计算化学公社
标题:
求助超算平台上用g09算了一个分子的opt/freq报错Error: segmentation violation
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作者Author:
AgOH
时间:
2023-12-5 00:16
标题:
求助超算平台上用g09算了一个分子的opt/freq报错Error: segmentation violation
老师们好，我在学校的超算平台上用g09算了一个分子的opt/freq，出现了一个报错，不知道该怎么处理想请教一下各位老师。
err文件：
Error: segmentation violation
rax 0000000000000000, rbx 0000000001263f80, rcx 000014a519ecb4bb
rdx 0000000000000000, rsp 00007ffc902dc068, rbp 00007ffc902dc090
rsi 000000000000000b, rdi 00000000000ae44e, r8 0000007d00001000
r9 000014a51aa2b200, r10 0000000000000006, r11 0000000000000202
r12 00007ffc902dc248, r13 00007ffc902dc250, r14 00007ffc902dc258
r15 0000142819c9f548
--- traceback not available
out文件末尾部分：
Number 0 0 0 0 0 0
Base 4472403 9902754 12270386 23370002 4453463 7540533
End 4473900 12255789 13467867 23377695 4472401 9899708
End1 4473900 12255789 13467867 23377695 4472401 9899708
Wr Pntr 4472403 9902754 12270386 23370002 4453463 7540533
Rd Pntr 4472403 9902754 12270386 23370002 4453463 7540533
Length 1497 2353035 1197481 7693 18938 2359175
Number 0 501 502 503 508 511
Base 25752714 6868656 6869656 13469171 2097152 6886967
End 27262976 6869656 6876081 13470081 2097182 7051994
End1 27262976 6869656 6876081 13470081 2097182 7051994
Wr Pntr 25752714 6868656 6869656 13469171 2097152 6886967
Rd Pntr 25752714 6868656 6869656 13469171 2097152 6886967
Length 1510262 1000 6425 910 30 165027
Number 512 520 521 522 524 526
Base 7057155 7092583 7540498 9899708 21013921 2097382
End 7059514 7092593 7540533 9902754 23370002 4453463
End1 7059514 7092593 7540533 9902754 23370002 4453463
Wr Pntr 7057155 7092583 7540498 9899708 21013921 2097382
Rd Pntr 7057155 7092583 7540498 9902754 21013921 2097382
Length 2359 10 35 3046 2356081 2356081
Number 528 530 532 534 536 538
Base 13842395 15039773 16237151 17434529 4473900 5671278
End 15039773 16237151 17434529 18631907 5671278 6868656
End1 15039773 16237151 17434529 18631907 5671278 6868656
Wr Pntr 13842395 15039773 16237151 17434529 4473900 5671278
Rd Pntr 13842395 15039773 16237151 17434529 5671278 6868656
Length 1197378 1197378 1197378 1197378 1197378 1197378
Number 551 552 561 562 563 565
Base 7092639 7092593 7085371 7085372 18631907 18633454
End 7092677 7092639 7085372 7092531 18633454 18634035
End1 7092677 7092639 7085372 7092531 18633454 18634035
Wr Pntr 7092639 7092593 7085371 7085372 18631907 18633454
Rd Pntr 7092639 7092593 7085371 7085372 18631907 18633454
Length 38 46 1 7159 1547 581
Number 575 577 579 580 581 582
Base 7092677 7092531 13839144 13839245 18634035 18637257
End 7540498 7092583 13839245 13842395 18637257 18641898
End1 7540498 7092583 13839245 13842395 18637257 18641898
Wr Pntr 7092677 7092531 13839144 13839245 18634035 18637257
Rd Pntr 7092677 7092531 13839144 13839245 18634035 18637257
Length 447821 52 101 3150 3222 4641
Number 583 584 603 605 619 634
Base 18641898 7059514 4472402 4472401 12255789 18642000
End 18642000 7060120 4472403 4472402 12270386 21013921
End1 18642000 7060120 4472403 4472402 12270386 21013921
Wr Pntr 18641898 7059514 4472402 4472401 12255789 18642000
Rd Pntr 18641898 7059514 4472402 4472401 12255789 21013921
Length 102 606 1 1 14597 2371921
Number 665 670 672 674 695 698
Base 7051994 6876081 13467867 13468230 7060120 13470081
End 7057155 6886967 13468230 13469171 7063279 13470687
End1 7057155 6886967 13468230 13469171 7063279 13470687
Wr Pntr 7051994 6876081 13467867 13468230 7060120 13470081
Rd Pntr 7051994 6886967 13467867 13468230 7060120 13470081
Length 5161 10886 363 941 3159 606
Number 701 780 989 993 997 998
Base 13470687 23377695 7063279 7083279 7083479 2097182
End 13839144 25752714 7083279 7083479 7085371 2097382
End1 13839144 25752714 7083279 7083479 7085371 2097382
Wr Pntr 13470687 23377695 7063279 7083279 7083479 2097182
Rd Pntr 13470687 25752714 7063279 7083279 7083479 2097382
Length 368457 2375019 20000 200 1892 200
dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 2097152
defal = T LstWrd = 4194304 FType=2 FMxFil=10000
Number 0
Base 2097152
End 4194304
End1 4194304
Wr Pntr 2097152
Rd Pntr 2097152
Length 2097152
Error termination in NtrErr:
NtrErr Called from FileIO.
输入文件部分：
%nprocshared=64
%mem=500GB
%chk=2segphos-ag-dipea.chk
#p opt freq
# B3LYP/genecp
按网上方法尝试过删除临时文件夹、删除输入文件中%chk=2segphos-ag-dipea.chk，但是仍然会出现同样的报错。
谢谢各位老师！
作者Author:
sobereva
时间:
2023-12-5 00:44
上传完整输入输出文件（过大就先压缩），说清楚可用硬盘空间、可用物理内存容量有多少
作者Author:
AgOH
时间:
2023-12-5 01:45
谢谢Sob老师回复！
平台上查询到的内存空间：
total used free shared buff/cache available
Mem: 527746232 25629724 483665568 4102916 18450940 494800016
Swap: 4194300 988428 3205872
查询到的磁盘空间：
Filesystem 1K-blocks Used Available Use% Mounted on
devtmpfs 263852824 0 263852824 0% /dev
tmpfs 263873116 172 263872944 1% /dev/shm
tmpfs 263873116 4108484 259764632 2% /run
tmpfs 263873116 0 263873116 0% /sys/fs/cgroup
/dev/mapper/cl-root 462765292 19042576 443722716 5% /
/dev/sda2 1038336 266336 772000 26% /boot
/dev/sda1 613184 7024 606160 2% /boot/efi
172.16.0.39:/nfsshare/studio 8314851328 6554852352 1340930048 84% /mnt/studio
tmpfs 52774620 0 52774620 0% /run/user/0
rdssg01 8040055046144 6558200725504 1481854320640 82% /dssg
tmpfs 52774620 0 52774620 0% /run/user/7325
tmpfs 52774620 0 52774620 0% /run/user/1822
tmpfs 52774620 0 52774620 0% /run/user/7694
192.168.51.3:/archive 12699432767488 17249918976 12682182848512 1% /mnt/cold_data
tmpfs 52774620 0 52774620 0% /run/user/8901
tmpfs 52774620 0 52774620 0% /run/user/1706
tmpfs 52774620 0 52774620 0% /run/user/1718
tmpfs 52774620 0 52774620 0% /run/user/3608
tmpfs 52774620 0 52774620 0% /run/user/1789
tmpfs 52774620 0 52774620 0% /run/user/5869
tmpfs 52774620 0 52774620 0% /run/user/4181
tmpfs 52774620 0 52774620 0% /run/user/7698
tmpfs 52774620 0 52774620 0% /run/user/8915
tmpfs 52774620 0 52774620 0% /run/user/7153
tmpfs 52774620 0 52774620 0% /run/user/5585
tmpfs 52774620 0 52774620 0% /run/user/7868
tmpfs 52774620 0 52774620 0% /run/user/1846
tmpfs 52774620 0 52774620 0% /run/user/7487
tmpfs 52774620 0 52774620 0% /run/user/2691
tmpfs 52774620 0 52774620 0% /run/user/4727
tmpfs 52774620 0 52774620 0% /run/user/8450
tmpfs 52774620 0 52774620 0% /run/user/8680
tmpfs 52774620 0 52774620 0% /run/user/3863
tmpfs 52774620 0 52774620 0% /run/user/1544
tmpfs 52774620 0 52774620 0% /run/user/5380
tmpfs 52774620 4 52774616 1% /run/user/1713
tmpfs 52774620 4 52774616 1% /run/user/5464
tmpfs 52774620 4 52774616 1% /run/user/1703
tmpfs 52774620 0 52774620 0% /run/user/8704
tmpfs 52774620 4 52774616 1% /run/user/3416
tmpfs 52774620 4 52774616 1% /run/user/3552
tmpfs 52774620 4 52774616 1% /run/user/1679
tmpfs 52774620 4 52774616 1% /run/user/2402
tmpfs 52774620 0 52774620 0% /run/user/3956
tmpfs 52774620 0 52774620 0% /run/user/4474
tmpfs 52774620 4 52774616 1% /run/user/7124
tmpfs 52774620 4 52774616 1% /run/user/7821
tmpfs 52774620 4 52774616 1% /run/user/8290
tmpfs 52774620 4 52774616 1% /run/user/8759
tmpfs 52774620 4 52774616 1% /run/user/2552
tmpfs 52774620 4 52774616 1% /run/user/2483
tmpfs 52774620 4 52774616 1% /run/user/3599
tmpfs 52774620 4 52774616 1% /run/user/2706
tmpfs 52774620 4 52774616 1% /run/user/8755
tmpfs 52774620 4 52774616 1% /run/user/3600
tmpfs 52774620 4 52774616 1% /run/user/3620
tmpfs 52774620 4 52774616 1% /run/user/1715
tmpfs 52774620 4 52774616 1% /run/user/8807
tmpfs 52774620 4 52774616 1% /run/user/7511
tmpfs 52774620 4 52774616 1% /run/user/8196
tmpfs 52774620 4 52774616 1% /run/user/1558
tmpfs 52774620 4 52774616 1% /run/user/7822
tmpfs 52774620 4 52774616 1% /run/user/7686
tmpfs 52774620 4 52774616 1% /run/user/1581
tmpfs 52774620 4 52774616 1% /run/user/7604
tmpfs 52774620 4 52774616 1% /run/user/8615
tmpfs 52774620 4 52774616 1% /run/user/8574
tmpfs 52774620 0 52774620 0% /run/user/5111
tmpfs 52774620 4 52774616 1% /run/user/4012
tmpfs 52774620 4 52774616 1% /run/user/6474
tmpfs 52774620 4 52774616 1% /run/user/8393
tmpfs 52774620 4 52774616 1% /run/user/1593
tmpfs 52774620 0 52774620 0% /run/user/8819
其他人在平台上算好像没有出过类似的问题
作者Author:
sobereva
时间:
2023-12-5 02:50
配体的基组改成6-311G(d,p)，基于之前最后一帧结构继续跑。去掉对当前毫无意义的弥散能节约巨量时间和内存消耗
仔细看
谈谈弥散函数和“月份”基组
http://sobereva.com/119
并且此体系应当带D3校正，仔细看
谈谈量子化学研究中什么时候用B3LYP泛函优化几何结构是适当的
http://sobereva.com/557
（
http://bbs.keinsci.com/thread-17899-1-1.html
）
谈谈“计算时是否需要加DFT-D3色散校正？”
http://sobereva.com/413
（
http://bbs.keinsci.com/thread-9772-1-1.html
）
内存超了。改成450GB
作者Author:
AgOH
时间:
2023-12-5 10:06
好的，谢谢老师！
作者Author:
NLJ
时间:
2024-6-28 10:42
AgOH 发表于 2023-12-5 10:06
**** 作者被禁止或删除 内容自动屏蔽 ****
请问最后解决了吗
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