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  1. LAMMPS (9 Nov 2018)
  2. using 1 OpenMP thread(s) per MPI task
  3. [scc-uh2:13887] *** Process received signal ***
  4. [scc-uh2:13887] Signal: Segmentation fault (11)
  5. [scc-uh2:13887] Signal code: Address not mapped (1)
  6. [scc-uh2:13887] Failing at address: 0xffffffffffffffff
  7. [scc-uh2:13887] [ 0] [scc-uh2:13911] *** Process received signal ***
  8. [scc-uh2:13911] Signal: Segmentation fault (11)
  9. [scc-uh2:13911] Signal code: Address not mapped (1)
  10. [scc-uh2:13911] Failing at address: 0x10
  11. [scc-uh2:13911] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b97f40fd7e0]
  12. [scc-uh2:13911] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x11bd5)[0x2b97ef7a7bd5]
  13. [scc-uh2:13911] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x146a8)[0x2b97ef7aa6a8]
  14. [scc-uh2:13911] [ 3] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b97ef7a9eb1]
  15. [scc-uh2:13911] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  16. [scc-uh2:13911] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d417]
  17. [scc-uh2:13911] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  18. [scc-uh2:13911] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  19. [scc-uh2:13911] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  20. [scc-uh2:13911] [ 9] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  21. [scc-uh2:13911] [10] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b97f4329d20]
  22. [scc-uh2:13911] [11] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  23. [scc-uh2:13911] *** End of error message ***
  24. variable ndim equal 2
  25. dimension ${ndim}
  26. dimension 2
  27. units si
  28.  
  29. atom_style meso/multiphase
  30. include vars.lmp
  31. [scc-uh2:13924] *** Process received signal ***
  32. [scc-uh2:13924] Signal: Segmentation fault (11)
  33. [scc-uh2:13924] Signal code: Address not mapped (1)
  34. [scc-uh2:13924] Failing at address: 0x10
  35. [scc-uh2:13924] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b23d94ef7e0]
  36. [scc-uh2:13924] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x11bd5)[0x2b23d4b99bd5]
  37. [scc-uh2:13924] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x146a8)[0x2b23d4b9c6a8]
  38. [scc-uh2:13924] [ 3] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b23d4b9beb1]
  39. [scc-uh2:13924] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  40. [scc-uh2:13924] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d417]
  41. [scc-uh2:13924] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  42. [scc-uh2:13924] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  43. [scc-uh2:13924] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  44. [scc-uh2:13924] [ 9] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  45. [scc-uh2:13924] [10] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b23d971bd20]
  46. [scc-uh2:13924] [11] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  47. [scc-uh2:13924] *** End of error message ***
  48. [scc-uh2:13926] *** Process received signal ***
  49. [scc-uh2:13926] Signal: Segmentation fault (11)
  50. [scc-uh2:13926] Signal code: Address not mapped (1)
  51. [scc-uh2:13926] Failing at address: 0x2f8
  52. [scc-uh2:13926] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b00b812a7e0]
  53. [scc-uh2:13926] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x14373)[0x2b00b37d7373]
  54. [scc-uh2:13926] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b00b37d6eb1]
  55. [scc-uh2:13926] [ 3] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  56. [scc-uh2:13926] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d3f9]
  57. [scc-uh2:13926] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  58. [scc-uh2:13926] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  59. [scc-uh2:13926] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  60. [scc-uh2:13926] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  61. [scc-uh2:13926] [ 9] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b00b8356d20]
  62. [scc-uh2:13926] [10] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  63. [scc-uh2:13926] *** End of error message ***
  64. [scc-uh2:13928] *** Process received signal ***
  65. [scc-uh2:13928] Signal: Segmentation fault (11)
  66. [scc-uh2:13928] Signal code: Invalid permissions (2)
  67. [scc-uh2:13928] Failing at address: 0x2b79193cb59c
  68. [scc-uh2:13928] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b7919b767e0]
  69. [scc-uh2:13928] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x11baa)[0x2b7915220baa]
  70. [scc-uh2:13928] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x146a8)[0x2b79152236a8]
  71. [scc-uh2:13928] [ 3] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b7915222eb1]
  72. [scc-uh2:13928] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  73. [scc-uh2:13928] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d3f9]
  74. [scc-uh2:13928] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  75. [scc-uh2:13928] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  76. [scc-uh2:13928] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  77. [scc-uh2:13928] [ 9] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  78. [scc-uh2:13928] [10] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b7919da2d20]
  79. [scc-uh2:13928] [11] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  80. [scc-uh2:13928] *** End of error message ***
  81. [scc-uh2:13954] *** Process received signal ***
  82. [scc-uh2:13954] Signal: Segmentation fault (11)
  83. [scc-uh2:13954] Signal code: Address not mapped (1)
  84. [scc-uh2:13954] Failing at address: 0x1
  85. [scc-uh2:13954] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b02238397e0]
  86. [scc-uh2:13954] [ 1] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d3f1]
  87. [scc-uh2:13954] [ 2] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  88. [scc-uh2:13954] [ 3] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  89. [scc-uh2:13954] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  90. [scc-uh2:13954] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  91. [scc-uh2:13954] [ 6] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b0223a65d20]
  92. [scc-uh2:13954] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  93. [scc-uh2:13954] *** End of error message ***
  94. [scc-uh2:13897] *** Process received signal ***
  95. [scc-uh2:13897] Signal: Segmentation fault (11)
  96. [scc-uh2:13897] Signal code: Address not mapped (1)
  97. [scc-uh2:13897] Failing at address: 0x10
  98. [scc-uh2:13897] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b00dabdb7e0]
  99. [scc-uh2:13897] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x11bd5)[0x2b00d6285bd5]
  100. [scc-uh2:13897] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x146a8)[0x2b00d62886a8]
  101. [scc-uh2:13897] [ 3] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b00d6287eb1]
  102. [scc-uh2:13897] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  103. [scc-uh2:13897] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d417]
  104. [scc-uh2:13897] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  105. [scc-uh2:13897] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  106. [scc-uh2:13897] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  107. [scc-uh2:13897] [ 9] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  108. [scc-uh2:13897] [10] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b00dae07d20]
  109. [scc-uh2:13897] [11] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  110. [scc-uh2:13897] *** End of error message ***
  111. [scc-uh2:13901] *** Process received signal ***
  112. [scc-uh2:13901] Signal: Segmentation fault (11)
  113. [scc-uh2:13901] Signal code: Invalid permissions (2)
  114. [scc-uh2:13901] Failing at address: 0x2b31a885e2c0
  115. [scc-uh2:13901] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b31a90b37e0]
  116. [scc-uh2:13901] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x11bd5)[0x2b31a475dbd5]
  117. [scc-uh2:13901] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x146a8)[0x2b31a47606a8]
  118. [scc-uh2:13901] [ 3] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b31a475feb1]
  119. [scc-uh2:13901] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  120. [scc-uh2:13901] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d417]
  121. [scc-uh2:13901] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  122. [scc-uh2:13901] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  123. [scc-uh2:13901] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  124. [scc-uh2:13901] [ 9] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  125. [scc-uh2:13901] [10] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b31a92dfd20]
  126. [scc-uh2:13901] [11] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  127. [scc-uh2:13901] *** End of error message ***
  128. # number of particles in each of the directions
  129. variable nx equal 51
  130. variable ny equal 51
  131. if "${ndim}==3" then "variable nz equal 6"
  132.  
  133. # size of the domain
  134. variable Lx equal 0.1
  135. variable Ly equal 0.1
  136. if "${ndim}==3" then "variable Lz equal ${Lx}/${nx}*${nz}"
  137. variable dx equal ${Lx}/${nx}
  138. variable dx equal 0.1/${nx}
  139. variable dx equal 0.1/51
  140.  
  141. variable sph_rho equal 1e3
  142. variable sph_rho_background equal 1.0
  143.  
  144. # parameter in EOS
  145. variable sph_gamma equal 1
  146.  
  147. # sound speed
  148. variable sph_c equal 5.77e-4
  149.  
  150. # viscosity
  151. variable sph_eta equal 1e-3
  152.  
  153. variable h equal 3*${dx}
  154. variable h equal 3*0.00196078431372549
  155. variable Nfreq equal 1000
  156.  
  157. # mass of one sph particles
  158. variable sph_mass equal ${dx}^${ndim}*${sph_rho}
  159. variable sph_mass equal 0.00196078431372549^${ndim}*${sph_rho}
  160. variable sph_mass equal 0.00196078431372549^2*${sph_rho}
  161. variable sph_mass equal 0.00196078431372549^2*1000
  162.  
  163. # radios of the cylinder
  164. variable cyl_r equal 2e-2
  165.  
  166. # body force
  167. variable gx equal 1.5e-7
  168.  
  169. # type of the flow particles
  170. variable g_type equal 1
  171.  
  172. # type of the cylinder particles
  173. variable d_type equal 2
  174. boundary p p p
  175. # create simulation box
  176. if ${ndim}==2 then "variable pLz equal ${dx}" "variable nLz equal 0" "region box block 0.0 ${Lx} 0.0 ${Ly} ${nLz} ${pLz} units box" else "region box block 0.0 ${Lx} 0.0 ${Ly} 0 ${Lz} units box"
  177. if 2==2 then "variable pLz equal ${dx}" "variable nLz equal 0" "region box block 0.0 ${Lx} 0.0 ${Ly} ${nLz} ${pLz} units box" else "region box block 0.0 ${Lx} 0.0 ${Ly} 0 ${Lz} units box"
  178. variable pLz equal ${dx}
  179. variable pLz equal 0.00196078431372549
  180. variable nLz equal 0
  181. region box block 0.0 ${Lx} 0.0 ${Ly} ${nLz} ${pLz} units box
  182. region box block 0.0 0.1 0.0 ${Ly} ${nLz} ${pLz} units box
  183. region box block 0.0 0.1 0.0 0.1 ${nLz} ${pLz} units box
  184. region box block 0.0 0.1 0.0 0.1 0 ${pLz} units box
  185. region box block 0.0 0.1 0.0 0.1 0 0.00196078431372549 units box
  186. /lib64/libpthread.so.0(+0xf7e0)[0x2b0d5f4597e0]
  187. [scc-uh2:13887] [ 1] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d3f1]
  188. [scc-uh2:13887] [ 2] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  189. [scc-uh2:13887] [ 3] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  190. [scc-uh2:13887] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  191. [scc-uh2:13887] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  192. [scc-uh2:13887] [ 6] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b0d5f685d20]
  193. [scc-uh2:13887] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  194. [scc-uh2:13887] *** End of error message ***
  195. [scc-uh2:13919] *** Process received signal ***
  196. [scc-uh2:13919] Signal: Segmentation fault (11)
  197. [scc-uh2:13919] Signal code: Invalid permissions (2)
  198. [scc-uh2:13919] Failing at address: 0x2b49b7bd4124
  199. [scc-uh2:13919] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b49b83787e0]
  200. [scc-uh2:13919] [ 1] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x11baa)[0x2b49b3a22baa]
  201. [scc-uh2:13919] [ 2] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(+0x146a8)[0x2b49b3a256a8]
  202. [scc-uh2:13919] [ 3] /share/pkg/intel/2018/install/daal/../tbb/lib/intel64_lin/gcc4.4/libtbbmalloc.so.2(scalable_aligned_realloc+0x61)[0x2b49b3a24eb1]
  203. [scc-uh2:13919] [ 4] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x66bbbb]
  204. [scc-uh2:13919] [ 5] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x43d3f9]
  205. [scc-uh2:13919] [ 6] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x411f26]
  206. [scc-uh2:13919] [ 7] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63f572]
  207. [scc-uh2:13919] [ 8] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x63b6cd]
  208. [scc-uh2:13919] [ 9] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x6676a1]
  209. [scc-uh2:13919] [10] /lib64/libc.so.6(__libc_start_main+0x100)[0x2b49b85a4d20]
  210. [scc-uh2:13919] [11] /projectnb/ryanlab/qth20/lammps_master/src/lmp_intel_cpu_openmpi[0x408ca9]
  211. [scc-uh2:13919] *** End of error message ***
  212. -------------------------------------------------------
  213. Primary job terminated normally, but 1 process returned
  214. a non-zero exit code. Per user-direction, the job has been aborted.
  215. -------------------------------------------------------
  216. --------------------------------------------------------------------------
  217. mpirun noticed that process rank 2 with PID 0 on node scc-uh2 exited on signal 11 (Segmentation fault).
  218. --------------------------------------------------------------------------
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