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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » Vasp&MedeA » 【求助】vasp并行安装mpich2的错误
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夕阳西下

金虫 (著名写手)

[交流] 【求助】vasp并行安装mpich2的错误已有4人参与

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。
不知道出了什么问题？大家帮帮忙。
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1楼2010-11-10 19:52:40
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youzhizhe(金币+1):谢谢。 2010-11-11 16:31:39
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
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2楼2010-11-10 20:15:08
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夕阳西下

金虫 (著名写手)
linux-pd32:~/vasp/vasp.4.6 # make
./preprocess 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？
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3楼2010-11-11 14:32:06
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小木虫(金币+0.5):给个红包，谢谢回帖交流
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Originally posted by 夕阳西下 at 2010-11-11 14:32:06:
linux-pd32:~/vasp/vasp.4.6 # make
./preprocess 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
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4楼2010-11-11 19:20:35
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夕阳西下

金虫 (著名写手)
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
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5楼2010-11-11 21:54:42
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youzhizhe(金币+2):谢谢交流。 2010-11-11 22:25:33
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
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6楼2010-11-11 22:05:50
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夕阳西下

金虫 (著名写手)
# 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
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7楼2010-11-12 10:06:30
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zzy870720z

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小木虫(金币+0.5):给个红包，谢谢回帖交流
zxzj05(金币+1):奖励回帖交流 2010-11-12 12:56:31
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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8楼2010-11-12 10:30:49
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夕阳西下

金虫 (著名写手)
引用回帖:
Originally posted by zzy870720z at 2010-11-12 10:30:49:
指定Blas时有错误
-lmkl_intel_lp64 -lguide -lpthread -lmkl_core -mkl_sequential
最后一个少一个l

我知道乐，谢谢

[ Last edited by 夕阳西下 on 2010-11-12 at 11:02 ]
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gougou531

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小木虫(金币+0.5):给个红包，谢谢回帖
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