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namd2_tut2_log

May 7th, 2015
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  1. Charmrun> IBVERBS version of charmrun
  2. Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
  3. Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
  4. Charm++> scheduler running in netpoll mode.
  5. CharmLB> Load balancer assumes all CPUs are same.
  6. Charm++> cpu affinity enabled.
  7. Charm++> Running on 6 unique compute nodes (64-way SMP).
  8. Charm++> cpu topology info is gathered in 0.035 seconds.
  9. Info: NAMD 2.10 for Linux-x86_64-ibverbs
  10. Info:
  11. Info: Please visit http://www.ks.uiuc.edu/Research/namd/
  12. Info: for updates, documentation, and support information.
  13. Info:
  14. Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
  15. Info: in all publications reporting results obtained with NAMD.
  16. Info:
  17. Info: Based on Charm++/Converse 60601 for net-linux-x86_64-ibverbs-iccstatic
  18. Info: Built Tue Dec 9 15:33:59 CST 2014 by jim on dakar.ks.uiuc.edu
  19. Info: 1 NAMD 2.10 Linux-x86_64-ibverbs 128 hydra-1 amylin
  20. Info: Running on 128 processors, 128 nodes, 6 physical nodes.
  21. Info: CPU topology information available.
  22. Info: Charm++/Converse parallel runtime startup completed at 0.119344 s
  23. Info: 99.0977 MB of memory in use based on /proc/self/stat
  24. Info: Configuration file is tut2.conf
  25. Info: Working in the current directory /home/local/amylin/namd_runs/tut2_alw
  26. TCL: Suspending until startup complete.
  27. Info: SIMULATION PARAMETERS:
  28. Info: TIMESTEP 2
  29. Info: NUMBER OF STEPS 0
  30. Info: STEPS PER CYCLE 10
  31. Info: PERIODIC CELL BASIS 1 61.567 0 0
  32. Info: PERIODIC CELL BASIS 2 0 62.362 0
  33. Info: PERIODIC CELL BASIS 3 0 0 66.264
  34. Info: PERIODIC CELL CENTER 30.8211 29.1624 17.7819
  35. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
  36. Info: LOAD BALANCER Centralized
  37. Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
  38. Info: LDB PERIOD 2000 steps
  39. Info: FIRST LDB TIMESTEP 50
  40. Info: LAST LDB TIMESTEP -1
  41. Info: LDB BACKGROUND SCALING 1
  42. Info: HOM BACKGROUND SCALING 1
  43. Info: PME BACKGROUND SCALING 1
  44. Info: REMOVING PATCHES FROM PROCESSOR 0
  45. Info: MIN ATOMS PER PATCH 40
  46. Info: INITIAL TEMPERATURE 310
  47. Info: CENTER OF MASS MOVING INITIALLY? NO
  48. Info: DIELECTRIC 1
  49. Info: EXCLUDE SCALED ONE-FOUR
  50. Info: 1-4 ELECTROSTATICS SCALED BY 1
  51. Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
  52. Info: DCD FILENAME tut2-run.dcd
  53. Info: DCD FREQUENCY 100
  54. Info: DCD FIRST STEP 100
  55. Info: DCD FILE WILL CONTAIN UNIT CELL DATA
  56. Info: XST FILENAME tut2-run.xst
  57. Info: XST FREQUENCY 100
  58. Info: NO VELOCITY DCD OUTPUT
  59. Info: NO FORCE DCD OUTPUT
  60. Info: OUTPUT FILENAME tut2-run
  61. Info: BINARY OUTPUT FILES WILL BE USED
  62. Info: RESTART FILENAME tut2-run.restart
  63. Info: RESTART FREQUENCY 100
  64. Info: BINARY RESTART FILES WILL BE USED
  65. Info: SWITCHING ACTIVE
  66. Info: SWITCHING ON 10
  67. Info: SWITCHING OFF 12
  68. Info: PAIRLIST DISTANCE 14
  69. Info: PAIRLIST SHRINK RATE 0.01
  70. Info: PAIRLIST GROW RATE 0.01
  71. Info: PAIRLIST TRIGGER 0.3
  72. Info: PAIRLISTS PER CYCLE 2
  73. Info: PAIRLISTS ENABLED
  74. Info: MARGIN 0.99
  75. Info: HYDROGEN GROUP CUTOFF 2.5
  76. Info: PATCH DIMENSION 17.49
  77. Info: ENERGY OUTPUT STEPS 100
  78. Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
  79. Info: TIMING OUTPUT STEPS 1000
  80. Info: PRESSURE OUTPUT STEPS 100
  81. Info: INTERACTIVE MD ACTIVE
  82. Info: INTERACTIVE MD PORT 3000
  83. Info: INTERACTIVE MD FREQ 1
  84. Info: LANGEVIN DYNAMICS ACTIVE
  85. Info: LANGEVIN TEMPERATURE 310
  86. Info: LANGEVIN USING BBK INTEGRATOR
  87. Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
  88. Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
  89. Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
  90. Info: TARGET PRESSURE IS 1.01325 BAR
  91. Info: OSCILLATION PERIOD IS 100 FS
  92. Info: DECAY TIME IS 50 FS
  93. Info: PISTON TEMPERATURE IS 310 K
  94. Info: PRESSURE CONTROL IS GROUP-BASED
  95. Info: INITIAL STRAIN RATE IS 0 0 0
  96. Info: CELL FLUCTUATION IS ANISOTROPIC
  97. Info: PARTICLE MESH EWALD (PME) ACTIVE
  98. Info: PME TOLERANCE 1e-06
  99. Info: PME EWALD COEFFICIENT 0.257952
  100. Info: PME INTERPOLATION ORDER 4
  101. Info: PME GRID DIMENSIONS 64 64 72
  102. Info: PME MAXIMUM GRID SPACING 1
  103. Info: Attempting to read FFTW data from FFTW_NAMD_2.10_Linux-x86_64-ibverbs.txt
  104. Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
  105. Info: Writing FFTW data to FFTW_NAMD_2.10_Linux-x86_64-ibverbs.txt
  106. Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
  107. Info: USING VERLET I (r-RESPA) MTS SCHEME.
  108. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
  109. Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
  110. Info: RIGID BONDS TO HYDROGEN : ALL
  111. Info: ERROR TOLERANCE : 1e-08
  112. Info: MAX ITERATIONS : 100
  113. Info: RIGID WATER USING SETTLE ALGORITHM
  114. Info: RANDOM NUMBER SEED 1431022278
  115. Info: USE HYDROGEN BONDS? NO
  116. Info: COORDINATE PDB solvate.pdb
  117. Info: STRUCTURE FILE solvate.psf
  118. Info: PARAMETER file: CHARMM format!
  119. Info: PARAMETERS par_all27_prot_lipid_na.inp
  120. Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
  121.  
  122. Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
  123. PREVIOUS VALUES k=130 theta0=107.5 k_ub=0 r_ub=0
  124. USING VALUES k=130 theta0=107 k_ub=0 r_ub=0
  125. Info: SUMMARY OF PARAMETERS:
  126. Info: 307 BONDS
  127. Info: 769 ANGLES
  128. Info: 1254 DIHEDRAL
  129. Info: 81 IMPROPER
  130. Info: 6 CROSSTERM
  131. Info: 190 VDW
  132. Info: 0 VDW_PAIRS
  133. Info: 0 NBTHOLE_PAIRS
  134. Info: TIME FOR READING PSF FILE: 0.355796
  135. Info: TIME FOR READING PDB FILE: 0.0494871
  136. Info:
  137. Info: ****************************
  138. Info: STRUCTURE SUMMARY:
  139. Info: 23410 ATOMS
  140. Info: 16023 BONDS
  141. Info: 9650 ANGLES
  142. Info: 3293 DIHEDRALS
  143. Info: 204 IMPROPERS
  144. Info: 74 CROSSTERMS
  145. Info: 0 EXCLUSIONS
  146. Info: 22808 RIGID BONDS
  147. Info: 47422 DEGREES OF FREEDOM
  148. Info: 7995 HYDROGEN GROUPS
  149. Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
  150. Info: 7995 MIGRATION GROUPS
  151. Info: 4 ATOMS IN LARGEST MIGRATION GROUP
  152. Info: TOTAL MASS = 141753 amu
  153. Info: TOTAL CHARGE = 1.0021e-06 e
  154. Info: MASS DENSITY = 0.92522 g/cm^3
  155. Info: ATOM DENSITY = 0.0920144 atoms/A^3
  156. Info: *****************************
  157. Info:
  158. Info: Entering startup at 0.597706 s, 107.484 MB of memory in use
  159. Info: Startup phase 0 took 0.00048399 s, 107.484 MB of memory in use
  160. Info: ADDED 28937 IMPLICIT EXCLUSIONS
  161. Info: Startup phase 1 took 0.596464 s, 112.309 MB of memory in use
  162. Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
  163. Info: NONBONDED TABLE SIZE: 769 POINTS
  164. Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
  165. Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
  166. Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
  167. Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
  168. Info: Startup phase 2 took 0.00318694 s, 113.68 MB of memory in use
  169. Info: Startup phase 3 took 0.000310898 s, 113.68 MB of memory in use
  170. Info: Startup phase 4 took 0.000774145 s, 113.859 MB of memory in use
  171. Info: Startup phase 5 took 0.000302792 s, 113.859 MB of memory in use
  172. Info: PATCH GRID IS 7 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
  173. Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY
  174. Info: REMOVING COM VELOCITY 0.0423901 -0.0038836 -0.0517072
  175. Info: LARGEST PATCH (16) HAS 408 ATOMS
  176. Info: TORUS A SIZE 128 USING 0 1 2 3 4 5
  177. Info: TORUS B SIZE 1 USING 0
  178. Info: TORUS C SIZE 1 USING 0
  179. Info: TORUS MINIMAL MESH SIZE IS 6 BY 1 BY 1
  180. Info: Placed 93.6508% of base nodes on same physical node as patch
  181. Info: Startup phase 6 took 0.0183611 s, 118.934 MB of memory in use
  182. Info: PME using 32 and 32 processors for FFT and reciprocal sum.
  183. Info: PME GRID LOCATIONS: 18 19 20 21 22 23 42 43 44 45 ...
  184. Info: PME TRANS LOCATIONS: 6 7 8 9 10 11 30 31 32 33 ...
  185. Info: PME USING 32 GRID NODES AND 32 TRANS NODES
  186. Info: Startup phase 7 took 0.00722313 s, 118.934 MB of memory in use
  187. Info: Startup phase 8 took 0.00290489 s, 119.121 MB of memory in use
  188. LDB: Central LB being created...
  189. Info: Startup phase 9 took 0.00150204 s, 119.121 MB of memory in use
  190. Info: CREATING 2205 COMPUTE OBJECTS
  191. Info: Interactive MD listening on port 3000.
  192. Info: Startup phase 10 took 0.00198007 s, 119.121 MB of memory in use
  193. Info: useSync: 1 useProxySync: 0
  194. Info: Startup phase 11 took 0.000352859 s, 119.121 MB of memory in use
  195. Info: Startup phase 12 took 8.60691e-05 s, 119.121 MB of memory in use
  196. Info: Finished startup at 1.23164 s, 119.121 MB of memory in use
  197.  
  198. TCL: Minimizing for 500 steps
  199. PRESSURE: 0 5.63084e+06 1.1698e+07 9.59469e+06 1.1698e+07 2.46061e+07 2.04317e+07 9.59469e+06 2.04317e+07 2.3612e+08
  200. GPRESSURE: 0 5.63046e+06 1.16973e+07 9.59467e+06 1.16973e+07 2.46053e+07 2.04311e+07 9.5944e+06 2.04318e+07 2.36123e+08
  201. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
  202. ENERGY: 0 7135.6061 2469.8713 263.9440 10.7318 -77937.259
  203. 0 81250017.4108 0.0000 0.0000 0.0000 81181960.3051 0.0000 81181960.3051 81181960.3051 0.0000 88785724.5439 88786370.5388 254416.7208 88785724.5439 88786370.5388
  204.  
  205. OPENING EXTENDED SYSTEM TRAJECTORY FILE
  206. MINIMIZER SLOWLY MOVING 64 ATOMS WITH BAD CONTACTS DOWNHILL
  207. PRESSURE: 1 226460 415643 169104 415643 799037 348028 169104 348028 1.72738e+07
  208. GPRESSURE: 1 227151 415200 169431 415093 799843 347526 168859 348544 1.72771e+07
  209. ENERGY: 1 7136.6146 2469.4022 264.0604 10.9865 -78541.4091 5589061.6541 0.0000 0.0000 0.0000 5520401.3086 0.0000 5520401.3086 5520401.3086 0.0000 6099760.6978 6101355.8161 254416.7208 6099760.6978 6101355.8161
  210.  
  211. MINIMIZER SLOWLY MOVING 50 ATOMS WITH BAD CONTACTS DOWNHILL
  212. The last position output (seq=1) takes 0.001 seconds, 119.121 MB of memory in use
  213. PRESSURE: 2 18152.9 33769 243.984 33769 60600 3028.03 243.984 3028.03 2.08337e+06
  214. GPRESSURE: 2 20003.4 33907.1 618.981 33938.6 62947.5 2555.28 200.226 3640.16 2.08574e+06
  215. ENERGY: 2 7136.7508 2469.8106 264.0604 10.9865 -78852.9306 668785.5723 0.0000 0.0000 0.0000 599814.2500 0.0000 599814.2500 599814.2500 0.0000 720707.9365 722896.1401 254416.7208 720707.9365 722896.1401
  216. [...]
  217.  
  218. [...]
  219.  
  220. [...]
  221.  
  222. [...]
  223.  
  224. [...]
  225.  
  226. [...]
  227.  
  228. WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 300
  229. LINE MINIMIZER BRACKET: DX 0.00119077 8.87972e-05 DU -60.5588 0.321072 DUDX -101481 -165.17 7420.56
  230. WRITING COORDINATES TO DCD FILE tut2-run.dcd AT STEP 300
  231. WRITING COORDINATES TO RESTART FILE AT STEP 300
  232. FINISHED WRITING RESTART COORDINATES
  233. WRITING VELOCITIES TO RESTART FILE AT STEP 300
  234. FINISHED WRITING RESTART VELOCITIES
  235. The last velocity output (seq=300) takes 0.001 seconds, 122.793 MB of memory in use
  236. PRESSURE: 301 -6942.71 -20.7237 -2.42685 -20.7237 -6897.49 71.912 -2.42685 71.912 -7058.36
  237. GPRESSURE: 301 -7004.07 -17.83 20.2445 -33.008 -6971.72 67.014 -7.6035 75.3538 -7128.76
  238. ENERGY: 301 3049.1382 2167.4278 229.0257 8.6775 -106366.1618 9530.5969 0.0000 0.0000 0.0000 -91381.2957 0.0000 -91381.2957 -91381.2957 0.0000 -6966.1857 -7034.8512 254416.7208 -6966.1857 -7034.8512
  239.  
  240. LINE MINIMIZER BRACKET: DX 0.00119077 8.87972e-06 DU -60.5588 0.00293496 DUDX -101481 -165.17 593.138
  241. PRESSURE: 302 -6942.87 -20.8812 -2.29513 -20.8812 -6897.49 72.0257 -2.29513 72.0257 -7058.44
  242. GPRESSURE: 302 -7004.07 -17.961 20.3121 -33.1101 -6971.57 67.1228 -7.53643 75.5033 -7128.56
  243. ENERGY: 302 3048.9750 2167.4166 229.0209 8.6750 -106365.9788 9530.5930 0.0000 0.0000 0.0000 -91381.2983 0.0000 -91381.2983 -91381.2983 0.0000 -6966.2680 -7034.7334 254416.7208 -6966.2680 -7034.7334
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