Project

General

Profile

Install EMAN2 » History » Version 74

Neil Voss, 02/12/2016 01:14 PM

1 1 Neil Voss
h1. Install EMAN2/SPARX
2
3 53 Amber Herold
*Before you begin:*
4 55 Amber Herold
Please note that Appion 2.2, Appion 2.2-redux and any earlier releases do not include any features that require EMAN2/SPARX to be installed. Appion 3.0, the development trunk and future releases will require this software.
5 69 Neil Voss
This documentation assumes you are using CentOS 6 (written as of CentOS 6.5)
6
It is best to install EMAN2/SPARX from source to get MPI working on a cluster or to avoid conflicts with having two different versions of python on your system. Binaries of EMAN2/SPARX all come with their own python pre-installed.
7 6 Neil Voss
8
9 55 Amber Herold
h2. Install pre-requisite packages for EMAN2 compiling
10 6 Neil Voss
11 27 Neil Voss
h3. yum based packages
12
13 7 Neil Voss
* Make sure EPEL is install, if not go here: [[Download additional Software (CentOS Specific)]]
14
* Use yum to install devel libraries:
15
<pre>
16 67 Neil Voss
sudo yum install fftw-devel gsl-devel boost-python numpy libjpeg-devel \
17 68 Neil Voss
 PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel libdb-devel \
18
 PyOpenGL ftgl-devel db4-devel python-argparse openmpi-devel python-pip
19 1 Neil Voss
</pre>
20 27 Neil Voss
21
22 3 Neil Voss
h2. Download the source
23
24
# To download the source code go to the link:
25
#* http://blake.bcm.edu/emanwiki/EMAN2
26 56 Amber Herold
# Click on *"Main EMAN2 Download Page"*
27 66 Neil Voss
# Click on *"Download EMAN 2"*, whichever is the latest release of EMAN. 
28
# Scroll down to *Source* to download the *eman2.1beta3.source.tar.gz* 
29 3 Neil Voss
30
h2. Work with the source
31
32
# go to the directory with the source code
33
# extract the archive:
34
<pre>
35 71 Neil Voss
tar zxvf eman2.12.source.tar.gz
36 1 Neil Voss
</pre>
37 15 Neil Voss
# go into directory
38
<pre>cd EMAN2/src/build</pre>
39 19 Neil Voss
# start configure script:
40 11 Neil Voss
<pre>cmake ../eman2/</pre>
41 1 Neil Voss
#* Note: alternatively you can run @ccmake ../eman2/@ and configure all the parameters
42 70 Neil Voss
<pre>
43
-- The C compiler identification is GNU 4.4.7
44
-- The CXX compiler identification is GNU 4.4.7
45
-- Check for working C compiler: /usr/bin/cc
46
-- Check for working C compiler: /usr/bin/cc -- works
47
-- Detecting C compiler ABI info
48
-- Detecting C compiler ABI info - done
49
-- Check for working CXX compiler: /usr/bin/c++
50
-- Check for working CXX compiler: /usr/bin/c++ -- works
51
-- Detecting CXX compiler ABI info
52
-- Detecting CXX compiler ABI info - done
53
-- Looking for fseek64
54
-- Looking for fseek64 - not found
55
-- Looking for fseeko
56
-- Looking for fseeko - found
57
-- Looking for ftell64
58
-- Looking for ftell64 - not found
59
-- Looking for ftello
60
-- Looking for ftello - found
61
-- Configuring done
62
-- Generating done
63
-- Build files have been written to: /emg/sw/EMAN2/src/build
64
</pre>
65 18 Neil Voss
# start compiling:
66
<pre>make</pre>
67 3 Neil Voss
# install to directory:
68 23 Neil Voss
<pre>sudo make install</pre>
69
70
h2. Set environmental variables
71
72
h3. bash
73
74
<pre>sudo nano /etc/profile.d/eman2.sh</pre>
75 24 Neil Voss
76
<pre>
77
export EMAN2DIR=/usr/local/EMAN2
78
export PATH=${EMAN2DIR}/bin:${PATH}
79 23 Neil Voss
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
80
export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin
81
</pre>
82 16 Neil Voss
83 51 Neil Voss
h3. c shell
84
85
<pre>sudo nano /etc/profile.d/eman2.csh</pre>
86
87
<pre>
88
setenv EMAN2DIR /usr/local/EMAN2
89
setenv PATH ${EMAN2DIR}/bin:${PATH}
90
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
91
setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin
92
</pre>
93
94
95 50 Neil Voss
h2. Install MyMPI
96 42 Neil Voss
97 63 Amber Herold
* First, add the openmpi module so that MyMPI can find it.
98
<pre>
99
module add openmpi-i386
100
-or-
101
module add openmpi-x86_64
102
</pre>
103
104 42 Neil Voss
* Download source: 
105 61 Amber Herold
From the main software page: http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222 scroll to *MPI Support*.
106
Click on *Download MPI Support*
107
Click on *pydusa-1.15es.tgz*
108 42 Neil Voss
* Extract:
109 61 Amber Herold
<pre>tar zxvf pydusa-1.15es.tgz</pre>
110 42 Neil Voss
* go into directory
111 61 Amber Herold
<pre>cd pydusa-1.15es</pre>
112 65 Amber Herold
&nbsp;
113 62 Amber Herold
If you are on a 64bit machine, you may have problems with the code finding the numpy headers:
114 65 Amber Herold
&nbsp;
115 34 Neil Voss
<pre>nano configure</pre>
116 65 Amber Herold
&nbsp;
117 54 Neil Voss
find the line:
118 1 Neil Voss
<pre>
119
elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then
120
   PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include"
121 54 Neil Voss
</pre>
122
and replace it with:
123 65 Amber Herold
&nbsp;
124 54 Neil Voss
<pre>
125 1 Neil Voss
elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then
126
   PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include"
127 46 Neil Voss
</pre>
128
* Configure:
129
<pre>
130
setenv MPIROOT /usr/lib64/openmpi
131
setenv MPIINC /usr/include/openmpi-x86_64
132
setenv MPILIB ${MPIROOT}/lib
133
setenv MPIBIN ${MPIROOT}/bin
134 1 Neil Voss
./configure
135
</pre>
136
<pre>
137
export MPIROOT=/usr/lib64/openmpi
138
export MPIINC=/usr/include/openmpi-x86_64
139
export MPILIB=${MPIROOT}/lib
140 47 Neil Voss
export MPIBIN=${MPIROOT}/bin
141 46 Neil Voss
./configure
142
</pre>
143 64 Amber Herold
Please ensure mpicc was found. If it is not found, a version of MPI will be installed that may cause errors. Look for the following error and correct this issue before moving on:
144
<pre>
145
configure: error: Unable to find mpicc! mpicc location can be specified with --with-mpicc
146
</pre>
147 65 Amber Herold
&nbsp;
148 46 Neil Voss
* compile the source:
149
<pre>make</pre>
150
* copy the mpi.so to site-packages with a different name:
151
<pre>
152 1 Neil Voss
sudo mkdir /usr/lib64/python2.6/site-packages/mympi/
153 52 Neil Voss
sudo touch /usr/lib64/python2.6/site-packages/mympi/__init__.py
154 1 Neil Voss
sudo cp -v src/mpi.so /usr/lib64/python2.6/site-packages/mympi/mpi.so
155
</pre>
156 47 Neil Voss
* create a wrapper around the wrapper:
157 1 Neil Voss
<pre>sudo nano /usr/lib64/python2.6/site-packages/mpi.py</pre>
158
<pre>
159
import ctypes
160
mpi = ctypes.CDLL('libmpi.so.1', ctypes.RTLD_GLOBAL)
161
from mympi.mpi import *
162
</pre>
163 50 Neil Voss
This needs to be done to avoid the error:
164
<pre>
165
python: symbol lookup error: 
166
  /usr/lib64/openmpi/lib/openmpi/mca_paffinity_hwloc.so: 
167
    undefined symbol: mca_base_param_reg_int
168
</pre>
169 1 Neil Voss
170
* test 1: 
171
<pre>
172
python -c 'import mpi'
173
python -c 'import sys; from mpi import mpi_init; mpi_init(len(sys.argv), sys.argv)'
174
</pre>
175
176 50 Neil Voss
* test 2: 
177
<pre>sxisac.py start.hdf</pre>
178
(Note: start.hdf does not need to exist, if it does not exist then it should exit with file not found)
179 42 Neil Voss
180 50 Neil Voss
h2. Test to see if code works
181
182
see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest
183
184
<pre>
185
cd EMAN2/test/rt
186
./rt.py
187
</pre>
188
189
h2. Install MyMPI for MPI functions
190
191
see http://sparx-em.org/sparxwiki/MPI-installation
192
or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup
193
194
This fixes this problem:
195
<pre>
196
    from mpi import mpi_init
197
ImportError: No module named mpi
198
</pre>
199
200
This module was very difficult to get working, it seems to be a poorly supported python wrapper for MPI. So, what we are going to do is compile the module, rename it, and create a wrapper. So, essentially we are creating a wrapper around the wrapper. We can only hope they switch to [http://mpi4py.scipy.org/ mpi4py] in the future.
201 34 Neil Voss
202 9 Neil Voss
h2. Documentation
203 3 Neil Voss
204 1 Neil Voss
* http://blake.bcm.edu/emanwiki/EMAN2/Install
205 2 Neil Voss
* http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ
206 31 Neil Voss
207 2 Neil Voss
______
208
209
[[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]]
210 1 Neil Voss
211
______