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marklau银虫 (小有名气)
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【求助】VASP使用出错,问题请教
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我按照http://muchong.com/bbs/viewthread.php?tid=1332100 安装的VASP 之前试过用ifc+mkl来装没有成功。用教程上的几个例子试了下,出现好几种错误。我将出现的错误贴在下面,请高手指点帮忙。 ------------------------------------------------------------------------------------- 1. vasp.4.6.28 25Jul05 complex POSCAR found : 1 types and 1 ions LDA part: xc-table for Pade appr. of Perdew POSCAR, INCAR and KPOINTS ok, starting setup WARNING: wrap around errors must be expected FFT: planning ... 1 reading WAVECAR entering main loop N E dE d eps ncg rms rms(c) DAV: 1 -0.338973130252E+01 -0.33897E+01 -0.12015E+03 3876 0.283E+02 DAV: 2 -0.487662410409E+01 -0.14869E+01 -0.14294E+01 4980 0.251E+01 DAV: 3 -0.488645576189E+01 -0.98317E-02 -0.98292E-02 4032 0.202E+00 DAV: 4 -0.488646366765E+01 -0.79058E-05 -0.79445E-05 5004 0.561E-02 DAV: 5 -0.488646367098E+01 -0.33273E-08 -0.34223E-08 3732 0.826E-04 0.770E-01 DAV: 6 -0.487366409615E+01 0.12800E-01 -0.40409E-03 3762 0.367E-01 0.460E-01 DAV: 7 -0.486631050449E+01 0.73536E-02 -0.89423E-03 3648 0.543E-01 0.254E-02 DAV: 8 -0.486630058326E+01 0.99212E-05 -0.31811E-05 3234 0.498E-02 Segmentation fault ----------------------------------------------------------------------------------- 2. vasp.4.6.28 25Jul05 complex POSCAR found : 1 types and 1 ions LDA part: xc-table for Pade appr. of Perdew WARNING: stress and forces are not correct POSCAR, INCAR and KPOINTS ok, starting setup WARNING: wrap around errors must be expected FFT: planning ... 1 reading WAVECAR WARNING: chargedensity file is incomplete ERROR: charge density could not be read from file CHGCAR for ICHARG>10 FORTRAN STOP ----------------------------------------------------------------------------------- 3. linux-n5rt:/home/VASP-example/Handson2/2_2_fccSi_dos # vasp vasp.4.6.28 25Jul05 complex POSCAR found : 1 types and 1 ions LDA part: xc-table for Pade appr. of Perdew POSCAR, INCAR and KPOINTS ok, starting setup WARNING: wrap around errors must be expected FFT: planning ... 1 reading WAVECAR WARNING: random wavefunctions but no delay for mixing, default for NELMDL entering main loop N E dE d eps ncg rms rms(c) DAV: 1 -0.338973130252E+01 -0.33897E+01 -0.12015E+03 3876 0.283E+02 DAV: 2 -0.487662410409E+01 -0.14869E+01 -0.14294E+01 4980 0.251E+01 DAV: 3 -0.488645576189E+01 -0.98317E-02 -0.98292E-02 4032 0.202E+00 DAV: 4 -0.488646366765E+01 -0.79058E-05 -0.79445E-05 5004 0.561E-02 DAV: 5 -0.488646367098E+01 -0.33273E-08 -0.34223E-08 3732 0.826E-04 0.770E-01 DAV: 6 -0.487366409615E+01 0.12800E-01 -0.40409E-03 3762 0.367E-01 0.460E-01 DAV: 7 -0.486631050449E+01 0.73536E-02 -0.89423E-03 3648 0.543E-01 0.254E-02 DAV: 8 -0.486630058326E+01 0.99212E-05 -0.31811E-05 3234 0.498E-02 *** glibc detected *** vasp: double free or corruption (!prev): 0x0000000001121df0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x2afa248b331e] /lib64/libc.so.6(__libc_free+0x6c)[0x2afa248b4d7c] vasp[0x5067a4] ======= Memory map: ======== 00400000-00c06000 r-xp 00000000 08:02 155614 /bin/vasp 00d05000-00d34000 rwxp 00805000 08:02 155614 /bin/vasp 00d34000-0119a000 rwxp 00d34000 00:00 0 [heap] 2afa243b4000-2afa243cf000 r-xp 00000000 08:02 20404 /lib64/ld-2.4.so 2afa243cf000-2afa243d5000 rwxp 2afa243cf000 00:00 0 2afa243f4000-2afa24446000 rwxp 2afa243f4000 00:00 0 2afa244ce000-2afa244d0000 rwxp 0001a000 08:02 20404 /lib64/ld-2.4.so 2afa244d0000-2afa244d8000 r-xp 00000000 08:02 20441 /lib64/librt-2.4.so 2afa244d8000-2afa245d7000 ---p 00008000 08:02 20441 /lib64/librt-2.4.so 2afa245d7000-2afa245d9000 rwxp 00007000 08:02 20441 /lib64/librt-2.4.so 2afa245d9000-2afa245ed000 r-xp 00000000 08:02 20437 /lib64/libpthread-2.4.so 2afa245ed000-2afa246ec000 ---p 00014000 08:02 20437 /lib64/libpthread-2.4.so 2afa246ec000-2afa246ee000 rwxp 00013000 08:02 20437 /lib64/libpthread-2.4.so 2afa246ee000-2afa246f2000 rwxp 2afa246ee000 00:00 0 2afa246f2000-2afa24746000 r-xp 00000000 08:02 20419 /lib64/libm-2.4.so 2afa24746000-2afa24845000 ---p 00054000 08:02 20419 /lib64/libm-2.4.so 2afa24845000-2afa24847000 rwxp 00053000 08:02 20419 /lib64/libm-2.4.so 2afa24847000-2afa24848000 rwxp 2afa24847000 00:00 0 2afa24848000-2afa2497e000 r-xp 00000000 08:02 20411 /lib64/libc-2.4.so 2afa2497e000-2afa24a7e000 ---p 00136000 08:02 20411 /lib64/libc-2.4.so 2afa24a7e000-2afa24a81000 r-xp 00136000 08:02 20411 /lib64/libc-2.4.so 2afa24a81000-2afa24a83000 rwxp 00139000 08:02 20411 /lib64/libc-2.4.so 2afa24a83000-2afa2533d000 rwxp 2afa24a83000 00:00 0 2afa25400000-2afa25421000 rwxp 2afa25400000 00:00 0 2afa25421000-2afa25500000 ---p 2afa25421000 00:00 0 2afa25500000-2afa2550d000 r-xp 00000000 08:02 33441 /lib64/libgcc_s.so.1 2afa2550d000-2afa2560c000 ---p 0000d000 08:02 33441 /lib64/libgcc_s.so.1 2afa2560c000-2afa2560d000 rwxp 0000c000 08:02 33441 /lib64/libgcc_s.so.1 7fff866df000-7fff866f6000 rwxp 7fff866df000 00:00 0 [stack]ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso] Aborted ------------------------------------------------------------------------------------- 4. linux-n5rt:/home/VASP-example/Handson4/4_5_Fe_dimer # vasp vasp.4.6.28 25Jul05 complex POSCAR found : 1 types and 2 ions ERROR: non collinear calculations require that VASP is compiled without the flag -DNGXhalf and -DNGZhalf FORTRAN STOP linux-n5rt:/home/VASP-example/Handson4/4_5_Fe_dimer # |
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2楼2009-05-18 20:39:27
marklau
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3楼2009-05-18 21:04:48
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4楼2009-05-18 21:23:24
marklau
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5楼2009-05-18 21:31:36
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ERROR: non collinear calculations require that VASP is compiled without the flag -DNGXhalf and -DNGZhalf FORTRAN STOP linux-n5rt:/home/VASP-example/Handson4/4_5_Fe_dimer # 从这个看起来,你在做那个handson上面的例子 先用benchment那个例子弄一下 |
6楼2009-05-18 21:47:45
marklau
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7楼2009-05-18 22:44:18
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8楼2009-05-18 23:48:16
veryman
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9楼2009-05-19 07:44:42
marklau
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可能是吧,贴出来,请大家看看 .SUFFIXES: .inc .f .f90 .F #----------------------------------------------------------------------- # Makefile for the PGI f90 (pgf90) compiler for Athlon Opteron systems # # The makefile was tested only under Linux on Intel platforms # # it might be required to change some of library pathes, since # LINUX installation vary a lot # Hence check ***ALL**** options in this makefile very carefully #----------------------------------------------------------------------- # # BLAS must be installed on the machine # there are several options: # 1) very slow but works: # retrieve the lapackage from ftp.netlib.org # and compile the blas routines (BLAS/SRC directory) # please use g77 or f77 for the compilation. When I tried to # use pgf77 or pgf90 for BLAS, VASP hang up when calling # ZHEEV (however this was with lapack 1.1 now I use lapack 2.0) # 2) most desirable: get an optimized BLAS # # the two most reliable packages around are presently: # 3a) Intels own optimised BLAS (PIII, P4, Itanium) # http://developer.intel.com/software/products/mkl/ # this is really excellent when you use Intel CPU's # # 3b) or obtain the atlas based BLAS routines # http://math-atlas.sourceforge.net/ # you certainly need atlas on the Athlon, since the mkl # routines are not optimal on the Athlon. # If you want to use atlas based BLAS, check the lines around LIB= # # 3c) mindblowing fast SSE2 (4 GFlops on P4, 2.53 GHz) # Kazushige Goto's BLAS # http://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=pgf90 # 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=8000 -DPGF90 -Davoidalloc \ # -DRPROMU_DGEMV -DRACCMU_DGEMV #----------------------------------------------------------------------- # general fortran flags (there must a trailing blank on this line) #----------------------------------------------------------------------- FFLAGS = -Mfree -tp k8-64 -i8 #----------------------------------------------------------------------- # optimization # no in depth tests done yet -O3 however seems to be sensible #----------------------------------------------------------------------- OFLAG=-O3 OFLAG_HIGH = $(OFLAG) OBJ_HIGH = OBJ_NOOPT = DEBUG = -O0 INLINE = $(OFLAG) #----------------------------------------------------------------------- # the following lines specify the position of BLAS and LAPACK # on Opteron, VASP works fastest with the libgoto library # so that's what I recommend #----------------------------------------------------------------------- # Atlas based libraries ATLASHOME= /usr/local/Linux_HAMMER64SSE2_2/lib BLAS= -L$(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/mkl/lib/32 -lmkl_p4 -lpthread # mkl.5.2 requires also to -lguide library # set -DRPROMU_DGEMV -DRACCMU_DGEMV in the CPP lines #BLAS=-L/opt/intel/mkl/lib/32 -lmkl_p4 -lguide -lpthread # even faster Kazushige Goto's BLAS # http://www.cs.utexas.edu/users/kgoto/signup_first.html #BLAS= /home/kresse/64/vasp.4.6/libgoto_opt64-r0.93.so # LAPACK, simplest use vasp.4.lib/lapack_double LAPACK= /root/vasp/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= -lmkl_lapack #----------------------------------------------------------------------- LIB = -L../vasp.4.lib -ldmy \ ../vasp.4.lib/linpack_double.o $(LAPACK) \ $(BLAS) # options for linking (for compiler version 6.X, 7.1) nothing is required LINK = -tp k8-64 #----------------------------------------------------------------------- # fft libraries: # VASP.4.6 can use fftw.3.0.X (http://www.fftw.org) # since this version is faster on P4 machines, we recommend to use it #----------------------------------------------------------------------- FFT3D = fft3dfurth.o fft3dlib.o FFT3D = fftw3d.o fft3dlib.o /usr/local/fftw-3.1.3/lib/libfftw3.a #======================================================================= # MPI section, uncomment the following lines # # one comment for users of mpich or lam: # You must *not* compile mpi with g77/f77, because f77/g77 # appends *two* underscores to symbols that contain already an # underscore (i.e. MPI_SEND becomes mpi_send__). The pgf90/ifc # compilers however append only one underscore. # Precompiled mpi version will also not work !!! # # We found that mpich.1.2.1 and lam-6.5.X to lam-7.0.4 are stable # mpich.1.2.1 was configured with # ./configure -prefix=/usr/local/mpich_nodvdbg -fc="pgf77 -Mx,119,0x200000" \ # -f90="pgf90 -Mx,119,0x200000" \ # --without-romio --without-mpe -opt=-O \ # # lam was configured with the line # ./configure -prefix /opt/libs/lam-7.0.4 --with-cflags=-O -with-fc=pgf77 \ # --with-f77flags=-O --without-romio # # please note that you might be able to use a lam or mpich version # compiled with f77/g77, but then you need to add the following # options: -Msecond_underscore (compilation) and -g77libs (linking) # # !!! Please do not send me any queries on how to install MPI, I will # certainly not answer them !!!! #======================================================================= #----------------------------------------------------------------------- # fortran linker for mpi: if you use LAM and compiled it with the options # suggested above, you can use the following line #----------------------------------------------------------------------- #FC=mpif77 #FCL=$(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 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) $(FFLAGS) -fastsse -Mipa=fast -c $*$(SUFFIX) |
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