Advertisement
thesketh

AdAA log file

Nov 5th, 2018
114
0
Never
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 6.80 KB | None | 0 0
  1. Charm++>ofi> provider: psm2
  2. Charm++>ofi> control progress: 2
  3. Charm++>ofi> data progress: 2
  4. Charm++>ofi> maximum inject message size: 64
  5. Charm++>ofi> eager maximum message size: 65536 (maximum header size: 40)
  6. Charm++>ofi> cq entries count: 8
  7. Charm++>ofi> use inject: 1
  8. Charm++>ofi> maximum rma size: 4294967295
  9. Charm++>ofi> mr mode: 0x2
  10. Charm++>ofi> use memory pool: 0
  11. Charm++>ofi> use request cache: 0
  12. Charm++>ofi> number of pre-allocated recvs: 8
  13. Charm++>ofi> exchanging addresses over OFI
  14. Charm++> Running in non-SMP mode: numPes 40
  15. Charm++> Using recursive bisection (scheme 3) for topology aware partitions
  16. Converse/Charm++ Commit ID: v6.8.2
  17. Warning> Randomization of virtual memory (ASLR) is turned on in the kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try running with '+isomalloc_sync'.
  18. CharmLB> Load balancer assumes all CPUs are same.
  19. Charm++> Running on 1 unique compute nodes (40-way SMP).
  20. Charm++> cpu topology info is gathered in 0.045 seconds.
  21. Info: NAMD 2.12 for Linux-x86_64
  22. Info:
  23. Info: Please visit http://www.ks.uiuc.edu/Research/namd/
  24. Info: for updates, documentation, and support information.
  25. Info:
  26. Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
  27. Info: in all publications reporting results obtained with NAMD.
  28. Info:
  29. Info: Based on Charm++/Converse 60800 for ofi-linux-x86_64-ifort-icc
  30. Info: Running on 40 processors, 40 nodes, 1 physical nodes.
  31. Info: CPU topology information available.
  32. Info: Charm++/Converse parallel runtime startup completed at 0.189006 s
  33. Info: 308.742 MB of memory in use based on /proc/self/stat
  34. Info: Configuration file is AdAA.conf
  35. Info: Working in the current directory /users/travis/Cameron/AdAA
  36. TCL: Suspending until startup complete.
  37. Info: SIMULATION PARAMETERS:
  38. Info: TIMESTEP 2
  39. Info: NUMBER OF STEPS 0
  40. Info: STEPS PER CYCLE 10
  41. Info: PERIODIC CELL BASIS 1 40.277 0 0
  42. Info: PERIODIC CELL BASIS 2 0 34.853 0
  43. Info: PERIODIC CELL BASIS 3 0 0 34.758
  44. Info: PERIODIC CELL CENTER 0.294979 0.528749 0.132491
  45. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
  46. Info: LOAD BALANCER Centralized
  47. Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
  48. Info: LDB PERIOD 2000 steps
  49. Info: FIRST LDB TIMESTEP 50
  50. Info: LAST LDB TIMESTEP -1
  51. Info: LDB BACKGROUND SCALING 1
  52. Info: HOM BACKGROUND SCALING 1
  53. Info: MIN ATOMS PER PATCH 40
  54. Info: INITIAL TEMPERATURE 298
  55. Info: CENTER OF MASS MOVING INITIALLY? NO
  56. Info: DIELECTRIC 1
  57. Info: EXCLUDE SCALED ONE-FOUR
  58. Info: 1-4 ELECTROSTATICS SCALED BY 1
  59. Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
  60. Info: DCD FILENAME AdAA.dcd
  61. Info: DCD FREQUENCY 2000
  62. Info: DCD FIRST STEP 2000
  63. Info: DCD FILE WILL CONTAIN UNIT CELL DATA
  64. Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
  65. Info: NO VELOCITY DCD OUTPUT
  66. Info: NO FORCE DCD OUTPUT
  67. Info: OUTPUT FILENAME AdAA
  68. Info: BINARY OUTPUT FILES WILL BE USED
  69. Info: RESTART FILENAME AdAA.restart
  70. Info: RESTART FREQUENCY 100
  71. Info: BINARY RESTART FILES WILL BE USED
  72. Info: SWITCHING ACTIVE
  73. Info: SWITCHING ON 10
  74. Info: SWITCHING OFF 12
  75. Info: PAIRLIST DISTANCE 14
  76. Info: PAIRLIST SHRINK RATE 0.01
  77. Info: PAIRLIST GROW RATE 0.01
  78. Info: PAIRLIST TRIGGER 0.3
  79. Info: PAIRLISTS PER CYCLE 2
  80. Info: PAIRLISTS ENABLED
  81. Info: MARGIN 2
  82. Info: HYDROGEN GROUP CUTOFF 2.5
  83. Info: PATCH DIMENSION 18.5
  84. Info: ENERGY OUTPUT STEPS 5000
  85. Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
  86. Info: TIMING OUTPUT STEPS 50000
  87. Info: PRESSURE OUTPUT STEPS 5000
  88. Info: LANGEVIN DYNAMICS ACTIVE
  89. Info: LANGEVIN TEMPERATURE 298
  90. Info: LANGEVIN USING BBK INTEGRATOR
  91. Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
  92. Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
  93. Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
  94. Info: TARGET PRESSURE IS 1.01325 BAR
  95. Info: OSCILLATION PERIOD IS 100 FS
  96. Info: DECAY TIME IS 50 FS
  97. Info: PISTON TEMPERATURE IS 298 K
  98. Info: PRESSURE CONTROL IS GROUP-BASED
  99. Info: INITIAL STRAIN RATE IS 0 0 0
  100. Info: CELL FLUCTUATION IS ISOTROPIC
  101. Info: USING VERLET I (r-RESPA) MTS SCHEME.
  102. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
  103. Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
  104. Info: RIGID BONDS TO HYDROGEN : ALL
  105. Info: ERROR TOLERANCE : 1e-08
  106. Info: MAX ITERATIONS : 100
  107. Info: RIGID WATER USING SETTLE ALGORITHM
  108. Info: RANDOM NUMBER SEED 1541429880
  109. Info: USE HYDROGEN BONDS? NO
  110. Info: COORDINATE PDB AdAA_wb.pdb
  111. Info: STRUCTURE FILE AdAA_wb.psf
  112. Info: PARAMETER file: CHARMM format!
  113. Info: PARAMETERS /users/travis/.charmm/par_all36_prot.prm
  114. Info: PARAMETERS /users/travis/.charmm/par_all36_carb.prm
  115. Info: PARAMETERS /users/travis/.charmm/par_all36_lipid.prm
  116. Info: PARAMETERS /users/travis/.charmm/par_all35_ethers.prm
  117. Info: PARAMETERS /users/travis/.charmm/par_all36_na.prm
  118. Info: PARAMETERS /users/travis/.charmm/par_all36_cgenff.prm
  119. Info: PARAMETERS /users/travis/.charmm/toppar_water_ions_namd.str
  120. Info: PARAMETERS /users/travis/.charmm/toppar_all36_prot_c36_d_aminoacids.str
  121. Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
  122. Info: SKIPPING rtf SECTION IN STREAM FILE
  123. Info: SKIPPING rtf SECTION IN STREAM FILE
  124. Info: SUMMARY OF PARAMETERS:
  125. Info: 991 BONDS
  126. Info: 2959 ANGLES
  127. Info: 7313 DIHEDRAL
  128. Info: 202 IMPROPER
  129. Info: 10 CROSSTERM
  130. Info: 370 VDW
  131. Info: 81 VDW_PAIRS
  132. Info: 0 NBTHOLE_PAIRS
  133. FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR CTD1 C NH1 CT1 (ATOMS 15 21 26 28)
  134. [0] Stack Traceback:
  135. [0:0] CmiAbortHelper+0x57 [0x12b06d7]
  136. [0:1] _Z8NAMD_diePKc+0x9d [0x66f31d]
  137. [0:2] _ZN10Parameters21assign_dihedral_indexEPcS0_S0_S0_P8dihedralii+0x233 [0xf5c0d3]
  138. [0:3] _ZN8Molecule13read_psf_fileEPcP10Parameters+0xcbb [0xed13db]
  139. [0:4] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x144 [0xecf2c4]
  140. [0:5] _ZN9NamdState13loadStructureEPKcS1_i+0x4dd [0xf244ed]
  141. [0:6] _ZN9NamdState14configListInitEP10ConfigList+0x332 [0xf26832]
  142. [0:7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0xc0 [0x103d5f0]
  143. [0:8] TclInvokeStringCommand+0x80 [0x2b1d52560550]
  144. [0:9] +0x34eb2 [0x2b1d52565eb2]
  145. [0:10] +0x35f1e [0x2b1d52566f1e]
  146. [0:11] Tcl_EvalEx+0x16 [0x2b1d52567446]
  147. [0:12] Tcl_FSEvalFileEx+0x202 [0x2b1d525cec12]
  148. [0:13] +0x47e81 [0x2b1d52578e81]
  149. [0:14] +0x34eb2 [0x2b1d52565eb2]
  150. [0:15] +0x35f1e [0x2b1d52566f1e]
  151. [0:16] Tcl_EvalEx+0x16 [0x2b1d52567446]
  152. [0:17] Tcl_FSEvalFileEx+0x202 [0x2b1d525cec12]
  153. [0:18] Tcl_EvalFile+0x27 [0x2b1d525ced77]
  154. [0:19] _ZN9ScriptTcl4loadEPc+0x10 [0x1039ad0]
  155. [0:20] main+0x4ca [0x68a04a]
  156. [0:21] __libc_start_main+0xf5 [0x2b1d532b6c05]
  157. [0:22] [0x5cf3e9]
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement