined reference to `MPI_Finalize'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(blacs_gridmap_.o): In function `blacs_gridmap_':
blacs_gridmap_.c:(.text+0x97): undefined reference to `MPI_Type_contiguous'
blacs_gridmap_.c:(.text+0xa4): undefined reference to `MPI_Type_commit'
blacs_gridmap_.c:(.text+0xbb): undefined reference to `MPI_Type_contiguous'
blacs_gridmap_.c:(.text+0xc8): undefined reference to `MPI_Type_commit'
blacs_gridmap_.c:(.text+0x334): undefined reference to `MPI_Comm_dup'
blacs_gridmap_.c:(.text+0x343): undefined reference to `MPI_Comm_rank'
blacs_gridmap_.c:(.text+0x380): undefined reference to `MPI_Comm_split'
blacs_gridmap_.c:(.text+0x399): undefined reference to `MPI_Comm_split'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(blacs_gridexit_.o): In function `blacs_gridexit_':
blacs_gridexit_.c:(.text+0xaa): undefined reference to `MPI_Comm_free'
blacs_gridexit_.c:(.text+0xba): undefined reference to `MPI_Comm_free'
blacs_gridexit_.c:(.text+0xc6): undefined reference to `MPI_Comm_free'
blacs_gridexit_.c:(.text+0xd6): undefined reference to `MPI_Comm_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(blacs_barrier_.o): In function `blacs_barrier_':
blacs_barrier_.c:(.text+0x82): undefined reference to `MPI_Barrier'
blacs_barrier_.c:(.text+0x93): undefined reference to `MPI_Barrier'
blacs_barrier_.c:(.text+0xa4): undefined reference to `MPI_Barrier'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgesd2d_.oo): In function `Csgesd2d':
sgesd2d_.c:(.text+0xd0): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgerv2d_.oo): In function `Csgerv2d':
sgerv2d_.c:(.text+0xbb): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(igebs2d_.oo): In function `Cigebs2d':
igebs2d_.c:(.text+0x16e): undefined reference to `MPI_Bcast'
igebs2d_.c:(.text+0x17a): undefined reference to `MPI_Type_free'
igebs2d_.c:(.text+0x2f8): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgebs2d_.oo): In function `Csgebs2d':
sgebs2d_.c:(.text+0x16e): undefined reference to `MPI_Bcast'
sgebs2d_.c:(.text+0x17a): undefined reference to `MPI_Type_free'
sgebs2d_.c:(.text+0x2f8): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(igebr2d_.oo): In function `Cigebr2d':
igebr2d_.c:(.text+0x194): undefined reference to `MPI_Bcast'
igebr2d_.c:(.text+0x1a0): undefined reference to `MPI_Type_free'
igebr2d_.c:(.text+0x346): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgebr2d_.oo): In function `Csgebr2d':
sgebr2d_.c:(.text+0x194): undefined reference to `MPI_Bcast'
sgebr2d_.c:(.text+0x1a0): undefined reference to `MPI_Type_free'
sgebr2d_.c:(.text+0x346): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgsum2d_.oo): In function `Csgsum2d':
sgsum2d_.c:(.text+0x2bd): undefined reference to `MPI_Reduce'
sgsum2d_.c:(.text+0x333): undefined reference to `MPI_Allreduce'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(sgamx2d_.oo): In function `Csgamx2d':
sgamx2d_.c:(.text+0x3f0): undefined reference to `MPI_Type_struct'
sgamx2d_.c:(.text+0x3ff): undefined reference to `MPI_Type_commit'
sgamx2d_.c:(.text+0x55a): undefined reference to `MPI_Op_create'
sgamx2d_.c:(.text+0x573): undefined reference to `MPI_Op_create'
sgamx2d_.c:(.text+0x5c8): undefined reference to `MPI_Reduce'
sgamx2d_.c:(.text+0x6bb): undefined reference to `MPI_Allreduce'
sgamx2d_.c:(.text+0x75c): undefined reference to `MPI_Op_free'
sgamx2d_.c:(.text+0x771): undefined reference to `MPI_Type_free'
sgamx2d_.c:(.text+0x9b5): undefined reference to `MPI_Type_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(blacs_get_.oo): In function `Cblacs_get':
blacs_get_.c:(.text+0x9f): undefined reference to `MPI_Attr_get'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(Cblacs_gridexit_.oo): In function `Cblacs_gridexit':
blacs_gridexit_.c:(.text+0x94): undefined reference to `MPI_Comm_free'
blacs_gridexit_.c:(.text+0xa4): undefined reference to `MPI_Comm_free'
blacs_gridexit_.c:(.text+0xb0): undefined reference to `MPI_Comm_free'
blacs_gridexit_.c:(.text+0xc0): undefined reference to `MPI_Comm_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_Ssend.o): In function `BI_Ssend':
BI_Ssend.c:(.text+0x49): undefined reference to `MPI_Send'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_Srecv.o): In function `BI_Srecv':
BI_Srecv.c:(.text+0x51): undefined reference to `MPI_Recv'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_Asend.o): In function `BI_Asend':
BI_Asend.c:(.text+0x63): undefined reference to `MPI_Isend'
BI_Asend.c:(.text+0x77): undefined reference to `MPI_Error_class'
BI_Asend.c:(.text+0x10d): undefined reference to `MPI_Isend'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_Arecv.o): In function `BI_Arecv':
BI_Arecv.c:(.text+0x63): undefined reference to `MPI_Irecv'
BI_Arecv.c:(.text+0x77): undefined reference to `MPI_Error_class'
BI_Arecv.c:(.text+0x10d): undefined reference to `MPI_Irecv'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_BeComb.o): In function `BI_BeComb':
BI_BeComb.c:(.text+0x218): undefined reference to `MPI_Sendrecv'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_BlacsAbort.o): In function `BI_BlacsAbort':
BI_BlacsAbort.c:(.text+0x2c): undefined reference to `MPI_Abort'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_BuffIsFree.o): In function `BI_BuffIsFree':
BI_BuffIsFree.c:(.text+0x30): undefined reference to `MPI_Testall'
BI_BuffIsFree.c:(.text+0x5e): undefined reference to `MPI_Waitall'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_Pack.o): In function `BI_Pack':
BI_Pack.c:(.text+0x3a): undefined reference to `MPI_Pack_size'
BI_Pack.c:(.text+0x90): undefined reference to `MPI_Pack'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_GetMpiGeType.o): In function `BI_GetMpiGeType':
BI_GetMpiGeType.c:(.text+0x3b): undefined reference to `MPI_Type_vector'
BI_GetMpiGeType.c:(.text+0x47): undefined reference to `MPI_Type_commit'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_TransUserComm.o): In function `BI_TransUserComm':
BI_TransUserComm.c:(.text+0x26): undefined reference to `MPI_Comm_group'
BI_TransUserComm.c:(.text+0x3c): undefined reference to `MPI_Group_incl'
BI_TransUserComm.c:(.text+0x4e): undefined reference to `MPI_Comm_create'
BI_TransUserComm.c:(.text+0x5a): undefined reference to `MPI_Group_free'
BI_TransUserComm.c:(.text+0x66): undefined reference to `MPI_Group_free'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(dwalltime00_.o): In function `dwalltime00_':
dwalltime00_.c:(.text+0x9): undefined reference to `MPI_Wtime'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacs.a(BI_Rsend.o): In function `BI_Rsend':
BI_Rsend.c:(.text+0x49): undefined reference to `MPI_Rsend'
/lustre/home/murugan/sgiopt/scalapack_installer_0.96/lib/blacsF77.a(Cblacs_pinfo.o): In function `Cblacs_pinfo':
blacs_pinfo_.c:(.text+0x21): undefined reference to `MPI_Initialized'
blacs_pinfo_.c:(.text+0x75): undefined reference to `MPI_Comm_size'
blacs_pinfo_.c:(.text+0x87): undefined reference to `MPI_Comm_rank'
make[1]: *** [/lustre/home/murugan/sgiopt/scalapack_installer_0.96/build/scalapack-1.8.0/TESTING/xspblas1tst] Error 1
make: *** [pblasexe] Error 2

----------------------------------------------

I would be grateful if some one helps me in solving this issue ?
karthikn234
 
Posts: 1
Joined: Tue Jul 26, 2011 2:10 pm

Re: scalapack installer error

Postby admin » Tue Aug 16, 2011 9:51 am

Could you explain how you compile a simple mpi program on your machine?
At the moment, the linking sequence does not seems to work because of mpi.
Do you have a mpicc available with your mpi distribution?
admin
Site Admin
 
Posts: 486
Joined: Wed Dec 08, 2004 7:07 pm


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