Job Running Error
Posted: Thu May 26, 2022 11:05 am
I am usually unable to submit job more then almost 90 atoms. Please have a look to error and suggest solution.
ERROR
WARNING: random wavefunctions but no delay for mixing, default for NELMDL
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 186419 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 186420 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 2 PID 186421 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===========================================================================
[glow]job script
[/glow]
#!/bin/bash
#PBS -q batch
#PBS -N testing
#PBS -l nodes=1:ppn=32
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=1
source /home/abdul/.bashrc
mpirun -np 32 /home/abdul/VASP/vasp.6.1.2.fixcell/bin/vasp_std > vasprun.l
[glow]POSCAR[/glow]
This file is generated by VASPKIT code
1.000000
14.0653711830732568 0.0000000000000000 0.0000000000000000
-7.0326378837600583 12.1817370217174652 0.0000000000000000
0.0000000000000000 0.0000000000000000 35.0135993958000000
In W Se Te
24 16 24 32
Direct
0.0008398486615709 0.0026303932638031 0.6395539078451030 In1
0.0008398486615709 0.5026303932638031 0.6395539078451030 In2
0.5008398486615709 0.0026303932638031 0.6395539078451030 In3
0.5008398486615709 0.5026303932638031 0.6395539078451030 In4
0.1685780852979015 0.3387844397100557 0.6393165815766640 In5
0.1685780852979015 0.8387844397100557 0.6393165815766640 In6
0.6685780852979015 0.3387844397100557 0.6393165815766640 In7
0.6685780852979015 0.8387844397100557 0.6393165815766640 In8
0.3368150410057580 0.1704069459662106 0.6395061673677972 In9
0.3368150410057580 0.6704069459662106 0.6395061673677972 In10
0.8368150410057580 0.1704069459662106 0.6395061673677972 In11
0.8368150410057580 0.6704069459662106 0.6395061673677972 In12
0.0000208924376611 0.0021745229119978 0.5597127532106815 In13
0.0000208924376611 0.5021745229119978 0.5597127532106815 In14
0.5000208924376611 0.0021745229119978 0.5597127532106815 In15
0.5000208924376611 0.5021745229119978 0.5597127532106815 In16
0.1684358981286210 0.3393404780794760 0.5595405345313570 In17
0.1684358981286210 0.8393404780794760 0.5595405345313570 In18
0.6684358981286210 0.3393404780794760 0.5595405345313570 In19
0.6684358981286210 0.8393404780794760 0.5595405345313570 In20
0.3372682688618494 0.1703286449131534 0.5597246691324855 In21
0.3372682688618494 0.6703286449131534 0.5597246691324855 In22
0.8372682688618494 0.1703286449131534 0.5597246691324855 In23
0.8372682688618494 0.6703286449131534 0.5597246691324855 In24
0.2459844288476805 0.0854796391002310 0.3713128147671061 W1
0.2459844288476805 0.5854796391002310 0.3713128147671061 W2
0.7459844288476805 0.0854796391002310 0.3713128147671061 W3
0.7459844288476805 0.5854796391002310 0.3713128147671061 W4
0.2461496886574750 0.3367528139602705 0.3713504010830440 W5 ..................................
[shadow]System Information[/shadow]
%Cpu(s): 28.9 us, 0.0 sy, 0.0 ni, 71.1 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 21129285+total, 17721987+free, 32960643+used, 11123176 buff/cache
KiB Swap: 4194300 total, 4194300 free, 0 used. 17762040+avail Mem
ERROR
WARNING: random wavefunctions but no delay for mixing, default for NELMDL
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 186419 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 186420 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 2 PID 186421 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===========================================================================
[glow]job script
[/glow]
#!/bin/bash
#PBS -q batch
#PBS -N testing
#PBS -l nodes=1:ppn=32
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=1
source /home/abdul/.bashrc
mpirun -np 32 /home/abdul/VASP/vasp.6.1.2.fixcell/bin/vasp_std > vasprun.l
[glow]POSCAR[/glow]
This file is generated by VASPKIT code
1.000000
14.0653711830732568 0.0000000000000000 0.0000000000000000
-7.0326378837600583 12.1817370217174652 0.0000000000000000
0.0000000000000000 0.0000000000000000 35.0135993958000000
In W Se Te
24 16 24 32
Direct
0.0008398486615709 0.0026303932638031 0.6395539078451030 In1
0.0008398486615709 0.5026303932638031 0.6395539078451030 In2
0.5008398486615709 0.0026303932638031 0.6395539078451030 In3
0.5008398486615709 0.5026303932638031 0.6395539078451030 In4
0.1685780852979015 0.3387844397100557 0.6393165815766640 In5
0.1685780852979015 0.8387844397100557 0.6393165815766640 In6
0.6685780852979015 0.3387844397100557 0.6393165815766640 In7
0.6685780852979015 0.8387844397100557 0.6393165815766640 In8
0.3368150410057580 0.1704069459662106 0.6395061673677972 In9
0.3368150410057580 0.6704069459662106 0.6395061673677972 In10
0.8368150410057580 0.1704069459662106 0.6395061673677972 In11
0.8368150410057580 0.6704069459662106 0.6395061673677972 In12
0.0000208924376611 0.0021745229119978 0.5597127532106815 In13
0.0000208924376611 0.5021745229119978 0.5597127532106815 In14
0.5000208924376611 0.0021745229119978 0.5597127532106815 In15
0.5000208924376611 0.5021745229119978 0.5597127532106815 In16
0.1684358981286210 0.3393404780794760 0.5595405345313570 In17
0.1684358981286210 0.8393404780794760 0.5595405345313570 In18
0.6684358981286210 0.3393404780794760 0.5595405345313570 In19
0.6684358981286210 0.8393404780794760 0.5595405345313570 In20
0.3372682688618494 0.1703286449131534 0.5597246691324855 In21
0.3372682688618494 0.6703286449131534 0.5597246691324855 In22
0.8372682688618494 0.1703286449131534 0.5597246691324855 In23
0.8372682688618494 0.6703286449131534 0.5597246691324855 In24
0.2459844288476805 0.0854796391002310 0.3713128147671061 W1
0.2459844288476805 0.5854796391002310 0.3713128147671061 W2
0.7459844288476805 0.0854796391002310 0.3713128147671061 W3
0.7459844288476805 0.5854796391002310 0.3713128147671061 W4
0.2461496886574750 0.3367528139602705 0.3713504010830440 W5 ..................................
[shadow]System Information[/shadow]
%Cpu(s): 28.9 us, 0.0 sy, 0.0 ni, 71.1 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 21129285+total, 17721987+free, 32960643+used, 11123176 buff/cache
KiB Swap: 4194300 total, 4194300 free, 0 used. 17762040+avail Mem