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标题: 测试xtb dock 官方demo时出现的内存问题 [打印本页]

作者
Author: 18217265596 时间: 2024-9-6 09:52
标题: 测试xtb dock 官方demo时出现的内存问题
xtb本体是ok的
寻思测试一下xtb dock module的官方demo
xtb dock amine.xyz cat.xyz --alpb dmso
my xtb version is * xtb version 6.7.1 (edcfbbe) compiled by 'albert@albert-system'

it had performed the docking process.but while opt the docked structure, memory err occured
the .out ends with

Optimizing 15 best structures with gfn2

.err ↓
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image             PC             Routine          Line       Source
xtb             000000000046E88A  Unknown             Unknown  Unknown
xtb             0000000002D1BD40  Unknown             Unknown  Unknown
xtb             000000000092A456  xtb_axis_mp_axis2       234  axis_trafo.f90
xtb             0000000000B12BC9  xtb_optimizer_mp_       356  optimizer.f90
xtb             0000000000A2754E  xtb_geoopt_mp_geo       147  geoopt_driver.f90
xtb             000000000052DDC7  xtb_docking_searc       907  search_nci.f90
xtb             000000000040662E  xtb_prog_dock_mp_       284  dock.f90
xtb             0000000000450E5A  MAIN__                   73  primary.f90
xtb             0000000000401E42  Unknown             Unknown  Unknown
xtb             0000000002D1298A  Unknown             Unknown  Unknown
xtb             0000000002D14227  Unknown             Unknown  Unknown
xtb             0000000000401D05  Unknown             Unknown  Unknown

full slurm job:

#SBATCH -n 32
#SBATCH --ntasks-per-node=32
#SBATCH -o %j.out
#SBATCH -e %j.err

module purge
module load openmpi

ulimit -s unlimited
ulimit -l unlimited
export OMP_NUM_THREADS=32
export OMP_STACKSIZE=256G

xtb dock amine.xyz cat.xyz --alpb dmso

forrtl: severe (151): allocatable array is already allocated
Image             PC             Routine          Line       Source
xtb             000000000049883F  Unknown             Unknown  Unknown
xtb             000000000069E771  xtb_gfnff_neighbo       672  neighbor.f90
xtb             000000000069F15E  xtb_gfnff_neighbo       100  neighbor.f90
xtb             00000000005EB938  xtb_gfnff_ini_mp_       192  gfnff_ini.f90
xtb             000000000054F2E4  xtb_docking_searc       1075  search_nci.f90
xtb             0000000000522A8E  xtb_docking_searc       262  search_nci.f90
xtb             000000000040662E  xtb_prog_dock_mp_       284  dock.f90
xtb             0000000000450E5A  MAIN__                   73  primary.f90
xtb             0000000000401E42  Unknown             Unknown  Unknown
xtb             0000000002D1298A  Unknown             Unknown  Unknown
xtb             0000000002D14227  Unknown             Unknown  Unknown

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