Install EMAN2 » History » Version 52
Neil Voss, 08/14/2012 12:27 PM
1 | 1 | Neil Voss | h1. Install EMAN2/SPARX |
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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. |
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4 | 2 | Neil Voss | |
5 | 6 | Neil Voss | This documentation assumes you are using CentOS 6 (written as of CentOS 6.2) |
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7 | h2. Install require pre-packages for EMAN2 compiling |
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8 | |||
9 | 27 | Neil Voss | h3. yum based packages |
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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: |
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13 | <pre> |
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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 |
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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. |
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22 | 26 | Neil Voss | <pre> |
23 | 1 | Neil Voss | sudo easy_install bsddb3 |
24 | </pre> |
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25 | 27 | Neil Voss | |
26 | 3 | Neil Voss | h2. Download the source |
27 | |||
28 | # To download the source code go to the link: |
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29 | #* http://blake.bcm.edu/emanwiki/EMAN2 |
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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) |
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33 | |||
34 | h2. Work with the source |
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35 | |||
36 | # go to the directory with the source code |
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37 | # extract the archive: |
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38 | <pre> |
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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> |
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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> |
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48 | 3 | Neil Voss | # install to directory: |
49 | 23 | Neil Voss | <pre>sudo make install</pre> |
50 | |||
51 | h2. Set environmental variables |
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52 | |||
53 | h3. bash |
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54 | |||
55 | <pre>sudo nano /etc/profile.d/eman2.sh</pre> |
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56 | 24 | Neil Voss | |
57 | <pre> |
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58 | export EMAN2DIR=/usr/local/EMAN2 |
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59 | export PATH=${EMAN2DIR}/bin:${PATH} |
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60 | 23 | Neil Voss | export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib |
61 | export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin |
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62 | </pre> |
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63 | 16 | Neil Voss | |
64 | 51 | Neil Voss | h3. c shell |
65 | |||
66 | <pre>sudo nano /etc/profile.d/eman2.csh</pre> |
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67 | |||
68 | <pre> |
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69 | setenv EMAN2DIR /usr/local/EMAN2 |
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70 | setenv PATH ${EMAN2DIR}/bin:${PATH} |
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71 | setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib |
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72 | setenv PYTHONPATH ${EMAN2DIR}/lib:${EMAN2DIR}/bin |
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73 | </pre> |
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74 | |||
75 | |||
76 | 50 | Neil Voss | h2. Install MyMPI |
77 | 42 | Neil Voss | |
78 | * Download source: |
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79 | 45 | Neil Voss | <pre>wget -O pydusa-1.15-sparx.tgz \ |
80 | 'http://sparx-em.org/sparxwiki/MPI-installation?action=AttachFile&do=get&target=pydusa-1.15-sparx.tgz'</pre> |
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81 | 42 | Neil Voss | * Extract: |
82 | <pre>tar zxvf pydusa-1.15-sparx.tgz</pre> |
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83 | * go into directory |
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84 | <pre>cd pydusa-1.15-sparx</pre> |
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85 | 34 | Neil Voss | <pre>nano configure</pre> |
86 | 1 | Neil Voss | <pre> |
87 | elif test -d ${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include; then |
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88 | PY_HEADER_NUMPY="-I${PY_PREFIX}/lib/python$PY_VERSION/site-packages/numpy/core/include" |
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89 | </pre><pre> |
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90 | elif test -d ${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include; then |
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91 | PY_HEADER_NUMPY="-I${PY_PREFIX}/lib64/python$PY_VERSION/site-packages/numpy/core/include" |
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92 | 46 | Neil Voss | </pre> |
93 | * Configure: |
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94 | <pre> |
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95 | setenv MPIROOT /usr/lib64/openmpi |
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96 | setenv MPIINC /usr/include/openmpi-x86_64 |
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97 | setenv MPILIB ${MPIROOT}/lib |
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98 | setenv MPIBIN ${MPIROOT}/bin |
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99 | 1 | Neil Voss | ./configure |
100 | </pre> |
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101 | <pre> |
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102 | export MPIROOT=/usr/lib64/openmpi |
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103 | export MPIINC=/usr/include/openmpi-x86_64 |
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104 | export MPILIB=${MPIROOT}/lib |
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105 | 47 | Neil Voss | export MPIBIN=${MPIROOT}/bin |
106 | 46 | Neil Voss | ./configure |
107 | </pre> |
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108 | * compile the source: |
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109 | <pre>make</pre> |
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110 | * copy the mpi.so to site-packages with a different name: |
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111 | <pre> |
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112 | 1 | Neil Voss | sudo mkdir /usr/lib64/python2.6/site-packages/mympi/ |
113 | 52 | Neil Voss | sudo touch /usr/lib64/python2.6/site-packages/mympi/__init__.py |
114 | 1 | Neil Voss | sudo cp -v src/mpi.so /usr/lib64/python2.6/site-packages/mympi/mpi.so |
115 | </pre> |
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116 | 47 | Neil Voss | * create a wrapper around the wrapper: |
117 | 1 | Neil Voss | <pre>sudo nano /usr/lib64/python2.6/site-packages/mpi.py</pre> |
118 | <pre> |
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119 | import ctypes |
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120 | mpi = ctypes.CDLL('libmpi.so.1', ctypes.RTLD_GLOBAL) |
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121 | from mympi.mpi import * |
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122 | </pre> |
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123 | 50 | Neil Voss | This needs to be done to avoid the error: |
124 | <pre> |
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125 | python: symbol lookup error: |
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126 | /usr/lib64/openmpi/lib/openmpi/mca_paffinity_hwloc.so: |
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127 | undefined symbol: mca_base_param_reg_int |
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128 | </pre> |
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129 | 1 | Neil Voss | |
130 | * test 1: |
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131 | <pre> |
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132 | python -c 'import mpi' |
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133 | python -c 'import sys; from mpi import mpi_init; mpi_init(len(sys.argv), sys.argv)' |
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134 | </pre> |
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135 | |||
136 | 50 | Neil Voss | * test 2: |
137 | <pre>sxisac.py start.hdf</pre> |
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138 | (Note: start.hdf does not need to exist, if it does not exist then it should exit with file not found) |
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139 | 42 | Neil Voss | |
140 | 50 | Neil Voss | h2. Test to see if code works |
141 | |||
142 | see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest |
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143 | |||
144 | <pre> |
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145 | cd EMAN2/test/rt |
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146 | ./rt.py |
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147 | </pre> |
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148 | |||
149 | h2. Install MyMPI for MPI functions |
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150 | |||
151 | see http://sparx-em.org/sparxwiki/MPI-installation |
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152 | or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup |
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153 | |||
154 | This fixes this problem: |
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155 | <pre> |
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156 | from mpi import mpi_init |
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157 | ImportError: No module named mpi |
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158 | </pre> |
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159 | |||
160 | 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. |
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161 | 34 | Neil Voss | |
162 | 9 | Neil Voss | h2. Documentation |
163 | 3 | Neil Voss | |
164 | 1 | Neil Voss | * http://blake.bcm.edu/emanwiki/EMAN2/Install |
165 | 2 | Neil Voss | * http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ |
166 | 31 | Neil Voss | |
167 | 2 | Neil Voss | ______ |
168 | |||
169 | [[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]] |
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170 | 1 | Neil Voss | |
171 | ______ |