The ABINIT Users Mailing List ( CLOSED )

[Alin M Elena <alin.elena@ichec.ie>]

Hi,

Just a wild guess. The problem may be in the configure. I had to modify it to 
make it to take the mvapich2

here are my notes on the compile
I had to change configure Here is the diff
alin@stokes2:/ichec/packages/abinit/5.8.3-intel/build> diff 
../abinit-5.8.3/configure ../abinit-5.8.3/configure.old
8111,8118c8111
< if test -x "${mpi_generic_prefix}/bin/mpicxx"; then
< mpi_generic_cxx="${mpi_generic_prefix}/bin/mpicxx"
< fi
<
< if test -x "${mpi_generic_prefix}/bin/mpirun.py"; then
< mpi_generic_runner="${mpi_generic_prefix}/bin/mpirun.py"
< fi
< if test -x "${mpi_generic_prefix}/bin/mpirun"; then
---


CXXFLAGS="-O3 -xSSSE3" CFLAGS="-O3 -xSSSE3" FCFLAGS="-O3 -xSSSE3" 
CFGFLAGS_NETCDF="--disable-utilities" ../abinit-5.8.3/configure --enable-
mpi="yes" --with-mpi-prefix=/ichec/packages/mvapich/1.2p1-intel --enable-
optlevel="aggressive" --enable-tricks="yes" --enable-netcdf="yes" --with-mpi-
level="2" --with-linalg-libs="-L$MKLROOT/lib/em64t -lmkl_intel_lp64 -
lmkl_intel_thread -lmkl_lapack -lmkl_core -liomp5 -lpthread" --with-scalapack-
includes="-I$MKLROOT/include" --with-scalapack-libs="-L$MKLROOT/lib/em64t -
lmkl_intel_lp64 -lmkl_intel_thread -lmkl_scalapack_lp64 -lmkl_lapack -
lmkl_core -liomp5 -lmkl_blacs_intelmpi_lp64 -lpthread" --enable-
scalapack="yes" --enable-fox --prefix=/ichec/packages/abinit/5.8.3-intel/

Alin


On Tuesday 22 September 2009 16:13:14 Luigi Genovese wrote:
> I never experience problems when putting -assume 2underscores in
> FCFLAGS. Let me know if it works for you
> 
> On Tue, Sep 22, 2009 at 4:13 PM, Jyh-Shyong <c00jsh00@nchc.org.tw> wrote:
> > Hi Luigi,
> >
> > After many attempts, I still failed to build parallel version of
> > bigdft-1.3 with cuda support.
> > In order to have cuda support, I have to include compiler option -assume
> > 2underscores,
> > however, this option fails to pass the mpi environment checking in
> > configure procedure.
> >
> > Configure options:
> > export  FC="/opt/mvapich2/intel/bin/mpif90 -assume 2underscores"
> > export  FCFLAGS=""
> > export  LDFLAGS=" "
> > export  LIBS=""
> > export  CC=icc
> > export  CPPFLAGS=""
> > export  CXX=icpc
> >
> > ./configure -prefix=/package/chem/bigdft --enable-cuda-gpu
> >  --with-cuda-path=/opt/cuda --with-lib-cutil
> > s=/opt/cuda/lib --with-ext-linalg="-lmkl_intel_lp64 -lmkl_sequential
> > -lmkl_core -lpthread -ldl -lsysfs"
> > --with-ext-linalg-path=-L/opt/intel/mkl/lib
> >
> >
> >
> > Basics:
> >  Fortran90 compiler:        /opt/mvapich2/intel/bin/mpif90 -assume
> > 2underscores
> >  Fortran90 compiler name:   intel
> >  Fortran90 flags:           -O2
> >  Linker flags:                -L/opt/intel/mkl/lib
> > -L$(top_builddir)/libXC/src
> >  Linked libraries:          -lxc -lmkl_intel_lp64 -lmkl_sequential
> > -lmkl_core -lpthread -ldl -lsysfs
> >
> > Build:
> >  Library ABINIT:            yes
> >  Library PSolver:           yes
> >  Library BigDFT:            yes
> >  Main binaries (cluster...):yes
> >  Minima hopping binary:     no
> >
> > Options:
> >  With MPI:                  Warning
> >  | Include dir.:            | Linker flags:            | Linked
> > libraries: | MPI2 support:           With optimised conv.:      yes
> >  With Cuda GPU conv.:       yes
> >  | NVidia Cuda Compiler:   /opt/cuda/bin/nvcc
> >  | Cuda flags:             -O3 --compiler-options -fno-strict-aliasing
> >  | GCC41HACK (gcc path):    | ext. cutil library:     /opt/cuda/lib
> >  |      cutil path:        /opt/cuda/lib
> >  With libXC:                yes
> >  | internal built:         yes
> >  | include dir.:           -I$(top_builddir)/libXC/src
> >
> > Installation paths:
> >  Source code location:      .
> >  Prefix:                    /package/chem/bigdft
> >  Exec prefix:               ${prefix}
> >  Binaries:                  ${exec_prefix}/bin
> >  Static libraries:          ${exec_prefix}/lib
> >  Fortran modules:           ${prefix}/include/intel
> >
> > Warnings:
> >  MPI:                       disabled by tests
> >
> >
> > In file config.log:
> > ....
> > configure:4965: checking for MPI capabilities
> > configure:4980: /opt/mvapich2/intel/bin/mpif90 -assume 2underscores -o
> > conftest -O2      conftest.f90   >&5
> > /tmp/ifortSVHO4q.o: In function `MAIN__':
> > conftest.f90:(.text+0x37): undefined reference to `mpi_init__'
> > configure:4986: $? = 1
> >
> > configure: failed program was:
> > | program main
> > |   include "mpif.h"
> > |
> > |   call MPI_INIT
> > | end
> >
> > configure:5002: result: no
> > configure:5070: WARNING: MPI is not working and has been disabled.
> > configure:5072: WARNING:   If you don't want to see this warning,
> > configure:5074: WARNING:   set --disable-mpi in the configure line.
> >
> > Eventually, the compilation built a serial version of bigdft with cuda
> > support.
> >
> >
> > If -assume 2underscores is not included:
> >
> > export  FC="/opt/mvapich2/intel/bin/mpif90"
> > export  FCFLAGS=""
> > export  LDFLAGS=" "
> > export  LIBS=""
> > export  CC=icc
> > export  CPPFLAGS=""
> > export  CXX=icpc
> >
> > ./configure -prefix=/package/chem/bigdft --enable-cuda-gpu
> >  --with-cuda-path=/opt/cuda --with-lib-cutil
> > s=/opt/cuda/lib --with-ext-linalg="-lmkl_intel_lp64 -lmkl_sequential
> > -lmkl_core -lpthread -ldl -lsysfs"
> > --with-ext-linalg-path=-L/opt/intel/mkl/lib
> >
> > ....
> > Basics:
> >  Fortran90 compiler:        /opt/mvapich2/intel/bin/mpif90
> >  Fortran90 compiler name:   intel
> >  Fortran90 flags:           -O2
> >  Linker flags:                -L/opt/intel/mkl/lib
> > -L$(top_builddir)/libXC/src
> >  Linked libraries:          -lxc -lmkl_intel_lp64 -lmkl_sequential
> > -lmkl_core -lpthread -ldl -lsysfs
> >
> > Build:
> >  Library ABINIT:            yes
> >  Library PSolver:           yes
> >  Library BigDFT:            yes
> >  Main binaries (cluster...):yes
> >  Minima hopping binary:     no
> >
> > Options:
> >  With MPI:                  yes
> >  | Include dir.:            | Linker flags:            | Linked
> > libraries: | MPI2 support:           yes
> >  With optimised conv.:      yes
> >  With Cuda GPU conv.:       yes
> >  | NVidia Cuda Compiler:   /opt/cuda/bin/nvcc
> >  | Cuda flags:             -O3 --compiler-options -fno-strict-aliasing
> >  | GCC41HACK (gcc path):    | ext. cutil library:     /opt/cuda/lib
> >  |      cutil path:        /opt/cuda/lib
> >  With libXC:                yes
> >  | internal built:         yes
> >  | include dir.:           -I$(top_builddir)/libXC/src
> >
> > Installation paths:
> >  Source code location:      .
> >  Prefix:                    /package/chem/bigdft
> >  Exec prefix:               ${prefix}
> >  Binaries:                  ${exec_prefix}/bin
> >  Static libraries:          ${exec_prefix}/lib
> >  Fortran modules:           ${prefix}/include/intel
> >
> > The compilation failed since subroutines in libGPU.a can not be
> > recognized.
> >
> > What would be the right combination of configure parameters so the
> > parallel version of bigdft which supports cuda?
> >
> > Thans for your help
> >
> > Jyh-Shyong Ho
> 

-- 
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  Mr  Alin M ELENA
  Irish Centre for High-End Computing -- www.ichec.ie
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  alin.elena@ichec.ie
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