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【求助】vasp并行安装mpich2的错误

作者 夕阳西下
来源: 小木虫 500 10 举报帖子
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linux-pd32:/tmp/mpich2-1.3 # ./configure -- prefix=/usr/mpich2-1.3
Configuring MPICH2 version 1.3 with  '--' 'prefix=/usr/mpich2-1.3'
Running on system: Linux linux-pd32 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for grep that handles long lines and -e... /usr/bin/grep
checking for fgrep... /usr/bin/grep -F
Executing mpich2prereq in /tmp/mpich2-1.3/src/mpid/ch3 with
Executing mpich2prereq in /tmp/mpich2-1.3/src/mpid/ch3/channels/nemesis
configure: ===== configuring src/mpl =====
configure: executing: /tmp/mpich2-1.3/src/mpl/configure  '--' 'prefix=/usr/mpich2-1.3' --disable-option-checking
configure: WARNING: you should use --build, --host, --target
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... configure: error: /bin/sh confdb/config.sub --disable-option-checking failed
configure: WARNING: cache variable ac_cv_build contains a newline
configure: error: MPL configure failed
linux-pd32:/tmp/mpich2-1.3 # make
make: *** 没有指明目标并且找不到 makefile。 停止。
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  • zzy870720z

    引用回帖:
    Originally posted by 夕阳西下 at 2010-11-10 19:52:40:
    linux-pd32:/tmp/mpich2-1.3 # ./configure -- prefix=/usr/mpich2-1.3
    Configuring MPICH2 version 1.3 with  '--' 'prefix=/usr/mpich2-1.3'
    Running on system: Linux linux-pd32 2.6.16.60-0.21-smp #1 SMP ...

    看make前面的一个error
    好像是configure出错了
    具体不太明白

  • 夕阳西下

    linux-pd32:~/vasp/vasp.4.6 # make
    ./preprocess <base.F | /usr/bin/cpp -P -C -traditional >base.f90 -DMPI  -DHOST=\"LinuxIFC\" -DIFC -Dkind8 -DNGZhalf -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DMPI_BLOCK=500 -DRPROMU_DGEMV  -DRACCMU_DGEMV
    mpif90 -FR -lowercase -assume byterecl  -O3 -xW -tpp7  -c base.f90
    ifort: command line remark #10148: option '-tp' not supported
    fortcom: No such file or directory
    ifort: error #10273: Fatal error in fortcom, terminated by 0x64
    make: *** [base.o] 错误 100
    大家帮我看看这个错误是怎么回事?

  • zzy870720z

    引用回帖:
    Originally posted by 夕阳西下 at 2010-11-11 14:32:06:
    linux-pd32:~/vasp/vasp.4.6 # make
    ./preprocess <base.F | /usr/bin/cpp -P -C -traditional >base.f90 -DMPI  -DHOST=\"LinuxIFC\" -DIFC -Dkind8 -DNGZhalf -DCACHE_SIZE=4000 -DPGF90 -Dav ...

    好像还是你编译器的问题
    可能还是你的ifort路径设置的问题

  • 夕阳西下

    opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_lapack.so: undefined reference to `mkl_blas_ztrmm'
    /opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_lapack.so: undefined reference to `mkl_pds_ladj_mod_pardiso'
    make: *** [vasp] 错误 1
    这个错误是怎么回事阿

  • zzy870720z

    引用回帖:
    Originally posted by 夕阳西下 at 2010-11-11 21:54:42:
    opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_lapack.so: undefined reference to `mkl_blas_ztrmm'
    /opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_lapack.so: undefined reference to `mkl_pds_lad ...

    给出的信息不全
    大致估计是你的makefile给出链接库不全
    可以把你的makefile贴出来看看
    主要是blas和lapack设置部分

  • 夕阳西下

    # 3c) mindblowing fast SSE2 (4 GFlops on P4, 2.53 GHz)
    #   Kazushige Goto's BLAS
    #   https://www.cs.utexas.edu/users/kgoto/signup_first.html
    #
    #-----------------------------------------------------------------------

    # all CPP processed fortran files have the extension .f90
    SUFFIX=.f90

    #-----------------------------------------------------------------------
    # fortran compiler and linker
    #-----------------------------------------------------------------------
    # FC=ifc
    # fortran linker
    # FCL=$(FC)


    #-----------------------------------------------------------------------
    # whereis CPP ?? (I need CPP, can't use gcc with proper options)
    # that's the location of gcc for SUSE 5.3
    #
    #  CPP_   =  /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C
    #
    # that's probably the right line for some Red Hat distribution:
    #
    #  CPP_   =  /usr/lib/gcc-lib/i386-redhat-linux/2.7.2.3/cpp -P -C
    #
    #  SUSE X.X, maybe some Red Hat distributions:

    CPP_ =  ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(SUFFIX)

    #-----------------------------------------------------------------------
    # possible options for CPP:
    # NGXhalf             charge density   reduced in X direction
    # wNGXhalf            gamma point only reduced in X direction
    # avoidalloc          avoid ALLOCATE if possible
    # IFC                 work around some IFC bugs
    # CACHE_SIZE          1000 for PII,PIII, 5000 for Athlon, 8000-12000 P4
    # RPROMU_DGEMV        use DGEMV instead of DGEMM in RPRO (depends on used BLAS)
    # RACCMU_DGEMV        use DGEMV instead of DGEMM in RACC (depends on used BLAS)
    #-----------------------------------------------------------------------

    # CPP     = $(CPP_)  -DHOST=\"LinuxIFC\" \
              -Dkind8 -DNGXhalf -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \
    #          -DRPROMU_DGEMV  -DRACCMU_DGEMV
    #-----------------------------------------------------------------------
    # general fortran flags  (there must a trailing blank on this line)
    #-----------------------------------------------------------------------

    FFLAGS =  -FR -lowercase -assume byterecl

    #-----------------------------------------------------------------------
    # optimization
    # we have tested whether higher optimisation improves performance
    # -axK  SSE1 optimization,  but also generate code executable on all mach.
    #       xK improves performance somewhat on XP, and a is required in order
    #       to run the code on older Athlons as well
    # -xW   SSE2 optimization
    # -axW  SSE2 optimization,  but also generate code executable on all mach.
    # -tpp6 P3 optimization
    # -tpp7 P4 optimization
    #-----------------------------------------------------------------------

    OFLAG=-O3 -xW -tpp7

    OFLAG_HIGH = $(OFLAG)
    OBJ_HIGH =
    OBJ_NOOPT =
    DEBUG  = -FR -O0
    INLINE = $(OFLAG)


    #-----------------------------------------------------------------------
    # the following lines specify the position of BLAS  and LAPACK
    # on P4, VASP works fastest with the libgoto library
    # so that's what I recommend
    #-----------------------------------------------------------------------

    # Atlas based libraries
    #ATLASHOME= $(HOME)/archives/BLAS_OPT/ATLAS/lib/Linux_P4SSE2/
    #BLAS=   -L$(ATLASHOME)  -lf77blas -latlas

    # use specific libraries (default library path might point to other libraries)
    #BLAS= $(ATLASHOME)/libf77blas.a $(ATLASHOME)/libatlas.a

    # use the mkl Intel libraries for p4 (www.intel.com)
    # mkl.5.1
    # set -DRPROMU_DGEMV  -DRACCMU_DGEMV in the CPP lines
    BLAS=-L/opt/intel/Compiler/11.1/073/mkl/lib/em64 -mkl_intel_lp64 -lguide -lpthread -lmkl_core -mkl_sequential
    # mkl.5.2 requires also to -lguide library
    # set -DRPROMU_DGEMV  -DRACCMU_DGEMV in the CPP lines
    #BLAS=-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -lmkl_intel_lp64 -lguide -lpthread -lmkl_core -mkl_sequential

    # even faster Kazushige Goto's BLAS
    # https://www.cs.utexas.edu/users/kgoto/signup_first.html
    # BLAS=  /opt/libs/libgoto/libgoto_p4_512-r0.6.so

    # LAPACK, simplest use vasp.4.lib/lapack_double
    LAPACK= ../vasp.4.lib/lapack_double.o

    # use atlas optimized part of lapack
    #LAPACK= ../vasp.4.lib/lapack_atlas.o  -llapack -lcblas

    # use the mkl Intel lapack
    LAPACK=-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -lmkl_lapack -lguide -lpthread

    #-----------------------------------------------------------------------

    # LIB  = -L../vasp.4.lib -ldmy \
         ../vasp.4.lib/linpack_double.o $(LAPACK) \
        $(BLAS)

    # options for linking (for compiler version 6.X, 7.1) nothing is required
    LINK    =
    # compiler version 7.0 generates some vector statments which are located
    # in the svml library, add the LIBPATH and the library (just in case)
    #LINK    =  -L/opt/intel/compiler70/ia32/lib/ -lsvml

    #-----------------------------------------------------------------------
    # fft libraries:
    # VASP.4.6 can use fftw.3.0.X (https://www.fftw.org)
    # since this version is faster on P4 machines, we recommend to use it
    #-----------------------------------------------------------------------

    #FFT3D   = fft3dfurth.o fft3dlib.o
    #FFT3D   = fftw3d.o fft3dlib.o   /opt/libs/fftw-3.0.1/lib/libfftw3.a


    #=======================================================================
    # MPI section, uncomment the following lines
    #
    # one comment for users of mpich or lam:
    # You must *not* compile mpi with g77/f77, because f77/g77
    # appends *two* underscores to symbols that contain already an
    # underscore (i.e. MPI_SEND becomes mpi_send__).  The pgf90/ifc
    # compilers however append only one underscore.
    # Precompiled mpi version will also not work !!!
    #
    # We found that mpich.1.2.1 and lam-6.5.X to lam-7.0.4 are stable
    # mpich.1.2.1 was configured with
    #  ./configure -prefix=/usr/local/mpich_nodvdbg -fc="pgf77 -Mx,119,0x200000"  \
    # -f90="pgf90 " \
    # --without-romio --without-mpe -opt=-O \
    #
    # lam was configured with the line
    #  ./configure  -prefix /opt/libs/lam-7.0.4 --with-cflags=-O -with-fc=ifc \
    # --with-f77flags=-O --without-romio
    #
    # please note that you might be able to use a lam or mpich version
    # compiled with f77/g77, but then you need to add the following
    # options: -Msecond_underscore (compilation) and -g77libs (linking)
    #
    # !!! Please do not send me any queries on how to install MPI, I will
    # certainly not answer them !!!!
    #=======================================================================
    #-----------------------------------------------------------------------
    # fortran linker for mpi: if you use LAM and compiled it with the options
    # suggested above,  you can use the following line
    #-----------------------------------------------------------------------

    FC=mpif90
    FCL=$(FC)

    #-----------------------------------------------------------------------
    # additional options for CPP in parallel version (see also above):
    # NGZhalf               charge density   reduced in Z direction
    # wNGZhalf              gamma point only reduced in Z direction
    # scaLAPACK             use scaLAPACK (usually slower on 100 Mbit Net)
    #-----------------------------------------------------------------------

    CPP    = $(CPP_) -DMPI  -DHOST=\"LinuxIFC\" -DIFC \
         -Dkind8 -DNGZhalf -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc \
         -DMPI_BLOCK=500  \
        -DRPROMU_DGEMV  -DRACCMU_DGEMV

    #-----------------------------------------------------------------------
    # location of SCALAPACK
    # if you do not use SCALAPACK simply uncomment the line SCA
    #-----------------------------------------------------------------------
    BLACS=$(HOME)/archives/SCALAPACK/BLACS/
    SCA_=$(HOME)/archives/SCALAPACK/SCALAPACK

    #SCA= $(SCA_)/libscalapack.a  \
    $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a $(BLACS)/LIB/blacs_MPI-LINUX-0.a $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a

    #SCA=

    #-----------------------------------------------------------------------
    # libraries for mpi
    #-----------------------------------------------------------------------

    LIB     = -L../vasp.4.lib -ldmy  \
          ../vasp.4.lib/linpack_double.o $(LAPACK) \
          $(SCA) $(BLAS)

    # FFT: fftmpi.o with fft3dlib of Juergen Furthmueller
    FFT3D   = fftmpi.o fftmpi_map.o fft3dlib.o

    # fftw.3.0.1 is slighly faster and should be used if available
    #FFT3D   = fftmpiw.o fftmpi_map.o fft3dlib.o   /opt/libs/fftw-3.0.1/lib/libfftw3.a

    #-----------------------------------------------------------------------
    # general rules and compile lines
    #-----------------------------------------------------------------------
    BASIC=   symmetry.o symlib.o   lattlib.o  random.o

    SOURCE=  base.o     mpi.o      smart_allocate.o      xml.o  \
             constant.o jacobi.o   main_mpi.o  scala.o   \
             asa.o      lattice.o  poscar.o   ini.o      setex.o     radial.o  \
             pseudo.o   mgrid.o    mkpoints.o wave.o      wave_mpi.o  $(BASIC) \
             nonl.o     nonlr.o    dfast.o    choleski2.o    \
             mix.o      charge.o   xcgrad.o   xcspin.o    potex1.o   potex2.o  \
             metagga.o  constrmag.o pot.o      cl_shift.o force.o    dos.o      elf.o    \
             tet.o      hamil.o    steep.o    \
             chain.o    dyna.o     relativistic.o LDApU.o sphpro.o  paw.o   us.o \
             ebs.o      wavpre.o   wavpre_noio.o broyden.o \
             dynbr.o    rmm-diis.o reader.o   writer.o   tutor.o xml_writer.o \
             brent.o    stufak.o   fileio.o   opergrid.o stepver.o  \
             dipol.o    xclib.o    chgloc.o   subrot.o   optreal.o   davidson.o \
             edtest.o   electron.o shm.o      pardens.o  paircorrection.o \
             optics.o   constr_cell_relax.o   stm.o    finite_diff.o \
             elpol.o    setlocalpp.o aedens.o
    INC=

    vasp: $(SOURCE) $(FFT3D) $(INC) main.o
            rm -f vasp
            $(FCL) -o vasp $(LINK) main.o  $(SOURCE)   $(FFT3D) $(LIB)
    makeparam: $(SOURCE) $(FFT3D) makeparam.o main.F $(INC)
            $(FCL) -o makeparam  $(LINK) makeparam.o $(SOURCE) $(FFT3D) $(LIB)
    zgemmtest: zgemmtest.o base.o random.o $(INC)
            $(FCL) -o zgemmtest $(LINK) zgemmtest.o random.o base.o $(LIB)
    dgemmtest: dgemmtest.o base.o random.o $(INC)
            $(FCL) -o dgemmtest $(LINK) dgemmtest.o random.o base.o $(LIB)
    ffttest: base.o smart_allocate.o mpi.o mgrid.o random.o ffttest.o $(FFT3D) $(INC)
            $(FCL) -o ffttest $(LINK) ffttest.o mpi.o mgrid.o random.o smart_allocate.o base.o $(FFT3D) $(LIB)
    kpoints: $(SOURCE) $(FFT3D) makekpoints.o main.F $(INC)
            $(FCL) -o kpoints $(LINK) makekpoints.o $(SOURCE) $(FFT3D) $(LIB)

    clean:
            -rm -f *.g *.f *.o *.L *.mod ; touch *.F

    main.o: main$(SUFFIX)
            $(FC) $(FFLAGS)$(DEBUG)  $(INCS) -c main$(SUFFIX)
    xcgrad.o: xcgrad$(SUFFIX)
            $(FC) $(FFLAGS) $(INLINE)  $(INCS) -c xcgrad$(SUFFIX)
    xcspin.o: xcspin$(SUFFIX)
            $(FC) $(FFLAGS) $(INLINE)  $(INCS) -c xcspin$(SUFFIX)

    makeparam.o: makeparam$(SUFFIX)
            $(FC) $(FFLAGS)$(DEBUG)  $(INCS) -c makeparam$(SUFFIX)

    makeparam$(SUFFIX): makeparam.F main.F
    #
    # MIND: I do not have a full dependency list for the include
    # and MODULES: here are only the minimal basic dependencies
    # if one strucuture is changed then touch_dep must be called
    # with the corresponding name of the structure
    #
    base.o: base.inc base.F
    mgrid.o: mgrid.inc mgrid.F
    constant.o: constant.inc constant.F
    lattice.o: lattice.inc lattice.F
    setex.o: setexm.inc setex.F
    pseudo.o: pseudo.inc pseudo.F
    poscar.o: poscar.inc poscar.F
    mkpoints.o: mkpoints.inc mkpoints.F
    wave.o: wave.inc wave.F
    nonl.o: nonl.inc nonl.F
    nonlr.o: nonlr.inc nonlr.F

    $(OBJ_HIGH):
            $(CPP)
            $(FC) $(FFLAGS) $(OFLAG_HIGH) $(INCS) -c $*$(SUFFIX)
    $(OBJ_NOOPT):
            $(CPP)
            $(FC) $(FFLAGS) $(INCS) -c $*$(SUFFIX)

    fft3dlib_f77.o: fft3dlib_f77.F
            $(CPP)
            $(F77) $(FFLAGS_F77) -c $*$(SUFFIX)

    .F.o:
            $(CPP)
            $(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)
    .F$(SUFFIX):
            $(CPP)
    $(SUFFIX).o:
            $(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)

    # special rules
    #-----------------------------------------------------------------------
    # these special rules are cummulative (that is once failed
    #   in one compiler version, stays in the list forever)
    # -tpp5|6|7 P, PII-PIII, PIV
    # -xW use SIMD (does not pay of on PII, since fft3d uses double prec)
    # all other options do no affect the code performance since -O1 is used
    #-----------------------------------------------------------------------

    fft3dlib.o : fft3dlib.F
            $(CPP)
            $(FC) -FR -lowercase -O1 -tpp7 -xW -unroll0  -vec_report3 -c $*$(SUFFIX)
    fft3dfurth.o : fft3dfurth.F
            $(CPP)
            $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)

    radial.o : radial.F
            $(CPP)
            $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)

    symlib.o : symlib.F
            $(CPP)
           $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)

    symmetry.o : symmetry.F
            $(CPP)
            $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)

    dynbr.o : dynbr.F
            $(CPP)
            $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)

    broyden.o : broyden.F
            $(CPP)
            $(FC) -FR -lowercase -O2 -c $*$(SUFFIX)

    us.o : us.F
            $(CPP)
            $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)

    wave.o : wave.F
            $(CPP)
            $(FC) -FR -lowercase -O0 -c $*$(SUFFIX)

    LDApU.o : LDApU.F
            $(CPP)
            $(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
    这是我的makefile,

  • zzy870720z

    指定Blas时有错误
    -lmkl_intel_lp64 -lguide -lpthread -lmkl_core -mkl_sequential
    最后一个少一个l

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