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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 » 请问有没有人用Vasp算过声子，我们组里还没有人会跑，各位大神，拜托，拜托
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tt-0-8

银虫 (小有名气)
引用回帖:
10楼: Originally posted by iamikaruk at 2012-10-31 09:22:50
基本上不需要修改什么吧？ubuntu的确是比较好装一点，不过suse只要有那几个库，应该也是没有问题的。...

安装numpy所提示错误：
Traceback (most recent call last):
  File "setup.py", line 3, in
    import numpy
  File "/root/Desktop/phonopy-1.2.1/numpy/__init__.py", line 127, in
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python intepreter from there.
安装numpy提示：
Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'
/bin/sh: svnversion: command not found
F2PY Version 2
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib64
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib64
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib64
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib64
  libraries f77blas,cblas,atlas not found in /usr/lib
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1414: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
  libraries blas not found in /usr/local/lib64
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib64
  libraries blas not found in /usr/lib
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1423: UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1426: UserWarning:
    Blas (http://www.netlib.org/blas/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [blas_src]) or by setting
    the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
  NOT AVAILABLE

/bin/sh: svnversion: command not found
lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib64
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib64
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
  libraries lapack_atlas not found in /usr/local/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
  libraries lapack_atlas not found in /usr/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib64
  libraries lapack_atlas not found in /usr/local/lib64
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib64
  libraries lapack_atlas not found in /usr/lib64
  libraries f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1330: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
  libraries lapack not found in /usr/local/lib64
  libraries lapack not found in /usr/local/lib
  libraries lapack not found in /usr/lib64
  libraries lapack not found in /usr/lib
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1341: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1344: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
  NOT AVAILABLE

running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
building library "npymath" sources
customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelFCompiler
Found executable /bin/ifort
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
Could not locate executable pgf77
customize AbsoftFCompiler
Could not locate executable f90
customize NAGFCompiler
Could not locate executable f95
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
_configtest.c:1: 警告：与内建函数‘exp’类型冲突
gcc -pthread _configtest.o -o _configtest
_configtest.o: In function `main':
/root/Desktop/phonopy/numpy-1.6.1/_configtest.c:6: undefined reference to `exp'
collect2: ld 返回 1
_configtest.o: In function `main':
/root/Desktop/phonopy/numpy-1.6.1/_configtest.c:6: undefined reference to `exp'
collect2: ld 返回 1
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
_configtest.c:1: 警告：与内建函数‘exp’类型冲突
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
conv_template:> build/src.linux-x86_64-2.6/numpy/core/src/npymath/npy_math.c
conv_template:> build/src.linux-x86_64-2.6/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-2.6/numpy/core/src/npymath/npy_math_complex.c
building extension "numpy.core._sort" sources
Generating build/src.linux-x86_64-2.6/numpy/core/include/numpy/config.h
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
_configtest.c:1:20: 错误：Python.h：没有那个文件或目录
_configtest.c:1:20: 错误：Python.h：没有那个文件或目录
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
  File "setup.py", line 196, in
    setup_package()
  File "setup.py", line 189, in setup_package
    configuration=configuration )
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/core.py", line 186, in setup
    return old_setup(**new_attr)
  File "/usr/lib64/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/usr/lib64/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/install.py", line 55, in run
    r = old_install.run(self)
  File "/usr/lib64/python2.6/distutils/command/install.py", line 582, in run
    self.run_command('build')
  File "/usr/lib64/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
  File "/usr/lib64/python2.6/distutils/command/build.py", line 134, in run
    self.run_command(cmd_name)
  File "/usr/lib64/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 152, in run
    self.build_sources()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 169, in build_sources
    self.build_extension_sources(ext)
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 385, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 410, in generate_config_h
    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/setup.py", line 41, in check_types
    out = check_types(*a, **kw)
  File "numpy/core/setup.py", line 271, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
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坚持就是胜利，哈哈
11楼2012-10-31 09:31:52
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

iamikaruk

木虫 (著名写手)
引用回帖:
11楼: Originally posted by tt-0-8 at 2012-10-31 09:31:52
安装numpy所提示错误：
Traceback (most recent call last):
  File "setup.py", line 3, in <module>
    import numpy
  File "/root/Desktop/phonopy-1.2.1/numpy/__init__.py", ...

BLAS和LAPACK库没有装，先用yum装上
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[img]http://osu.ppy.sh/stat2/iamikaruk-0.png[/img]
12楼2012-10-31 10:24:26
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xcid

银虫 (小有名气)
我在VASP主页的帮助文件上用下面指令在虚拟机Ubantu系统上运行，怎么下载不下来呀？
% sudo apt-get install python-dev python-numpy \
  python-matplotlib python-tk python-lxml python-yaml
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小菜一碟
13楼2012-10-31 16:01:29
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xcid

银虫 (小有名气)
引用回帖:
12楼: Originally posted by iamikaruk at 2012-10-31 10:24:26
BLAS和LAPACK库没有装，先用yum装上...

你好，请问我们组计算机有个大的服务器，服务器上有主机，还有三台台式机通过内部网连到服务器上，那么请问那个phonoy程序是不是应该装在服务器的主机上，可是主机有没有联网，怎么装呀？
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小菜一碟
14楼2012-11-01 13:45:55
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

iamikaruk

木虫 (著名写手)
★ ★ ★ ★ ★
sunyang1988: 金币+5, 谢谢热心帮助 2012-11-01 19:21:42
引用回帖:
14楼: Originally posted by xcid at 2012-11-01 13:45:55
你好，请问我们组计算机有个大的服务器，服务器上有主机，还有三台台式机通过内部网连到服务器上，那么请问那个phonoy程序是不是应该装在服务器的主机上，可是主机有没有联网，怎么装呀？...

phonopy是个处理程序，你完全不用把它装到大服务器上。你随便找一个台式机装个ubuntu就行了。
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[img]http://osu.ppy.sh/stat2/iamikaruk-0.png[/img]
15楼2012-11-01 13:51:05
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