计算化学公社
标题: 求助在Ubuntu 中运行G16 在shell中出现Segmentation fault报错，但log中没有提示 [打印本页]
作者Author: zhangzhiyuanscu 时间: 2022-6-29 10:04
标题: 求助在Ubuntu 中运行G16 在shell中出现Segmentation fault报错，但log中没有提示
我是新手。在运行g16时遇到了“Segmentation fault”报错。该报错打印在Shell中，在log文件里面我没有找到相应的错误提示。完全相同的输入文件在另外一台服务器中可以正常的运行，算出结果。
另外，尝试将内存改为1000WM或者去掉%mem，以及去掉%nproc没有解决问题，报错相同。
我在网上找了一些回答都是单纯针对C/C++的，例如：
1.(139条消息) Segmentation Fault错误原因总结_喜欢恋着风的博客-CSDN博客_segmentationfault
2.Segmentation fault细谈 - 知乎 (zhihu.com)
对于怎么从g16软件的层面或者直接从linux的层面解决问题暂时没有找到。
因为我不会C/C++所以看完之后也不知道该怎么办。希望站中的老师们能帮忙找一找原因，不胜感激！
我的gjf输入文件如下：--------------------------------------------------------------------------------------------
%chk=/home/server/gw/chk/Mg-MEDJOW-2.chk
%mem=5GB
%nproc=32
# M062X/Def2SVP opt freq
Mg-MEDJOW-2
1 1
Mg1 -3.3382 5.6034 5.0723
O1 -4.6535 6.5395 6.3997
C1 -5.9757 6.2507 6.0305
O2 -6.2124 5.5478 5.0624
C2 -7.0224 6.8798 6.9265
C3 -6.547 7.6459 7.9766
C4 -7.4135 8.2674 8.8577
C5 -8.7609 8.1507 8.7276
C6 -9.3132 7.384 7.6785
C7 -10.716 7.2595 7.5389
C8 -11.2558 6.5223 6.5304
C9 -10.4365 5.8838 5.6268
C10 -9.0791 5.976 5.7228
C11 -8.4434 6.7294 6.7514
H1 -5.4836 7.7801 8.1375
H2 -7.0083 8.861 9.6705
H3 -9.4162 8.6496 9.434
H4 -11.3703 7.7588 8.2459
H5 -12.3336 6.4376 6.4383
H6 -10.8772 5.2985 4.8265
H7 -8.4921 5.4507 4.9815
-----------------------------------------------------------------------------------------------------------
报错后的log文件如下：
-----------------------------------------------------------------------------------------------------------
Entering Gaussian System, Link 0=g16
Initial command:
/home/zzy/sw/g16/l1.exe "/home/zzy/sw/tmp/Gau-11960.inp" -scrdir="/home/zzy/sw/tmp/"
Entering Link 1 = /home/zzy/sw/g16/l1.exe PID= 11962.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016,
Gaussian, Inc. All Rights Reserved.
This is part of the Gaussian(R) 16 program. It is based on
the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.),
the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.),
the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
University), and the Gaussian 82(TM) system (copyright 1983,
Carnegie Mellon University). Gaussian is a federally registered
trademark of Gaussian, Inc.
This software contains proprietary and confidential information,
including trade secrets, belonging to Gaussian, Inc.
This software is provided under written license and may be
used, copied, transmitted, or stored only in accord with that
written license.
The following legend is applicable only to US Government
contracts under FAR:
RESTRICTED RIGHTS LEGEND
Use, reproduction and disclosure by the US Government is
subject to restrictions as set forth in subparagraphs (a)
and (c) of the Commercial Computer Software - Restricted
Rights clause in FAR 52.227-19.
Gaussian, Inc.
340 Quinnipiac St., Bldg. 40, Wallingford CT 06492
---------------------------------------------------------------
Warning -- This program may not be used in any manner that
competes with the business of Gaussian, Inc. or will provide
assistance to any competitor of Gaussian, Inc. The licensee
of this program is prohibited from giving any competitor of
Gaussian, Inc. access to this program. By using this program,
the user acknowledges that Gaussian, Inc. is engaged in the
business of creating and licensing software in the field of
computational chemistry and represents and warrants to the
licensee that it is not a competitor of Gaussian, Inc. and that
it will not use this program in any manner prohibited above.
---------------------------------------------------------------
Cite this work as:
Gaussian 16, Revision A.03,
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone,
G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich,
J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian,
J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young,
F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone,
T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega,
G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda,
J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai,
T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta,
F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin,
V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand,
K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar,
J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi,
J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas,
J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
******************************************
Gaussian 16: ES64L-G16RevA.03 25-Dec-2016
28-Jun-2022
******************************************
%chk=/home/zzy/gw/chk/Mg-MEDJOW-2-L.chk
%mem=5GB
%nproc=32
Will use up to 32 processors via shared memory.
------------------------
# M062X/Def2SVP opt freq
------------------------
1/18=20,19=15,26=3,38=1/1,3;
2/9=110,12=2,17=6,18=5,40=1/2;
3/5=43,7=101,11=2,25=1,30=1,71=1,74=-55/1,2,3;
4//1;
5/5=2,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
7//1,2,3,16;
1/18=20,19=15,26=3/3(2);
2/9=110/2;
99//99;
2/9=110/2;
3/5=43,7=101,11=2,25=1,30=1,71=1,74=-55/1,2,3;
4/5=5,16=3,69=1/1;
5/5=2,38=5/2;
7//1,2,3,16;
1/18=20,19=15,26=3/3(-5);
2/9=110/2;
6/7=2,8=2,9=2,10=2,19=2,28=1/1;
99/9=1/99;
--------------------------------------------------------------------------------------------------------------------
作者Author: abin 时间: 2022-6-29 18:21
你到底有多少内存？
多少个处理器核心？
作者Author: Lucas_xin 时间: 2022-6-29 19:13
把chk的绝对路径删掉试试
作者Author: sobereva 时间: 2022-6-29 21:05
首先先确保Gaussian已经按下文正确安装了，Default.Route没不当设置
Gaussian的安装方法及运行时的相关问题
http://sobereva.com/439（http://bbs.keinsci.com/thread-10814-1-1.html）
另外，不管能不能运行，%mem=5GB结合%nproc=32这种设置都是荒谬的，没理由就给这么丁点内存
然后按3L说的去掉%chk再试，至少确保%chk指定的路径有读写权限，而且相应目录是确实存在的
若还不行，应当是Gaussian和软硬件环境兼容性问题。说明操作系统和CPU的详细信息
作者Author: sun0615 时间: 2023-3-20 17:16
这通常是系统内存不足，怎么改input file都没用的，只算一个H也会跳Segmentation fault。
举个例子，我今天在阿里云开了一台免费的V*S，一个vcpu，1G内存
进入系统后，发现可用的内存根本没多少，跑g09直接跳Segmentation fault
Top看到的信息:
KiB Mem : 1008348 total, 158488 free, 101380 used, 748480 buff/cache
V*S系统默认的SWAP是0，我新增了一个4G的SWAP就可以正常执行了。
KiB Swap: 4194300 total, 4194300 free, 0 used. 748480 avail Mem
Linux新增SWAP请参考https://hoohoo.top/blog/7937896/
题外话:
其实拿免费的V*S来跑Gaussian实际的应用价值不大，因为太慢了。我只是好奇阿里云的Intel 8269CY和Oracle的AMD EPYC 7551效能差异多少，都用一个免费的vcpu相比，阿里云的速度差不多是Oracle的两倍多。
作者Author: abin 时间: 2023-3-20 20:31
V*S都是超售的……
这种比较没有意义。
租用bare metal 机器做测试。
作者Author: tiandikuoyuan 时间: 2023-6-3 19:04
用hyper-v搭建的centos虚拟机上运行的时候发现出现了同样的问题，应该是虚拟机使用了动态内存，系统会根据使用量为虚拟机分配内存以增加宿主机的内存。把动态内存关掉就好了。
| 欢迎光临 计算化学公社 (http://bbs.keinsci.com/) |
Powered by Discuz! X3.3 |