Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]
Posted: Sat Aug 08, 2020 8:08 pm
Dear abinit users and developers,
I have configured and compiled abinit -8.10.3 in a HPC-cluster running Cent OS 7. Abinit is configured with below configuration file. I am using Intel parallel_studio_xe_2019 update 4 cluster edition.
n199.ac:
The netcdf version 4.1.1 is and libxc version 3.0.0 are used.
The abinit program was configured and compiled without any error message. But, when I try to run the Si calculation I am getting "Program received signal SIGSEGV: Segmentation fault - invalid memory reference" error and the program stops. The err file shows the below message:
I am attaching the input file, output file and config.log file.
Please, suggest me the solution for this problem.
Thank you
Shivaprasad
PhD student
IIT Mandi, India.
I have configured and compiled abinit -8.10.3 in a HPC-cluster running Cent OS 7. Abinit is configured with below configuration file. I am using Intel parallel_studio_xe_2019 update 4 cluster edition.
n199.ac:
Code: Select all
FC="mpif90"
CC="mpicc"
CXX="mpicxx"
enable_mpi="yes"
enable_openmp="yes"
enable_mpi-io="yes"
with_tardir="/home/shiva/.abinit/tarballs"
enable_fallbacks="yes"
with_trio_flavor="netcdf"
with_fft_flavor="fftw3"
with_linalg_flavor="mkl"
with_dft_flavor="libxc"
The abinit program was configured and compiled without any error message. But, when I try to run the Si calculation I am getting "Program received signal SIGSEGV: Segmentation fault - invalid memory reference" error and the program stops. The err file shows the below message:
Code: Select all
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
libi40iw-i40iw_vmapped_qp: failed to pin memory for SQ
libi40iw-i40iw_ucreate_qp: failed to map QP
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2B44CA4C5697
#1 0x2B44CA4C5CDE
#2 0x2B44CC83B3AF
#3 0x2B455CE4AB76
#0 0x2B7104E85697
#4 0x2B44C61EF7A2
#1 0x2B7104E85CDE
#5 0x2B44C4051DC5#2 0x2B71071FB3AF
#3 0x2B719780AB76
#4 0x2B7100BAF7A2
#5 0x2B70FEA11DC5
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2B51FEC3C697
#1 0x2B51FEC3CCDE
#2 0x2B5200FB23AF
#3 0x2B52915C1B76
#4 0x2B51FA9667A2
#5 0x2B51F87C8DC5
#0 0x2B0B7F1E5697
#1 0x2B0B7F1E5CDE
#2 0x2B0B8155B3AF
#3 0x2B0C11B6AB76
#4 0x2B0B7AF0F7A2
#5 0x2B0B78D71DC5
#6 0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#6 0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#7 0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#7 0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#8 0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#8 0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#9 0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#9 0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#6 0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#7 0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#6 0x1192FC1 in __m_cgtools_MOD_cg_zdotc at m_cgtools.F90:728
#7 0x1193170 in __m_cgtools_MOD_dotprod_g at m_cgtools.F90:1364
#10 0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#10 0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#8 0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#8 0xAA4FF3 in __m_cgwf_MOD_cgwf at m_cgwf.F90:499
#9 0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#9 0x598482 in __m_vtowfk_MOD_vtowfk at m_vtowfk.F90:408
#11 0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#10 0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#11 0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#12 0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#10 0x57D7B6 in __m_vtorho_MOD_vtorho at m_vtorho.F90:943
#12 0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#11 0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#13 0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#11 0x5475C4 in __m_scfcv_core_MOD_scfcv_core at m_scfcv_core.F90:1536
#12 0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#14 0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#13 0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#12 0x53B3D4 in __m_scfcv_MOD_scfcv_scfcv at m_scfcv.F90:746
#15 0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#14 0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#13 0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#16 0x40C2EE in MAIN__ at abinit.F90:444
#13 0x52B453 in __m_gstate_MOD_gstate at m_gstate.F90:1331
#15 0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#14 0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#16 0x40C2EE in MAIN__ at abinit.F90:444
#14 0x428A09 in __m_gstateimg_MOD_gstateimg at m_gstateimg.F90:566
#15 0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#15 0x417682 in __m_driver_MOD_driver at m_driver.F90:705 (discriminator 2)
#16 0x40C2EE in MAIN__ at abinit.F90:444
#16 0x40C2EE in MAIN__ at abinit.F90:444
I am attaching the input file, output file and config.log file.
Please, suggest me the solution for this problem.
Thank you
Shivaprasad
PhD student
IIT Mandi, India.