Hi, I have been trying to run siesta with OpenMP to reduce memory usage. I tried openmpi and intelmpi with both rel-MaX-1 and psml-support git branches. All of them successfully compiled but segment fault at runtime. Does anyone know how to fix this?
The command to run siesta for rel-MaX-1 with intelmpi is mpirun -np 8 -ppn 8 -genv OMP_NUM_THREADS=16 -genv OMP_STACKSIZE=512m /path/to/siesta < job.fdf The error message (other versions have similar error messages) is: … InitMesh: MESH = 432 x 432 x 128 = 23887872 InitMesh: Mesh cutoff (required, used) = 100.000 100.983 Ry New grid distribution [1]: sub = 2 New grid distribution [2]: sub = 2 New grid distribution [3]: sub = 2 Setting up quadratic distribution... [r452:20712:0:20712] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x1477c8021000) [r452:20715:0:20715] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x14e5e4004000) [r452:20709:0:20709] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x14b7d0d51000) [r452:20714:0:20714] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x14e9155fb000) [r452:20716:0:20716] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x15356e7b7000) [r452:20713:0:20713] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x152b1e544000) [r452:20711:0:20711] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x148f5e2f7000) [r452:20710:0:20710] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x14f6c64ee000) ==== backtrace (tid: 20709) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 000014B9DB022DD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 000014B9D8D2D6A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown ==== backtrace (tid: 20715) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 000014E7EE2D5DD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 000014E7EBFE06A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown ==== backtrace (tid: 20714) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= ==== backtrace (tid: 20713) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= ==== backtrace (tid: 20712) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= ==== backtrace (tid: 20716) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 000014EB1F8CCDD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 000014EB1D5D76A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 0000152D28815DD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 0000152D265206A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 00001479DA673DD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 00001479D837E6A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 0000153778A88DD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 00001537767936A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown ==== backtrace (tid: 20711) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= ==== backtrace (tid: 20710) ==== 0 0x0000000000055799 ucs_debug_print_backtrace() ???:0 1 0x0000000000012dd0 .annobin_sigaction.c() sigaction.c:0 2 0x00000000004a054b diag3g_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diag3g.F:156 3 0x0000000000456152 m_diagon_mp_diagon_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/diagon.F:309 4 0x00000000005c0a75 m_compute_dm_mp_compute_dm_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/compute_dm.F:202 5 0x0000000000608299 m_siesta_forces_mp_siesta_forces_() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta_forces.F90:347 6 0x0000000000c2f85f MAIN__() /ocean/projects/phy200062p/mistguy/softwares/siesta-rel-MaX-1/Src/siesta.F:85 7 0x00000000004225e2 main() ???:0 8 0x00000000000236a3 __libc_start_main() ???:0 9 0x00000000004224ee _start() ???:0 ================================= forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 00001491685C8DD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 00001491662D36A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source siesta 000000000142757A Unknown Unknown Unknown libpthread-2.28.s 000014F8D07BFDD0 Unknown Unknown Unknown siesta 00000000004A054B diag3g_ 156 diag3g.F siesta 0000000000456152 m_diagon_mp_diago 309 diagon.F siesta 00000000005C0A75 m_compute_dm_mp_c 202 compute_dm.F siesta 0000000000608299 m_siesta_forces_m 347 siesta_forces.F90 siesta 0000000000C2F85F MAIN__ 85 siesta.F siesta 00000000004225E2 Unknown Unknown Unknown libc-2.28.so 000014F8CE4CA6A3 __libc_start_main Unknown Unknown siesta 00000000004224EE Unknown Unknown Unknown Best, Chong Wang
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
