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  1. niksh@NX5-1:~/D1-D4/test$ ./MDis min.conf
  2. ===============================
  3. MDis version trunk
  4. (built Sep 7 2012 21:36:16)
  5. [With MPI support]
  6. ===============================
  7. Running on host 'NX5-1', Fri Sep 7 21:45:11 2012
  8.  
  9. Args: ./MDis min.conf
  10. ===============================
  11. Parsing 'min.conf' parameters file...
  12. device 0
  13. name d1_out00
  14. structure ../Build/psf/<name>.psf
  15. coordinates ../Build/pdb/<name>.pdb
  16. parameters ../charmmcommon/param19_eef1.inp
  17. topologies ../charmmcommon/toph19_eef1.inp
  18. paratype CHARMM19
  19. damping 0.15
  20. 1-4 scale
  21. scale14 0.4
  22. nbtype rdieshift
  23. nbcutoff 0.75
  24. nbswitch 0.65
  25. pairsfreq 100
  26. pairscutoff 1.2
  27. possiblepairsfreq 1000
  28. possiblepairscutoff 1.6
  29. pairslistextension 256
  30. RB_Enabled no
  31. sasa on
  32. sasaparameters ../charmmcommon/sasa_parameters.par
  33. sasapairslistcutoff 1.0
  34. sasapairsfreq 100
  35. repulsiveboundary off
  36. pbc off
  37. integrator sd
  38. timestep 0.001
  39. firstrun 1
  40. runnum 1
  41. numsteps 1000000
  42. seed 17171111
  43. temperature 0
  44. outputname dat/<name>_<run>_min.dat
  45. outputfreq 1000
  46. dcdfile dcd/<name>_<run>_min.dcd
  47. dcdfreq 10000
  48. restartcoord restart/<name>_restart_<run>_min.coord.pdb
  49. restartvel restart/<name>_restart_<run>_min.vel.pdb
  50. restartfreq 100000
  51. finalcoord pdb/<name>.pdb
  52. finalvel pdb/<name>_vel.pdb
  53. restartkey restart/<name>_restart.txt
  54. outputlegend dat/<name>_legend.txt
  55. Creating fictional parameter 'mpi_rank' with value '0'
  56. Using default value for parameter mpi_device_auto: 'mpi_device_auto' = 'NO'
  57. 'device' = '0'
  58. Using default value for parameter mpi_device_0: 'mpi_device_0' = '0'
  59. Creating fictional parameter 'mpi_device_current' with value '0'
  60. 'device' = '0'
  61. 'mpi_device_current' = '0'
  62. Using default value for parameter firststep: 'firststep' = '0'
  63. 'numsteps' = ' 1000000'
  64. Using default value for parameter totaltime: 'totaltime' = '-1.000000'
  65. 'timestep' = ' 0.001'
  66. Total simulation time is 1000.000061ps.
  67. Using default value for parameter run: 'run' = '-1'
  68. 'firstrun' = ' 1'
  69. 'runnum' = ' 1'
  70. Will run 1 trajectories, starting from trajectory 1
  71. .'seed' = ' 17171111'
  72. 'mpi_rank' = '0'
  73. 'structure' = ' ../Build/psf/<name>.psf'
  74. 'coordinates' = '../Build/pdb/<name>.pdb'
  75. Using default value for parameter velocities: 'velocities' = 'NONE'
  76. 'parameters' = ' ../charmmcommon/param19_eef1.inp'
  77. 'topologies' = ' ../charmmcommon/toph19_eef1.inp'
  78. 'paratype' = ' CHARMM19'
  79. 'restartkey' = ' restart/<name>_restart.txt'
  80. Using default value for parameter mpi_firstrun_auto: 'mpi_firstrun_auto' = 'YES'
  81. Creating fictional parameter 'restartcount' with value '0'
  82. Reading force-field data from '../charmmcommon/param19_eef1.inp'.
  83. Found:
  84. 87 bond types.
  85. 212 angle types.
  86. 47 dihedral types.
  87. 50 improper types.
  88. 0 CMAP corrections types.
  89. 20 non-bonded types.
  90. *** buffer overflow detected ***: ./MDis terminated
  91. ======= Backtrace: =========
  92. /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7fbfb55cc007]
  93. /lib/x86_64-linux-gnu/libc.so.6(+0x107f00)[0x7fbfb55caf00]
  94. ./MDis(_Z13readNonBondedP8_IO_FILEP10ForceField+0x186)[0x42a7d6]
  95. ./MDis(_Z12readCHARMMFFPKcP10ForceFieldPc+0x1ad)[0x42ba0d]
  96. ./MDis(main+0x2ad)[0x41e4dd]
  97. /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fbfb54e476d]
  98. ./MDis[0x4207d5]
  99. ======= Memory map: ========
  100. 00400000-004d1000 r-xp 00000000 08:06 11665430 /home/niksh/UML/MDis/trunk/MDis
  101. 006d0000-006d4000 r--p 000d0000 08:06 11665430 /home/niksh/UML/MDis/trunk/MDis
  102. 006d4000-006d5000 rw-p 000d4000 08:06 11665430 /home/niksh/UML/MDis/trunk/MDis
  103. 006d5000-006db000 rw-p 00000000 00:00 0
  104. 01781000-019cb000 rw-p 00000000 00:00 0 [heap]
  105. 7fbfaeac4000-7fbfaead1000 r-xp 00000000 08:05 16914028 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
  106. 7fbfaead1000-7fbfaecd0000 ---p 0000d000 08:05 16914028 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
  107. 7fbfaecd0000-7fbfaecd1000 r--p 0000c000 08:05 16914028 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
  108. 7fbfaecd1000-7fbfaecd2000 rw-p 0000d000 08:05 16914028 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
  109. 7fbfaecd2000-7fbfaecdc000 r-xp 00000000 08:05 16913887 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
  110. 7fbfaecdc000-7fbfaeedc000 ---p 0000a000 08:05 16913887 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
  111. 7fbfaeedc000-7fbfaeedd000 r--p 0000a000 08:05 16913887 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
  112. 7fbfaeedd000-7fbfaeede000 rw-p 0000b000 08:05 16913887 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
  113. 7fbfaeede000-7fbfaeef4000 r-xp 00000000 08:05 16913867 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
  114. 7fbfaeef4000-7fbfaf0f4000 ---p 00016000 08:05 16913867 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
  115. 7fbfaf0f4000-7fbfaf0f5000 r--p 00016000 08:05 16913867 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
  116. 7fbfaf0f5000-7fbfaf0f6000 rw-p 00017000 08:05 16913867 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
  117. 7fbfaf0f6000-7fbfaf0f9000 r-xp 00000000 08:05 16914039 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
  118. 7fbfaf0f9000-7fbfaf2f8000 ---p 00003000 08:05 16914039 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
  119. 7fbfaf2f8000-7fbfaf2f9000 r--p 00002000 08:05 16914039 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
  120. 7fbfaf2f9000-7fbfaf2fa000 rw-p 00003000 08:05 16914039 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
  121. 7fbfaf500000-7fbfaf502000 r-xp 00000000 08:05 16913915 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
  122. 7fbfaf502000-7fbfaf701000 ---p 00002000 08:05 16913915 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
  123. 7fbfaf701000-7fbfaf702000 r--p 00001000 08:05 16913915 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
  124. 7fbfaf702000-7fbfaf703000 rw-p 00002000 08:05 16913915 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
  125. 7fbfaf703000-7fbfaf706000 r-xp 00000000 08:05 16913891 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
  126. 7fbfaf706000-7fbfaf905000 ---p 00003000 08:05 16913891 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
  127. 7fbfaf905000-7fbfaf906000 r--p 00002000 08:05 16913891 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
  128. 7fbfaf906000-7fbfaf907000 rw-p 00003000 08:05 16913891 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
  129. 7fbfaf907000-7fbfaf90f000 r-xp 00000000 08:05 16913902 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
  130. 7fbfaf90f000-7fbfafb0e000 ---p 00008000 08:05 16913902 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
  131. 7fbfafb0e000-7fbfafb0f000 r--p 00007000 08:05 16913902 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
  132. 7fbfafb0f000-7fbfafb10000 rw-p 00008000 08:05 16913902 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
  133. 7fbfafb10000-7fbfafb1b000 r-xp 00000000 08:05 16913874 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
  134. 7fbfafb1b000-7fbfafd1a000 ---p 0000b000 08:05 16913874 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
  135. 7fbfafd1a000-7fbfafd1b000 r--p 0000a000 08:05 16913874 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
  136. 7fbfafd1b000-7fbfafd1c000 rw-p 0000b000 08:05 16913874 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
  137. 7fbfafd1c000-7fbfafd9c000 rw-p 00000000 00:00 0
  138. 7fbfafd9c000-7fbfafda2000 r-xp 00000000 08:05 16913904 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
  139. 7fbfafda2000-7fbfaffa1000 ---p 00006000 08:05 16913904 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
  140. 7fbfaffa1000-7fbfaffa2000 r--p 00005000 08:05 16913904 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
  141. 7fbfaffa2000-7fbfaffa3000 rw-p 00006000 08:05 16913904 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
  142. 7fbfaffa3000-7fbfaffa6000 r-xp 00000000 08:05 16914050 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
  143. 7fbfaffa6000-7fbfb01a5000 ---p 00003000 08:05 16914050 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
  144. 7fbfb01a5000-7fbfb01a6000 r--p 00002000 08:05 16914050 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
  145. 7fbfb01a6000-7fbfb01a7000 rw-p 00003000 08:05 16914050 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
  146. 7fbfb07e2000-7fbfb07e6000 r-xp 00000000 08:05 16913894 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
  147. 7fbfb07e6000-7fbfb09e5000 ---p 00004000 08:05 16913894 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
  148. 7fbfb09e5000-7fbfb09e6000 r--p 00003000 08:05 16913894 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
  149. 7fbfb09e6000-7fbfb09e7000 rw-p 00004000 08:05 16913894 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
  150. 7fbfb0beb000-7fbfb0bff000 r-xp 00000000 08:05 16914047 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
  151. 7fbfb0bff000-7fbfb0dfe000 ---p 00014000 08:05 16914047 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
  152. 7fbfb0dfe000-7fbfb0dff000 r--p 00013000 08:05 16914047 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
  153. 7fbfb0dff000-7fbfb0e00000 rw-p 00014000 08:05 16914047 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
  154. 7fbfb101b000-7fbfb1020000 r-xp 00000000 08:05 16913905 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
  155. 7fbfb1020000-7fbfb121f000 ---p 00005000 08:05 16913905 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
  156. 7fbfb121f000-7fbfb1220000 r--p 00004000 08:05 16913905 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
  157. 7fbfb1220000-7fbfb1221000 rw-p 00005000 08:05 16913905 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
  158. 7fbfb1221000-7fbfb1226000 r-xp 00000000 08:05 16914055 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
  159. 7fbfb1226000-7fbfb1425000 ---p 00005000 08:05 16914055 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
  160. 7fbfb1425000-7fbfb1426000 r--p 00004000 08:05 16914055 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
  161. 7fbfb1426000-7fbfb1427000 rw-p 00005000 08:05 16914055 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
  162. 7fbfb143e000-7fbfb1441000 r-xp 00000000 08:05 16913917 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
  163. 7fbfb1441000-7fbfb1640000 ---p 00003000 08:05 16913917 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
  164. 7fbfb1640000-7fbfb1641000 r--p 00002000 08:05 16913917 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
  165. 7fbfb1641000-7fbfb1642000 rw-p 00003000 08:05 16913917 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
  166. 7fbfb1642000-7fbfb1644000 r-xp 00000000 08:05 16779797 /usr/lib/openmpi/lib/libmca_common_sm.so.2.0.0
  167. 7fbfb1644000-7fbfb1843000 ---p 00002000 08:05 16779797 /usr/lib/openmpi/lib/libmca_common_sm.so.2.0.0
  168. 7fbfb1843000-7fbfb1844000 r--p 00001000 08:05 16779797 /usr/lib/openmpi/lib/libmca_common_sm.so.2.0.0
  169. 7fbfb1844000-7fbfb1845000 rw-p 00002000 08:05 16779797 /usr/lib/openmpi/lib/libmca_common_sm.so.2.0.0
  170. 7fbfb1845000-7fbfb1847000 r-xp 00000000 08:05 16913895 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
  171. 7fbfb1847000-7fbfb1a46000 ---p 00002000 08:05 16913895 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
  172. 7fbfb1a46000-7fbfb1a47000 r--p 00001000 08:05 16913895 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
  173. 7fbfb1a47000-7fbfb1a48000 rw-p 00002000 08:05 16913895 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
  174. 7fbfb1a48000-7fbfb1a4b000 r-xp 00000000 08:05 16913908 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
  175. 7fbfb1a4b000-7fbfb1c4a000 ---p 00003000 08:05 16913908 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
  176. 7fbfb1c4a000-7fbfb1c4b000 r--p 00002000 08:05 16913908 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
  177. 7fbfb1c4b000-7fbfb1c4c000 rw-p 00003000 08:05 16913908 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
  178. 7fbfb1c4c000-7fbfb1c4d000 r-xp 00000000 08:05 16913901 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
  179. 7fbfb1c4d000-7fbfb1e4c000 ---p 00001000 08:05 16913901 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
  180. 7fbfb1e4c000-7fbfb1e4d000 r--p 00000000 08:05 16913901 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
  181. 7fbfb1e4d000-7fbfb1e4e000 rw-p 00001000 08:05 16913901 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
  182. 7fbfb1e4e000-7fbfb1e51000 r-xp 00000000 08:05 16914044 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
  183. 7fbfb1e51000-7fbfb2050000 ---p 00003000 08:05 16914044 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
  184. 7fbfb2050000-7fbfb2051000 r--p 00002000 08:05 16914044 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
  185. 7fbfb2051000-7fbfb2052000 rw-p 00003000 08:05 16914044 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
  186. 7fbfb2052000-7fbfb2054000 r-xp 00000000 08:05 16913877 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
  187. 7fbfb2054000-7fbfb2253000 ---p 00002000 08:05 16913877 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
  188. 7fbfb2253000-7fbfb2254000 r--p 00001000 08:05 16913877 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
  189. 7fbfb2254000-7fbfb2255000 rw-p 00002000 08:05 16913877 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
  190. 7fbfb2255000-7fbfb2261000 r-xp 00000000 08:05 1446196 /lib/x86_64-linux-gnu/libnss_files-2.15.so
  191. 7fbfb2261000-7fbfb2460000 ---p 0000c000 08:05 1446196 /lib/x86_64-linux-gnu/libnss_files-2.15.so
  192. 7fbfb2460000-7fbfb2461000 r--p 0000b000 08:05 1446196 /lib/x86_64-linux-gnu/libnss_files-2.15.so
  193. 7fbfb2461000-7fbfb2462000 rw-p 0000c000 08:05 1446196 /lib/x86_64-linux-gnu/libnss_files-2.15.so
  194. 7fbfb2462000-7fbfb246c000 r-xp 00000000 08:05 1446200 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
  195. 7fbfb246c000-7fbfb266c000 ---p 0000a000 08:05 1446200 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
  196. 7fbfb266c000-7fbfb266d000 r--p 0000a000 08:05 1446200 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
  197. 7fbfb266d000-7fbfb266e000 rw-p 0000b000 08:05 1446200 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
  198. 7fbfb266e000-7fbfb2685000 r-xp 00000000 08:05 1446190 /lib/x86_64-linux-gnu/libnsl-2.15.so
  199. 7fbfb2685000-7fbfb2884000 ---p 00017000 08:05 1446190 /lib/x86_64-linux-gnu/libnsl-2.15.so
  200. 7fbfb2884000-7fbfb2885000 r--p 00016000 08:05 1446190 /lib/x86_64-linux-gnu/libnsl-2.15.so
  201. 7fbfb2885000-7fbfb2886000 rw-p 00017000 08:05 1446190 /lib/x86_64-linux-gnu/libnsl-2.15.so
  202. 7fbfb2886000-7fbfb2888000 rw-p 00000000 00:00 0
  203. 7fbfb2888000-7fbfb2890000 r-xp 00000000 08:05 1446192 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
  204. 7fbfb2890000-7fbfb2a8f000 ---p 00008000 08:05 1446192 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
  205. 7fbfb2a8f000-7fbfb2a90000 r--p 00007000 08:05 1446192 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
  206. 7fbfb2a90000-7fbfb2a91000 rw-p 00008000 08:05 1446192 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
  207. 7fbfb2a91000-7fbfb2a95000 r-xp 00000000 08:05 16913879 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
  208. 7fbfb2a95000-7fbfb2c94000 ---p 00004000 08:05 16913879 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
  209. 7fbfb2c94000-7fbfb2c95000 r--p 00003000 08:05 16913879 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
  210. 7fbfb2c95000-7fbfb2c96000 rw-p 00004000 08:05 16913879 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
  211. 7fbfb2c96000-7fbfb2c99000 r-xp 00000000 08:05 16914032 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
  212. 7fbfb2c99000-7fbfb2e99000 ---p 00003000 08:05 16914032 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
  213. 7fbfb2e99000-7fbfb2e9a000 r--p 00003000 08:05 16914032 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
  214. 7fbfb2e9a000-7fbfb2e9b000 rw-p 00004000 08:05 16914032 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
  215. 7fbfb2e9b000-7fbfb2eaa000 r-xp 00000000 08:05 16913875 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
  216. 7fbfb2eaa000-7fbfb30a9000 ---p 0000f000 08:05 16913875 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
  217. 7fbfb30a9000-7fbfb30aa000 r--p 0000e000 08:05 16913875 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
  218. 7fbfb30aa000-7fbfb30ab000 rw-p 0000f000 08:05 16913875 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
  219. 7fbfb30ab000-7fbfb30ae000 r-xp 00000000 08:05 16913882 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
  220. 7fbfb30ae000-7fbfb32ad000 ---p 00003000 08:05 16913882 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
  221. 7fbfb32ad000-7fbfb32ae000 r--p 00002000 08:05 16913882 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
  222. 7fbfb32ae000-7fbfb32af000 rw-p 00003000 08:05 16913882 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
  223. 7fbfb32af000-7fbfb32b4000 r-xp 00000000 08:05 16913911 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
  224. 7fbfb32b4000-7fbfb34b3000 ---p 00005000 08:05 16913911 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
  225. 7fbfb34b3000-7fbfb34b4000 r--p 00004000 08:05 16913911 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
  226. 7fbfb34b4000-7fbfb34b5000 rw-p 00005000 08:05 16913911 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
  227. 7fbfb34b6000-7fbfb34b8000 r-xp 00000000 08:05 16913892 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
  228. 7fbfb34b8000-7fbfb36b7000 ---p 00002000 08:05 16913892 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
  229. 7fbfb36b7000-7fbfb36b8000 r--p 00001000 08:05 16913892 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
  230. 7fbfb36b8000-7fbfb36b9000 rw-p 00002000 08:05 16913892 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
  231. 7fbfb36b9000-7fbfb36bb000 r-xp 00000000 08:05 16914034 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
  232. 7fbfb36bb000-7fbfb38ba000 ---p 00002000 08:05 16914034 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
  233. 7fbfb38ba000-7fbfb38bb000 r--p 00001000 08:05 16914034 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
  234. 7fbfb38bb000-7fbfb38bc000 rw-p 00002000 08:05 16914034 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
  235. 7fbfb38bc000-7fbfb38bd000 r-xp 00000000 08:05 16914041 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
  236. 7fbfb38bd000-7fbfb3abc000 ---p 00001000 08:05 16914041 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
  237. 7fbfb3abc000-7fbfb3abd000 r--p 00000000 08:05 16914041 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
  238. 7fbfb3abd000-7fbfb3abe000 rw-p 00001000 08:05 16914041 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
  239. 7fbfb3abe000-7fbfb3ad6000 r-xp 00000000 08:05 1446229 /lib/x86_64-linux-gnu/libresolv-2.15.so
  240. 7fbfb3ad6000-7fbfb3cd6000 ---p 00018000 08:05 1446229 /lib/x86_64-linux-gnu/libresolv-2.15.so
  241. 7fbfb3cd6000-7fbfb3cd7000 r--p 00018000 08:05 1446229 /lib/x86_64-linux-gnu/libresolv-2.15.so
  242. 7fbfb3cd7000-7fbfb3cd8000 rw-p 00019000 08:05 1446229 /lib/x86_64-linux-gnu/libresolv-2.15.so
  243. 7fbfb3cd8000-7fbfb3cda000 rw-p 00000000 00:00 0
  244. 7fbfb3cda000-7fbfb3cf0000 r-xp 00000000 08:05 1446256 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
  245. 7fbfb3cf0000-7fbfb3eef000 ---p 00016000 08:05 1446256 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
  246. 7fbfb3eef000-7fbfb3ef0000 r--p 00015000 08:05 1446256 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
  247. 7fbfb3ef0000-7fbfb3ef1000 rw-p 00016000 08:05 1446256 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
  248. 7fbfb3ef1000-7fbfb3efc000 r-xp 00000000 08:05 1446215 /lib/x86_64-linux-gnu/libpci.so.3.1.8
  249. 7fbfb3efc000-7fbfb40fb000 ---p 0000b000 08:05 1446215 /lib/x86_64-linux-gnu/libpci.so.3.1.8
  250. 7fbfb40fb000-7fbfb40fc000 r--p 0000a000 08:05 1446215 /lib/x86_64-linux-gnu/libpci.so.3.1.8
  251. 7fbfb40fc000-7fbfb40fd000 rw-p 0000b000 08:05 1446215 /lib/x86_64-linux-gnu/libpci.so.3.1.8
  252. 7fbfb40fd000-7fbfb4106000 r-xp 00000000 08:05 13502687 /usr/lib/libnuma.so.1
  253. 7fbfb4106000-7fbfb4306000 ---p 00009000 08:05 13502687 /usr/lib/libnuma.so.1
  254. 7fbfb4306000-7fbfb4307000 r--p 00009000 08:05 13502687 /usr/lib/libnuma.so.1
  255. 7fbfb4307000-7fbfb4308000 rw-p 0000a000 08:05 13502687 /usr/lib/libnuma.so.1
  256. 7fbfb4308000-7fbfb4459000 r-xp 00000000 08:05 13511345 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
  257. 7fbfb4459000-7fbfb4658000 ---p 00151000 08:05 13511345 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
  258. 7fbfb4658000-7fbfb4660000 r--p 00150000 08:05 13511345 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
  259. 7fbfb4660000-7fbfb4662000 rw-p 00158000 08:05 13511345 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
  260. 7fbfb4662000-7fbfb4663000 rw-p 00000000 00:00 0
  261. 7fbfb4663000-7fbfb4687000 r-xp 00000000 08:05 13502692 /usr/lib/x86_64-linux-gnu/libhwloc.so.4.1.4
  262. 7fbfb4687000-7fbfb4887000 ---p 00024000 08:05 13502692 /usr/lib/x86_64-linux-gnu/libhwloc.so.4.1.4
  263. 7fbfb4887000-7fbfb4888000 r--p 00024000 08:05 13502692 /usr/lib/x86_64-linux-gnu/libhwloc.so.4.1.4
  264. 7fbfb4888000-7fbfb4889000 rw-p 00025000 08:05 13502692 /usr/lib/x86_64-linux-gnu/libhwloc.so.4.1.4
  265. 7fbfb4889000-7fbfb488c000 r-xp 00000000 08:05 16914045 /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc.so
  266. 7fbfb488c000-7fbfb4a8b000 ---p 00003000 08:05 16914045 /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc.so
  267. 7fbfb4a8b000-7fbfb4a8c000 r--p 00002000 08:05 16914045 /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc.so
  268. 7fbfb4a8c000-7fbfb4a8d000 rw-p 00003000 08:05 16914045 /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc.so
  269. 7fbfb4a8d000-7fbfb4a95000 r-xp 00000000 08:05 13511104 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
  270. 7fbfb4a95000-7fbfb4c95000 ---p 00008000 08:05 13511104 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
  271. 7fbfb4c95000-7fbfb4c96000 r--p 00008000 08:05 13511104 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
  272. 7fbfb4c96000-7fbfb4c97000 rw-p 00009000 08:05 13511104 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
  273. 7fbfb4c97000-7fbfb4c99000 r-xp 00000000 08:05 1446249 /lib/x86_64-linux-gnu/libutil-2.15.so
  274. 7fbfb4c99000-7fbfb4e98000 ---p 00002000 08:05 1446249 /lib/x86_64-linux-gnu/libutil-2.15.so
  275. 7fbfb4e98000-7fbfb4e99000 r--p 00001000 08:05 1446249 /lib/x86_64-linux-gnu/libutil-2.15.so
  276. 7fbfb4e99000-7fbfb4e9a000 rw-p 00002000 08:05 1446249 /lib/x86_64-linux-gnu/libutil-2.15.so
  277. 7fbfb4e9a000-7fbfb4ea1000 r-xp 00000000 08:05 1446231 /lib/x86_64-linux-gnu/librt-2.15.so
  278. 7fbfb4ea1000-7fbfb50a0000 ---p 00007000 08:05 1446231 /lib/x86_64-linux-gnu/librt-2.15.so
  279. 7fbfb50a0000-7fbfb50a1000 r--p 00006000 08:05 1446231 /lib/x86_64-linux-gnu/librt-2.15.so
  280. 7fbfb50a1000-7fbfb50a2000 rw-p 00007000 08:05 1446231 /lib/x86_64-linux-gnu/librt-2.15.so
  281. 7fbfb50a2000-7fbfb50a4000 r-xp 00000000 08:05 1446158 /lib/x86_64-linux-gnu/libdl-2.15.so
  282. 7fbfb50a4000-7fbfb52a4000 ---p 00002000 08:05 1446158 /lib/x86_64-linux-gnu/libdl-2.15.so
  283. 7fbfb52a4000-7fbfb52a5000 r--p 00002000 08:05 1446158 /lib/x86_64-linux-gnu/libdl-2.15.so
  284. 7fbfb52a5000-7fbfb52a6000 rw-p 00003000 08:05 1446158 /lib/x86_64-linux-gnu/libdl-2.15.so
  285. 7fbfb52a6000-7fbfb52be000 r-xp 00000000 08:05 1446225 /lib/x86_64-linux-gnu/libpthread-2.15.so
  286. 7fbfb52be000-7fbfb54bd000 ---p 00018000 08:05 1446225 /lib/x86_64-linux-gnu/libpthread-2.15.so
  287. 7fbfb54bd000-7fbfb54be000 r--p 00017000 08:05 1446225 /lib/x86_64-linux-gnu/libpthread-2.15.so
  288. 7fbfb54be000-7fbfb54bf000 rw-p 00018000 08:05 1446225 /lib/x86_64-linux-gnu/libpthread-2.15.so
  289. 7fbfb54bf000-7fbfb54c3000 rw-p 00000000 00:00 0
  290. 7fbfb54c3000-7fbfb5676000 r-xp 00000000 08:05 1446145 /lib/x86_64-linux-gnu/libc-2.15.so
  291. 7fbfb5676000-7fbfb5875000 ---p 001b3000 08:05 1446145 /lib/x86_64-linux-gnu/libc-2.15.so
  292. 7fbfb5875000-7fbfb5879000 r--p 001b2000 08:05 1446145 /lib/x86_64-linux-gnu/libc-2.15.so
  293. 7fbfb5879000-7fbfb587b000 rw-p 001b6000 08:05 1446145 /lib/x86_64-linux-gnu/libc-2.15.so
  294. 7fbfb587b000-7fbfb5880000 rw-p 00000000 00:00 0
  295. 7fbfb5880000-7fbfb5895000 r-xp 00000000 08:05 1446166 /lib/x86_64-linux-gnu/libgcc_s.so.1
  296. 7fbfb5895000-7fbfb5a94000 ---p 00015000 08:05 1446166 /lib/x86_64-linux-gnu/libgcc_s.so.1
  297. 7fbfb5a94000-7fbfb5a95000 r--p 00014000 08:05 1446166 /lib/x86_64-linux-gnu/libgcc_s.so.1
  298. 7fbfb5a95000-7fbfb5a96000 rw-p 00015000 08:05 1446166 /lib/x86_64-linux-gnu/libgcc_s.so.1
  299. 7fbfb5a96000-7fbfb5b8f000 r-xp 00000000 08:05 1446177 /lib/x86_64-linux-gnu/libm-2.15.so
  300. 7fbfb5b8f000-7fbfb5d8e000 ---p 000f9000 08:05 1446177 /lib/x86_64-linux-gnu/libm-2.15.so
  301. 7fbfb5d8e000-7fbfb5d8f000 r--p 000f8000 08:05 1446177 /lib/x86_64-linux-gnu/libm-2.15.so
  302. 7fbfb5d8f000-7fbfb5d90000 rw-p 000f9000 08:05 1446177 /lib/x86_64-linux-gnu/libm-2.15.so
  303. 7fbfb5d90000-7fbfb5e72000 r-xp 00000000 08:05 13511264 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
  304. 7fbfb5e72000-7fbfb6071000 ---p 000e2000 08:05 13511264 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
  305. 7fbfb6071000-7fbfb6079000 r--p 000e1000 08:05 13511264 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
  306. 7fbfb6079000-7fbfb607b000 rw-p 000e9000 08:05 13511264 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
  307. 7fbfb607b000-7fbfb6090000 rw-p 00000000 00:00 0
  308. 7fbfb6090000-7fbfb61c7000 r-xp 00000000 08:05 16779802 /usr/lib/openmpi/lib/libmpi.so.1.0.2
  309. 7fbfb61c7000-7fbfb63c6000 ---p 00137000 08:05 16779802 /usr/lib/openmpi/lib/libmpi.so.1.0.2
  310. 7fbfb63c6000-7fbfb63cb000 r--p 00136000 08:05 16779802 /usr/lib/openmpi/lib/libmpi.so.1.0.2
  311. 7fbfb63cb000-7fbfb63dc000 rw-p 0013b000 08:05 16779802 /usr/lib/openmpi/lib/libmpi.so.1.0.2
  312. 7fbfb63dc000-7fbfb63f5000 rw-p 00000000 00:00 0
  313. 7fbfb63f5000-7fbfb640c000 r-xp 00000000 08:05 16779805 /usr/lib/openmpi/lib/libmpi_cxx.so.1.0.1
  314. 7fbfb640c000-7fbfb660c000 ---p 00017000 08:05 16779805 /usr/lib/openmpi/lib/libmpi_cxx.so.1.0.1
  315. 7fbfb660c000-7fbfb660e000 r--p 00017000 08:05 16779805 /usr/lib/openmpi/lib/libmpi_cxx.so.1.0.1
  316. 7fbfb660e000-7fbfb660f000 rw-p 00019000 08:05 16779805 /usr/lib/openmpi/lib/libmpi_cxx.so.1.0.1
  317. 7fbfb660f000-7fbfb666a000 r-xp 00000000 08:05 14031007 /usr/local/cuda/lib64/libcudart.so.4.2.9
  318. 7fbfb666a000-7fbfb686a000 ---p 0005b000 08:05 14031007 /usr/local/cuda/lib64/libcudart.so.4.2.9
  319. 7fbfb686a000-7fbfb686b000 r--p 0005b000 08:05 14031007 /usr/local/cuda/lib64/libcudart.so.4.2.9
  320. 7fbfb686b000-7fbfb686c000 rw-p 0005c000 08:05 14031007 /usr/local/cuda/lib64/libcudart.so.4.2.9
  321. 7fbfb686c000-7fbfb686d000 rw-p 00000000 00:00 0
  322. 7fbfb686d000-7fbfb688f000 r-xp 00000000 08:05 1446125 /lib/x86_64-linux-gnu/ld-2.15.so
  323. 7fbfb6a72000-7fbfb6a7a000 rw-p 00000000 00:00 0
  324. 7fbfb6a8a000-7fbfb6a8f000 rw-p 00000000 00:00 0
  325. 7fbfb6a8f000-7fbfb6a90000 r--p 00022000 08:05 1446125 /lib/x86_64-linux-gnu/ld-2.15.so
  326. 7fbfb6a90000-7fbfb6a92000 rw-p 00023000 08:05 1446125 /lib/x86_64-linux-gnu/ld-2.15.so
  327. 7fffe0384000-7fffe03a5000 rw-p 00000000 00:00 0 [stack]
  328. 7fffe03c6000-7fffe03c7000 r-xp 00000000 00:00 0 [vdso]
  329. ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
  330. [NX5-1:19908] *** Process received signal ***
  331. [NX5-1:19908] Signal: Aborted (6)
  332. [NX5-1:19908] Signal code: (-6)
  333. [NX5-1:19908] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364c0) [0x7fbfb54f94c0]
  334. [NX5-1:19908] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7fbfb54f9445]
  335. [NX5-1:19908] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) [0x7fbfb54fcbab]
  336. [NX5-1:19908] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x73e2e) [0x7fbfb5536e2e]
  337. [NX5-1:19908] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37) [0x7fbfb55cc007]
  338. [NX5-1:19908] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x107f00) [0x7fbfb55caf00]
  339. [NX5-1:19908] [ 6] ./MDis(_Z13readNonBondedP8_IO_FILEP10ForceField+0x186) [0x42a7d6]
  340. [NX5-1:19908] [ 7] ./MDis(_Z12readCHARMMFFPKcP10ForceFieldPc+0x1ad) [0x42ba0d]
  341. [NX5-1:19908] [ 8] ./MDis(main+0x2ad) [0x41e4dd]
  342. [NX5-1:19908] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fbfb54e476d]
  343. [NX5-1:19908] [10] ./MDis() [0x4207d5]
  344. [NX5-1:19908] *** End of error message ***
  345. Aborted (core dumped)
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