fluidity install on Cluster

1.编译器安装 gcc4.6 openmpi python

HOME_PATH= /hpcdata1/xiaozhong/

1.1.gmp & mpc & mpfr

1.1.1.gmp-6.0.0

$ tar -xvf gmp-6.0.0a.tar.bz2

$ cd gmp-6.0.0

./configure --prefix=/hpcdata1/xiaozhong/public/gmp-6.0.0  \

--enable-cxx

make -j4

make install

1.1.2.mpfr-3.1.2

$ tar -xvf mpfr-3.1.2.tar.bz2

$ cd mpfr-3.1.2

./configure --prefix=/hpcdata1/xiaozhong/public/mpfr-3.1.2  \

--with-gmp=/hpcdata1/xiaozhong/public/gmp-6.0.0

make -j4

make install

1.1.3.mpc

$ tar -xvf mpc-1.0.2.tar.gz

$ cd mpc-1.0.2

./configure --prefix=/hpcdata1/xiaozhong/public/mpc-1.0.2  \

--with-gmp=/hpcdata1/xiaozhong/public/gmp-6.0.0   \

--with-mpfr=/hpcdata1/xiaozhong/public/mpfr-3.1.2

make -j4

make install

1.1.4.set environment path

$ vi ~/.bashrc

edit .bashrc

export LD_LIBRARY_PATH=/hpcdata1/xiaozhong/public/mpc-1.0.2/lib:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/hpcdata1/xiaozhong/public/gmp-6.0.0/lib:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/hpcdata1/xiaozhong/public/mpfr-3.1.2/lib:$LD_LIBRARY_PATH

1.2.gcc-4.6

$ tar -xvf gcc-4.6.4.tar

$ cd gcc-4.6.4

./configure  \

--prefix=/hpcdata1/xiaozhong/public/gcc-4.6.4  \

--with-mpc=/hpcdata1/xiaozhong/public/mpc-1.0.2  \

--with-mpfr=/hpcdata1/xiaozhong/public/mpfr-3.1.2  \

--with-gmp=/hpcdata1/xiaozhong/public/gmp-6.0.0  \

--enable-languages=c,c++,fortran

make -j4

make install

set environment path

要将动态链接库位置添加到 LD_LIBRARY_PATH 内，否则编译好程序无法运行

export PATH=/hpcdata1/xiaozhong/public/gcc-4.6.4/bin:$PATH

export LD_LIBRARY_PATH=/hpcdata1/xiaozhong/public/gcc-4.6.4/lib:$LD_LIBRARY_PATH

export LD_LIBRARY_PATH=/hpcdata1/xiaozhong/public/gcc-4.6.4/lib64:$LD_LIBRARY_PATH

1.3.openmpi-1.8.3

$ tar -xvf openmpi-1.8.3.tar

$ cd openmpi-1.8.3

./configure  \

--prefix=/hpcdata1/xiaozhong/public/openmpi-1.8.3  \

CC=gcc  \

CXX=g++  \

FC=gfortran \

CFLAGS=-fgnu89-inline

make -j4

make install

edit .bashrc

export PATH=/hpcdata1/xiaozhong/public/openmpi-1.8.3/bin:$PATH

export LD_LIBRARY_PATH=/hpcdata1/xiaozhong/public/openmpi-1.8.3/lib:$LD_LIBRARY_PATH

1.4.python

1.4.1.python 2.7

$ wget --no-check-certificate http://python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2

$ tar -xvf Python-2.7.3.tar.bz2

$ make

the system print:

Python build finished, but the necessary bits to build these modules were not found:

_tkinter           bsddb185           dl

imageop            sunaudiodev

To find the necessary bits, look in setup.py in detect_modules() for the module's name.

无视，继续

$ make install

1.4.2.setuptools

$ tar -xvf setuptools-12.0.5.tar.gz

$ cd setuptools-12.0.5

$ su

python setup.py install --prefix=/hpcdata1/xiaozhong/public

此时在/hpcdata1/xiaozhong/public目录下生成lib/python2.7/site-packages目录，运行里面setuptools-12.0.5-py2.7.egg脚本，便在/usr/local/bin/目录下生成easy_install程序。

sudo sh ./setuptools-12.0.5-py2.7.egg

测试

easy_install numpy


Searching for numpy

Reading https://pypi.python.org/simple/numpy/

Download error on https://pypi.python.org/simple/numpy/: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed -- Some packages may not be found!

Couldn't find index page for 'numpy' (maybe misspelled?)

Scanning index of all packages (this may take a while)

Reading https://pypi.python.org/simple/

Download error on https://pypi.python.org/simple/: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed -- Some packages may not be found!

No local packages or download links found for numpy

error: Could not find suitable distribution for Requirement.parse('numpy')

curl的证书太老了需要下载最新的证书

下载最新的证书文件

$ wget http://curl.haxx.se/ca/cacert.pem

更名为ca-bundle.crt放置到默认目录

$ mv cacert.pem ca-bundle.crt

$ mv ca-bundle.crt /etc/pki/tls/certs

还是不能用！！！

1.4.3.numpy 源程序安装

首先添加安装位置到PYTHONPATH环境变量中，edit .bashrc

export PYTHONPATH=/hpcdata1/xiaozhong/public/lib/python2.7/site-packages/:$PYTHONPATH


$ tar -xvf numpy-1.9.2.tar.gz

$ cd setuptools-12.0.5

$ python setup.py install --prefix=/hpcdata1/xiaozhong/public

不成功？

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