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  1. [11:34:32] Project: 6015 (Run 1, Clone 236, Gen 75)
  2. [11:34:32]
  3. [11:34:32] Assembly optimizations on if available.
  4. [11:34:32] Entering M.D.
  5. Starting 4 threads
  6. NNODES=4, MYRANK=1, HOSTNAME=thread #1
  7. NNODES=4, MYRANK=0, HOSTNAME=thread #0
  8. NNODES=4, MYRANK=3, HOSTNAME=thread #3
  9. NNODES=4, MYRANK=2, HOSTNAME=thread #2
  10. Reading file work/wudata_07.tpr, VERSION 4.0.99_development_20090605 (single precision)
  11. Note: tpx file_version 68, software version 70
  12. Making 1D domain decomposition 4 x 1 x 1
  13. starting mdrun 'Protein in POPC'
  14. 38000004 steps, 76000.0 ps (continuing from step 37500004, 75000.0 ps).
  15.  
  16. t = 75000.008 ps: Water molecule starting at atom 61581 can not be settled.
  17. Check for bad contacts and/or reduce the timestep.
  18.  
  19. t = 75000.010 ps: Water molecule starting at atom 69522 can not be settled.
  20. Check for bad contacts and/or reduce the timestep.
  21.  
  22. t = 75000.010 ps: Water molecule starting at atom 40203 can not be settled.
  23. Check for bad contacts and/or reduce the timestep.
  24. [11:34:39] Completed 0 out of 500000 steps (0%)
  25. [11:34:39] CoreStatus = 0 (0)
  26. [11:34:39] Sending work to server
  27. [11:34:39] Project: 6015 (Run 1, Clone 236, Gen 75)
  28. [11:34:39] - Error: Could not get length of results file work/wuresults_07.dat
  29. [11:34:39] - Error: Could not read unit 07 file. Removing from queue.
  30. [11:34:39] - Preparing to get new work unit...
  31. [11:34:39] Cleaning up work directory
  32. [11:35:01] + Attempting to get work packet
  33. [11:35:01] Passkey found
  34. [11:35:01] - Connecting to assignment server
  35. [11:35:03] - Successful: assigned to (130.237.232.140).
  36. [11:35:03] + News From Folding@Home: Welcome to Folding@Home
  37. [11:35:03] Loaded queue successfully.
  38. [11:35:15] + Closed connections
  39. [11:35:20]
  40. [11:35:20] + Processing work unit
  41. [11:35:20] Core required: FahCore_a3.exe
  42. [11:35:20] Core found.
  43. [11:35:20] Working on queue slot 08 [June 6 11:35:20 UTC]
  44. [11:35:20] + Working ...
  45. [11:35:20]
  46. [11:35:20] *------------------------------*
  47. [11:35:20] Folding@Home Gromacs SMP Core
  48. [11:35:20] Version 2.21 (May 10, 2010)
  49. [11:35:20]
  50. [11:35:20] Preparing to commence simulation
  51. [11:35:20] - Ensuring status. Please wait.
  52. [11:35:29] - Looking at optimizations...
  53. [11:35:29] - Working with standard loops on this execution.
  54. [11:35:29] - Created dyn
  55. [11:35:29] - Files status OK
  56. [11:35:30] - Expanded 1797980 -> 2392545 (decompressed 133.0 percent)
  57. [11:35:30] Called DecompressByteArray: compressed_data_size=1797980 data_size=2392545, decompressed_data_size=2392545 diff=0
  58. [11:35:30] - Digital signature verified
  59. [11:35:30]
  60. [11:35:30] Project: 6015 (Run 1, Clone 236, Gen 75)
  61. [11:35:30]
  62. [11:35:30] Entering M.D.
  63. Starting 4 threads
  64. NNODES=4, MYRANK=0, HOSTNAME=thread #0
  65. NNODES=4, MYRANK=3, HOSTNAME=thread #3
  66. NNODES=4, MYRANK=1, HOSTNAME=thread #1
  67. NNODES=4, MYRANK=2, HOSTNAME=thread #2
  68. Reading file work/wudata_08.tpr, VERSION 4.0.99_development_20090605 (single precision)
  69. Note: tpx file_version 68, software version 70
  70. Making 1D domain decomposition 4 x 1 x 1
  71. starting mdrun 'Protein in POPC'
  72. 38000004 steps, 76000.0 ps (continuing from step 37500004, 75000.0 ps).
  73.  
  74. t = 75000.008 ps: Water molecule starting at atom 61581 can not be settled.
  75. Check for bad contacts and/or reduce the timestep.
  76. [11:35:36] Completed 0 out of 500000 steps (0%)
  77.  
  78. Step 37500005, time 75000 (ps) LINCS WARNING
  79. relative constraint deviation after LINCS:
  80. rms 114074.825128, max 12513528.000000 (between atoms 16886 and 16887)
  81. bonds that rotated more than 90 degrees:
  82. atom 1 atom 2 angle previous, current, constraint length
  83.  
  84. Step 37500005, time 75000 (ps) LINCS WARNING
  85. relative constraint deviation after LINCS:
  86. rms 1333368.277217, max 107107288.000000 (between atoms 16886 and 16883)
  87. bonds that rotated more than 90 degrees:
  88. atom 1 atom 2 angle previous, current, constraint length
  89. 16890 16893 105.4 0.1610 1367.0081 0.1610
  90. 16890 16892 101.8 0.1480 1367.0148 0.1480
  91. 16890 16891 90.9 0.1480 1367.0176 0.1480
  92. 16893 16890 105.4 0.1610 1367.0081 0.1610
  93. 16892 16890 101.8 0.1480 1367.0148 0.1480
  94. 16891 16890 90.9 0.1480 1367.0176 0.1480
  95.  
  96. t = 75000.010 ps: Water molecule starting at atom 40203 can not be settled.
  97. Check for bad contacts and/or reduce the timestep.
  98.  
  99. t = 75000.010 ps: Water molecule starting at atom 69522 can not be settled.
  100. Check for bad contacts and/or reduce the timestep.
  101. [11:35:37] CoreStatus = 0 (0)
  102. [11:35:37] Sending work to server
  103. [11:35:37] Project: 6015 (Run 1, Clone 236, Gen 75)
  104. [11:35:37] - Error: Could not get length of results file work/wuresults_08.dat
  105. [11:35:37] - Error: Could not read unit 08 file. Removing from queue.
  106. [11:35:37] - Preparing to get new work unit...
  107. [11:35:37] Cleaning up work directory
  108. [11:35:58] + Attempting to get work packet
  109. [11:35:58] Passkey found
  110. [11:35:58] - Connecting to assignment server
  111. [11:36:00] - Successful: assigned to (130.237.232.140).
  112. [11:36:00] + News From Folding@Home: Welcome to Folding@Home
  113. [11:36:00] Loaded queue successfully.
  114. [11:36:10] + Closed connections
  115. [11:36:15]
  116. [11:36:15] + Processing work unit
  117. [11:36:15] Core required: FahCore_a3.exe
  118. [11:36:15] Core found.
  119. [11:36:15] Working on queue slot 09 [June 6 11:36:15 UTC]
  120. [11:36:15] + Working ...
  121. [11:36:15]
  122. [11:36:15] *------------------------------*
  123. [11:36:15] Folding@Home Gromacs SMP Core
  124. [11:36:15] Version 2.21 (May 10, 2010)
  125. [11:36:15]
  126. [11:36:15] Preparing to commence simulation
  127. [11:36:15] - Ensuring status. Please wait.
  128. [11:36:24] - Looking at optimizations...
  129. [11:36:24] - Working with standard loops on this execution.
  130. [11:36:24] - Created dyn
  131. [11:36:24] - Files status OK
  132. [11:36:25] - Expanded 1797980 -> 2392545 (decompressed 133.0 percent)
  133. [11:36:25] Called DecompressByteArray: compressed_data_size=1797980 data_size=2392545, decompressed_data_size=2392545 diff=0
  134. [11:36:25] - Digital signature verified
  135. [11:36:25]
  136. [11:36:25] Project: 6015 (Run 1, Clone 236, Gen 75)
  137. [11:36:25]
  138. [11:36:25] Entering M.D.
  139. Starting 4 threads
  140. NNODES=4, MYRANK=0, HOSTNAME=thread #0
  141. NNODES=4, MYRANK=3, HOSTNAME=thread #3
  142. NNODES=4, MYRANK=1, HOSTNAME=thread #1
  143. NNODES=4, MYRANK=2, HOSTNAME=thread #2
  144. Reading file work/wudata_09.tpr, VERSION 4.0.99_development_20090605 (single precision)
  145. Note: tpx file_version 68, software version 70
  146. Making 1D domain decomposition 4 x 1 x 1
  147. starting mdrun 'Protein in POPC'
  148. 38000004 steps, 76000.0 ps (continuing from step 37500004, 75000.0 ps).
  149. [11:36:31] Completed 0 out of 500000 steps (0%)
  150.  
  151. t = 75000.008 ps: Water molecule starting at atom 61581 can not be settled.
  152. Check for bad contacts and/or reduce the timestep.
  153.  
  154. t = 75000.010 ps: Water molecule starting at atom 76296 can not be settled.
  155. Check for bad contacts and/or reduce the timestep.
  156.  
  157. t = 75000.010 ps: Water molecule starting at atom 49758 can not be settled.
  158. Check for bad contacts and/or reduce the timestep.
  159. [11:36:31] CoreStatus = 0 (0)
  160. [11:36:31] Sending work to server
  161. [11:36:31] Project: 6015 (Run 1, Clone 236, Gen 75)
  162. [11:36:31] - Error: Could not get length of results file work/wuresults_09.dat
  163. [11:36:31] - Error: Could not read unit 09 file. Removing from queue.
  164. [11:36:31] - Preparing to get new work unit...
  165. [11:36:31] Cleaning up work directory
  166. [11:36:53] + Attempting to get work packet
  167. [11:36:53] Passkey found
  168. [11:36:53] - Connecting to assignment server
  169. [11:36:55] - Successful: assigned to (130.237.232.140).
  170. [11:36:55] + News From Folding@Home: Welcome to Folding@Home
  171. [11:36:55] Loaded queue successfully.
  172. [11:37:05] + Closed connections
  173. [11:37:10]
  174. [11:37:10] + Processing work unit
  175. [11:37:10] Core required: FahCore_a3.exe
  176. [11:37:10] Core found.
  177. [11:37:10] Working on queue slot 00 [June 6 11:37:10 UTC]
  178. [11:37:10] + Working ...
  179. [11:37:10]
  180. [11:37:10] *------------------------------*
  181. [11:37:10] Folding@Home Gromacs SMP Core
  182. [11:37:10] Version 2.21 (May 10, 2010)
  183. [11:37:10]
  184. [11:37:10] Preparing to commence simulation
  185. [11:37:10] - Ensuring status. Please wait.
  186. [11:37:19] - Looking at optimizations...
  187. [11:37:19] - Working with standard loops on this execution.
  188. [11:37:19] - Created dyn
  189. [11:37:19] - Files status OK
  190. [11:37:20] - Expanded 1797980 -> 2392545 (decompressed 133.0 percent)
  191. [11:37:20] Called DecompressByteArray: compressed_data_size=1797980 data_size=2392545, decompressed_data_size=2392545 diff=0
  192. [11:37:20] - Digital signature verified
  193. [11:37:20]
  194. [11:37:20] Project: 6015 (Run 1, Clone 236, Gen 75)
  195. [11:37:20]
  196. [11:37:20] Entering M.D.
  197. Starting 4 threads
  198. NNODES=4, MYRANK=3, HOSTNAME=thread #3
  199. NNODES=4, MYRANK=0, HOSTNAME=thread #0
  200. NNODES=4, MYRANK=1, HOSTNAME=thread #1
  201. NNODES=4, MYRANK=2, HOSTNAME=thread #2
  202. Reading file work/wudata_00.tpr, VERSION 4.0.99_development_20090605 (single precision)
  203. Note: tpx file_version 68, software version 70
  204. Making 1D domain decomposition 4 x 1 x 1
  205. starting mdrun 'Protein in POPC'
  206. 38000004 steps, 76000.0 ps (continuing from step 37500004, 75000.0 ps).
  207.  
  208. t = 75000.008 ps: Water molecule starting at atom 61581 can not be settled.
  209. Check for bad contacts and/or reduce the timestep.
  210. [11:37:26] Completed 0 out of 500000 steps (0%)
  211.  
  212. t = 75000.010 ps: Water molecule starting at atom 40203 can not be settled.
  213. Check for bad contacts and/or reduce the timestep.
  214.  
  215. t = 75000.010 ps: Water molecule starting at atom 69522 can not be settled.
  216. Check for bad contacts and/or reduce the timestep.
  217. [11:37:26] CoreStatus = 0 (0)
  218. [11:37:26] Sending work to server
  219. [11:37:26] Project: 6015 (Run 1, Clone 236, Gen 75)
  220. [11:37:26] - Error: Could not get length of results file work/wuresults_00.dat
  221. [11:37:26] - Error: Could not read unit 00 file. Removing from queue.
  222. [11:37:26] - Preparing to get new work unit...
  223. [11:37:26] Cleaning up work directory
  224. [11:37:48] + Attempting to get work packet
  225. [11:37:48] Passkey found
  226. [11:37:48] - Connecting to assignment server
  227. [11:37:49] - Successful: assigned to (130.237.232.140).
  228. [11:37:49] + News From Folding@Home: Welcome to Folding@Home
  229. [11:37:49] Loaded queue successfully.
  230. [11:38:00] + Closed connections
  231. [11:38:05]
  232. [11:38:05] + Processing work unit
  233. [11:38:05] Core required: FahCore_a3.exe
  234. [11:38:05] Core found.
  235. [11:38:05] Working on queue slot 01 [June 6 11:38:05 UTC]
  236. [11:38:05] + Working ...
  237. [11:38:05]
  238. [11:38:05] *------------------------------*
  239. [11:38:05] Folding@Home Gromacs SMP Core
  240. [11:38:05] Version 2.21 (May 10, 2010)
  241. [11:38:05]
  242. [11:38:05] Preparing to commence simulation
  243. [11:38:05] - Ensuring status. Please wait.
  244. [11:38:14] - Looking at optimizations...
  245. [11:38:14] - Working with standard loops on this execution.
  246. [11:38:14] - Created dyn
  247. [11:38:14] - Files status OK
  248. [11:38:15] - Expanded 1797980 -> 2392545 (decompressed 133.0 percent)
  249. [11:38:15] Called DecompressByteArray: compressed_data_size=1797980 data_size=2392545, decompressed_data_size=2392545 diff=0
  250. [11:38:15] - Digital signature verified
  251. [11:38:15]
  252. [11:38:15] Project: 6015 (Run 1, Clone 236, Gen 75)
  253. [11:38:15]
  254. [11:38:15] Entering M.D.
  255. Starting 4 threads
  256. NNODES=4, MYRANK=0, HOSTNAME=thread #0
  257. NNODES=4, MYRANK=1, HOSTNAME=thread #1
  258. NNODES=4, MYRANK=2, HOSTNAME=thread #2
  259. NNODES=4, MYRANK=3, HOSTNAME=thread #3
  260. Reading file work/wudata_01.tpr, VERSION 4.0.99_development_20090605 (single precision)
  261. Note: tpx file_version 68, software version 70
  262. Making 1D domain decomposition 4 x 1 x 1
  263. starting mdrun 'Protein in POPC'
  264. 38000004 steps, 76000.0 ps (continuing from step 37500004, 75000.0 ps).
  265.  
  266. t = 75000.008 ps: Water molecule starting at atom 61581 can not be settled.
  267. Check for bad contacts and/or reduce the timestep.
  268. [11:38:21] Completed 0 out of 500000 steps (0%)
  269.  
  270. t = 75000.010 ps: Water molecule starting at atom 76296 can not be settled.
  271. Check for bad contacts and/or reduce the timestep.
  272.  
  273. t = 75000.010 ps: Water molecule starting at atom 40203 can not be settled.
  274. Check for bad contacts and/or reduce the timestep.
  275. [11:38:21] CoreStatus = 0 (0)
  276. [11:38:21] Sending work to server
  277. [11:38:21] Project: 6015 (Run 1, Clone 236, Gen 75)
  278. [11:38:21] - Error: Could not get length of results file work/wuresults_01.dat
  279. [11:38:21] - Error: Could not read unit 01 file. Removing from queue.
  280. [11:38:21] - Preparing to get new work unit...
  281. [11:38:21] Cleaning up work directory
  282. [11:38:43] + Attempting to get work packet
  283. [11:38:43] Passkey found
  284. [11:38:43] - Connecting to assignment server
  285. [11:38:44] - Successful: assigned to (130.237.232.140).
  286. [11:38:44] + News From Folding@Home: Welcome to Folding@Home
  287. [11:38:45] Loaded queue successfully.
  288. [11:39:03] + Closed connections
  289. [11:39:08]
  290. [11:39:08] + Processing work unit
  291. [11:39:08] Core required: FahCore_a3.exe
  292. [11:39:08] Core found.
  293. [11:39:08] Working on queue slot 02 [June 6 11:39:08 UTC]
  294. [11:39:08] + Working ...
  295. [11:39:08]
  296. [11:39:08] *------------------------------*
  297. [11:39:08] Folding@Home Gromacs SMP Core
  298. [11:39:08] Version 2.21 (May 10, 2010)
  299. [11:39:08]
  300. [11:39:08] Preparing to commence simulation
  301. [11:39:08] - Ensuring status. Please wait.
  302. [11:39:17] - Looking at optimizations...
  303. [11:39:17] - Working with standard loops on this execution.
  304. [11:39:17] - Created dyn
  305. [11:39:17] - Files status OK
  306. [11:39:18] - Expanded 1797980 -> 2392545 (decompressed 133.0 percent)
  307. [11:39:18] Called DecompressByteArray: compressed_data_size=1797980 data_size=2392545, decompressed_data_size=2392545 diff=0
  308. [11:39:18] - Digital signature verified
  309. [11:39:18]
  310. [11:39:18] Project: 6015 (Run 1, Clone 236, Gen 75)
  311. [11:39:18]
  312. [11:39:18] Entering M.D.
  313. Starting 4 threads
  314. NNODES=4, MYRANK=3, HOSTNAME=thread #3
  315. NNODES=4, MYRANK=0, HOSTNAME=thread #0
  316. NNODES=4, MYRANK=2, HOSTNAME=thread #2
  317. NNODES=4, MYRANK=1, HOSTNAME=thread #1
  318. Reading file work/wudata_02.tpr, VERSION 4.0.99_development_20090605 (single precision)
  319. Note: tpx file_version 68, software version 70
  320. Making 1D domain decomposition 4 x 1 x 1
  321. starting mdrun 'Protein in POPC'
  322. 38000004 steps, 76000.0 ps (continuing from step 37500004, 75000.0 ps).
  323.  
  324. t = 75000.008 ps: Water molecule starting at atom 61581 can not be settled.
  325. Check for bad contacts and/or reduce the timestep.
  326. [11:39:24] Completed 0 out of 500000 steps (0%)
  327.  
  328. t = 75000.010 ps: Water molecule starting at atom 69522 can not be settled.
  329. Check for bad contacts and/or reduce the timestep.
  330.  
  331. t = 75000.010 ps: Water molecule starting at atom 40203 can not be settled.
  332. Check for bad contacts and/or reduce the timestep.
  333. [11:39:25] CoreStatus = 0 (0)
  334. [11:39:25] Sending work to server
  335. [11:39:25] Project: 6015 (Run 1, Clone 236, Gen 75)
  336. [11:39:25] - Error: Could not get length of results file work/wuresults_02.dat
  337. [11:39:25] - Error: Could not read unit 02 file. Removing from queue.
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