errors in beta version

raguelmoon's picture
Submitted by raguelmoon on Mon, 11/29/2010 - 16:15

Hi
There is error when new beta version starts to write restart file in the end. I tired with both beta versions and also changed system. Error is:

Total # of neighbors = 216699
Ave neighs/atom = 5.28534
Neighbor list builds = 5595
Dangerous builds = 0
System init for write_restart ...
*** glibc detected *** lmp_fedora: free(): invalid pointer: 0xb0de6008 ***
*** glibc detected *** lmp_fedora: free(): invalid pointer: 0xb0e58008 ***
*** glibc detected *** lmp_fedora: double free or corruption (out): 0xb0dc8008 ***
======= Backtrace: =========
======= Backtrace: =========
/lib/libc.so.6(+0x6f1e1)[0x7bc1e1]
======= Backtrace: =========
/lib/libc.so.6(+0x6f1e1)[0x5041e1]
/lib/libc.so.6(+0x6f1e1)[0xb8e1e1]
lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15)[0x818b503]
lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15)[0x818b503]
lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15)[0x818b503]
lmp_fedora(_ZN9LAMMPS_NS6Memory23destroy_3d_double_arrayEPPPd+0x26)[0x818b636]
lmp_fedora(_ZN9LAMMPS_NS6Memory23destroy_3d_double_arrayEPPPd+0x26)[0x818b636]
lmp_fedora(_ZN9LAMMPS_NS6Memory23destroy_3d_double_arrayEPPPd+0x26)[0x818b636]
lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD1Ev+0x8e)[0x8127a66]
lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD1Ev+0x8e)[0x8127a66]
lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD0Ev+0x12)[0x8127ae8]
lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD0Ev+0x12)[0x8127ae8]
lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD0Ev+0x12)[0x8127ae8]
lmp_fedora(_ZN9LAMMPS_NS6Modify10delete_fixEPKc+0x58)[0x8196e1e]
lmp_fedora(_ZN9LAMMPS_NS6Modify10delete_fixEPKc+0x58)[0x8196e1e]
lmp_fedora(_ZN9LAMMPS_NS6Modify10delete_fixEPKc+0x58)[0x8196e1e]
lmp_fedora(_ZN9LAMMPS_NS8PairGranD1Ev+0x2f)[0x81cec09]
lmp_fedora(_ZN9LAMMPS_NS8PairGranD1Ev+0x2f)[0x81cec09]
lmp_fedora(_ZN9LAMMPS_NS8PairGranD1Ev+0x2f)[0x81cec09]
lmp_fedora(_ZN9LAMMPS_NS20PairGranHookeHistoryD1Ev+0x17)[0x81d1089]
lmp_fedora(_ZN9LAMMPS_NS20PairGranHookeHistoryD1Ev+0x17)[0x81d1089]
lmp_fedora(_ZN9LAMMPS_NS20PairGranHookeHistoryD1Ev+0x17)[0x81d1089]
lmp_fedora(_ZN9LAMMPS_NS20PairGranHertzHistoryD0Ev+0x18)[0x81cf40e]
lmp_fedora(_ZN9LAMMPS_NS20PairGranHertzHistoryD0Ev+0x18)[0x81cf40e]
lmp_fedora(_ZN9LAMMPS_NS20PairGranHertzHistoryD0Ev+0x18)[0x81cf40e]
lmp_fedora(_ZN9LAMMPS_NS5ForceD1Ev+0x8e)[0x817a8ec]
lmp_fedora(_ZN9LAMMPS_NS5ForceD1Ev+0x8e)[0x817a8ec]
lmp_fedora(_ZN9LAMMPS_NS5ForceD1Ev+0x8e)[0x817a8ec]
lmp_fedora(_ZN9LAMMPS_NS5ForceD0Ev+0x12)[0x817a974]
lmp_fedora(_ZN9LAMMPS_NS5ForceD0Ev+0x12)[0x817a974]
lmp_fedora(_ZN9LAMMPS_NS5ForceD0Ev+0x12)[0x817a974]
lmp_fedora(_ZN9LAMMPS_NS6LAMMPS7destroyEv+0x46)[0x8188012]
lmp_fedora(_ZN9LAMMPS_NS6LAMMPS7destroyEv+0x46)[0x8188012]
lmp_fedora(_ZN9LAMMPS_NS6LAMMPS7destroyEv+0x46)[0x8188012]
lmp_fedora(_ZN9LAMMPS_NS6LAMMPSD1Ev+0x12)[0x8188326]
lmp_fedora(_ZN9LAMMPS_NS6LAMMPSD1Ev+0x12)[0x8188326]
lmp_fedora(main+0x74)[0x818b0f0]
/lib/libc.so.6(__libc_start_main+0xe6)[0x763cc6]
lmp_fedora(main+0x74)[0x818b0f0]
/lib/libc.so.6(__libc_start_main+0xe6)[0x4abcc6]
00110000-001a6000 r-xp 00000000 fd:00 3151747 /usr/lib/openmpi/lib/libmpi.so.0.0.2 (deleted)
001a6000-001b4000 rw-p 00095000 fd:00 3151747 /usr/lib/openmpi/lib/libmpi.so.0.0.2 (deleted)
001b4000-001bc000 rw-p 00000000 00:00 0
001bc000-001d3000 r-xp 00000000 fd:00 1704074 /lib/libpthread-2.12.so (deleted)
001d3000-001d4000 r--p 00016000 fd:00 1704074 /lib/libpthread-2.12.so (deleted)
001d4000-001d5000 rw-p 00017000 fd:00 1704074 /lib/libpthread-2.12.so (deleted)
001d5000-001d7000 rw-p 00000000 00:00 0
001d7000-001d9000 r-xp 00000000 fd:00 3151804 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
001d9000-001da000 rw-p 00001000 fd:00 3151804 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
001da000-001e9000 r-xp 00000000 fd:00 3151801 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
001e9000-001ea000 rw-p 0000e000 fd:00 3151801 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
001ea000-001ee000 r-xp 00000000 fd:00 3151819 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
001ee000-001ef000 rw-p 00003000 fd:00 3151819 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
001ef000-001f2000 r-xp 00000000 fd:00 3151788 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
001f2000-001f3000 rw-p 00002000 fd:00 3151788 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
001f3000-001f5000 r-xp 00000000 fd:00 3151763 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
001f5000-001f6000 rw-p 00001000 fd:00 3151763 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
001f6000-001f9000 r-xp 00000000 fd:00 3151814 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
001f9000-001fa000 rw-p 00002000 fd:00 3151814 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
001fa000-001fc000 r-xp 00000000 fd:00 3151798 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
001fc000-001fd000 rw-p 00001000 fd:00 3151798 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
001fd000-001ff000 r-xp 00000000 fd:00 3151811 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
001ff000-00200000 rw-p 00002000 fd:00 3151811 /usr/lib/op00110000-00115000 r-xp 00000000 fd:00 3151818 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
00115000-00116000 rw-p 00004000 fd:00 3151818 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
00116000-00118000 r-xp 00000000 fd:00 3151763 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
00118000-00119000 rw-p 00001000 fd:00 3151763 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
00119000-0011c000 r-xp 00000000 fd:00 3151797 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
0011c000-0011d000 rw-p 00002000 fd:00 3151797 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
0011d000-0011f000 r-xp 00000000 fd:00 3151811 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
0011f000-00120000 rw-p 00002000 fd:00 3151811 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
00120000-00121000 r-xp 00000000 fd:00 3151822 /usr/lib/openmpi/lib/openmpi/mca_topo_unity.so
00121000-00122000 rw-p 00000000 fd:00 3151822 /usr/lib/openmpi/lib/openmpi/mca_topo_unity.so
00124000-0013a000 r-xp 00000000 fd:00 3151809 /usr/lilmp_fedora(_ZN9LAMMPS_NS6LAMMPSD1Ev+0x12)[0x8188326]
b/openmpi/lib/openmpi/mca_pml_ob1.so
0013a000-0013b000 rw-p 00015000 fd:00 3151809 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
00144000-00147000 r-xp 00000000 fd:00 3151767 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
00147000-00148000 rw-p 00002000 fd:00 3151767 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
00148000-0014f000 r-xp 00000000 fd:00 3151772 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
0014f000-00150000 rw-p 00006000 fd:00 3151772 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
00150000-00155000 r-xp 00000000 fd:00 3151776 /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
00155000-00156000 rw-p 00004000 fd:00 3151776 /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
0016d000-00172000 r-xp 00000000 fd:00 3151768 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
00172000-00173000 rw-p 00004000 fd:00 3151768 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
00173000-0018d000 r-xp 00000000 fd:00 3151778 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
0018d000-0018e000 rw-p 00019000 fd:00 3151778 [localhost:07402] *** Process received signal ***
[localhost:07402] Signal: Aborted (6)
[localhost:07402] Signal code: (-6)
lmp_fedora[0x80a3011]
======= Memory map: ========
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
001d1000-001d3000 r-xp 00000000 fd:00 3151782 /usr/lib/openmpi/lib/openmpi/mca_ess_env.so
001d3000-001d4000 rw-p 00001000 fd:00 3151782 /usr/lib/openmpi/lib/openmpi/mca_ess_env.so
001ee000-00203000 r-xp 00000000 fd:00 3151749 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.1
00203000-00205000 rw-p 00014000 fd:00 3151749 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.1
0027a000-0027d000 r-xp 00000000 fd:00 1704056 /lib/libdl-2.12.so (deleted)
0027d000-0027e000 r--p 00002000 fd:00 1704056 /lib/libdl-2.12.so (deleted)
0027e000-0027f000 rw-p 00003000 fd:00 1704056 /lib/libdl-2.12.so (deleted)
0027f000-0035e000 r-xp 00000000 fd:00 2374087 /usr/lib/libstdc++.so.6.0.13 (deleted)[localhost:07401] *** Process received signal ***
[localhost:07401] Signal: Aborted (6)
[localhost:07401] Signal code: (-6)
[localhost:07400] *** Process received signal ***
[localhost:07400] Signal: Aborted (6)
[localhost:07400] Signal code: (-6)
[localhost:07402] [ 0] [0x37140c]
[localhost:07402] [ 1] [0x371424]
[localhost:07402] [ 2] /lib/libc.so.6(gsignal+0x51) [0x777d71]
[localhost:07402] [ 3] /lib/libc.so.6(abort+0x17a) [0x77964a]
[localhost:07402] [ 4] /lib/libc.so.6(+0x68d9d) [0x7b5d9d]
[localhost:07402] [ 5] /lib/libc.so.6(+0x6f1e1) [0x7bc1e1]
[localhost:07402] [ 6] lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15) [0x818b503]
[localhost:07402] [ 7] lmp_fedora(_ZN9LAMMPS_NS6Memory23destroy_3d_double_arrayEPPPd+0x26) [0x818b636]
[localhost:07402] [ 8] lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD1Ev+0x8e) [0x8127a66]
[localhost:07402] [ 9] lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD0Ev+0x12) [0x8127ae8]
[localhost:07402] [10] lmp_fedora(_ZN9LAMMPS_NS6Modify10delete_fixEPKc+0x58) [0x8196e1e]
[localhost:07402] [11] lmp_fedora(_ZN9LAMMPS_NS8PairGranD1Ev+0x2f) [0x81cec09]
[localhost:07402] [12] lmp_fedora(_ZN9LAMMPS_NS20PairGranHookeHistoryD1Ev+0x17) [0x81d1089]
[localhost:07402] [13] lmp_fedora(_ZN9LAMMPS_NS20PairGranHertzHistoryD0Ev+0x18) [0x81cf40e]
[localhost:07402] [14] lmp_fedora(_ZN9LAMMPS_NS5ForceD1Ev+0x8e) [0x817a8ec]
[localhost:07402] [15] lmp_fedora(_ZN9LAMMPS_NS5ForceD0Ev+0x12) [0x817a974]
[localhost:07402] [16] lmp_fedora(_ZN9LAMMPS_NS6LAMMPS7destroyEv+0x46) [0x8188012]
[localhost:07402] [17] lmp_fedora(_ZN9LAMMPS_NS6LAMMPSD1Ev+0x12) [0x8188326]
[localhost:07402] [18] lmp_fedora(main+0x74) [0x818b0f0]
[localhost:07402] [19] /lib/libc.so.6(__libc_start_main+0xe6) [0x763cc6]
[localhost:07402] [20] lmp_fedora() [0x80a3011]
[localhost:07402] *** End of error message ***
[localhost:07400] [ 0] [0x6a440c]
[localhost:07400] [ 1] [0x6a4424]
[localhost:07400] [ 2] /lib/libc.so.6(gsignal+0x51) [0x4bfd71]
[localhost:07400] [ 3] /lib/libc.so.6(abort+0x17a) [0x4c164a]
[localhost:07400] [ 4] /lib/libc.so.6(+0x68d9d) [0x4fdd9d]
[localhost:07400] [ 5] /lib/libc.so.6(+0x6f1e1) [0x5041e1]
[localhost:07400] [ 6] lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15) [0x818b503]
[localhost:07400] [ 7] lmp_fedora(_ZN9LAMMPS_NS6Memory23destroy_3d_double_arrayEPPPd+0x26) [0x818b636]
[localhost:07400] [ 8] lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD1Ev+0x8e) [0x8127a66]
[localhost:07400] [ 9] lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD0Ev+0x12) [0x8127ae8]
[localhost:07400] [10] lmp_fedora(_ZN9LAMMPS_NS6Modify10delete_fixEPKc+0x58) [0x8196e1e]
[localhost:07400] [11] lmp_fedora(_ZN9LAMMPS_NS8PairGranD1Ev+0x2f) [0x81cec09]
[localhost:07400] [12] lmp_fedora(_ZN9LAMMPS_NS20PairGranHookeHistoryD1Ev+0x17) [0x81d1089]
[localhost:07400] [13] lmp_fedora(_ZN9LAMMPS_NS20PairGranHertzHistoryD0Ev+0x18) [0x81cf40e]
[localhost:07400] [14] lmp_fedora(_ZN9LAMMPS_NS5ForceD1Ev+0x8e) [0x817a8ec]
[localhost:07400] [15] lmp_fedora(_ZN9LAMMPS_NS5ForceD0Ev+0x12) [0x817a974]
[localhost:07400] [16] lmp_fedora(_ZN9LAMMPS_NS6LAMMPS7destroyEv+0x46) [0x8188012]
[localhost:07400] [17] lmp_fedora(_ZN9LAMMPS_NS6LAMMPSD1Ev+0x12) [0x8188326]
[localhost:07400] [18] lmp_fedora(main+0x74) [0x818b0f0]
[localhost:07400] [19] /lib/libc.so.6(__libc_start_main+0xe6) [0x4abcc6]
[localhost:07400] [20] lmp_fedora() [0x80a3011]
[localhost:07400] *** End of error message ***
[localhost:07401] [ 0] [0xa1140c]
[localhost:07401] [ 1] [0xa11424]
[localhost:07401] [ 2] /lib/libc.so.6(gsignal+0x51) [0xb49d71]
[localhost:07401] [ 3] /lib/libc.so.6(abort+0x17a) [0xb4b64a]
[localhost:07401] [ 4] /lib/libc.so.6(+0x68d9d) [0xb87d9d]
[localhost:07401] [ 5] /lib/libc.so.6(+0x6f1e1) [0xb8e1e1]
[localhost:07401] [ 6] lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15) [0x818b503]
[localhost:07401] [ 7] lmp_fedora(_ZN9LAMMPS_NS6Memory23destroy_3d_double_arrayEPPPd+0x26) [0x818b636]
[localhost:07401] [ 8] lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD1Ev+0x8e) [0x8127a66]
[localhost:07401] [ 9] lmp_fedora(_ZN9LAMMPS_NS17FixContactHistoryD0Ev+0x12) [0x8127ae8]
[localhost:07401] [10] lmp_fedora(_ZN9LAMMPS_NS6Modify10delete_fixEPKc+0x58) [0x8196e1e]
[localhost:07401] [11] lmp_fedora(_ZN9LAMMPS_NS8PairGranD1Ev+0x2f) [0x81cec09]
[localhost:07401] [12] lmp_fedora(_ZN9LAMMPS_NS20PairGranHookeHistoryD1Ev+0x17) [0x81d1089]
[localhost:07401] [13] lmp_fedora(_ZN9LAMMPS_NS20PairGranHertzHistoryD0Ev+0x18) [0x81cf40e]
[localhost:07401] [14] lmp_fedora(_ZN9LAMMPS_NS5ForceD1Ev+0x8e) [0x817a8ec]
[localhost:07401] [15] lmp_fedora(_ZN9LAMMPS_NS5ForceD0Ev+0x12) [0x817a974]
[localhost:07401] [16] lmp_fedora(_ZN9LAMMPS_NS6LAMMPS7destroyEv+0x46) [0x8188012]
[localhost:07401] [17] lmp_fedora(_ZN9LAMMPS_NS6LAMMPSD1Ev+0x12) [0x8188326]
[localhost:07401] [18] lmp_fedora(main+0x74) [0x818b0f0]
[localhost:07401] [19] /lib/libc.so.6(__libc_start_main+0xe6) [0xb35cc6]
[localhost:07401] [20] lmp_fedora() [0x80a3011]
[localhost:07401] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 7402 on node localhost.localdomain exited on signal 6 (Aborted).
--------------------------------------------------------------------------
[ram@localhost force]$

Thanks..
Ram

Forums:

sajjadjeeven | Mon, 11/29/2010 - 16:36

HI!
I am facing the same problem,the both beta versions cannot make restart file.However without making restart file of an input file,it works well.
The message i got at the end of simulation is"

System init for write_restart ...
*** glibc detected *** lmp_fedora: double free or corruption (out): 0x09d030d0 ***
*** glibc detected *** lmp_fedora: double free or corruption (!prev): 0x08db7688 ***
======= Backtrace: =========
/lib/libc.so.6[0x669231/lib/libc.so.6[0x5ae231]
lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15)[0x81bbc51]
lmp_fedora(_ZN9LAMMPS_NS12WriteRestart5writeEPc+0x821)[0x8268cb9]
lmp_fedora(_ZN9LAMMPS_NS12WriteRestart5writeEPc+0x821)[0x8268cb9]
lmp_fedora(_ZN9LAMMPS_NS12WriteRestart7commandEiPPc+0x180)[0x8268e44]
lmp_fedora(_ZN9LAMMPS_NS12WriteRestart7commandEiPPc+0x180)[0x8268e44]
lmp_fedora(_ZN9LAMMPS_NS5Input15execute_commandEv+0x107b)[0x81b4ff9]
lmp_fedora(_ZN9LAMMPS_NS5Input15execute_commandEv+0x107b)[0x81b4ff9]
lmp_fedora(_ZN9LAMMPS_NS5Input4fileEv+0x276)[0x81b52b2]
lmp_fedora(_ZN9LAMMPS_NS5Input4fileEv+0x276)[0x81b52b2]
lmp_fedora(main+0x68)[0x81bb72c]
/lib/libc.so.6(__libc_start_main+0xe6)[0x60fa66]
lmp_fedora(main+0x68)[0x81bb72c]
/lib/libc.so.6(__libc_start_main+0xe6)[0x554a66]
lmp_fedora[0x80a1181]
======= Memory map: ========
00110000-00112000 r-xp 00000000 08:08 688500 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
00112000-00113000 rw-p 00001000 08:08 688500 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
00113000-00116000 r-xp 00000000 08:08 1852161 /usr/lib/libplpa.so.0.0.1
00116000-00117000 rw-p 00003000 08:08 1852161 /usr/lib/libplpa.so.0.0.1
00117000-0011a000 r-xp 00000000 08:08 688484 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
0011a000-0011b000 rw-p 00002000 08:08 688484 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
0011b000-00126000 r-xp 00000000 08:08 729299 /lib/libnss_files-2.10.1.so
00126000-00127000 r--p 0000a000 08:08 729299 /lib/libnss_files-2.10.1.so
00127000-00128000 rw-p 0000b000 08:08 729299 /lib/libnss_files-2.10.1.so
00128000-0012a000 r-xp 00000000 08:08 688458 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
0012a000-0012b000 rw-p 00001000 08:08 688458 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
0012b000-0012d000 r-xp 00000000 08:08 688459 lmp_fedora[0x80a1181]
======= Memory map: ========
/usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
0012d000-0012e000 rw-p 00001000 08:08 688459 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
0012e000-00131000 r-xp 00000000 08:08 688493 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
00131000-00132000 rw-p 00002000 08:08 688493 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
00132000-00134000 r-xp 00000000 08:08 688441 /usr/lib/openmpi/lib/libmca_common_sm.so.1.0.0
00134000-00135000 rw-p 00001000 08:08 688441 /usr/lib/openmpi/lib/libmca_common_sm.so.1.0.0
0014c000-00161000 r-xp 00000000 08:08 688505 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
00161000-00162000 rw-p 00015000 08:08 688505 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
0016c000-0016f000 r-xp 00000000 08:08 688463 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
0016f000-00170000 rw-p 00002000 08:08 688463 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
00170000-00175000 r-xp 00000000 08:08 688464 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
00175000-00176000 rw-p 00004000 08:08 688464 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
00176000-0017a000 r-xp 00000000 08:08 688469 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
0017a000-0017b000 rw-p 00003000 08:08 688469 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
0017b000-0017e000 r-xp 00000000 08:08 688470 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
0017e000-0017f000 rw-p 00002000 08:08 688470 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
0017f000-00189000 r-xp 00000000 08:08 688498 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
00189000-0018a000 rw-p 0000a000 08:08 688498 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
001f7000-00217000 r-xp 00000000 08:08 730689 /lib/ld-2.10.1.so
00217000-00218000 r--p 0001f000 08:08 730689 /lib/ld-2.10.1.so
00218000-00219000 rw-p 00020000 08:08 730689 /lib/ld-2.10.1.so
0021e000-0021f000 r-xp 0021e000 00:00 0 [vdso]
002c5000-002c8000 r-xp 00000000 08:08 688460 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
002c8000-002c9000 rw-p 00003000 08:08 688460 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
002c9000-002d4000 r-xp 00000000 08:08 688465 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
002d4000-002d5000 rw-p 0000b000 08:08 688465 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
002d5000-00355000 rw-p 002d5000 00:00 0
0038f000-00392000 r-xp 00000000 08:08 730696 /lib/libdl-2.10.1.so
00392000-00393000 r--p 00002000 08:08 730696 /lib/libdl-2.10.1.so
00393000-00394000 rw-p 00003000 08:08 730696 /lib/libdl-2.10.1.so
00396000-003bc000 r-xp 00000000 08:08 730701 /lib/libm-2.10.1.so
003bc000-003bd000 r--p 00025000 08:08 730701 /lib/libm-2.10.1.so
003bd000-003be000 rw-p 00026000 08:08 730701 /lib/libm-2.10.1.so
003c0000-003d6000 r-xp 00000000 08:08 730691 /lib/libpthread-2.10.1.so
003d6000-003d7000 ---p 00016000 08:08 730691 /lib/libpthread-2.10.1.so
003d7000-003d8000 r--p 00016000 08:08 730691 /lib/libpthread-2.10.1.so
003d8000-003d9000 rw-p 00017000 08:08 730691 /lib/libpthread-2.10.1.so
003d9000-003db000 rw-p 003d9000 00:00 0
003dd000-00428000 r-xp 00000000 08:08 688692 /usr/lib/openmpi/lib/libopen-pal.so.0.0.0
00428000-0042a000 rw-p 0004b000 08:08 688692 /usr/lib/openmpi/lib/libopen-pal.so.0.0.0
0042a000-0044c000 rw-p 0042a000 00:00 0
0044e000-00494000 r-xp 00000000 08:08 688451 /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
00494000-00496000 rw-p 00046000 08:08 688451 /usr/lib/openmpi/lib/libopen-rte.so.0.0.0
00496000-00497000 rw-p 00496000 00:00 0
00499000-00528000 r-xp 00000000 08:08 688688 /usr/lib/openmpi/lib/libmpi.so.0.0.1
00528000-00536000 rw-p 0008e000 08:08 688688 /usr/lib/openmpi/lib/libmpi.so.0.0.1
00536000-0053e000 rw-p 00536000 00:00 0
005e3000-005f7000 r-xp 00000000 08:08 688445 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.0
005f7000-005f9000 rw-p 00013000 08:08 688445 /usr/lib/openmpi/lib/libmpi_cxx.so.0.0.0
005f9000-00764000 r-xp 00000000 08:08 730690 /lib/libc-2.10.1.so
00764000-00765000 ---p 0016b000 08:08 730690 /lib/libc-2.10.1.so
00765000-00767000 r--p 0016b000 08:08 730690 /lib/libc-2.10.1.so
00767000-00768000 rw-p 0016d000 08:08 730690 /lib/libc-2.10.1.so
00768000-0076b000 rw-p 00768000 00:00 0
00777000-00779000 r-xp 00000000 08:08 688471 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
00779000-0077a000 rw-p 00001000 08:08 688471 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
00795000-00798000 r-xp 00000000 08:08 688473 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
00798000-00799000 rw-p 00002000 08:08 688473 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
007d1000-007d6000 r-xp 00000000 08:08 688472 /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
007d6000-007d7000 rw-p 00004000 08:08 688472 /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so
00870000-00873000 r-xp 00000000 08:08 688516 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
00873000-00874000 rw-p 00003000 08:08 688516 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
008c1000-008ce000 r-xp 00000000 08:08 688499 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
008ce000-008cf000 rw-p 0000c000 08:08 688499 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
008f2000-0091c000 r-xp 00000000 08:08 730705 /lib/libgcc_s-4.4.0-20090506.so.1
0091c000-0091d000 rw-p 00029000 08:08 730705 /lib/libgcc_s-4.4.0-20090506.so.1
009d6000-009d7000 r-xp 00000000 08:08 688519 /usr/lib/openmpi/lib/openmpi/mca_topo_unity.so
009d7000-009d8000 rw-p 00000000 08:08 688519 /usr/lib/openmpi/lib/openmpi/mca_topo_unity.so
009ed000-00a04000 r-xp 00000000 08:08 688474 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
00a04000-00a05000 rw-p 00016000 08:08 688474 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
00a47000-00a48000 r-xp 00000000 08:08 688492 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
00a48000-00a49000 rw-p 00000000 08:08 688492 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
00a56000-00a58000 r-xp 00000000 08:08 688507 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
00a58000-00a59000 rw-p 00001000 08:--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 7276 on node localhost.localdomain exited on signal 6 (Aborted).
--------------------------------------------------------------------------
[localhost:07275] *** Process received signal ***
[localhost:07275] Signal: Aborted (6)
[localhost:07275] Signal code: (-6)
[localhost:07276] *** Process received signal ***
[localhost:07276] Signal: Aborted (6)
[localhost:07276] Signal code: (-6)
[localhost:07275] [ 0] [0xa3540c]
[localhost:07275] [ 1] [0xa35424]
[localhost:07275] [ 2] /lib/libc.so.6(gsignal+0x51) [0x5697c1]
[localhost:07275] [ 3] /lib/libc.so.6(abort+0x182) [0x56b092]
[localhost:07275] [ 4] /lib/libc.so.6 [0x5a7dad]
[localhost:07276] [ 0] [0x21e40c]
[localhost:07276] [ 1] [0x21e424]
[localhost:07275] [ 5] /lib/libc.so.6 [0x5ae231]
[localhost:07276] [ 2] /lib/libc.so.6(gsignal+0x51) [0x6247c1]
[localhost:07276] [ 3] /lib/libc.so.6(abort+0x182) [0x626092]
[localhost:07276] [ 4] /lib/libc.so.6 [0x662dad]
[localhost:07276] [ 5] /lib/libc.so.6 [0x669231]
[localhost:07276] [ 6] lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15) [0x81bbc51]
[localhost:07276] [ 7] lmp_fedora(_ZN9LAMMPS_NS12WriteRestart5writeEPc+0x821) [0x8268cb9]
[localhost:07276] [ 8] lmp_fedora(_ZN9LAMMPS_NS12WriteRestart7commandEiPPc+0x180) [0x8268e44]
[localhost:07276] [ 9] lmp_fedora(_ZN9LAMMPS_NS5Input15execute_commandEv+0x107b) [0x81b4ff9]
[localhost:07276] [10] lmp_fedora(_ZN9LAMMPS_NS5Input4fileEv+0x276) [0x81b52b2]
[localhost:07276] [11] lmp_fedora(main+0x68) [0x81bb72c]
[localhost:07276] [12] /lib/libc.so.6(__libc_start_main+0xe6) [0x60fa66]
[localhost:07275] [ 6] lmp_fedora(_ZN9LAMMPS_NS6Memory5sfreeEPv+0x15) [0x81bbc51]
[localhost:07276] [13] lmp_fedora [0x80a1181]
[localhost:07276] *** End of error message ***
[localhost:07275] [ 7] lmp_fedora(_ZN9LAMMPS_NS12WriteRestart5writeEPc+0x821) [0x8268cb9]
[localhost:07275] [ 8] lmp_fedora(_ZN9LAMMPS_NS12WriteRestart7commandEiPPc+0x180) [0x8268e44]
[localhost:07275] [ 9] lmp_fedora(_ZN9LAMMPS_NS5Input15execute_commandEv+0x107b) [0x81b4ff9]
[localhost:07275] [10] lmp_fedora(_ZN9LAMMPS_NS5Input4fileEv+0x276) [0x81b52b2]
[localhost:07275] [11] lmp_fedora(main+0x68) [0x81bb72c]
[localhost:07275] [12] /lib/libc.so.6(__libc_start_main+0xe6) [0x554a66]
[localhost:07275] [13] lmp_fedora [0x80a1181]
[localhost:07275] *** End of error message ***
[sajjad@localhost rec]$ "
sajjad

raguelmoon's picture

raguelmoon | Mon, 12/06/2010 - 23:36

Hi,
There is still errors when it reads restart file. How can I reduce number of particle-tri contacts in restart file?
Error is:

LIGGGHTS 1.2.2beta based on lammps-10Mar10
Reading restart file ...
orthogonal box = (-0.001 -0.001 -0.001) to (0.226 0.226 0.21)
2 by 2 by 1 processor grid
411387 atoms
Resetting global state of Fix xwalls Style wall/gran/hertz/history from restart file info
Resetting per-atom state of Fix xwalls Style wall/gran/hertz/history from restart file info
Resetting global state of Fix ywalls Style wall/gran/hertz/history from restart file info
Resetting per-atom state of Fix ywalls Style wall/gran/hertz/history from restart file info
Resetting global state of Fix zwalls Style wall/gran/hertz/history from restart file info
Resetting per-atom state of Fix zwalls Style wall/gran/hertz/history from restart file info
Resetting global state of Fix pts1 Style particletemplate/sphere from restart file info
particledistribution/discrete (id pdd1): distribution based on mass%:
pts1: d=3.000000e-03 (bounding sphere) mass%=100.000000%
particledistribution/discrete (id pdd1): distribution based on number%:
pts1: d=3.000000e-03 (bounding sphere) number%=100.000000%
Resetting global state of Fix pdd1 Style particledistribution/discrete from restart file info

Importing STL file 'stl/int2.stl'
Solid body detected in STL file
End of solid body detected in STL file.
WARNING: STL face normals were not normalized, normalizing
Mesh calculations running. This may take a while...finished!

Import of 1200 triangles completed successfully!

Mesh calculations running. This may take a while...finished!
Resetting global state of Fix cad2 Style mesh/gran/stressanalysis from restart file info
INFO: Growing number of particle-tri contacts out of restart
INFO: Maxmimum number of particle-tri contacts >6 at step 100000, growing array
[localhost:09951] *** Process received signal ***
[localhost:09951] Signal: Segmentation fault (11)
[localhost:09951] Signal code: Address not mapped (1)
[localhost:09951] Failing at address: (nil)
[localhost:09949] *** Process received signal ***
[localhost:09949] Signal: Segmentation fault (11)
[localhost:09949] Signal code: Address not mapped (1)
[localhost:09949] Failing at address: (nil)
[localhost:09951] [ 0] [0x8e940c]
[localhost:09951] [ 1] beta2(_ZN9LAMMPS_NS11FixWallGran23grow_arrays_maxtritouchEi+0xd6) [0x8174664]
[localhost:09951] [ 2] beta2(_ZN9LAMMPS_NS11FixWallGran7restartEPc+0xa0) [0x8174c10]
[localhost:09951] [ 3] beta2(_ZN9LAMMPS_NS6Modify7add_fixEiPPc+0x28a5) [0x8199cd1]
[localhost:09951] [ 4] beta2(_ZN9LAMMPS_NS5Input3fixEv+0x24) [0x8184c7c]
[localhost:09951] [ 5] beta2(_ZN9LAMMPS_NS5Input15execute_commandEv+0x504) [0x818637e]
[localhost:09951] [ 6] beta2(_ZN9LAMMPS_NS5Input4fileEv+0x276) [0x81871ac]
[localhost:09951] [ 7] beta2(main+0x68) [0x818b124]
[localhost:09951] [ 8] /lib/libc.so.6(__libc_start_main+0xe6) [0x6e0cc6]
[localhost:09951] [ 9] beta2() [0x80a3011]
[localhost:09951] *** End of error message ***
[localhost:09949] [ 0] [0x31240c]
[localhost:09949] [ 1] beta2(_ZN9LAMMPS_NS11FixWallGran23grow_arrays_maxtritouchEi+0xd6) [0x8174664]
[localhost:09949] [ 2] beta2(_ZN9LAMMPS_NS11FixWallGran7restartEPc+0xa0) [0x8174c10]
[localhost:09949] [ 3] beta2(_ZN9LAMMPS_NS6Modify7add_fixEiPPc+0x28a5) [0x8199cd1]
[localhost:09949] [ 4] beta2(_ZN9LAMMPS_NS5Input3fixEv+0x24) [0x8184c7c]
[localhost:09949] [ 5] beta2(_ZN9LAMMPS_NS5Input15execute_commandEv+0x504) [0x818637e]
[localhost:09949] [ 6] beta2(_ZN9LAMMPS_NS5Input4fileEv+0x276) [0x81871ac]
[localhost:09949] [ 7] beta2(main+0x68) [0x818b124]
[localhost:09949] [ 8] /lib/libc.so.6(__libc_start_main+0xe6) [0x6e0cc6]
[localhost:09949] [ 9] beta2() [0x80a3011]
[localhost:09949] *** End of error message ***
[localhost:09950] *** Process received signal ***
[localhost:09950] Signal: Segmentation fault (11)
[localhost:09950] Signal code: Address not mapped (1)
[localhost:09950] Failing at address: (nil)
[localhost:09952] *** Process received signal ***
[localhost:09952] Signal: Segmentation fault (11)
[localhost:09952] Signal code: Address not mapped (1)
[localhost:09952] Failing at address: (nil)
[localhost:09950] [ 0] [0x64940c]
[localhost:09950] [ 1] beta2(_ZN9LAMMPS_NS11FixWallGran23grow_arrays_maxtritouchEi+0xd6) [0x8174664]
[localhost:09950] [ 2] beta2(_ZN9LAMMPS_NS11FixWallGran7restartEPc+0xa0) [0x8174c10]
[localhost:09950] [ 3] beta2(_ZN9LAMMPS_NS6Modify7add_fixEiPPc+0x28a5) [0x8199cd1]
[localhost:09950] [ 4] beta2(_ZN9LAMMPS_NS5Input3fixEv+0x24) [0x8184c7c]
[localhost:09950] [ 5] beta2(_ZN9LAMMPS_NS5Input15execute_commandEv+0x504) [0x818637e]
[localhost:09950] [ 6] beta2(_ZN9LAMMPS_NS5Input4fileEv+0x276) [0x81871ac]
[localhost:09950] [ 7] beta2(main+0x68) [0x818b124]
[localhost:09950] [ 8] /lib/libc.so.6(__libc_start_main+0xe6) [0x6e0cc6]
[localhost:09950] [ 9] beta2() [0x80a3011]
[localhost:09950] *** End of error message ***
[localhost:09952] [ 0] [0x46640c]
[localhost:09952] [ 1] beta2(_ZN9LAMMPS_NS11FixWallGran23grow_arrays_maxtritouchEi+0xd6) [0x8174664]
[localhost:09952] [ 2] beta2(_ZN9LAMMPS_NS11FixWallGran7restartEPc+0xa0) [0x8174c10]
[localhost:09952] [ 3] beta2(_ZN9LAMMPS_NS6Modify7add_fixEiPPc+0x28a5) [0x8199cd1]
[localhost:09952] [ 4] beta2(_ZN9LAMMPS_NS5Input3fixEv+0x24) [0x8184c7c]
[localhost:09952] [ 5] beta2(_ZN9LAMMPS_NS5Input15execute_commandEv+0x504) [0x818637e]
[localhost:09952] [ 6] beta2(_ZN9LAMMPS_NS5Input4fileEv+0x276) [0x81871ac]
[localhost:09952] [ 7] beta2(main+0x68) [0x818b124]
[localhost:09952] [ 8] /lib/libc.so.6(__libc_start_main+0xe6) [0x6e0cc6]
[localhost:09952] [ 9] beta2() [0x80a3011]
[localhost:09952] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 9949 on node localhost.localdomain exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Thanks,
Ram

Ram

ckloss's picture

ckloss | Tue, 12/07/2010 - 00:04

Ram,

try to move grow_arrays(atom->nmax); at line 940 in fix_wall_gran.cpp to line 933 and recompile - I guess that should resolve the issue.

Christoph

sajjadjeeven | Fri, 12/03/2010 - 03:10

Hi!
I have checked the new 1.2.2 .It works fine for two processor system also.
thanks
sajjad