fluidity install on Cluster

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？