Install EMAN2 » History » Version 87
Neil Voss, 05/23/2016 03:03 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 | 81 | Neil Voss | sudo yum install fftw-devel gsl-devel boost148-python numpy libjpeg-devel \ |
17 | PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel boost148-devel \ |
||
18 | 85 | Neil Voss | PyOpenGL db4-devel python-argparse openmpi-devel python-pip freeglut-devel ftgl-devel |
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 | 1 | Neil Voss | <pre>cmake ../eman2/</pre> |
41 | 11 | Neil Voss | #* Note: alternatively you can run @ccmake ../eman2/@ and configure all the parameters |
42 | 75 | Neil Voss | #* I had to disable ftgl (fonts in OpenGL) to get 2.12 to compile. |
43 | 82 | Neil Voss | #* I had to manually set BOOST_LIBRARY=/usr/lib64/boost148/libboost_python.so |
44 | 84 | Neil Voss | #* I had to manually set BOOST_INCLUDE_PATH=/usr/include/boost148 |
45 | #* I had to manually set FREETYPE_INCLUDE_PATH=/usr/include/freetype2/ |
||
46 | 87 | Neil Voss | #* I had to manually set FTGL_INCLUDE_PATH=/usr/include/FTGL/ |
47 | #* I had to manually set FTGL_LIBRARY=/usr/lib64/libftgl.so |
||
48 | 70 | Neil Voss | <pre> |
49 | -- The C compiler identification is GNU 4.4.7 |
||
50 | -- The CXX compiler identification is GNU 4.4.7 |
||
51 | -- Check for working C compiler: /usr/bin/cc |
||
52 | -- Check for working C compiler: /usr/bin/cc -- works |
||
53 | -- Detecting C compiler ABI info |
||
54 | -- Detecting C compiler ABI info - done |
||
55 | -- Check for working CXX compiler: /usr/bin/c++ |
||
56 | -- Check for working CXX compiler: /usr/bin/c++ -- works |
||
57 | -- Detecting CXX compiler ABI info |
||
58 | -- Detecting CXX compiler ABI info - done |
||
59 | -- Looking for fseek64 |
||
60 | -- Looking for fseek64 - not found |
||
61 | -- Looking for fseeko |
||
62 | -- Looking for fseeko - found |
||
63 | -- Looking for ftell64 |
||
64 | -- Looking for ftell64 - not found |
||
65 | -- Looking for ftello |
||
66 | -- Looking for ftello - found |
||
67 | -- Configuring done |
||
68 | -- Generating done |
||
69 | -- Build files have been written to: /emg/sw/EMAN2/src/build |
||
70 | </pre> |
||
71 | 18 | Neil Voss | # start compiling: |
72 | <pre>make</pre> |
||
73 | 3 | Neil Voss | # install to directory: |
74 | 23 | Neil Voss | <pre>sudo make install</pre> |
75 | |||
76 | h2. Set environmental variables |
||
77 | |||
78 | h3. bash |
||
79 | |||
80 | <pre>sudo nano /etc/profile.d/eman2.sh</pre> |
||
81 | 24 | Neil Voss | |
82 | <pre> |
||
83 | export EMAN2DIR=/usr/local/EMAN2 |
||
84 | export PATH=${EMAN2DIR}/bin:${PATH} |
||
85 | 23 | Neil Voss | export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib |
86 | export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin |
||
87 | </pre> |
||
88 | 16 | Neil Voss | |
89 | 51 | Neil Voss | h3. c shell |
90 | |||
91 | <pre>sudo nano /etc/profile.d/eman2.csh</pre> |
||
92 | |||
93 | <pre> |
||
94 | setenv EMAN2DIR /usr/local/EMAN2 |
||
95 | setenv PATH ${EMAN2DIR}/bin:${PATH} |
||
96 | setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib |
||
97 | setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin |
||
98 | </pre> |
||
99 | |||
100 | |||
101 | 50 | Neil Voss | h2. Install MyMPI |
102 | 42 | Neil Voss | |
103 | 63 | Amber Herold | * First, add the openmpi module so that MyMPI can find it. |
104 | <pre> |
||
105 | module add openmpi-i386 |
||
106 | -or- |
||
107 | module add openmpi-x86_64 |
||
108 | </pre> |
||
109 | |||
110 | 42 | Neil Voss | * Download source: |
111 | 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*. |
112 | Click on *Download MPI Support* |
||
113 | Click on *pydusa-1.15es.tgz* |
||
114 | 42 | Neil Voss | * Extract: |
115 | 61 | Amber Herold | <pre>tar zxvf pydusa-1.15es.tgz</pre> |
116 | 42 | Neil Voss | * go into directory |
117 | 61 | Amber Herold | <pre>cd pydusa-1.15es</pre> |
118 | 65 | Amber Herold | |
119 | 62 | Amber Herold | If you are on a 64bit machine, you may have problems with the code finding the numpy headers: |
120 | 65 | Amber Herold | |
121 | 34 | Neil Voss | <pre>nano configure</pre> |
122 | 65 | Amber Herold | |
123 | 54 | Neil Voss | find the line: |
124 | 1 | Neil Voss | <pre> |
125 | elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then |
||
126 | PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include" |
||
127 | 54 | Neil Voss | </pre> |
128 | and replace it with: |
||
129 | 65 | Amber Herold | |
130 | 54 | Neil Voss | <pre> |
131 | 1 | Neil Voss | elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then |
132 | PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include" |
||
133 | 46 | Neil Voss | </pre> |
134 | * Configure: |
||
135 | <pre> |
||
136 | setenv MPIROOT /usr/lib64/openmpi |
||
137 | setenv MPIINC /usr/include/openmpi-x86_64 |
||
138 | setenv MPILIB ${MPIROOT}/lib |
||
139 | setenv MPIBIN ${MPIROOT}/bin |
||
140 | 1 | Neil Voss | ./configure |
141 | </pre> |
||
142 | <pre> |
||
143 | export MPIROOT=/usr/lib64/openmpi |
||
144 | export MPIINC=/usr/include/openmpi-x86_64 |
||
145 | export MPILIB=${MPIROOT}/lib |
||
146 | 47 | Neil Voss | export MPIBIN=${MPIROOT}/bin |
147 | 46 | Neil Voss | ./configure |
148 | </pre> |
||
149 | 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: |
150 | <pre> |
||
151 | configure: error: Unable to find mpicc! mpicc location can be specified with --with-mpicc |
||
152 | </pre> |
||
153 | 65 | Amber Herold | |
154 | 46 | Neil Voss | * compile the source: |
155 | <pre>make</pre> |
||
156 | * copy the mpi.so to site-packages with a different name: |
||
157 | <pre> |
||
158 | 1 | Neil Voss | sudo mkdir /usr/lib64/python2.6/site-packages/mympi/ |
159 | 52 | Neil Voss | sudo touch /usr/lib64/python2.6/site-packages/mympi/__init__.py |
160 | 1 | Neil Voss | sudo cp -v src/mpi.so /usr/lib64/python2.6/site-packages/mympi/mpi.so |
161 | </pre> |
||
162 | 47 | Neil Voss | * create a wrapper around the wrapper: |
163 | 1 | Neil Voss | <pre>sudo nano /usr/lib64/python2.6/site-packages/mpi.py</pre> |
164 | <pre> |
||
165 | import ctypes |
||
166 | mpi = ctypes.CDLL('libmpi.so.1', ctypes.RTLD_GLOBAL) |
||
167 | from mympi.mpi import * |
||
168 | </pre> |
||
169 | 50 | Neil Voss | This needs to be done to avoid the error: |
170 | <pre> |
||
171 | python: symbol lookup error: |
||
172 | /usr/lib64/openmpi/lib/openmpi/mca_paffinity_hwloc.so: |
||
173 | undefined symbol: mca_base_param_reg_int |
||
174 | </pre> |
||
175 | 1 | Neil Voss | |
176 | * test 1: |
||
177 | <pre> |
||
178 | python -c 'import mpi' |
||
179 | python -c 'import sys; from mpi import mpi_init; mpi_init(len(sys.argv), sys.argv)' |
||
180 | </pre> |
||
181 | |||
182 | 50 | Neil Voss | * test 2: |
183 | <pre>sxisac.py start.hdf</pre> |
||
184 | (Note: start.hdf does not need to exist, if it does not exist then it should exit with file not found) |
||
185 | 42 | Neil Voss | |
186 | 50 | Neil Voss | h2. Test to see if code works |
187 | |||
188 | see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest |
||
189 | |||
190 | <pre> |
||
191 | cd EMAN2/test/rt |
||
192 | ./rt.py |
||
193 | </pre> |
||
194 | |||
195 | h2. Install MyMPI for MPI functions |
||
196 | |||
197 | see http://sparx-em.org/sparxwiki/MPI-installation |
||
198 | or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup |
||
199 | |||
200 | This fixes this problem: |
||
201 | <pre> |
||
202 | from mpi import mpi_init |
||
203 | ImportError: No module named mpi |
||
204 | </pre> |
||
205 | |||
206 | 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. |
||
207 | 34 | Neil Voss | |
208 | 9 | Neil Voss | h2. Documentation |
209 | 3 | Neil Voss | |
210 | 1 | Neil Voss | * http://blake.bcm.edu/emanwiki/EMAN2/Install |
211 | 2 | Neil Voss | * http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ |
212 | 31 | Neil Voss | |
213 | 2 | Neil Voss | ______ |
214 | |||
215 | [[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]] |
||
216 | 1 | Neil Voss | |
217 | ______ |