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  1.  
  2. rr186@spectre2.le.ac.uk's password:
  3. Last login: Thu Mar 23 15:37:13 2017 from host-53-211.ph.le.ac.uk
  4.  
  5. Welcome to the SPECTRE2 service
  6. ===============================
  7.  
  8. SPECTRE2 documentation can be found at:
  9. http://www2.le.ac.uk/offices/itservices/resources/is/rcs/hpc/spectre
  10. This documentation is currently being updated for SPECTRE2
  11.  
  12. Contact rcs.support@le.ac.uk to report problems.
  13.  
  14. Please mention SPECTRE2 in your email.
  15.  
  16. *** Upcoming Service Days ***
  17.  
  18. Wed 29 March 2017
  19. Wed 17 May 2017
  20. Wed 28 June 2017
  21. Wed 26 July 2017
  22. Wed 30 August 2017
  23.  
  24.  
  25. *********************************************
  26.  
  27. Default SCRATCHDIR is /scratch/spectre/r/rr186
  28. Default TMPDIR is /scratch/spectre/r/rr186
  29.  
  30. *********************************************
  31.  
  32. [rr186@spectre12 ~]$ cd finalproject1/
  33. [rr186@spectre12 finalproject1]$ cd 1M_pre_ms_to_wd/
  34. [rr186@spectre12 1M_pre_ms_to_wd]$ ls
  35. checks.md5 final_profile.data inlist mesa_dir.rb plot.py rn
  36. ck get-pip.py inlist_1.0 mk plotters src
  37. clean grid6.mp4 LOGS photos png star
  38. final.mod hr.mp4 make plot_data re
  39. [rr186@spectre12 1M_pre_ms_to_wd]$ display png/grid6_00
  40. grid6_000015.png grid6_000375.png grid6_000735.png grid6_001095.png
  41. grid6_000030.png grid6_000390.png grid6_000750.png grid6_001110.png
  42. grid6_000045.png grid6_000405.png grid6_000765.png grid6_001125.png
  43. grid6_000060.png grid6_000420.png grid6_000780.png grid6_001140.png
  44. grid6_000075.png grid6_000435.png grid6_000795.png grid6_001155.png
  45. grid6_000090.png grid6_000450.png grid6_000810.png grid6_001170.png
  46. grid6_000105.png grid6_000465.png grid6_000825.png grid6_001185.png
  47. grid6_000120.png grid6_000480.png grid6_000840.png grid6_001200.png
  48. grid6_000135.png grid6_000495.png grid6_000855.png grid6_001215.png
  49. grid6_000150.png grid6_000510.png grid6_000870.png grid6_001230.png
  50. grid6_000165.png grid6_000525.png grid6_000885.png grid6_001245.png
  51. grid6_000180.png grid6_000540.png grid6_000900.png grid6_001260.png
  52. grid6_000195.png grid6_000555.png grid6_000915.png grid6_001275.png
  53. grid6_000210.png grid6_000570.png grid6_000930.png grid6_001290.png
  54. grid6_000225.png grid6_000585.png grid6_000945.png grid6_001305.png
  55. grid6_000240.png grid6_000600.png grid6_000960.png grid6_001320.png
  56. grid6_000255.png grid6_000615.png grid6_000975.png grid6_001335.png
  57. grid6_000270.png grid6_000630.png grid6_000990.png grid6_001350.png
  58. grid6_000285.png grid6_000645.png grid6_001005.png grid6_001365.png
  59. grid6_000300.png grid6_000660.png grid6_001020.png grid6_001380.png
  60. grid6_000315.png grid6_000675.png grid6_001035.png grid6_001395.png
  61. grid6_000330.png grid6_000690.png grid6_001050.png grid6_001410.png
  62. grid6_000345.png grid6_000705.png grid6_001065.png grid6_001425.png
  63. [rr186@spectre12 1M_pre_ms_to_wd]$ display png/grid6_0003
  64. grid6_000300.png grid6_000330.png grid6_000360.png grid6_000390.png
  65. grid6_000315.png grid6_000345.png grid6_000375.png
  66. [rr186@spectre12 1M_pre_ms_to_wd]$ display png/grid6_000360.png
  67. [rr186@spectre12 1M_pre_ms_to_wd]$ nano plot.py
  68. [rr186@spectre12 1M_pre_ms_to_wd]$ python plot.py
  69. 35 in profiles.index file ...
  70. Found and load nearest profile for cycle 800
  71. reading LOGS/profile22.data ...
  72. reading ...100%
  73.  
  74. failed to get the current screen resources
  75. Closing profile tool ...
  76. [rr186@spectre12 1M_pre_ms_to_wd]$ ^C
  77. [rr186@spectre12 1M_pre_ms_to_wd]$ failed to get the current screen resources
  78. -bash: failed: command not found
  79. [rr186@spectre12 1M_pre_ms_to_wd]$ ^C
  80. [rr186@spectre12 1M_pre_ms_to_wd]$ python
  81. Python 2.7.13 |Anaconda 4.3.1 (64-bit)| (default, Dec 20 2016, 23:09:15)
  82. [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
  83. Type "help", "copyright", "credits" or "license" for more information.
  84. Anaconda is brought to you by Continuum Analytics.
  85. Please check out: http://continuum.io/thanks and https://anaconda.org
  86. >>> d = mesa.mesa_profile("LOGS", 001440)
  87. Traceback (most recent call last):
  88. File "<stdin>", line 1, in <module>
  89. NameError: name 'mesa' is not defined
  90. >>> import mesa
  91. >>> d = mesa.mesa_profile("LOGS", 001440)
  92. 35 in profiles.index file ...
  93. Found and load nearest profile for cycle 800
  94. reading LOGS/profile22.data ...
  95. reading ...100%
  96.  
  97. >>> help(d.density_profile)
  98.  
  99. >>> import mesa_reader as mr
  100. Traceback (most recent call last):
  101. File "<stdin>", line 1, in <module>
  102. ImportError: No module named mesa_reader
  103. >>> exit()
  104. Closing profile tool ...
  105. [rr186@spectre12 1M_pre_ms_to_wd]$ ls
  106. checks.md5 final_profile.data inlist mesa_dir.rb plot.py rn
  107. ck get-pip.py inlist_1.0 mk plotters src
  108. clean grid6.mp4 LOGS photos png star
  109. final.mod hr.mp4 make plot_data re
  110. [rr186@spectre12 1M_pre_ms_to_wd]$ ls ../..
  111. 2nd year file.txt NuGridpy-0.1.6401-py2.7.egg
  112. anaconda2 finalproject1 pair
  113. Anaconda2-4.3.1-Linux-x86_64.sh include pgplot
  114. Assess learning py
  115. bin lib py_mesa_reader
  116. core.11526 lib64 README
  117. core.11701 libexec share
  118. cwork __MACOSX site.py
  119. Desktop man site.pyc
  120. Downloads matplotlib tutorial
  121. easy-install.pth mesa
  122. extern MesaWorkshop
  123. [rr186@spectre12 1M_pre_ms_to_wd]$ ls ../../mesa/s
  124. sample/ star/ svnup
  125. [rr186@spectre12 1M_pre_ms_to_wd]$ ls ~
  126. 2nd year file.txt NuGridpy-0.1.6401-py2.7.egg
  127. anaconda2 finalproject1 pair
  128. Anaconda2-4.3.1-Linux-x86_64.sh include pgplot
  129. Assess learning py
  130. bin lib py_mesa_reader
  131. core.11526 lib64 README
  132. core.11701 libexec share
  133. cwork __MACOSX site.py
  134. Desktop man site.pyc
  135. Downloads matplotlib tutorial
  136. easy-install.pth mesa
  137. extern MesaWorkshop
  138. [rr186@spectre12 1M_pre_ms_to_wd]$ ls ~/py_mesa_reader/
  139. .git/ mesa_reader/ README.md setup.py
  140. [rr186@spectre12 1M_pre_ms_to_wd]$ cp -R ~/py_mesa_reader/mesa_reader/ .
  141. [rr186@spectre12 1M_pre_ms_to_wd]$ ls
  142. checks.md5 final_profile.data inlist mesa_dir.rb plot_data re
  143. ck get-pip.py inlist_1.0 mesa_reader plot.py rn
  144. clean grid6.mp4 LOGS mk plotters src
  145. final.mod hr.mp4 make photos png star
  146. [rr186@spectre12 1M_pre_ms_to_wd]$ python
  147. Python 2.7.13 |Anaconda 4.3.1 (64-bit)| (default, Dec 20 2016, 23:09:15)
  148. [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
  149. Type "help", "copyright", "credits" or "license" for more information.
  150. Anaconda is brought to you by Continuum Analytics.
  151. Please check out: http://continuum.io/thanks and https://anaconda.org
  152. >>> import mesa_reader
  153. >>> p = profile_data()
  154. Traceback (most recent call last):
  155. File "<stdin>", line 1, in <module>
  156. NameError: name 'profile_data' is not defined
  157. >>> l = MesaLogDir("./LOGS")
  158. Traceback (most recent call last):
  159. File "<stdin>", line 1, in <module>
  160. NameError: name 'MesaLogDir' is not defined
  161. >>> l = mesa_reader.MesaLogDir("./LOGS")
  162. >>> p = l.profile.data()
  163. Traceback (most recent call last):
  164. File "<stdin>", line 1, in <module>
  165. AttributeError: MesaLogDir instance has no attribute 'profile'
  166. >>> p = l.profile_data()
  167. >>> xlabel("Radius")
  168. Traceback (most recent call last):
  169. File "<stdin>", line 1, in <module>
  170. NameError: name 'xlabel' is not defined
  171. >>> %pylab
  172. File "<stdin>", line 1
  173. %pylab
  174. ^
  175. SyntaxError: invalid syntax
  176. >>> exit
  177. Use exit() or Ctrl-D (i.e. EOF) to exit
  178. >>>
  179. [rr186@spectre12 1M_pre_ms_to_wd]$ ipython
  180. Python 2.7.13 |Anaconda 4.3.1 (64-bit)| (default, Dec 20 2016, 23:09:15)
  181. Type "copyright", "credits" or "license" for more information.
  182.  
  183. IPython 5.1.0 -- An enhanced Interactive Python.
  184. ? -> Introduction and overview of IPython's features.
  185. %quickref -> Quick reference.
  186. help -> Python's own help system.
  187. object? -> Details about 'object', use 'object??' for extra details.
  188.  
  189. In [1]: %pylab
  190. Using matplotlib backend: Qt5Agg
  191. Populating the interactive namespace from numpy and matplotlib
  192.  
  193. In [2]: failed to get the current screen resources
  194. QXcbConnection: XCB error: 170 (Unknown), sequence: 164, resource id: 90, major0
  195. In [2]:
  196.  
  197. In [2]: import mesa_reader as mr
  198.  
  199. In [3]: l = MesaLogDir("./LOGS")
  200. ---------------------------------------------------------------------------
  201. NameError Traceback (most recent call last)
  202. <ipython-input-3-8d3e882c1434> in <module>()
  203. ----> 1 l = MesaLogDir("./LOGS")
  204.  
  205. NameError: name 'MesaLogDir' is not defined
  206.  
  207. In [4]: l = mr.MesaLogDir("./LOGS")
  208.  
  209. In [5]: p = l.profile_data()
  210.  
  211. In [6]: p
  212. Out[6]: <mesa_reader.MesaData instance at 0x2aaad646b758>
  213.  
  214. In [7]: p.Rho
  215. Out[7]:
  216. array([ 2.13518742e-09, 2.13518742e-09, 2.13518743e-09, ...,
  217. 3.65829961e+06, 3.65843063e+06, 3.65854067e+06])
  218.  
  219. In [8]: import matplotlib
  220.  
  221. In [9]: plot(p.Rho)
  222. Out[9]: [<matplotlib.lines.Line2D at 0x2aaad64d98d0>]
  223.  
  224. In [10]:
  225.  
  226. In [10]: plot.loglog(p.Rho)
  227. ---------------------------------------------------------------------------
  228. AttributeError Traceback (most recent call last)
  229. <ipython-input-10-6c19130d10c9> in <module>()
  230. ----> 1 plot.loglog(p.Rho)
  231.  
  232. AttributeError: 'function' object has no attribute 'loglog'
  233.  
  234. In [11]: plt.yscale('log')
  235.  
  236. In [12]: plt.xscale('log')
  237.  
  238. In [13]: plot(p.Rho)
  239. Out[13]: [<matplotlib.lines.Line2D at 0x2aaadf4c8f50>]
  240.  
  241. In [14]:
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