Appion Home » History » Version 19
Amber Herold, 03/31/2010 04:08 PM
1 | 19 | Amber Herold | h1. Complete Installation |
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2 | 1 | Eric Hou | |
3 | 11 | Amber Herold | h1. Complete Installation |
4 | 6 | Amber Herold | |
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6 | 1 | Eric Hou | |
7 | 16 | Amber Herold | |
8 | 11 | Amber Herold | h2. Four Parts of Leginon System |
9 | 1 | Eric Hou | |
10 | 11 | Amber Herold | |
11 | 16 | Amber Herold | !http://emg.nysbc.org/software/leginon/images/images/Leg_Proj_parts.png! |
12 | 1 | Eric Hou | |
13 | 11 | Amber Herold | Leginon as a system that we distribute can be divided into three parts: |
14 | 1 | Eric Hou | |
15 | 6 | Amber Herold | |
16 | 16 | Amber Herold | |
17 | 11 | Amber Herold | h2. Processing Server (Python-side) |
18 | 1 | Eric Hou | |
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20 | 11 | Amber Herold | Python (and some c) scripts that handle instrument control, data acquisition, and |
21 | processing. |
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22 | 1 | Eric Hou | |
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26 | 16 | Amber Herold | |
27 | 11 | Amber Herold | h2. Database Server (MySQL-side) |
28 | 1 | Eric Hou | |
29 | 11 | Amber Herold | |
30 | a MySQL server that handles the database |
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31 | |||
32 | |||
33 | 1 | Eric Hou | |
34 | 11 | Amber Herold | |
35 | 16 | Amber Herold | |
36 | 11 | Amber Herold | h2. Web Server (PHP-side) |
37 | |||
38 | |||
39 | This includes php and Java scripts at a webserver that we will create to retrieve image |
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40 | and metadata from the database and file-storage system. |
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42 | |||
43 | 1 | Eric Hou | |
44 | 11 | Amber Herold | |
45 | 16 | Amber Herold | |
46 | 11 | Amber Herold | h2. File Server |
47 | |||
48 | |||
49 | This is up to you to set up to store lots of data coming out of Leginon system. |
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54 | 1 | Eric Hou | |
55 | 11 | Amber Herold | |
56 | 16 | Amber Herold | |
57 | 11 | Amber Herold | h2. What is in this chapter |
58 | |||
59 | |||
60 | |||
61 | Leginon runs under both the Linux and Microsoft Windows Operating systems. However, the |
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62 | current php-mrctool can not be installed on Windows which means mrc images can not be viewed |
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63 | on the web. See the section on Possible Computer Set-up Configurations for details. |
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64 | |||
65 | |||
66 | The many components for the Leginon system are divided into packages and need to be |
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67 | installed separately. It has been integrated with several third party software packages that |
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68 | are necessary for its operation. The installation documentation will describe how to set-up |
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69 | Leginon and give hints as to how to install and set-up the necessary third-party software. |
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70 | This documentation is not intended to support the additional, but necessary third-party |
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71 | software. |
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72 | |||
73 | |||
74 | There has been interest in installing Leginon under Mac OS X. While this is possible in |
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75 | theory, we have not been successful in installing a fully functional system. The two main |
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76 | problems are (1) compilation of php-mrctool from the pre-installed php and (2) wxPython on Mac |
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77 | is unable to hide bitmap objects which makes Leginon graphical user interface difficult to |
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78 | use. |
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79 | |||
80 | |||
81 | 15 | Amber Herold | See <link linkend="InstT_install">Installation Troubleshooting</link> and "Leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2 searching |
82 | 11 | Amber Herold | for "install" if you run into problems. |
83 | |||
84 | |||
85 | 1 | Eric Hou | |
86 | 11 | Amber Herold | |
87 | 16 | Amber Herold | |
88 | 11 | Amber Herold | h2. Possible Computer Set-up Configurations |
89 | |||
90 | |||
91 | |||
92 | Computer(s) used for the whole Leginon system need to support five functions: |
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93 | * TEM/Camera control and data output (by python-side packages of Leginon |
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94 | system) |
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95 | |||
96 | |||
97 | *The computer attached to the microscope/camera is used for this function. |
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98 | Therefore, it is on a Windows computer. |
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99 | |||
100 | |||
101 | * General Leginon operation such as target selection and image processing (processing |
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102 | server of Leginon system) |
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103 | |||
104 | |||
105 | * Image data storage. |
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106 | |||
107 | |||
108 | * Other meta-data storage through MySQL database (by database server of Leginon |
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109 | system) |
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110 | |||
111 | |||
112 | * Web server (using PHP-side of Leginon system). |
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113 | |||
114 | |||
115 | *Important* The MRC module that is used to load mrc formatted files to the web |
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116 | pages is not compiled on Windows. Therefore, this function must be on a linux box unless |
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117 | you don't need to see the images*** |
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118 | |||
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120 | |||
121 | |||
122 | |||
123 | The five functions can be distributed to five different computers on a network or all on |
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124 | one single computer. However, since the latter minimal setup requires the use of the computer |
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125 | attached to the microscope for all functions, it is not advisable. |
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126 | |||
127 | |||
128 | Processing server of Leginion is a multi-platform software, meaning it can run on both |
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129 | Microsoft Windows and Linux. It is also inherently designed to utilize distributed systems on |
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130 | a network. MySQL used in the database server is also supported by multiple platforms. This is |
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131 | not true for the Web server because the custom MRC module used in the web viewer only compiles |
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132 | on linux machines. Therefore, one of the computer not part of the microscope must be a linux. |
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133 | The following examples show several arrangements that take advantage of distributed system. |
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134 | Other combinations are possible, but will basically be variations on one of the following |
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135 | themes. |
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136 | 1 | Eric Hou | |
137 | 11 | Amber Herold | |
138 | 16 | Amber Herold | |
139 | 11 | Amber Herold | h2. A: 1 Windows computer (attached to the Microscope) & 1 Linux computer (for all |
140 | other functions, separate from the Microscope) (Good for single user and small-scale |
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141 | acquisition) |
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142 | |||
143 | |||
144 | |||
145 | |||
146 | |||
147 | * Install the latest processing server side of Leginon release (and supporting |
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148 | packages) on the Windows computer controlling the microscope and on the Linux computer |
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149 | which is to run Leginon image acquisition and processing. |
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150 | |||
151 | |||
152 | * Install the additional modules needed for CCD camera and film interaction on the |
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153 | Windows computer controlling the microscope. |
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154 | |||
155 | |||
156 | * Install MySQL, PHP, the Apache Web Server, and dbem tools only on the Linux |
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157 | computer that will perform these functions, (i.e. NOT the computer controlling the |
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158 | microscope). |
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165 | 1 | Eric Hou | |
166 | 11 | Amber Herold | |
167 | 16 | Amber Herold | |
168 | 11 | Amber Herold | h2. B: 1 Windows computer (attached to the Microscope) & 4 Linux computers (one for |
169 | each function) (Good for multiple microsopes, users and large-scale acquisition) |
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170 | |||
171 | |||
172 | |||
173 | This is the set-up at NRAMM. It has the processing server side of Leginon installed on |
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174 | the Windows computer attached to the microscope and on the Linux computer that is used for |
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175 | running Leginon. A second Linux machine is dedicated to the database while the web-based |
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176 | viewer is hosted by another server. |
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177 | |||
178 | |||
179 | |||
180 | |||
181 | * Install the python-side Leginon (and supporting packages) on the Windows computer |
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182 | controlling the microscope and on the Linux computer that is to run Leginon. You can |
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183 | make the latter installation accessable to any numbers of linux computers on your |
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184 | network. |
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185 | |||
186 | |||
187 | * Install MySQL, PHP, the Apache Web Server, and dbem tools on the second Linux |
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188 | computer that will serve as the database/web server/PHP host. |
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189 | |||
190 | |||
191 | * The computer hosting the data storage should be accessable by all linux |
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192 | boxes. |
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199 | 1 | Eric Hou | |
200 | 11 | Amber Herold | |
201 | 16 | Amber Herold | |
202 | 11 | Amber Herold | h2. C: 1 Windows computer (attached to the Microscope), 1 Windows computer running python- |
203 | and MySQL-side functions and 1 Linux computer as web server (Has been applied |
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204 | successfully) |
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205 | |||
206 | |||
207 | |||
208 | The data storage may be on one of these computers that is accessable by other |
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209 | computers. |
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214 | 1 | Eric Hou | |
215 | 11 | Amber Herold | |
216 | 16 | Amber Herold | |
217 | 11 | Amber Herold | h2. Ports that Leginon system uses: |
218 | |||
219 | |||
220 | |||
221 | This information is useful if you want to open specific ports between computers with a |
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222 | firewall in between. |
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223 | |||
224 | |||
225 | |||
226 | |||
227 | * MySQL normally uses port 3306 (but configurable in /etc/my.cnf) |
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228 | |||
229 | |||
230 | * Leginon Client running on TEM host: port 55555 |
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231 | |||
232 | |||
233 | * Leginon main program on the processing server: dynamically assigned ports between |
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234 | 49152 and 65535 |
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235 | |||
236 | |||
237 | There is no strict port assignment since we could potentially have more than one |
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238 | Leginon process running on the same linux host talking to different TEM hosts. It is |
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239 | probably good enough if you only worry about opening up the first few of those ports in |
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240 | your firewall (maybe 49152 through 49160, or something like that). |
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241 | |||
242 | |||
243 | See more discussion at Leginon bulletin board thread on ""network problem, Leginon not seeing |
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244 | 15 | Amber Herold | tecnai host":http://emg.nysbc.org/bb/viewtopic.php?t=7 " |
245 | 11 | Amber Herold | |
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251 | 1 | Eric Hou | |
252 | 11 | Amber Herold | |
253 | 16 | Amber Herold | |
254 | 15 | Amber Herold | h2. Where to Register and download Leginon system |
255 | 11 | Amber Herold | |
256 | |||
257 | |||
258 | "http://www.leginon.org/":http://www.leginon.org is the home. Please |
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259 | register if you want to recieve support from Leginon team. |
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260 | |||
261 | 1 | Eric Hou | |
262 | * python-side Leginon packages |
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263 | |||
264 | 11 | Amber Herold | |
265 | 16 | Amber Herold | direct link: "http://emg.nysbc.org/software/leginon/":http://emg.nysbc.org/software/leginon/ * mrctools: including the tools for reading mrc images on the web |
266 | 11 | Amber Herold | |
267 | |||
268 | 16 | Amber Herold | direct link: "http://emg.nysbc.org/software/mrctools/":http://emg.nysbc.org/software/mrctools/ * dbemtools: including the tools for administration and webviewing |
269 | 1 | Eric Hou | |
270 | 11 | Amber Herold | |
271 | 16 | Amber Herold | direct link: "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/ * project tools (optional): For administration and webviewing of projects |
272 | 11 | Amber Herold | |
273 | |||
274 | 16 | Amber Herold | direct link: "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/ h2. Processing server-side Leginon Installation |
275 | 11 | Amber Herold | |
276 | |||
277 | |||
278 | 1 | Eric Hou | For the lack of better name, processing server-side Leginon refers to packages that |
279 | 11 | Amber Herold | performs the general functions of image acquisition and processing. The instructions here are |
280 | 1 | Eric Hou | for Linux. Refer to Windows Installation for Windows specific instructions. |
281 | 11 | Amber Herold | |
282 | |||
283 | 16 | Amber Herold | |
284 | 11 | Amber Herold | h2. Download svn checkout script from Leginon website |
285 | |||
286 | |||
287 | |||
288 | "http://www.leginon.org/":http://www.leginon.org/ Download |
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289 | 15 | Amber Herold | svnget-1.6.sh to a convenient location such as your home directory. |
290 | 11 | Amber Herold | |
291 | |||
292 | |||
293 | |||
294 | 16 | Amber Herold | |
295 | 11 | Amber Herold | h2. Check out SVN Source Files from the depository |
296 | |||
297 | |||
298 | |||
299 | run svnget-1.6.sh. It does the |
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300 | 17 | Amber Herold | following:<pre>mkdir Leginon-1.6-ALL |
301 | 11 | Amber Herold | cd Leginon-1.6-ALL |
302 | svn co http://emg.nysbc.org/svn/leginon/branches/1.6 Leginon |
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303 | 1 | Eric Hou | svn co http://emg.nysbc.org/svn/pyami/branches/leg1.6 pyami |
304 | 11 | Amber Herold | svn co http://emg.nysbc.org/svn/pyScope/branches/leg1.6 pyScope |
305 | svn co http://emg.nysbc.org/svn/sinedon/branches/leg1.6 sinedon |
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306 | svn co http://emg.nysbc.org/svn/numextension/branches/leg1.6 numextension |
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307 | svn co http://emg.nysbc.org/svn/libcv/branches/leg1.6 libcv |
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308 | svn co http://emg.nysbc.org/svn/ImageViewer/branches/leg1.6 ImageViewer</pre> |
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309 | |||
310 | |||
311 | If the process fails, you probably do not have svn client installed. Skip to "Install |
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312 | the supporting packages first if missing:", then try this again. |
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313 | |||
314 | |||
315 | |||
316 | |||
317 | 16 | Amber Herold | |
318 | 11 | Amber Herold | h2. Perform system check: |
319 | |||
320 | |||
321 | |||
322 | In addition to the downloads from our svn depository, there are several other |
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323 | requirements that you will get either from your OS installation source, or from its |
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324 | respective website. The system check in the Leginon package checks your system to see if you |
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325 | already have these requirements |
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326 | |||
327 | 1 | Eric Hou | |
328 | 11 | Amber Herold | |
329 | <pre>cd your_download_area/Leginon-1.6-ALL/Leginon |
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330 | python syscheck.py</pre> |
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331 | |||
332 | |||
333 | |||
334 | If python is not installed, this, of course will not run. If you see any lines like "*** |
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335 | Failed...", then you have something missing. Otherwise, everything should result in |
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336 | "OK". |
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337 | |||
338 | |||
339 | |||
340 | |||
341 | 16 | Amber Herold | |
342 | 11 | Amber Herold | h2. Install the supporting packages first if missing: |
343 | |||
344 | |||
345 | |||
346 | Follow the instruction for your specific Linux distribution. |
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347 | 1 | Eric Hou | |
348 | 11 | Amber Herold | |
349 | For example, SUSE users can use YaST to install them; RedHat and CentOS users can use |
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350 | yum. |
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351 | |||
352 | |||
353 | *SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK |
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354 | package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from |
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355 | http://repos.opensuse.org/science (need to specify your SuSE version and machine |
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356 | etc.) |
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357 | |||
358 | |||
359 | 1 | Eric Hou | |
360 | 11 | Amber Herold | |
361 | 16 | Amber Herold | |
362 | 11 | Amber Herold | h2. Required supporting packages: |
363 | |||
364 | 1 | Eric Hou | |
365 | 11 | Amber Herold | |
366 | 14 | Amber Herold | |
367 | 11 | Amber Herold | |_.Name:|_.Download site:|_.yum package name|_.SuSE rpm name| |
368 | 15 | Amber Herold | |Python 2.4 or newer|"http://www.python.org":http://www.python.org |python|python-devel| |
369 | |wxPython 2.5.2.8 or newer|"http://www.wxpython.org":http://www.wxpython.org |wxPython|python-wxGTK| |
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370 | |MySQL Python client 1.2 or newer|"http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python |MySQL-python|python-mysql| |
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371 | |Python Imaging Library (PIL) 1.1.4 or newer|"http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/ |python-imaging|python-imaging| |
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372 | |Python XML module 0.8.3 or newer|"http://pyxml.sourceforge.net":http://pyxml.sourceforge.net |PyXML|python-xml| |
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373 | 1 | Eric Hou | |NumPy 1.0.1 or newer|"http://www.scipy.org":http://www.scipy.org |numpy|numpy| |
374 | 15 | Amber Herold | |SciPy 0.5.1 (tested, others may work)*|"http://www.scipy.org":http://www.scipy.org , "http://repos.opensuse.org/science":http://repos.opensuse.org/science *|scipy|python-scipy| |
375 | 11 | Amber Herold | |
376 | |||
377 | |||
378 | |||
379 | *SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK |
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380 | package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from |
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381 | http://repos.opensuse.org/science (need to specify your SuSE version and machine |
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382 | 1 | Eric Hou | etc.) |
383 | 11 | Amber Herold | |
384 | |||
385 | |||
386 | |||
387 | 16 | Amber Herold | |
388 | 11 | Amber Herold | h2. Optional supporting packages: |
389 | |||
390 | |||
391 | |||
392 | |||
393 | |||
394 | * For using Matlab to explore holefinding algorithm (Matlab HoleFinder) |
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395 | |||
396 | |||
397 | 16 | Amber Herold | pymat: "http://sourceforge.net/projects/pymat":http://sourceforge.net/projects/pymat h2. Install the packages you downloaded from svn depository |
398 | 11 | Amber Herold | |
399 | |||
400 | |||
401 | Here are the packages you need to install with python installer inside the |
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402 | Leginon-1.6-ALL folder. |
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403 | 1 | Eric Hou | |
404 | 11 | Amber Herold | |
405 | 14 | Amber Herold | |
406 | 11 | Amber Herold | |_.Name:|_.Purpose:| |
407 | | Leginon|modular TEM image acquisition| |
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408 | | pyami|general functions| |
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409 | | pyScope|microscope control and monitoring| |
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410 | | sinedon|Leginon/database interaction| |
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411 | | numExtension|c extension for numerical processing| |
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412 | | libCV|small c library of algorithm from computer vision field| |
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413 | | ImageViewer|image viewing for tomography| |
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414 | |||
415 | |||
416 | |||
417 | |||
418 | |||
419 | |||
420 | * run syscheck.py again to make sure you have everything. |
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421 | |||
422 | 1 | Eric Hou | |
423 | 19 | Amber Herold | * Install the package in _each folder_ with commands |
424 | 11 | Amber Herold | like |
425 | these<pre>cd /your_download_area/Leginon-1.6-ALL/Leginon |
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426 | 1 | Eric Hou | python setup.py install |
427 | 11 | Amber Herold | |
428 | cd ../pyami |
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429 | python setup.py install |
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430 | cd ../pyScope |
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431 | python setup.py install |
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432 | cd ../sinedon |
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433 | python setup.py install |
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434 | cd ../numextension |
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435 | python setup.py install |
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436 | cd ../libcv |
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437 | python setup.py install |
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438 | cd ../ImageViewer |
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439 | python setup.py install</pre> |
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440 | |||
441 | |||
442 | |||
443 | |||
444 | |||
445 | |||
446 | |||
447 | |||
448 | 16 | Amber Herold | |
449 | 11 | Amber Herold | h2. python-site-package-path: where the installed python |
450 | packages went: |
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451 | |||
452 | |||
453 | Python installer put the packages you installed to its site-packages directory. This |
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454 | enable all users on the same computer to access them. The easiest way to find where your |
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455 | installed package is called by python is to load a module from the package using interactive |
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456 | python command lines like this: |
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457 | |||
458 | |||
459 | |||
460 | |||
461 | * Start python command line from shell |
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462 | |||
463 | |||
464 | |||
465 | <pre>> python</pre> |
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466 | |||
467 | |||
468 | |||
469 | * Import a module from the package. Let's try sinedon here. All packages installed |
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470 | through the above setup.py script should go to the same place. |
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471 | |||
472 | |||
473 | |||
474 | <pre>python> import sinedon</pre> |
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475 | |||
476 | |||
477 | |||
478 | 1 | Eric Hou | * If the module is loaded successfully, call the module attribute __path__ (two |
479 | 11 | Amber Herold | underscrolls before "path" and two underscrolls after) will return the location of the |
480 | module it is loaded from |
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481 | |||
482 | |||
483 | |||
484 | <pre>python> sinedon.__path__ |
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485 | |||
486 | RETURNS, For example, |
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487 | python> <module 'sinedon' from '/usr/lib/python2.5/site-packages/sinedon/__init__.pyc'> </pre> |
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488 | |||
489 | |||
490 | In this case, /usr/lib/python2.5/site-packages/ is your python-site-package-path. |
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491 | If you go to that directory, you will find all the packages you just installed. |
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492 | |||
493 | |||
494 | |||
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496 | |||
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499 | |||
500 | 16 | Amber Herold | |
501 | 11 | Amber Herold | h2. Configure leginon.cfg: |
502 | |||
503 | |||
504 | Leginon can be configured at three levels: |
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505 | |||
506 | |||
507 | |||
508 | |||
509 | * A skeleton (default) configuration file is available: |
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510 | |||
511 | 1 | Eric Hou | |
512 | 11 | Amber Herold | |
513 | 19 | Amber Herold | <pre> _<link linkend="package_path">[python-site-package-path]</link>_/Leginon/config/default.cfg</pre> |
514 | 11 | Amber Herold | |
515 | |||
516 | |||
517 | * Configurations for all users |
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518 | 1 | Eric Hou | |
519 | 11 | Amber Herold | |
520 | |||
521 | 19 | Amber Herold | <pre> _<link linkend="package_path">[python-site-package-path]</link>_/Leginon/config/leginon.cfg</pre> |
522 | 11 | Amber Herold | |
523 | |||
524 | |||
525 | 1 | Eric Hou | Example of the configuration that you should set: (Here we assume your leginon |
526 | 11 | Amber Herold | database is named "dbemdata", and Leginon log into the database as a user named |
527 | "usr_object" with no password |
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528 | set).<pre>[Images] |
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529 | 19 | Amber Herold | path: _your_storage_disk_path_/leginon |
530 | 11 | Amber Herold | </pre> |
531 | |||
532 | 1 | Eric Hou | |
533 | 11 | Amber Herold | * Configurations for individual users that overrides the all-user configuration if |
534 | exists |
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535 | |||
536 | |||
537 | |||
538 | <pre> ~/leginon.cfg</pre> |
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539 | |||
540 | 1 | Eric Hou | |
541 | 11 | Amber Herold | |
542 | This configuration should include all the minimal configuration above and |
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543 | additional configuration for individual user for |
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544 | convenience<pre>[User] |
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545 | 19 | Amber Herold | Fullname: _your_name_ #The name you entered in the leginon administration web page. Note that it is case sensitive</pre> |
546 | 11 | Amber Herold | |
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552 | |||
553 | |||
554 | 16 | Amber Herold | |
555 | 11 | Amber Herold | h2. Names used in the example installation |
556 | |||
557 | |||
558 | From this point on, you will need to enter database user names for different |
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559 | configuration files and settings. These are NOT Leginon user names but what is required by |
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560 | MySQL database interaction. Consistent names are essential. In the example shown here, the |
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561 | leginon database is called "dbemdata", the project database is called "projectdata". The |
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562 | MySQL user name are the same, "usr_object", and in this case without a password. |
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563 | |||
564 | |||
565 | |||
566 | |||
567 | 16 | Amber Herold | |
568 | 11 | Amber Herold | h2. Configure sinedon.cfg: |
569 | |||
570 | |||
571 | Sinedon is designed to be able to interact with multiple databases. It can be |
||
572 | configured at global or user level. |
||
573 | |||
574 | |||
575 | |||
576 | |||
577 | * An example configuration file is available at: |
||
578 | |||
579 | |||
580 | |||
581 | <pre>/your_download_area/Leginon-1.6-ALL/sinedon/examples/sinedon.cfg</pre> |
||
582 | |||
583 | 1 | Eric Hou | |
584 | 11 | Amber Herold | |
585 | * Configurations for all users should be placed at the following path |
||
586 | |||
587 | |||
588 | |||
589 | 19 | Amber Herold | <pre> _<link linkend="package_path">[python-site-package-path]</link>_/sinedon/sinedon.cfg</pre> |
590 | 11 | Amber Herold | |
591 | |||
592 | |||
593 | 1 | Eric Hou | * Modify host,db,user,passwd to what is used. Note that the user here is MySQL user |
594 | 11 | Amber Herold | Leginon uses to communicate with the database for all Leginon users. For Leginon that |
595 | uses Project database, set the following: |
||
596 | |||
597 | |||
598 | |||
599 | <pre>[global] |
||
600 | 19 | Amber Herold | host: _your_database_host_ |
601 | 11 | Amber Herold | user: usr_object |
602 | passwd: |
||
603 | |||
604 | [projectdata] |
||
605 | db: projectdata |
||
606 | |||
607 | [leginondata] |
||
608 | db: dbemdata |
||
609 | </pre> |
||
610 | |||
611 | 1 | Eric Hou | |
612 | 11 | Amber Herold | |
613 | * Add database configuration if you intend to use grid-inserting robot. The Robot2 |
||
614 | module uses the database to communicate to the robot. Applications that carries the |
||
615 | name "Robot" requires this to be set. In general, using the same database as the |
||
616 | general leginon database is fine. |
||
617 | |||
618 | |||
619 | |||
620 | <pre>[robot2] |
||
621 | db: dbemdata</pre> |
||
622 | |||
623 | |||
624 | |||
625 | |||
626 | |||
627 | |||
628 | |||
629 | |||
630 | 1 | Eric Hou | |
631 | 11 | Amber Herold | |
632 | |||
633 | 16 | Amber Herold | |
634 | 11 | Amber Herold | h2. Database Server-side Installation |
635 | |||
636 | |||
637 | |||
638 | The following is for the computer that hosts the databases. This involves installing MySQL |
||
639 | server and creation/configuration of the leginon and project databases. |
||
640 | |||
641 | 1 | Eric Hou | |
642 | 11 | Amber Herold | |
643 | 14 | Amber Herold | |
644 | 11 | Amber Herold | |
645 | 15 | Amber Herold | |_.Name:|_.Download site:| |
646 | 1 | Eric Hou | |MySQL-Server 5.0 or higher|"http://www.mysql.com":http://www.mysql.com | |
647 | 15 | Amber Herold | |MySQL-Client 5.0 or higher|"http://www.mysql.com":http://www.mysql.com | |
648 | 11 | Amber Herold | |
649 | |||
650 | |||
651 | |||
652 | 16 | Amber Herold | |
653 | 11 | Amber Herold | h2. MySQL |
654 | |||
655 | |||
656 | |||
657 | |||
658 | |||
659 | * Install MySQL-Server |
||
660 | |||
661 | |||
662 | |||
663 | |||
664 | * Use your package installer (yum, zypper, YaST) if available. |
||
665 | |||
666 | 1 | Eric Hou | |
667 | 11 | Amber Herold | OR |
668 | |||
669 | |||
670 | 16 | Amber Herold | * Download the latest MySQL-server RPM for Linux from "www.mysql.com":http://www.mysql.com * Install the MySQL-server rpm: |
671 | 11 | Amber Herold | |
672 | |||
673 | <pre> rpm -Uvh MySQL-server-5.0.xx-y.i386.rpm</pre> |
||
674 | (substitute correct version numbers) |
||
675 | |||
676 | |||
677 | |||
678 | |||
679 | |||
680 | |||
681 | * Install MySQL-Client |
||
682 | |||
683 | |||
684 | |||
685 | |||
686 | * Use your package installer (yum, zypper, YaST) if available. |
||
687 | |||
688 | |||
689 | OR |
||
690 | |||
691 | |||
692 | 16 | Amber Herold | * Download the latest MySQL-client RPM for Linux from "www.mysql.com":http://www.mysql.com * Install the MySQL-client rpm: |
693 | 11 | Amber Herold | |
694 | |||
695 | <pre> rpm -Uvh MySQL-client-5.0.xx-y.i386.rpm</pre> |
||
696 | (substitute correct version numbers) |
||
697 | |||
698 | |||
699 | |||
700 | |||
701 | |||
702 | |||
703 | * MySQL configuration file is usually located in /usr/share/mysql. There are |
||
704 | several examples there: |
||
705 | |||
706 | |||
707 | |||
708 | <pre>> ls /usr/share/mysql/my* |
||
709 | /usr/share/mysql/my-huge.cnf |
||
710 | /usr/share/mysql/my-innodb-heavy-4G.cnf |
||
711 | /usr/share/mysql/my-large.cnf |
||
712 | /usr/share/mysql/my-medium.cnf |
||
713 | /usr/share/mysql/my-small.cnf |
||
714 | > </pre> |
||
715 | |||
716 | |||
717 | |||
718 | * Configure my.cnf in /etc using my-huge.cnf as the template |
||
719 | |||
720 | |||
721 | |||
722 | |||
723 | * <pre>> cp /usr/share/mysql/my-huge.cnf /etc/my.cnf</pre> |
||
724 | |||
725 | |||
726 | |||
727 | * Edit /etc/my.cnf to add or change query cache variables like these: |
||
728 | |||
729 | <pre>query_cache_type= 1 |
||
730 | query_cache_size = 100M |
||
731 | query_cache_limit= 100M</pre> |
||
732 | |||
733 | |||
734 | |||
735 | |||
736 | |||
737 | |||
738 | |||
739 | * start MySQL Server |
||
740 | |||
741 | <pre> >/etc/init.d/mysqld start</pre> |
||
742 | |||
743 | on some installation, |
||
744 | |||
745 | <pre> >/etc/init.d/mysql start</pre> |
||
746 | |||
747 | For future reference: start | stop | restart MySQL Server with similar |
||
748 | commands: |
||
749 | |||
750 | <pre> >/etc/init.d/mysqld start |
||
751 | >/etc/init.d/mysqld stop |
||
752 | >/etc/init.d/mysqld restart</pre> |
||
753 | |||
754 | If you want to start MySQL automatically at boot on SuSE |
||
755 | |||
756 | <pre> SuSE >chkconfig mysql on |
||
757 | </pre> |
||
758 | |||
759 | * For future reference, the database location will be: |
||
760 | |||
761 | |||
762 | |||
763 | <pre>> cd /var/lib/mysql |
||
764 | Directory: /var/lib/mysql |
||
765 | > ls |
||
766 | yourdbserver.pid |
||
767 | ib_logfile0 |
||
768 | mysql |
||
769 | mysql.sock |
||
770 | test |
||
771 | > </pre> |
||
772 | |||
773 | |||
774 | |||
775 | * Create leginon database, here we call <link linkend="db_example_names" |
||
776 | >dbemdata</link> |
||
777 | |||
778 | <pre> >mysqladmin create dbemdata</pre> |
||
779 | |||
780 | |||
781 | |||
782 | * Create project database, here we call <link linkend="db_example_names" |
||
783 | >projectdata</link> (optional) |
||
784 | |||
785 | <pre> >mysqladmin create projectdata</pre> |
||
786 | |||
787 | |||
788 | |||
789 | * Connect to mysql db |
||
790 | |||
791 | <pre>>mysql mysql |
||
792 | |||
793 | mysql> select user, password, host from user; |
||
794 | +------+----------+-----------+ |
||
795 | | user | password | host | |
||
796 | +------+----------+-----------+ |
||
797 | | root | | localhost | |
||
798 | | root | | host1 | |
||
799 | | | | host1 | |
||
800 | | | | localhost | |
||
801 | +------+----------+-----------+ |
||
802 | 4 rows in set (0.00 sec)</pre> |
||
803 | |||
804 | |||
805 | |||
806 | * Create and grant privileges to a user called <link linkend="db_example_names" |
||
807 | >usr_object</link> for the databases on both the localhost and other hosts involved. |
||
808 | For example, use wild card '%' for all hosts. You may also set specific privilege to |
||
809 | the user. See MySQL Reference Manual for details |
||
810 | |||
811 | <pre>mysql> create user usr_object@'localhost'; |
||
812 | mysql> grant all privileges on dbemdata.* to usr_object@'localhost'; |
||
813 | mysql> grant all privileges on projectdata.* to usr_object@'localhost';</pre> |
||
814 | |||
815 | Similarly, |
||
816 | 1 | Eric Hou | |
817 | 11 | Amber Herold | <pre>mysql> create usr_object@'%'; |
818 | mysql> grant all privileges on dbemdata.* to usr_object@'%'; |
||
819 | mysql> grant all privileges on projectdata.* to usr_object@'%'; |
||
820 | </pre> |
||
821 | |||
822 | * Change Root passworld |
||
823 | |||
824 | 19 | Amber Herold | <pre>mysql> update user set password=password('_a passwd_') where user="root"; |
825 | 1 | Eric Hou | Query OK, 2 rows affected (0.01 sec) |
826 | 11 | Amber Herold | Rows matched: 2 Changed: 2 Warnings: 0 |
827 | 1 | Eric Hou | |
828 | 11 | Amber Herold | mysql>^D or exit;</pre> |
829 | From now on, you will need to specify the password to connect to the database as |
||
830 | root user like this: |
||
831 | |||
832 | <pre>>mysql -u root -p mysql</pre> |
||
833 | |||
834 | 19 | Amber Herold | _***If your password change does not take effect in your next |
835 | 11 | Amber Herold | database connection, you will need to flush the mysql pivileges cache as mysql root |
836 | and connecting with you old password (or no password in the above |
||
837 | 19 | Amber Herold | case):_ |
838 | 11 | Amber Herold | |
839 | <pre>>mysql -u root mysql</pre> |
||
840 | <pre>mysql> flush privileges; |
||
841 | mysql>^D or exit;</pre> |
||
842 | |||
843 | * Check MySQL variables |
||
844 | |||
845 | <pre>>mysql -u usr_object dbemdata |
||
846 | |||
847 | mysql> SHOW VARIABLES LIKE 'query%'; |
||
848 | +------------------------------+-----------+ |
||
849 | | Variable_name | Value | |
||
850 | +------------------------------+-----------+ |
||
851 | | ft_query_expansion_limit | 20 | |
||
852 | | have_query_cache | YES | |
||
853 | | long_query_time | 10 | |
||
854 | | query_alloc_block_size | 8192 | |
||
855 | | query_cache_limit | 104857600 | <<---This should correspond to your change |
||
856 | | query_cache_min_res_unit | 4096 | |
||
857 | | query_cache_size | 104857600 | <<---This should correspond to your change |
||
858 | | query_cache_type | ON | <<---This should correspond to your change |
||
859 | | query_cache_wlock_invalidate | OFF | |
||
860 | | query_prealloc_size | 8192 | |
||
861 | +------------------------------+-----------+ |
||
862 | 10 rows in set (0.00 sec) |
||
863 | |||
864 | mysql> exit;</pre> |
||
865 | |||
866 | |||
867 | |||
868 | * Make sure MySQL is running |
||
869 | |||
870 | <pre>prompt:~> mysqlshow |
||
871 | +--------------+ |
||
872 | | Databases | |
||
873 | +--------------+ |
||
874 | | mysql | |
||
875 | 1 | Eric Hou | | dbemdata | |
876 | 11 | Amber Herold | | projectdata | |
877 | +--------------+</pre> |
||
878 | |||
879 | |||
880 | |||
881 | * Or check with the following php script (if already installed) |
||
882 | |||
883 | <pre><? |
||
884 | 1 | Eric Hou | mysql_connect('your_host.your_institute.edu', 'usr_object', '','dbemdata'); |
885 | 11 | Amber Herold | echo mysql_stat(); |
886 | ?> </pre> |
||
887 | |||
888 | |||
889 | Output |
||
890 | |||
891 | <pre> Uptime: 1452562 Threads: 1 Questions: 618 Slow queries: 0 Opens: 117 Flush tables: 1 Open tables: 106 Queries per second avg: 0.000</pre> |
||
892 | |||
893 | |||
894 | |||
895 | |||
896 | |||
897 | |||
898 | |||
899 | |||
900 | |||
901 | 16 | Amber Herold | |
902 | 11 | Amber Herold | h2. Web server set up and Installation |
903 | |||
904 | |||
905 | |||
906 | The following applies to the computer that will host the web-accessable image viewers ( a |
||
907 | part of dbem tools) and project manager (a part of project tools). |
||
908 | 1 | Eric Hou | |
909 | 11 | Amber Herold | |
910 | 16 | Amber Herold | |
911 | 11 | Amber Herold | h2. Differences between Linux flavors |
912 | |||
913 | |||
914 | |||
915 | Different Linux flavors often put web server and mysql-related files in different |
||
916 | locations. This can be confusing. From experience, we found the equivalent on CentOS vs |
||
917 | SuSE. Here we list them for reference. If your system use a different naming and you are |
||
918 | willing to share your experience, please send us the list. We will add it here: |
||
919 | |||
920 | 1 | Eric Hou | |
921 | 11 | Amber Herold | |
922 | 14 | Amber Herold | |_.File or Command Head|_.CentOS|_.SuSE| |
923 | 11 | Amber Herold | | php.ini|/etc/| /etc/php5/apache2/| |
924 | | httpd.conf|/etc/httpd/conf/|/etc/php5/apache2/| |
||
925 | | default document_root|/var/www/html/|/srv/www/htdocs/| |
||
926 | | apache start/stop/restart command head|/etc/init.d/httpd|/etc/init.d/apache2| |
||
927 | | mysql start/stop/restart command head|/etc/init.d/mysqld|/etc/init.d/mysql| |
||
928 | |||
929 | |||
930 | 1 | Eric Hou | |
931 | |||
932 | 11 | Amber Herold | |
933 | |||
934 | 16 | Amber Herold | |
935 | 11 | Amber Herold | h2. Prerequisites for dbemtools, projecttools, and mrctools extension |
936 | |||
937 | |||
938 | |||
939 | The dbemtools are mostly php scripts that run at the web server. The followings are |
||
940 | required before installation of dbemtools and the mrc extension that handles mrc files to be |
||
941 | displayed. Some of these packages may be found on the SuSE Linux DVD or included in common |
||
942 | 1 | Eric Hou | package repository. MySQL and the Apache Web Server can be downloaded from their respective |
943 | websites. |
||
944 | 11 | Amber Herold | |
945 | 1 | Eric Hou | |
946 | 11 | Amber Herold | |
947 | 14 | Amber Herold | |_.Name:|_.Download site:|_.yum package name|_.SuSE rpm name| |
948 | 11 | Amber Herold | | Apache|"www.apache.org":http://www.apache.org | httpd| apache2| |
949 | 15 | Amber Herold | | php|"www.php.net":http://www.php.net | php| php| |
950 | | php-devel*|"rpmfind.net/linux/RPM/Development_Languages_PHP.html":http://rpmfind.net/linux/RPM/Development_Languages_PHP.html | php-devel| php-devel| |
||
951 | | php-gd (including GD library, its development libraries and header *)|"www.php.ned/gd":http://www.libgd.org (Use gd2)| php-gd, gd-devel| php-gd,gd-devel| |
||
952 | | fftw3 library (including development libraries and header *)|"www.fftw.org":http://www.fftw.org (Use fftw3.x)| fftw3-devel| fftw3-devel| |
||
953 | |||
954 | 11 | Amber Herold | |
955 | |||
956 | |||
957 | * mrctools are compiled and added to php extension with php-devel package. Mrctools use |
||
958 | GD and FFTW3 that need to be compiled from their development libraries while the extension |
||
959 | is compiled. If GD and FFTW3 sources were downloaded and compiled directly on your computer, |
||
960 | these development files are included. If (as in most cases) GD and FFTW3 are installed from |
||
961 | rpm, they are not included. An error message will appear when you attempt to compile |
||
962 | mrctools. In this case, you will need separate download and installation of GD-devel and |
||
963 | FFTW3-devel. Search "http://rpmfind.net/linux/rpm2html/":http://rpmfind.ned/linux/rpm2html/ for GD-devel and FFTW3-devel for the rpm |
||
964 | 15 | Amber Herold | distribution needed for your system. |
965 | 1 | Eric Hou | |
966 | 11 | Amber Herold | |
967 | |||
968 | |||
969 | 16 | Amber Herold | |
970 | 11 | Amber Herold | h2. Installation tools |
971 | 1 | Eric Hou | |
972 | 11 | Amber Herold | |
973 | |||
974 | Use the installation tools available for your linux distribution. |
||
975 | |||
976 | |||
977 | |||
978 | |||
979 | * For example, Use yum utility to install. |
||
980 | |||
981 | |||
982 | * For example, Use the SuSE Linux YaST2 utility or zypper (openSuSE 10.2 and above) |
||
983 | to install. |
||
984 | |||
985 | |||
986 | * "A list of required CENTOS |
||
987 | 1 | Eric Hou | rpms and instruction":http://emg.nysbc.org/bb/viewtopic.php?t=238 can be found at dbemtools bulletin board at |
988 | 11 | Amber Herold | leginon.org. |
989 | 15 | Amber Herold | |
990 | 11 | Amber Herold | |
991 | |||
992 | |||
993 | |||
994 | |||
995 | |||
996 | |||
997 | 16 | Amber Herold | |
998 | 11 | Amber Herold | h2. PHP, PHP-devel, gd, and fftw3 |
999 | |||
1000 | |||
1001 | Install the packages using your installation tools if available. For example, to |
||
1002 | install gd as php extension you may use |
||
1003 | |||
1004 | |||
1005 | |||
1006 | 17 | Amber Herold | <pre>CentOS> yum install php-gd |
1007 | 11 | Amber Herold | SuSE10.2 and above> zypper install php-gd</pre> |
1008 | |||
1009 | |||
1010 | |||
1011 | |||
1012 | |||
1013 | 16 | Amber Herold | |
1014 | 11 | Amber Herold | h2. Configure php.ini |
1015 | |||
1016 | |||
1017 | |||
1018 | Edit the following two sections in php.ini (found as /etc/php.ini on CentOS and |
||
1019 | 1 | Eric Hou | /etc/php5/apache2/php.ini on SuSE) so that they look like the following: |
1020 | 11 | Amber Herold | |
1021 | |||
1022 | |||
1023 | <pre>register_argc_argv = On</pre> |
||
1024 | |||
1025 | |||
1026 | |||
1027 | |||
1028 | <pre>short_open_tag = On</pre> |
||
1029 | |||
1030 | |||
1031 | |||
1032 | |||
1033 | <pre>max_execution_time = 300 ; Maximum execution time of each script, in seconds |
||
1034 | max_input_time = 300 ; Maximum amount of time each script may spend parsing request data |
||
1035 | memory_limit = 256M ; Maximum amount of memory a script may consume (8MB)</pre> |
||
1036 | |||
1037 | |||
1038 | |||
1039 | You may want to increase max_input_time and memory_limit if the server is heavily used. |
||
1040 | At NRAMM, max_input_time=600 and memory_limit=4000M. |
||
1041 | |||
1042 | |||
1043 | |||
1044 | |||
1045 | 16 | Amber Herold | |
1046 | 11 | Amber Herold | h2. Apache Web Server |
1047 | |||
1048 | |||
1049 | |||
1050 | |||
1051 | |||
1052 | * Install the Apache Web Server with the YaST or yum utility. |
||
1053 | |||
1054 | |||
1055 | * Find "httpd.conf". |
||
1056 | |||
1057 | |||
1058 | This is /etc/httpd/conf/httpd.conf on CentOS and /etc/php5/apache2/httpd.conf on |
||
1059 | SuSE |
||
1060 | |||
1061 | |||
1062 | * Edit the "httpd.conf" configuration file to look like the following: |
||
1063 | |||
1064 | |||
1065 | |||
1066 | <pre><IfModule mod_dir.c> |
||
1067 | DirectoryIndex index.htm index.shtm index.html index.shtml index.php |
||
1068 | </IfModule></pre> |
||
1069 | |||
1070 | |||
1071 | 1 | Eric Hou | (Note: It may be possible to edit httpd.conf in YaST2 as well.) |
1072 | 11 | Amber Herold | |
1073 | |||
1074 | * Restart the web server. |
||
1075 | |||
1076 | |||
1077 | |||
1078 | <pre>apachectl restart |
||
1079 | or |
||
1080 | /etc/init.d/httpd restart (ON CentOS) |
||
1081 | or |
||
1082 | /etc/init.d/apache2 restart (ON SuSE)</pre> |
||
1083 | |||
1084 | |||
1085 | |||
1086 | If you want to start the web server automatically at boot on SuSE |
||
1087 | |||
1088 | <pre> SuSE >chkconfig apache2 on |
||
1089 | </pre> |
||
1090 | |||
1091 | |||
1092 | |||
1093 | 1 | Eric Hou | |
1094 | 11 | Amber Herold | |
1095 | |||
1096 | |||
1097 | 16 | Amber Herold | |
1098 | 11 | Amber Herold | h2. Check php information |
1099 | 1 | Eric Hou | |
1100 | 11 | Amber Herold | |
1101 | Create the following info.php in your web server document root directory (/var/www/html |
||
1102 | on CentOS. /srv/www/htdocs on SuSE. You can find its location in httpd.conf mentioned above |
||
1103 | under the line starting |
||
1104 | DocumentRoot).<pre><?php |
||
1105 | phpinfo(); |
||
1106 | ?></pre> |
||
1107 | |||
1108 | 1 | Eric Hou | |
1109 | 11 | Amber Herold | Visit this page at http://yourhost/info.php |
1110 | |||
1111 | |||
1112 | You will see comprehensive tables of php and apache information, including the location |
||
1113 | of the addition .ini files, extension, include path, and what extension is enabled. |
||
1114 | |||
1115 | |||
1116 | Here is an example screen shot of the part of the info.php page that tells you where |
||
1117 | php.ini and other configuration files are. |
||
1118 | |||
1119 | |||
1120 | |||
1121 | 16 | Amber Herold | !http://emg.nysbc.org/software/leginon/images/images/phpini.png! |
1122 | 11 | Amber Herold | |
1123 | |||
1124 | 1 | Eric Hou | |
1125 | 11 | Amber Herold | |
1126 | |||
1127 | 16 | Amber Herold | |
1128 | 11 | Amber Herold | h2. mrctools Installation |
1129 | |||
1130 | |||
1131 | |||
1132 | mrctools are installed as php extension and are required for displaying mrc files live |
||
1133 | on the web browser. |
||
1134 | |||
1135 | 1 | Eric Hou | |
1136 | 16 | Amber Herold | |
1137 | 11 | Amber Herold | h2. Install php-devel packages on the web server if missing: |
1138 | |||
1139 | |||
1140 | You can check whether php-devel is installed by |
||
1141 | typing<pre> >phpize</pre> |
||
1142 | |||
1143 | |||
1144 | Follow the instruction for your specific Linux distribution. |
||
1145 | |||
1146 | |||
1147 | For example, SUSE users can use YaST or zypper to install them |
||
1148 | |||
1149 | |||
1150 | |||
1151 | |||
1152 | 16 | Amber Herold | |
1153 | 11 | Amber Herold | h2. php-GD/FFTW3-devel |
1154 | |||
1155 | |||
1156 | |||
1157 | Follow instructions from the download site. These may be included already. If not, |
||
1158 | mrctools installation will fail. |
||
1159 | |||
1160 | |||
1161 | |||
1162 | 1 | Eric Hou | |
1163 | 16 | Amber Herold | |
1164 | 11 | Amber Herold | h2. mrctools Installation |
1165 | |||
1166 | |||
1167 | |||
1168 | mrctools are installed from php devel directory. This is usually /usr/include/php/ext |
||
1169 | where you will find other php extension source such as gd. After the installation, mrc.so |
||
1170 | should be placed in php's extension directory (Look for "extension_dir" in |
||
1171 | 1 | Eric Hou | http://your_host/<link linkend="install_infophp">info.php</link> |
1172 | 11 | Amber Herold | |
1173 | |||
1174 | |||
1175 | |||
1176 | 15 | Amber Herold | * Download dbem tools from "http://emg.nysbc.org/software/mrctools":http://emg.nysbc.org/software/mrctools . |
1177 | 11 | Amber Herold | |
1178 | |||
1179 | 15 | Amber Herold | * Follow the instruction at "http://emg.nysbc.org/software/mrctools/mrc_so.php":http://emg.nysbc.org/software/mrctools/mrc_so.php for installation and |
1180 | 1 | Eric Hou | testing. The next session about checking php information can also help debugging the |
1181 | 11 | Amber Herold | installation |
1182 | |||
1183 | |||
1184 | |||
1185 | |||
1186 | |||
1187 | |||
1188 | |||
1189 | |||
1190 | 16 | Amber Herold | |
1191 | 11 | Amber Herold | h2. Check php information |
1192 | |||
1193 | |||
1194 | |||
1195 | Visit or refresh http://yourhost/info.php <link linkend="install_infophp">which you |
||
1196 | created earlier</link>. It should have a section looking like this (The version should |
||
1197 | correspond to what you've just installed): |
||
1198 | |||
1199 | |||
1200 | |||
1201 | 16 | Amber Herold | !http://emg.nysbc.org/software/leginon/images/images/phpmrc.png! |
1202 | 11 | Amber Herold | |
1203 | |||
1204 | |||
1205 | If mrc is not listed, the extension did not get added at the right order. |
||
1206 | |||
1207 | |||
1208 | |||
1209 | |||
1210 | 16 | Amber Herold | |
1211 | 11 | Amber Herold | h2. Alternative approach if mrc module does not show up in info.php output |
1212 | |||
1213 | |||
1214 | |||
1215 | * find in the <link linkend="install_infophp">info.php web page</link> the location |
||
1216 | of "additional .ini files parsed" in the first table (such as |
||
1217 | /etc/php.d/conf.d/*). |
||
1218 | |||
1219 | |||
1220 | * Go to the directory and make a copy of any ini file to use as a template for |
||
1221 | mrc.ini |
||
1222 | |||
1223 | |||
1224 | |||
1225 | <pre>>cd [additional_ini_directory] |
||
1226 | >cp gd.ini mrc.ini</pre> |
||
1227 | |||
1228 | |||
1229 | |||
1230 | * Edit mrc.ini to the following |
||
1231 | |||
1232 | 1 | Eric Hou | |
1233 | 11 | Amber Herold | |
1234 | <pre>; comment out next line to disable mrc extension in php |
||
1235 | extension=mrc.so</pre> |
||
1236 | |||
1237 | |||
1238 | |||
1239 | * Comment out mrc extension from php.ini (found in /etc/php.ini/ on a typical PHP |
||
1240 | installation) |
||
1241 | |||
1242 | |||
1243 | |||
1244 | <pre>;extension=mrc.so</pre> |
||
1245 | |||
1246 | |||
1247 | |||
1248 | * restart your webserver |
||
1249 | |||
1250 | |||
1251 | |||
1252 | <pre>> /etc/init.d/httpd restart</pre> |
||
1253 | |||
1254 | |||
1255 | |||
1256 | |||
1257 | |||
1258 | |||
1259 | |||
1260 | |||
1261 | |||
1262 | 16 | Amber Herold | |
1263 | 11 | Amber Herold | h2. Web Viewing Tools (dbemtools) Linux |
1264 | Installation |
||
1265 | |||
1266 | |||
1267 | |||
1268 | php and java scripts for viewing images and Leginon information through the web |
||
1269 | server. |
||
1270 | |||
1271 | |||
1272 | |||
1273 | |||
1274 | 15 | Amber Herold | * Download dbem tools from "http://emg.nysbc.org/software/dbemtools":http://emg.nysbc.org/software/dbemtools . |
1275 | 11 | Amber Herold | |
1276 | |||
1277 | * Unpack the package in your [webdirectory] |
||
1278 | |||
1279 | |||
1280 | |||
1281 | <pre>>cd [webdirectory] #/var/www/html in this example |
||
1282 | [webdirectory>tar zxvf dbem_1_5_1.tgz</pre> |
||
1283 | |||
1284 | |||
1285 | |||
1286 | * Copy config.php.template to config.php and edit the latter by adding these MySQL |
||
1287 | parameters: |
||
1288 | |||
1289 | "config.php" should be located in /var/www/html/dbem_1_5_1/ on CentOS and |
||
1290 | /srv/www/htdocs/dbem_1_5_1/ on SuSE. |
||
1291 | |||
1292 | |||
1293 | |||
1294 | <pre><? |
||
1295 | // ---define dbem web tools base ---// |
||
1296 | define('BASE_URL',"/dbem_1_5_1/"; |
||
1297 | // --- Leginon Viewer Configuration --- // |
||
1298 | |||
1299 | 1 | Eric Hou | // --- Set your leginon MySQL database server parameters |
1300 | 11 | Amber Herold | |
1301 | $DB_HOST = "[your database host]"; |
||
1302 | $DB_USER = "<link linkend="db_example_names">usr_object</link>"; |
||
1303 | $DB_PASS = ""; |
||
1304 | $DB = "<link linkend="db_example_names">dbemdata</link>"; |
||
1305 | |||
1306 | // --- XML test dataset |
||
1307 | $XML_DATA = "test/viewerdata.xml"; |
||
1308 | |||
1309 | // --- Project database config |
||
1310 | |||
1311 | 1 | Eric Hou | $PROJECT_URL = "/project_1_2"; |
1312 | 11 | Amber Herold | $PROJECT_DB_HOST = "[your database host]"; |
1313 | $PROJECT_DB_USER = "<link linkend="db_example_names">usr_object</link>"; |
||
1314 | $PROJECT_DB_PASS = ""; |
||
1315 | $PROJECT_DB = "<link linkend="db_example_names">projectdata</link>"; |
||
1316 | </pre> |
||
1317 | |||
1318 | |||
1319 | |||
1320 | * Test the set-up by visiting http://yourhost/dbem_1_5_1 |
||
1321 | 1 | Eric Hou | |
1322 | 11 | Amber Herold | |
1323 | |||
1324 | |||
1325 | |||
1326 | |||
1327 | |||
1328 | |||
1329 | 16 | Amber Herold | |
1330 | 11 | Amber Herold | h2. Project management tools Linux Installation |
1331 | |||
1332 | |||
1333 | |||
1334 | Leginon sessions can be catagorized into different projects. The projects are created |
||
1335 | and viewed trhough a set of web tools. To access them, install the tools on the web server. |
||
1336 | The same project management tools are also used to create and track appion processing |
||
1337 | databases. If you want to use our processing pipeline, Appion, in the future, you must |
||
1338 | install this. |
||
1339 | |||
1340 | |||
1341 | 16 | Amber Herold | |
1342 | 11 | Amber Herold | h2. Prerequisites for project tools |
1343 | |||
1344 | |||
1345 | |||
1346 | installed dbemtools and its prerequisites |
||
1347 | |||
1348 | |||
1349 | |||
1350 | |||
1351 | 16 | Amber Herold | |
1352 | 11 | Amber Herold | h2. project tools |
1353 | |||
1354 | |||
1355 | Current release: project 1.2. |
||
1356 | |||
1357 | |||
1358 | |||
1359 | |||
1360 | 15 | Amber Herold | * Download project tools from "http://emg.nysbc.org/software/dbemtools":http://emg.nysbc.org/software/dbemtools . |
1361 | 11 | Amber Herold | |
1362 | |||
1363 | * Unpack the package in your [webdirectory] |
||
1364 | |||
1365 | 1 | Eric Hou | |
1366 | 11 | Amber Herold | |
1367 | <pre>>cd [webdirectory] #/var/www/html in this example |
||
1368 | [webdirectory]>tar zxvf project_1_2.tgz</pre> |
||
1369 | |||
1370 | |||
1371 | |||
1372 | 1 | Eric Hou | * Go to the uncompressed directory |
1373 | 17 | Amber Herold | project_1_2.<pre>> cd project_1_2</pre> |
1374 | 11 | Amber Herold | |
1375 | |||
1376 | 19 | Amber Herold | * Copy config.php.template to _config.php_ |
1377 | 11 | Amber Herold | |
1378 | |||
1379 | |||
1380 | <pre>> cp config.php.template to config.php</pre> |
||
1381 | |||
1382 | |||
1383 | |||
1384 | 19 | Amber Herold | * Edit _config.php_: You need to insert these MySQL |
1385 | 11 | Amber Herold | parameters in project tool's config.php |
1386 | |||
1387 | |||
1388 | |||
1389 | 1 | Eric Hou | <pre>// --- Project Configuration --- // |
1390 | 11 | Amber Herold | |
1391 | // --- Leginon database config |
||
1392 | $DBEM_PATH="../dbem_1_5_1/"; |
||
1393 | |||
1394 | $DB_HOST = "[your database host]"; |
||
1395 | $DB_USER = "usr_object"; |
||
1396 | 1 | Eric Hou | $DB_PASS = ""; |
1397 | 11 | Amber Herold | $DB = "<link linkend="db_example_names">dbemdata</link>"; |
1398 | |||
1399 | // --- Project database config |
||
1400 | $PROJECT_DB_HOST = "[your database host]"; |
||
1401 | 1 | Eric Hou | $PROJECT_DB_USER = "<link linkend="db_example_names">usr_object</link>"; |
1402 | 11 | Amber Herold | $PROJECT_DB_PASS = ""; |
1403 | $PROJECT_DB = "<link linkend="db_example_names">projectdata</link>"; |
||
1404 | </pre> |
||
1405 | |||
1406 | |||
1407 | |||
1408 | * Test the set-up by visiting http://yourhost/project_1_2 |
||
1409 | |||
1410 | |||
1411 | |||
1412 | |||
1413 | |||
1414 | |||
1415 | |||
1416 | |||
1417 | |||
1418 | |||
1419 | 16 | Amber Herold | |
1420 | 11 | Amber Herold | h2. Other Tools |
1421 | |||
1422 | |||
1423 | This section includes tools that may help with Leginon development. |
||
1424 | |||
1425 | |||
1426 | 16 | Amber Herold | |
1427 | 11 | Amber Herold | h2. phpMyAdmin |
1428 | |||
1429 | |||
1430 | |||
1431 | |||
1432 | |||
1433 | 16 | Amber Herold | * Download phpMyAdmin from Yast2 or "www.phpmyadmin.net":http://www.phpmyadmin.net * Download phpMyAdmin into the directory where the web server has been |
1434 | 11 | Amber Herold | installed. |
1435 | |||
1436 | |||
1437 | |||
1438 | |||
1439 | |||
1440 | |||
1441 | * Check phpMyAdmin installation: |
||
1442 | |||
1443 | |||
1444 | |||
1445 | <pre>>rpm -qa |grep -i phpmyadmin </pre> |
||
1446 | |||
1447 | |||
1448 | |||
1449 | * Install from tarball: |
||
1450 | |||
1451 | |||
1452 | |||
1453 | <pre>> cd [webdirectory] |
||
1454 | [webdirectory]>tar zxvf phpMyAdmin-2.x.tar.gz</pre> |
||
1455 | |||
1456 | |||
1457 | |||
1458 | or Install with yum if availabe: |
||
1459 | |||
1460 | |||
1461 | |||
1462 | <pre>> yum install phpMyAdmin</pre> |
||
1463 | |||
1464 | |||
1465 | |||
1466 | * Create phpMyAdmin configuration file called config.inc.php from a |
||
1467 | sample. |
||
1468 | |||
1469 | |||
1470 | |||
1471 | <pre>[webdirectory]>cd phpMyAdmin |
||
1472 | (if you install with yum, the program directory is /usr/share/phpMyAdmin) |
||
1473 | |||
1474 | > cp config.sample.inc.php config.inc.php |
||
1475 | </pre> |
||
1476 | |||
1477 | |||
1478 | |||
1479 | * Make sure these are set correctly in <emphasis role="bold" |
||
1480 | >config.inc.php</emphasis>. Note that these are for MySQL which we set earlier. |
||
1481 | You can set specific user, but it is safer just leave it blank. |
||
1482 | |||
1483 | |||
1484 | |||
1485 | <pre> |
||
1486 | $cfg['Servers'][$i]['host'] = '[your host]'; |
||
1487 | $cfg['Servers'][$i]['port'] = ''; |
||
1488 | $cfg['Servers'][$i]['socket'] = ''; |
||
1489 | $cfg['Servers'][$i]['connect_type'] = 'tcp'; |
||
1490 | $cfg['Servers'][$i]['extension'] = 'mysql'; |
||
1491 | $cfg['Servers'][$i]['compress'] = FALSE; |
||
1492 | $cfg['Servers'][$i]['controluser'] = ''; |
||
1493 | $cfg['Servers'][$i]['auth_type'] = 'http'; |
||
1494 | $cfg['Servers'][$i]['user'] = ''; |
||
1495 | $cfg['Servers'][$i]['password'] = ''; |
||
1496 | </pre> |
||
1497 | |||
1498 | |||
1499 | |||
1500 | * For additional security, you may restrict mysql root access |
||
1501 | |||
1502 | |||
1503 | |||
1504 | <pre> |
||
1505 | 1 | Eric Hou | $cfg['Servers'][$i]['AllowRoot'] = FALSE; |
1506 | 11 | Amber Herold | </pre> |
1507 | |||
1508 | |||
1509 | |||
1510 | 1 | Eric Hou | * If you want to access phpMyAdmin from another computer, you can add it to its |
1511 | 11 | Amber Herold | web access configuration file found as /etc/httpd/conf.d/phpMyAdmin.conf in a |
1512 | typical installation |
||
1513 | |||
1514 | |||
1515 | 1 | Eric Hou | |
1516 | 11 | Amber Herold | <pre> |
1517 | <Directory /usr/share/phpMyAdmin/> |
||
1518 | order deny,allow |
||
1519 | deny from all |
||
1520 | allow from 127.0.0.1 |
||
1521 | allow from YOUR_IP_ADDRESS |
||
1522 | </Directory> |
||
1523 | </pre> |
||
1524 | |||
1525 | |||
1526 | |||
1527 | |||
1528 | |||
1529 | |||
1530 | |||
1531 | |||
1532 | |||
1533 | |||
1534 | |||
1535 | |||
1536 | |||
1537 | 16 | Amber Herold | |
1538 | 11 | Amber Herold | h2. Windows installation |
1539 | |||
1540 | |||
1541 | |||
1542 | 16 | Amber Herold | |
1543 | 11 | Amber Herold | h2. Processing-side Leginon Windows Installation |
1544 | |||
1545 | |||
1546 | |||
1547 | 16 | Amber Herold | |
1548 | 11 | Amber Herold | h2. Install Python and Support Packages (Note that python 2.5 must be used): |
1549 | |||
1550 | |||
1551 | |||
1552 | This list does not include pyton XML module because it is included in the python |
||
1553 | package for window. |
||
1554 | |||
1555 | 1 | Eric Hou | |
1556 | 11 | Amber Herold | |
1557 | 14 | Amber Herold | |_.Name:|_.Download site:| |
1558 | 11 | Amber Herold | |Python 2.5*|"http://www.python.org":http://www.python.org | |
1559 | 15 | Amber Herold | |Python for Windows extension (pywin32) |"http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/ | |
1560 | |wxPython 2.5.2.8 or newer|"http://www.wxpython.org":http://www.wxpython.org | |
||
1561 | |MySQL Python client 1.2 or newer|"http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python | |
||
1562 | |Python Imaging Library (PIL) 1.1.4 or newer|"http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/ | |
||
1563 | |NumPy 1.0b5 (tested, others may work)|"http://www.scipy.org":http://www.scipy.org | |
||
1564 | |SciPy 0.5.1 or newer|"http://www.scipy.org":http://www.scipy.org | |
||
1565 | |Tortoise SVN client|"http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org | |
||
1566 | |||
1567 | 11 | Amber Herold | |
1568 | |||
1569 | 1 | Eric Hou | |
1570 | 11 | Amber Herold | *Python 2.5 is the only python version that we have compiled numExtension. libCV and |
1571 | comarray in. Therefore no other python version works for now. |
||
1572 | |||
1573 | |||
1574 | Execute the installer file and follow the directions. |
||
1575 | |||
1576 | |||
1577 | |||
1578 | 1 | Eric Hou | |
1579 | 16 | Amber Herold | |
1580 | 11 | Amber Herold | h2. Packages required from NRAMM |
1581 | |||
1582 | |||
1583 | |||
1584 | Here are the packages you need to install with python installer |
||
1585 | |||
1586 | 1 | Eric Hou | |
1587 | 11 | Amber Herold | |
1588 | 14 | Amber Herold | |_.Name:|_.Purpose:| |
1589 | 11 | Amber Herold | | Leginon|modular TEM image acquisition| |
1590 | | pyami|general functions| |
||
1591 | | sinedon|Leginon/database interaction| |
||
1592 | | pyScope|microscope control and monitoring| |
||
1593 | | ImageViewer|image viewing for tomography| |
||
1594 | |||
1595 | |||
1596 | |||
1597 | |||
1598 | Because numextension and libCV requires extra compilers, we have created window |
||
1599 | 1 | Eric Hou | installer for them for python 2.5 and made them available through "http://www.leginon.org/":http://www.leginon.org/ |
1600 | |||
1601 | 14 | Amber Herold | |_.Downloadfile Name|_.Installed Python Package File|_.Purpose:| |
1602 | 13 | Amber Herold | |NumExtension-1.2.0.win32-py2.5.exe|numextension.pyd|c extension for numerical processing| |
1603 | 11 | Amber Herold | |libCV-0.2.win32-py2.5.exe|libCV.pyd|small c library of algorithm from computer vision field| |
1604 | |||
1605 | |||
1606 | 1 | Eric Hou | |
1607 | 11 | Amber Herold | |
1608 | |||
1609 | |||
1610 | 16 | Amber Herold | |
1611 | 11 | Amber Herold | h2. Check out SVN Source Files from the depository |
1612 | |||
1613 | |||
1614 | |||
1615 | Use your mouse to do the following |
||
1616 | * Create Leginon-1.6-ALL directory somewhere at your convenience |
||
1617 | |||
1618 | |||
1619 | * Change directory into Leginon-1.6-ALL |
||
1620 | |||
1621 | 1 | Eric Hou | |
1622 | 11 | Amber Herold | * Right-click the mouse botton in this directory window and select Tortoise svn |
1623 | 17 | Amber Herold | Checkout in the menu:!http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! |
1624 | 1 | Eric Hou | |
1625 | 11 | Amber Herold | |
1626 | * Set up svn checkout window like this for <link linkend="windows_packages">EACH |
||
1627 | 17 | Amber Herold | of the leginon packages</link>.!http://emg.nysbc.org/software/leginon/images/images/svnco.png! |
1628 | 11 | Amber Herold | |
1629 | |||
1630 | 1 | Eric Hou | |
1631 | 11 | Amber Herold | |
1632 | |||
1633 | |||
1634 | |||
1635 | 16 | Amber Herold | |
1636 | 11 | Amber Herold | h2. Install the packages you downloaded from NRAMM svn depository |
1637 | |||
1638 | 1 | Eric Hou | |
1639 | 11 | Amber Herold | |
1640 | |||
1641 | |||
1642 | * Start a command line Window from Start Menu |
||
1643 | |||
1644 | |||
1645 | * Install the package in each folder with commands such as |
||
1646 | <pre>cd Your_Download_Place\Leginon-1.6-ALL\leginon |
||
1647 | c:\\python25\python.exe setup.py install</pre> |
||
1648 | |||
1649 | |||
1650 | |||
1651 | |||
1652 | |||
1653 | |||
1654 | |||
1655 | |||
1656 | 16 | Amber Herold | |
1657 | 11 | Amber Herold | h2. Download the two Window Installer Files from Leginon website |
1658 | |||
1659 | |||
1660 | |||
1661 | "http://www.leginon.org/":http://www.leginon.org/ h2. Install individual packages |
||
1662 | 15 | Amber Herold | |
1663 | 11 | Amber Herold | |
1664 | |||
1665 | Excute the installer files and follow the instruction. |
||
1666 | |||
1667 | |||
1668 | |||
1669 | |||
1670 | 16 | Amber Herold | |
1671 | 11 | Amber Herold | h2. Mapping Drives: |
1672 | |||
1673 | |||
1674 | |||
1675 | If you plan to run Leginon directly on the Windows machine, such as in <link |
||
1676 | linkend="config_C">configuration C</link>, and your data files are served through a |
||
1677 | Samba server on a Linux machine, you will need to map the network drive. For example, if |
||
1678 | your Samba server has a hostname your_smbserver, and you have set up a share called |
||
1679 | [your_share_point] which points to /your_data_path/ and leginon data will be saved under a |
||
1680 | folder in /your_data_path/leginon/ |
||
1681 | 1 | Eric Hou | |
1682 | 11 | Amber Herold | |
1683 | |||
1684 | |||
1685 | * Start, My Computer |
||
1686 | 1 | Eric Hou | |
1687 | 11 | Amber Herold | |
1688 | * Tools menu, Map network drive |
||
1689 | 1 | Eric Hou | |
1690 | 11 | Amber Herold | |
1691 | * Use an unmapped drive such as Z: |
||
1692 | |||
1693 | 1 | Eric Hou | Enter shared path in Windows format |
1694 | 17 | Amber Herold | as<pre>\\your_smbserver\your_share_point</pre> |
1695 | 11 | Amber Herold | |
1696 | |||
1697 | * Add the drive and the Linux path to leginon.cfg on the Windows machine |
||
1698 | 17 | Amber Herold | as<pre>[Drive Mapping] |
1699 | 11 | Amber Herold | Z:/your_data_path</pre> |
1700 | |||
1701 | |||
1702 | * Add image path to leginon.cfg on the Windows machine in Linux format |
||
1703 | 17 | Amber Herold | as<pre>[Images] |
1704 | 11 | Amber Herold | path:/your_data_path/leginon</pre> |
1705 | |||
1706 | |||
1707 | |||
1708 | |||
1709 | |||
1710 | |||
1711 | |||
1712 | |||
1713 | 16 | Amber Herold | |
1714 | 11 | Amber Herold | h2. Configure leginon.cfg: |
1715 | |||
1716 | |||
1717 | Follow instruction in "<link linkend="leginon_cfg">Configure leginon.cfg</link>" in |
||
1718 | the section for Linux installation but note the location of the configuration files |
||
1719 | follows. In addition, if the storage disk is mapped onto the Windows PC as drive Z, this |
||
1720 | mapping should be included in leginon.cfg. See above. |
||
1721 | |||
1722 | |||
1723 | |||
1724 | |||
1725 | * Configurations for all users |
||
1726 | |||
1727 | |||
1728 | |||
1729 | 1 | Eric Hou | <pre> <Python directory>\Lib\site-packages\Leginon\config\leginon.cfg</pre> |
1730 | 11 | Amber Herold | |
1731 | |||
1732 | Example: |
||
1733 | <pre> C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg</pre> |
||
1734 | |||
1735 | |||
1736 | * Configurations for individual users |
||
1737 | |||
1738 | |||
1739 | |||
1740 | <pre> <Home directory>\leginon.cfg</pre> |
||
1741 | |||
1742 | |||
1743 | Example: |
||
1744 | <pre> C:\Documents and Settings\Leginon User\leginon.cfg </pre> |
||
1745 | |||
1746 | |||
1747 | * A skeleton (default) configuration file is available: |
||
1748 | |||
1749 | |||
1750 | |||
1751 | <pre> C:\Python25\Lib\site-packages\Leginon\config\default.cfg</pre> |
||
1752 | |||
1753 | |||
1754 | |||
1755 | |||
1756 | |||
1757 | |||
1758 | |||
1759 | |||
1760 | 1 | Eric Hou | |
1761 | 16 | Amber Herold | |
1762 | 11 | Amber Herold | h2. Configure sinedon.cfg: |
1763 | |||
1764 | |||
1765 | Sinedon is designed to be able to interact with multiple databases. |
||
1766 | |||
1767 | Follow instruction in "<link linkend="sinedon_cfg">Configure sinedon.cfg</link>" in |
||
1768 | the section for Linux installation but note the location of the configuration files |
||
1769 | follows. |
||
1770 | |||
1771 | |||
1772 | |||
1773 | |||
1774 | * For all users, put sinedon.cfg with the installed package |
||
1775 | as<pre>C:\Python25\Lib\site-packages\sinedon\sinedon.cfg</pre> |
||
1776 | |||
1777 | |||
1778 | * Your home directory on |
||
1779 | Windows:<pre>C:\Documents and Settings\your_name></pre> |
||
1780 | |||
1781 | |||
1782 | * the skeleton sinedon configuration file |
||
1783 | is<pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre> |
||
1784 | |||
1785 | |||
1786 | |||
1787 | |||
1788 | |||
1789 | |||
1790 | |||
1791 | |||
1792 | 16 | Amber Herold | |
1793 | 11 | Amber Herold | h2. Create Leginon and Leginon Client shortcut in Start menu menu under Leginon |
1794 | |||
1795 | |||
1796 | 1 | Eric Hou | |
1797 | 11 | Amber Herold | This instruction refers to Windows XP |
1798 | |||
1799 | |||
1800 | |||
1801 | |||
1802 | * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new |
||
1803 | 1 | Eric Hou | folder named Leginon. |
1804 | 11 | Amber Herold | |
1805 | |||
1806 | * In another window, go |
||
1807 | 17 | Amber Herold | to<pre>C:\Python25\Lib\site-packages\Leginon</pre> |
1808 | 11 | Amber Herold | |
1809 | |||
1810 | 1 | Eric Hou | * Create a shortcut from start-leginon.py as Leginon and a shortcut from |
1811 | 11 | Amber Herold | launcher.py as Leginon Client. |
1812 | |||
1813 | |||
1814 | * Move the two shortcuts into |
||
1815 | 17 | Amber Herold | <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre> |
1816 | 11 | Amber Herold | |
1817 | |||
1818 | |||
1819 | |||
1820 | |||
1821 | |||
1822 | |||
1823 | |||
1824 | 16 | Amber Herold | |
1825 | 11 | Amber Herold | h2. Additional Software (Optional): |
1826 | 1 | Eric Hou | |
1827 | 11 | Amber Herold | |
1828 | TightVNC (http://www.tightvnc.com) |
||
1829 | |||
1830 | |||
1831 | |||
1832 | |||
1833 | |||
1834 | |||
1835 | |||
1836 | |||
1837 | 16 | Amber Herold | |
1838 | 11 | Amber Herold | h2. Database server Windows Installation |
1839 | |||
1840 | |||
1841 | |||
1842 | 16 | Amber Herold | |
1843 | 11 | Amber Herold | h2. We do not do this at NRAMM. Please follow the instruction in Linux installation and |
1844 | modify it for Windows at your own risk. |
||
1845 | |||
1846 | |||
1847 | |||
1848 | For a good Windows specific instruction for general PHP configuration with MySQL for |
||
1849 | Apache 2 in Windows, try http://www.artfulsoftware.com/php_mysql_win.html. |
||
1850 | |||
1851 | |||
1852 | |||
1853 | |||
1854 | |||
1855 | |||
1856 | |||
1857 | |||
1858 | 16 | Amber Herold | |
1859 | 1 | Eric Hou | h2. Additional installation on the microscope computer: |
1860 | 11 | Amber Herold | |
1861 | |||
1862 | |||
1863 | The full leginon and its supporting packages need to be installed on the Windows computer |
||
1864 | controlling the microscope. Additional programs are required for communication with the CCD |
||
1865 | and extra functions for Tecnai scripting not supported as default by FEI Tecnai |
||
1866 | microscopes |
||
1867 | |||
1868 | |||
1869 | 16 | Amber Herold | |
1870 | 11 | Amber Herold | h2. Required supporting programs for the CCD camera from camera makers |
1871 | |||
1872 | |||
1873 | |||
1874 | Install and register the following programs for CCD cameras from the two makes: |
||
1875 | |||
1876 | 1 | Eric Hou | |
1877 | |||
1878 | 14 | Amber Herold | |_.Camera Make:|_.File:| |
1879 | 11 | Amber Herold | | Gatan|TecnaiCCD.dll| |
1880 | | Tietz|CAMC4.exe*| |
||
1881 | |||
1882 | |||
1883 | |||
1884 | |||
1885 | * We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA. |
||
1886 | Replacing it with an earlier version of CAMC4.exe resolved the problem. |
||
1887 | |||
1888 | |||
1889 | |||
1890 | |||
1891 | 16 | Amber Herold | |
1892 | 11 | Amber Herold | h2. Additional Package required from NRAMM for Gatan camera or camera that uses TIA |
1893 | |||
1894 | |||
1895 | |||
1896 | For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install |
||
1897 | 1 | Eric Hou | with python |
1898 | 11 | Amber Herold | |
1899 | 1 | Eric Hou | |
1900 | |||
1901 | |_.SVN Package Name|_.Installed Python Package Name|_.Reason for update:| |
||
1902 | 11 | Amber Herold | |comarray|comarray|com module output conversion to array| |
1903 | |||
1904 | |||
1905 | |||
1906 | |||
1907 | |||
1908 | |||
1909 | * <link linkend="window_svn">Check out the comarray package</link> from svn |
||
1910 | depository with your SVN client |
||
1911 | |||
1912 | 17 | Amber Herold | <pre>cd Leginon-1.6-ALL |
1913 | 11 | Amber Herold | svn co http://emg.nysbc.org/svn/comarray/branches/leg1.6 comarray</pre> |
1914 | |||
1915 | * Start a command line Window from Start Menu |
||
1916 | 1 | Eric Hou | |
1917 | 11 | Amber Herold | |
1918 | * Install the package with commands such as |
||
1919 | <pre>cd Your_Download_Place\Leginon-1.6-ALL\comarray |
||
1920 | c:\\python25\python.exe setup.py install</pre> |
||
1921 | |||
1922 | |||
1923 | |||
1924 | |||
1925 | |||
1926 | |||
1927 | |||
1928 | |||
1929 | 16 | Amber Herold | |
1930 | 11 | Amber Herold | h2. Supporting programs for film exposure |
1931 | |||
1932 | |||
1933 | |||
1934 | Install the following if you need film exposure on FEI Tecnai TEM through Leginon, |
||
1935 | available through FEI. Please contact Max Otten: <email>mto@feico.com</email> and request |
||
1936 | 1 | Eric Hou | for adaexp.exe that works with your version of Tecnai user interface program. |
1937 | |||
1938 | 11 | Amber Herold | |
1939 | 14 | Amber Herold | |
1940 | 13 | Amber Herold | |_.Name:|_.File:| |
1941 | 11 | Amber Herold | | exposure adaptor|adaexp.exe| |
1942 | |||
1943 | |||
1944 | |||
1945 | |||
1946 | |||
1947 | |||
1948 | 16 | Amber Herold | |
1949 | 11 | Amber Herold | h2. Register adaexep.exe |
1950 | |||
1951 | |||
1952 | |||
1953 | * From the command prompt: |
||
1954 | |||
1955 | <pre>adaexp.exe /regserver</pre> |
||
1956 | |||
1957 | * From the program start menu under pyScope or |
||
1958 | C:\Python25\Lib\site-packages\pyScope\ |
||
1959 | |||
1960 | <pre>updatecom.py</pre> |
||
1961 | |||
1962 | |||
1963 | |||
1964 | |||
1965 | |||
1966 | |||
1967 | |||
1968 | 16 | Amber Herold | |
1969 | 11 | Amber Herold | h2. Modify instruments.cfg: |
1970 | |||
1971 | 1 | Eric Hou | |
1972 | 11 | Amber Herold | |
1973 | Sinedon now have full control of database interaction, therefore, the database |
||
1974 | configuration in leginon.cfg is no longer needed. |
||
1975 | |||
1976 | |||
1977 | |||
1978 | |||
1979 | * Modify the file instruments.cfg in the installed pyScope directory to that for |
||
1980 | your microscope and camera. For example, if your microscope uses Tecnai Scripting |
||
1981 | Interface and you have a Gatan camera that you interface through |
||
1982 | DigitalMicrograph: |
||
1983 | |||
1984 | |||
1985 | |||
1986 | <pre>[tem] |
||
1987 | class: tecnai.Tecnai |
||
1988 | [camera] |
||
1989 | class: gatan.Gatan</pre> |
||
1990 | |||
1991 | 1 | Eric Hou | |
1992 | 11 | Amber Herold | |
1993 | The file contains other examples of microscope and camera drivers that we |
||
1994 | distribute from NRAMM. |
||
1995 | |||
1996 | |||
1997 | |||
1998 | |||
1999 | |||
2000 | |||
2001 | |||
2002 | |||
2003 | 16 | Amber Herold | |
2004 | 11 | Amber Herold | h2. Run updatecom.py |
2005 | |||
2006 | |||
2007 | |||
2008 | From a command line window: |
||
2009 | |||
2010 | |||
2011 | |||
2012 | <pre>cd C:\python25\Lib\Site-Packages\pyScope |
||
2013 | C:\python25\python.exe updatecom.py</pre> |
||
2014 | |||
2015 | |||
2016 | |||
2017 | This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py, |
||
2018 | in the same directory. |
||
2019 | |||
2020 | |||
2021 | |||
2022 | |||
2023 | 16 | Amber Herold | |
2024 | 11 | Amber Herold | h2. Additional setup on Tietz PXL camera (optional) |
2025 | |||
2026 | |||
2027 | |||
2028 | The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like |
||
2029 | to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that |
||
2030 | get camera dimension in tietz.py of pyScope package. |
||
2031 | |||
2032 | 1 | Eric Hou | |
2033 | 11 | Amber Herold | * Go to C:\Python25\Lib\site-packages\pyScope\ |
2034 | |||
2035 | |||
2036 | * Edit tietz.py with a plain text editor |
||
2037 | |||
2038 | |||
2039 | * Find the lines: |
||
2040 | |||
2041 | |||
2042 | |||
2043 | <pre> def getCameraSize(self): |
||
2044 | # {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}} |
||
2045 | x = self._getParameterValue('cpTotalDimensionX') |
||
2046 | 1 | Eric Hou | y = self._getParameterValue('cpTotalDimensionY') |
2047 | 11 | Amber Herold | return {'x': x, 'y': y} |
2048 | </pre> |
||
2049 | |||
2050 | |||
2051 | 1 | Eric Hou | |
2052 | 11 | Amber Herold | * Change the last line to: |
2053 | |||
2054 | |||
2055 | |||
2056 | <pre> return {'x': 2048, 'y': 2048}</pre> |
||
2057 | |||
2058 | |||
2059 | |||
2060 | |||
2061 | 1 | Eric Hou | |
2062 | 11 | Amber Herold | |
2063 | |||
2064 | 16 | Amber Herold | |
2065 | 11 | Amber Herold | h2. Additional Software (Optional): |
2066 | |||
2067 | |||
2068 | TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room |
||
2069 | just to open the column valves. |
||
2070 | 1 | Eric Hou | |
2071 | 11 | Amber Herold | |
2072 | |||
2073 | |||
2074 | |||
2075 | |||
2076 | |||
2077 | |||
2078 | 16 | Amber Herold | |
2079 | 11 | Amber Herold | h2. What is next |
2080 | |||
2081 | 1 | Eric Hou | |
2082 | 11 | Amber Herold | |
2083 | 16 | Amber Herold | |
2084 | 11 | Amber Herold | h2. Perform Administration Setup |
2085 | |||
2086 | 1 | Eric Hou | |
2087 | 11 | Amber Herold | See Next chapter on <link linkend="addusers">Leginon Administration Tools</link>. |
2088 | |||
2089 | |||
2090 | |||
2091 | 1 | Eric Hou | |
2092 | 11 | Amber Herold | |
2093 | 16 | Amber Herold | |
2094 | 11 | Amber Herold | h2. Create a test project |
2095 | |||
2096 | |||
2097 | See the chapter on <link linkend="project">Project Management Tools</link>. |
||
2098 | |||
2099 | |||
2100 | |||
2101 | 1 | Eric Hou | |
2102 | 16 | Amber Herold | |
2103 | 11 | Amber Herold | h2. Perform Microscope Setup and Test run |
2104 | |||
2105 | |||
2106 | See the chapter on <link linkend="runleg_chapter">Start Leginon</link>. |
||
2107 | |||
2108 | |||
2109 | |||
2110 | |||
2111 | |||
2112 | 1 | Eric Hou | |
2113 | 16 | Amber Herold | |
2114 | 11 | Amber Herold | h2. Backup Practices |
2115 | |||
2116 | |||
2117 | |||
2118 | 16 | Amber Herold | |
2119 | 11 | Amber Herold | h2. Ideal setup: |
2120 | |||
2121 | |||
2122 | |||
2123 | 16 | Amber Herold | |
2124 | 11 | Amber Herold | h2. Regular computer backup |
2125 | 1 | Eric Hou | |
2126 | 11 | Amber Herold | |
2127 | |||
2128 | To protect your program installation. |
||
2129 | |||
2130 | |||
2131 | |||
2132 | |||
2133 | 16 | Amber Herold | |
2134 | 11 | Amber Herold | h2. Full backup of the databases every night |
2135 | 1 | Eric Hou | |
2136 | 11 | Amber Herold | |
2137 | |||
2138 | The database is the metadata generated by Leginon named "dbemdata" in the installation |
||
2139 | example. |
||
2140 | |||
2141 | |||
2142 | |||
2143 | |||
2144 | 16 | Amber Herold | |
2145 | 11 | Amber Herold | h2. Full/Incremental/differential backup of the images |
2146 | |||
2147 | |||
2148 | 1 | Eric Hou | |
2149 | 11 | Amber Herold | The image files located in [your storage disk] should be backup in full at least once |
2150 | a month, and nightly in differential or incremental mode. |
||
2151 | |||
2152 | |||
2153 | |||
2154 | |||
2155 | 1 | Eric Hou | |
2156 | 11 | Amber Herold | |
2157 | 16 | Amber Herold | |
2158 | 11 | Amber Herold | h2. Current NRAMM setup: |
2159 | |||
2160 | |||
2161 | |||
2162 | Because our tape backup system is not on-site and the data have to transfer over slow |
||
2163 | network to perform the task, we have not been able to backup in the ideal setting. Here is |
||
2164 | what we currently do: |
||
2165 | |||
2166 | |||
2167 | 16 | Amber Herold | |
2168 | 11 | Amber Herold | h2. Regular computer backup |
2169 | |||
2170 | |||
2171 | |||
2172 | TSRI Research Computing provides regular back up service that does full backup of the |
||
2173 | computers every four weeks and incremental backup every night. The full backup expires in |
||
2174 | 4 months and the incremental backup one month. We do this for the computers running |
||
2175 | Leginon main program, the database server, as well as the web server. |
||
2176 | |||
2177 | |||
2178 | |||
2179 | |||
2180 | 16 | Amber Herold | |
2181 | 11 | Amber Herold | h2. Regular backup & tar of the databases every night |
2182 | |||
2183 | |||
2184 | |||
2185 | On top of the TSRI backup, we also tar the database everynight and store it on the |
||
2186 | institutional tape library. |
||
2187 | 16 | Amber Herold | |
2188 | 11 | Amber Herold | |
2189 | |||
2190 | |||
2191 | |||
2192 | h2. rsync to a tape library of the image storage disk |
||
2193 | |||
2194 | |||
2195 | |||
2196 | As our image storage disks total 15T byte, we currently use rsync function to update a |
||
2197 | copy on our institutional tape library. It creates new files, updates old files, but does |
||
2198 | not remove old files on the tape if it is removed on the storage disk. We do not think |
||
2199 | this is the best solution since it is not possible to retrieve old files that have been |
||
2200 | modified on a later time. |