Project

General

Profile

Install EMAN2 » History » Version 36

Neil Voss, 08/13/2012 09:47 PM

1 1 Neil Voss
h1. Install EMAN2/SPARX
2
3
It is best to install EMAN2/SPARX from source, so that do not have conflicts with having two different versions of python on your system. Binaries of EMAN2/SPARX all come with their own python pre-installed.
4 2 Neil Voss
5 6 Neil Voss
This documentation assumes you are using CentOS 6 (written as of CentOS 6.2)
6
7
h2. Install require pre-packages for EMAN2 compiling
8
9 27 Neil Voss
h3. yum based packages
10
11 7 Neil Voss
* Make sure EPEL is install, if not go here: [[Download additional Software (CentOS Specific)]]
12
* Use yum to install devel libraries:
13
<pre>
14 10 Neil Voss
sudo yum install fftw-devel gsl-devel boost-python numpy \
15 12 Neil Voss
 PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel \
16 8 Neil Voss
 PyOpenGL ftgl-devel db4-devel python-argparse openmpi-devel
17 1 Neil Voss
</pre>
18 27 Neil Voss
19
h3. bsddb3
20
21
Additionally you need to install the python-bsddb3 library (not available via YUM). I just use the pypi easy_installer, yum will never know.
22 26 Neil Voss
<pre>
23 1 Neil Voss
sudo easy_install bsddb3
24
</pre>
25 27 Neil Voss
26 3 Neil Voss
h2. Download the source
27
28
# To download the source code go to the link:
29
#* http://blake.bcm.edu/emanwiki/EMAN2
30 17 Neil Voss
# Click on *"Current stable version - direct link"*
31 3 Neil Voss
# Go under the heading "Source" at bottom of page
32
# Click to download the *eman-source-2.xx.tar.gz* file (as of August 2012, 2.xx is 2.06)
33
34
h2. Work with the source
35
36
# go to the directory with the source code
37
# extract the archive:
38
<pre>
39 4 Neil Voss
tar zxvf eman-source-2.06.tar.gz
40 1 Neil Voss
</pre>
41 15 Neil Voss
# go into directory
42
<pre>cd EMAN2/src/build</pre>
43 19 Neil Voss
# start configure script:
44 11 Neil Voss
<pre>cmake ../eman2/</pre>
45 15 Neil Voss
#* Note: alternatively you can run @ccmake ../eman2/@ and configure all the parameters
46 18 Neil Voss
# start compiling:
47
<pre>make</pre>
48 3 Neil Voss
# install to directory:
49 23 Neil Voss
<pre>sudo make install</pre>
50
51
h2. Set environmental variables
52
53
h3. bash
54
55
<pre>sudo nano /etc/profile.d/eman2.sh</pre>
56 24 Neil Voss
57
<pre>
58
export EMAN2DIR=/usr/local/EMAN2
59
export PATH=${EMAN2DIR}/bin:${PATH}
60 23 Neil Voss
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
61
export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin
62
</pre>
63 16 Neil Voss
64
h2. Test to see if code works
65
66
see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest
67
68
<pre>
69
cd EMAN2/test/rt
70
./rt.py
71 3 Neil Voss
</pre>
72 1 Neil Voss
73 31 Neil Voss
h2. Install MyMPI for SPARX MPI functions
74
75
see http://sparx-em.org/sparxwiki/MPI-installation
76 32 Neil Voss
or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup
77 31 Neil Voss
78 33 Neil Voss
This fixes this problem:
79
<pre>
80
    from mpi import mpi_init
81
ImportError: No module named mpi
82
</pre>
83
84 34 Neil Voss
h3. to install
85
* Download source
86
* tar zxvf
87
* cd directory
88 35 Neil Voss
* setenv MPIINC /usr/include/openmpi-x86_64/
89
* ./configure --with-mpicc=/usr/lib64/openmpi/bin/mpicc
90 34 Neil Voss
** if it fails you need to change these lines in configure
91
<pre>nano configure</pre>
92
<pre>
93
elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then
94
   PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include"
95
</pre><pre>
96
elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then
97
   PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include"
98
</pre>
99 36 Neil Voss
* make
100 34 Neil Voss
101 9 Neil Voss
h2. Documentation
102 3 Neil Voss
103 1 Neil Voss
* http://blake.bcm.edu/emanwiki/EMAN2/Install
104 2 Neil Voss
* http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ
105 31 Neil Voss
106 2 Neil Voss
______
107
108
[[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]]
109 1 Neil Voss
110
______