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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 » Abinit » abinit安装出错
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lingzhe

铜虫 (初入文坛)

[求助] abinit安装出错

??8??linux-redhat 5.4 ???????abinit-7.4.2????????????????????C++??fortran??mpich2?????????????????????????????????


mpd &
[1] 22087
[root@kongzhe abinit-7.4.2]# configuration file /etc/mpd.conf is accessible by others
change permissions to allow read and write access only by you




# ./config/scripts/makemake
[makemake] Starting at 2013/09/15 01:58:48 +0000
[makemake] -------------------------------------
[makemake] === Source tree consistency ===
[makemake]   Enabling write permission for all dirs & files
[makemake] === Source tree update ===
[makemake]   Generating CPP option dumper
[makemake]   Updating routines inside 57_iovars
[makemake]   Removing build examples
[makemake]   Generating build examples
[makemake] Updating Fortran interfaces
[makemake] ---> running ./config/scripts/abilint  --dependencies --dump_dtset bindings/parser/dtset.pickle . . 1>abilint.out 2>&1
[makemake]   Generating dtset source files
[makemake] === Build system update ===
[makemake]   Resetting configuration dumper
[makemake]   Generating macros for the Autotools
[makemake]   Generating macros for dumpers
[makemake]   Generating macros for environment variables
[makemake]   Generating macros for command-line options
[makemake]   Generating macros for hints
[makemake]   Generating macros for debugging
[makemake]   Generating macros for default optimizations
[makemake]   Generating macros for per-directory optimizations
[makemake]   Generating macros for core libraries
[makemake]   Generating macros for fallback linking
    make-macros-linking: Could not find config file (fallbacks/config/specs/fallbacks.conf).
    make-macros-linking: Aborting now.
[makemake] Aborting now!



#./configure
????????
Summary of important options:

  * C compiler      : gnu version 4.1
  * Fortran compiler: gnu version 4.1
  * architecture    : intel xeon (64 bits)

  * debugging       : basic
  * optimizations   : standard

  * OpenMP enabled  : no (collapse: ignored)
  * MPI    enabled  : no
  * MPI-IO enabled  : no
  * GPU    enabled  : no (flavor: none)

  * TRIO   flavor = none
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = netlib-fallback (libs: ignored)
  * ALGO   flavor = none (libs: ignored)
  * FFT    flavor = none (libs: ignored)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = none

Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>"




#make
..............................................
/bin/sh ./config.status
config.status: creating doc/Makefile
config.status: creating config.dump
config.status: creating config.pc
config.status: creating config.sh
config.status: creating config/wrappers/wrap-fc
config.status: creating fallbacks/config.mk
config.status: creating src/incs/Makefile
config.status: creating src/mods/Makefile
config.status: creating src/16_hideleave/m_build_info.F90
config.status: creating tests/config.sh
config.status: creating tests/tests.env
config.status: creating tests/tests-install.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/01_gsl_ext/Makefile
config.status: creating src/01_interfaces_ext/Makefile
config.status: creating src/01_linalg_ext/Makefile
config.status: creating src/01_macroavnew_ext/Makefile
config.status: creating src/02_clib/Makefile
config.status: creating src/10_defs/Makefile
config.status: creating src/11_memory_mpi/Makefile
config.status: creating src/11_qespresso_ext/Makefile
config.status: creating src/12_hide_mpi/Makefile
config.status: creating src/14_hidewrite/Makefile
config.status: creating src/15_gpu_toolbox/Makefile
config.status: creating src/16_hideleave/Makefile
config.status: creating src/18_timing/Makefile
config.status: creating src/27_toolbox_oop/Makefile
config.status: creating src/28_numeric_noabirule/Makefile
config.status: creating src/32_util/Makefile
config.status: creating src/41_geometry/Makefile
config.status: creating src/42_libpaw/Makefile
config.status: creating src/42_nlstrain/Makefile
config.status: creating src/42_parser/Makefile
config.status: creating src/43_ptgroups/Makefile
config.status: creating src/43_wvl_wrappers/Makefile
config.status: creating src/44_abitypes_defs/Makefile
config.status: creating src/45_geomoptim/Makefile
config.status: creating src/47_xml/Makefile
config.status: creating src/49_gw_toolbox_oop/Makefile
config.status: creating src/51_manage_mpi/Makefile
config.status: creating src/52_fft_mpi_noabirule/Makefile
config.status: creating src/52_manage_cuda/Makefile
config.status: creating src/53_abiutil/Makefile
config.status: creating src/53_ffts/Makefile
config.status: creating src/53_spacepar/Makefile
config.status: creating src/56_mixing/Makefile
config.status: creating src/56_recipspace/Makefile
config.status: creating src/56_xc/Makefile
config.status: creating src/57_iopsp_parser/Makefile
config.status: creating src/57_iovars/Makefile
config.status: creating src/59_io_mpi/Makefile
config.status: creating src/61_ionetcdf/Makefile
config.status: creating src/62_cg_noabirule/Makefile
config.status: creating src/62_iowfdenpot/Makefile
config.status: creating src/62_occeig/Makefile
config.status: creating src/62_poisson/Makefile
config.status: creating src/62_wvl_wfs/Makefile
config.status: creating src/63_bader/Makefile
config.status: creating src/64_atompaw/Makefile
config.status: creating src/65_lotf_base/Makefile
config.status: creating src/65_nonlocal/Makefile
config.status: creating src/65_psp/Makefile
config.status: creating src/66_paw/Makefile
config.status: creating src/66_wfs/Makefile
config.status: creating src/67_common/Makefile
config.status: creating src/68_dmft/Makefile
config.status: creating src/68_lotf/Makefile
config.status: creating src/68_recursion/Makefile
config.status: creating src/68_rsprc/Makefile
config.status: creating src/69_wfdesc/Makefile
config.status: creating src/70_gw/Makefile
config.status: creating src/71_bse/Makefile
config.status: creating src/72_response/Makefile
config.status: creating src/77_ddb/Makefile
config.status: creating src/77_lwf/Makefile
config.status: creating src/77_suscep/Makefile
config.status: creating src/79_seqpar_mpi/Makefile
config.status: creating src/83_cut3d/Makefile
config.status: creating src/95_drive/Makefile
config.status: creating src/98_main/Makefile
config.status: creating src/libs/Makefile
config.status: creating tests/Nightly/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing dump-optim commands
/bin/sh: /config/scripts/make-optim-dumper: No such file or directory
config.status: executing script-perms commands
config.status: executing long-lines commands
/bin/sh: /config/scripts/shrink-src-files: No such file or directory
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /root/abinit-7.4.2/config/gnu/missing --run autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[1]: Entering directory `/root/abinit-7.4.2'
Making all in fallbacks
make[2]: Entering directory `/root/abinit-7.4.2/fallbacks'
make fox
make[3]: Entering directory `/root/abinit-7.4.2/fallbacks'
The build of fox has been disabled
make[3]: Leaving directory `/root/abinit-7.4.2/fallbacks'
Checking build of fox fallback
test -e stamps/fox-install-stamp
make libxc
make[3]: Entering directory `/root/abinit-7.4.2/fallbacks'
The build of libxc has been disabled
make[3]: Leaving directory `/root/abinit-7.4.2/fallbacks'
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make linalg
make[3]: Entering directory `/root/abinit-7.4.2/fallbacks'
cd sources/lapack-abinit_6.10 && make -j 5
make[4]: Entering directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10'
cd blas && make
make[5]: Entering directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10/blas'
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c caxpy.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c ccopy.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c cdotc.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c cdotu.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c cgbmv.f
cdotu.f:0: 错误??march= 所带?????native)??正??cdotu.f:0: 错误??mtune= 所带?????native)??正??make[5]: *** [cdotu.o] 错误 1
make[5]: *** 正在等待未完??的任务....
caxpy.f:0: 错误??march= 所带?????native)??正??cdotc.f:0: 错误??march= 所带?????native)??正??caxpy.f:0: 错误??mtune= 所带?????native)??正??cdotc.f:0: 错误??mtune= 所带?????native)??正??cgbmv.f:0: 错误??march= 所带?????native)??正??cgbmv.f:0: 错误??mtune= 所带?????native)??正??make[5]: *** [cdotc.o] 错误 1
ccopy.f:0: 错误??march= 所带?????native)??正??ccopy.f:0: 错误??mtune= 所带?????native)??正??make[5]: *** [caxpy.o] 错误 1
make[5]: *** [cgbmv.o] 错误 1
make[5]: *** [ccopy.o] 错误 1
make[5]: Leaving directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10/blas'
make[4]: *** [all_targets] 错误 2
make[4]: Leaving directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10'
make[3]: *** [stamps/linalg-build-stamp] 错误 2
make[3]: Leaving directory `/root/abinit-7.4.2/fallbacks'
make[2]: [all-local] 错误 2 (忽略)
Checking build of linalg fallback
test -e stamps/linalg-install-stamp
make[2]: *** [all-local] 错误 1
make[2]: Leaving directory `/root/abinit-7.4.2/fallbacks'
make[1]: *** [all-recursive] 错误 1
make[1]: Leaving directory `/root/abinit-7.4.2'
make: *** [all] 错误 2
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1楼 2013-09-13 11:06:14
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

souledge

专家顾问 (著名写手)
这小乱码贴的，咋看得懂啊……
赞一下 回复此楼
思想重于技巧，内涵重于表象
2楼2013-09-13 15:23:44
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

lingzhe

铜虫 (初入文坛)
引用回帖:
2楼: Originally posted by souledge at 2013-09-13 15:23:44
这小乱码贴的，咋看得懂啊……

不好意思，没注意成乱码了。乱码就是错误，所带参数不正确


#make
..............................................
/bin/sh ./config.status
config.status: creating doc/Makefile
config.status: creating config.dump
config.status: creating config.pc
config.status: creating config.sh
config.status: creating config/wrappers/wrap-fc
config.status: creating fallbacks/config.mk
config.status: creating src/incs/Makefile
config.status: creating src/mods/Makefile
config.status: creating src/16_hideleave/m_build_info.F90
config.status: creating tests/config.sh
config.status: creating tests/tests.env
config.status: creating tests/tests-install.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/01_gsl_ext/Makefile
config.status: creating src/01_interfaces_ext/Makefile
config.status: creating src/01_linalg_ext/Makefile
config.status: creating src/01_macroavnew_ext/Makefile
config.status: creating src/02_clib/Makefile
config.status: creating src/10_defs/Makefile
config.status: creating src/11_memory_mpi/Makefile
config.status: creating src/11_qespresso_ext/Makefile
config.status: creating src/12_hide_mpi/Makefile
config.status: creating src/14_hidewrite/Makefile
config.status: creating src/15_gpu_toolbox/Makefile
config.status: creating src/16_hideleave/Makefile
config.status: creating src/18_timing/Makefile
config.status: creating src/27_toolbox_oop/Makefile
config.status: creating src/28_numeric_noabirule/Makefile
config.status: creating src/32_util/Makefile
config.status: creating src/41_geometry/Makefile
config.status: creating src/42_libpaw/Makefile
config.status: creating src/42_nlstrain/Makefile
config.status: creating src/42_parser/Makefile
config.status: creating src/43_ptgroups/Makefile
config.status: creating src/43_wvl_wrappers/Makefile
config.status: creating src/44_abitypes_defs/Makefile
config.status: creating src/45_geomoptim/Makefile
config.status: creating src/47_xml/Makefile
config.status: creating src/49_gw_toolbox_oop/Makefile
config.status: creating src/51_manage_mpi/Makefile
config.status: creating src/52_fft_mpi_noabirule/Makefile
config.status: creating src/52_manage_cuda/Makefile
config.status: creating src/53_abiutil/Makefile
config.status: creating src/53_ffts/Makefile
config.status: creating src/53_spacepar/Makefile
config.status: creating src/56_mixing/Makefile
config.status: creating src/56_recipspace/Makefile
config.status: creating src/56_xc/Makefile
config.status: creating src/57_iopsp_parser/Makefile
config.status: creating src/57_iovars/Makefile
config.status: creating src/59_io_mpi/Makefile
config.status: creating src/61_ionetcdf/Makefile
config.status: creating src/62_cg_noabirule/Makefile
config.status: creating src/62_iowfdenpot/Makefile
config.status: creating src/62_occeig/Makefile
config.status: creating src/62_poisson/Makefile
config.status: creating src/62_wvl_wfs/Makefile
config.status: creating src/63_bader/Makefile
config.status: creating src/64_atompaw/Makefile
config.status: creating src/65_lotf_base/Makefile
config.status: creating src/65_nonlocal/Makefile
config.status: creating src/65_psp/Makefile
config.status: creating src/66_paw/Makefile
config.status: creating src/66_wfs/Makefile
config.status: creating src/67_common/Makefile
config.status: creating src/68_dmft/Makefile
config.status: creating src/68_lotf/Makefile
config.status: creating src/68_recursion/Makefile
config.status: creating src/68_rsprc/Makefile
config.status: creating src/69_wfdesc/Makefile
config.status: creating src/70_gw/Makefile
config.status: creating src/71_bse/Makefile
config.status: creating src/72_response/Makefile
config.status: creating src/77_ddb/Makefile
config.status: creating src/77_lwf/Makefile
config.status: creating src/77_suscep/Makefile
config.status: creating src/79_seqpar_mpi/Makefile
config.status: creating src/83_cut3d/Makefile
config.status: creating src/95_drive/Makefile
config.status: creating src/98_main/Makefile
config.status: creating src/libs/Makefile
config.status: creating tests/Nightly/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing dump-optim commands
/bin/sh: /config/scripts/make-optim-dumper: No such file or directory
config.status: executing script-perms commands
config.status: executing long-lines commands
/bin/sh: /config/scripts/shrink-src-files: No such file or directory
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /root/abinit-7.4.2/config/gnu/missing --run autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[1]: Entering directory `/root/abinit-7.4.2'
Making all in fallbacks
make[2]: Entering directory `/root/abinit-7.4.2/fallbacks'
make fox
make[3]: Entering directory `/root/abinit-7.4.2/fallbacks'
The build of fox has been disabled
make[3]: Leaving directory `/root/abinit-7.4.2/fallbacks'
Checking build of fox fallback
test -e stamps/fox-install-stamp
make libxc
make[3]: Entering directory `/root/abinit-7.4.2/fallbacks'
The build of libxc has been disabled
make[3]: Leaving directory `/root/abinit-7.4.2/fallbacks'
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make linalg
make[3]: Entering directory `/root/abinit-7.4.2/fallbacks'
cd sources/lapack-abinit_6.10 && make -j 5
make[4]: Entering directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10'
cd blas && make
make[5]: Entering directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10/blas'
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c caxpy.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c ccopy.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c cdotc.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c cdotu.f
gfortran -ffixed-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -g -O2 -I/root/abinit-7.4.2/fallbacks/exports/include -c cgbmv.f
cdotu.f:0: 错误：-march= 所带参数(native)不正确
cdotu.f:0: 错误：-mtune= 所带参数(native)不正确
make[5]: *** [cdotu.o] 错误 1
make[5]: *** 正在等待未完成的任务....
caxpy.f:0: 错误：-march= 所带参数(native)不正确
cdotc.f:0: 错误：-march= 所带参数(native)不正确
caxpy.f:0: 错误：-mtune= 所带参数(native)不正确
cdotc.f:0: 错误：-mtune= 所带参数(native)不正确
cgbmv.f:0: 错误：-march= 所带参数(native)不正确
cgbmv.f:0: 错误：-mtune= 所带参数(native)不正确
make[5]: *** [cdotc.o] 错误 1
ccopy.f:0: 错误：-march= 所带参数(native)不正确
ccopy.f:0: 错误：-mtune= 所带参数(native)不正确
make[5]: *** [caxpy.o] 错误 1
make[5]: *** [cgbmv.o] 错误 1
make[5]: *** [ccopy.o] 错误 1
make[5]: Leaving directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10/blas'
make[4]: *** [all_targets] 错误 2
make[4]: Leaving directory `/root/abinit-7.4.2/fallbacks/sources/lapack-abinit_6.10'
make[3]: *** [stamps/linalg-build-stamp] 错误 2
make[3]: Leaving directory `/root/abinit-7.4.2/fallbacks'
make[2]: [all-local] 错误 2 (忽略)
Checking build of linalg fallback
test -e stamps/linalg-install-stamp
make[2]: *** [all-local] 错误 1
make[2]: Leaving directory `/root/abinit-7.4.2/fallbacks'
make[1]: *** [all-recursive] 错误 1
make[1]: Leaving directory `/root/abinit-7.4.2'
make: *** [all] 错误 2
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3楼2013-09-13 16:14:02
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

souledge

专家顾问 (著名写手)
★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
lingzhe(cenwanglai代发): 金币+5, 楼主到处找怎么给你金币呢 2013-09-17 11:37:56
lingzhe(sunyang1988代发): 金币+45, 代转金币 2013-09-23 13:48:11
引用回帖:
3楼: Originally posted by lingzhe at 2013-09-13 16:14:02
不好意思，没注意成乱码了。乱码就是错误，所带参数不正确


#make
..............................................
/bin/sh ./config.status
config.status: creating doc/Makefile
config.status: crea ...

科学网的blog中有一篇：http://blog.sciencenet.cn/blog-90975-427216.html。
如果由于小木虫的原因不容易查看，特摘抄如下（LZ的GNU Fortran正好是4.1版本）：
引用回帖:
1，如果使用gcc-4.1编译的openmpi, 后面abinit在make时会出现编译问题:
error: bad value (native) for -mtune= switch
所以重新安装gcc-4.5.0.

2 安装gcc-4.5.0之前要安装三个程序包，分别为：gmp-4.3.2，mpfr-2.4.2，mpc-0.8.1。按顺序安装到自己目录中，
$ ../configure --prefix="/home/zjma/program/gmp-4.3.2"
$../configure --prefix="/home/zjma/program/mpfr-2.4.2" --with-gmp="/home/zjma/program/gmp-4.3.2/"
$../configure --prefix="/home/zjma/program/mpc-0.8.1" --with-gmp="/home/zjma/program/gmp-4.3.2/" --with-mpfr="/home/zjma/program/mpfr-2.4.2/"

3 安装gcc-4.5.0
$ ../configure --prefix="/home/zjma/program/gcc-4.5.0" --with-gmp="/home/zjma/program/gmp-4.3.2/" --with-mpfr="/home/zjma/program/mpfr-2.4.2/" --with-mpc="/home/zjma/program/mpc-0.8.1/"
$ make
$ make install

4 使用gcc-4.5.0重新编译openmpi-1.4
$ ../configure FC="/home/zjma/program/gcc-4.5.0/bin/gfortran" CC="/home/zjma/program/gcc-4.5.0/bin/gcc" CXX="/home/zjma/program/gcc-4.5.0/bin/g++"  F77="/home/zjma/program/gcc-4.5.0/bin/gfortran" --prefix="/home/zjma/program/openmpi-1.4.2"
$ make
$ make install

5 下载abinit6.6.1的所有插件到~/.abinit/tarballs/下
地址：http://www.abinit.org/downloads/plug-in-sources

6 使用新编译的openmpi安装并行版abinit6.6.1
$ ../configure --prefix="/home/zjma/abinit-6.6.1" --with-mpi-prefix="/home/zjma/program/openmpi-1.4.2/" --enable-mpi="yes"  | tee 1
$ make
$ make install

不一定要完全按照上述博客中的来做，因为GCC系列编译器已经升级到非常高的版本了。而且，不一定要使用OpenMPI，具体要看服务器上是什么的。至于Abinit，显然就用最新版本了。
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思想重于技巧，内涵重于表象
4楼2013-09-14 12:15:30
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daofengwalan

金虫 (小有名气)
请问楼主的问题解决了吗？
我也是遇到类似的问题，MPI装的是MPICH2，是直接sudo aptget安装的，./configure的时候，也是找不到mpi：
  * OpenMP enabled  : no (collapse: ignored)
  * MPI    enabled  : no
  * MPI-IO enabled  : no
  * GPU    enabled  : no (flavor: none)
使用which mpirun命令查看，得到
/usr/local/bin/mpirun
这种情况，在.／的时候应该怎么设置？
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5楼2014-05-12 10:06:14
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