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Apr 25, 2024 02:15 AM
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1. 准备工作
1.1 软件下载
- 下载 MobaXterm 终端软件(点我下载) 方便后面的操作,sftp 和 ssh 在一个界面非常友好,支持 x11 转发,全能终端工具,方便后面的操作
- 下载 GAMESS 软件包(点我下载)
1.2 修改 Ubuntu 源
更换源保证以后的下载速度。
修改
sources.list
文件把里面的全部删掉,修改成下面的:
修改完后,进行更新
1.3 安装一些包
首先安装
tmux
这样就能保证后台一直运行,就算断连也可以后台运作使用命令
tmux new -s gamess
建立一个 gamess 后台窗口,更多的 tumux 命令看这个(点我打开)一次性安装常见的 build 需要的各种组件:
2. Intel mkl 安装
使用命令:
包比较大,慢慢等待下载,我们已经使用 tmux 了,所以不用担心服务器断连。
下载完成后,使用命令
运行包,稍等一下,MobaXterm 会弹出可视化安装界面。
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fcea8c0ee-ea47-4a5f-bcac-e0cccf23c78e%2FUntitled.png?table=block&id=34e7a221-ffd0-43fa-bd09-1fbfed6c43e3&t=34e7a221-ffd0-43fa-bd09-1fbfed6c43e3&width=720&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F4d2cc17a-b234-4601-b992-f64a395b5ab2%2FUntitled.png?table=block&id=ff1d9b19-c898-41b4-8381-05fc10c97dda&t=ff1d9b19-c898-41b4-8381-05fc10c97dda&width=720&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F9c022146-1995-435f-9f7e-680cbb9d67b2%2FUntitled.png?table=block&id=63c0aa76-b58d-4a04-9067-57ccc0c41e78&t=63c0aa76-b58d-4a04-9067-57ccc0c41e78&width=720&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F40bbba2f-495c-4229-a156-996e3aca6673%2FUntitled.png?table=block&id=608700d5-e07f-420f-a1fc-6dc140562cd9&t=608700d5-e07f-420f-a1fc-6dc140562cd9&width=720&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F60a38f2a-f8bd-4ca7-9b25-805a0f2ad53b%2FUntitled.png?table=block&id=80d8df9c-dd9c-4ecb-b781-0797c92c5eef&t=80d8df9c-dd9c-4ecb-b781-0797c92c5eef&width=720&cache=v2)
最后慢慢等待安装
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F4deb75fe-efbf-45a1-998c-1b86f5ab947f%2FUntitled.png?table=block&id=36f35af0-3c13-4e02-9868-043e5b1c75dd&t=36f35af0-3c13-4e02-9868-043e5b1c75dd&width=720&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fb25723a8-1021-4d67-a7e9-c821297294ba%2FUntitled.png?table=block&id=b49579eb-b167-4c68-adec-72464b01ff7a&t=b49579eb-b167-4c68-adec-72464b01ff7a&width=720&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F5d8fdfdb-c7bf-4f98-a2d2-a9fb4b91e51f%2FUntitled.png?table=block&id=0f1e2aad-aab6-4dae-b3cb-47bed84402dc&t=0f1e2aad-aab6-4dae-b3cb-47bed84402dc&width=720&cache=v2)
3. GAMESS 安装
3.1 准备工作
将下载好的 GAMESS 软件包上传到服务器,MobaXterm 直接拖过去就行了。
进入家目录,然后解压
3.2 查看 gfortran 版本号
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F3c94ee9e-436b-4453-87e6-b1a497b6ca7d%2FUntitled.png?table=block&id=0e5c5473-d76f-4b6a-9f51-42b299d6e320&t=0e5c5473-d76f-4b6a-9f51-42b299d6e320&width=960&cache=v2)
记住这个数字 9.4 后面要用
3.3 GAMESS 设置
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F0fb6400b-762a-4768-ac4c-3428c0d818f8%2FUntitled.png?table=block&id=c20b62f0-b11b-4df4-a8da-6afe55e7e3ce&t=c20b62f0-b11b-4df4-a8da-6afe55e7e3ce&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fe1bf4e7f-3c45-4c7f-981f-c23924c12b71%2FUntitled.png?table=block&id=46514997-3162-4b84-8265-1640d8ad9d2a&t=46514997-3162-4b84-8265-1640d8ad9d2a&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F7df22bf4-1c5d-4ec0-a569-f2198b9a28ca%2FUntitled.png?table=block&id=3c05ba8d-88d2-47d0-9a08-0b67c34d819b&t=3c05ba8d-88d2-47d0-9a08-0b67c34d819b&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fe361619f-95fa-4f7b-944b-718f8a3888b2%2FUntitled.png?table=block&id=1115948c-7549-4546-a550-1f92251ef70e&t=1115948c-7549-4546-a550-1f92251ef70e&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fd14a5279-a4cc-4892-bbaf-088587db3b45%2FUntitled.png?table=block&id=d8d521a8-1ee8-4b34-9671-3b062da21ebc&t=d8d521a8-1ee8-4b34-9671-3b062da21ebc&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F6abc7d7e-2ad9-48a3-94fb-06161428fbbe%2FUntitled.png?table=block&id=bfe482b2-cb38-491f-a421-f326f18930bd&t=bfe482b2-cb38-491f-a421-f326f18930bd&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F234df792-bc67-4602-8ad6-59dcb17a78ee%2FUntitled.png?table=block&id=54c344d2-5bbe-423b-b5d4-fd5fe5ccab48&t=54c344d2-5bbe-423b-b5d4-fd5fe5ccab48&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F9e7a502a-fefb-4c65-8ec2-2e81cc4fa0b6%2FUntitled.png?table=block&id=4f7a67e6-acfa-498f-8ae6-d20fdcf1a2aa&t=4f7a67e6-acfa-498f-8ae6-d20fdcf1a2aa&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F7ec8512e-ff1b-4da3-8dad-c2f203b78b0b%2FUntitled.png?table=block&id=f9fc2127-5b81-4d4d-b1eb-8e3e9df6bf45&t=f9fc2127-5b81-4d4d-b1eb-8e3e9df6bf45&width=960&cache=v2)
下面填入这个
/opt/intel/oneapi/mkl/2022.0.2
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Ffc590970-2508-4e63-bd06-7fe9e55eedc1%2FUntitled.png?table=block&id=fa589d9e-a8e8-44f4-a259-41f5f6075a98&t=fa589d9e-a8e8-44f4-a259-41f5f6075a98&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F4b544673-f256-4e2c-9cd8-28f29ec979f1%2FUntitled.png?table=block&id=87b2ea03-0df8-4bee-811b-07496ad664e7&t=87b2ea03-0df8-4bee-811b-07496ad664e7&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F0afda21c-b313-48eb-96c0-4d0d178f182c%2FUntitled.png?table=block&id=f24ace92-a3d0-4419-a523-7763e3642846&t=f24ace92-a3d0-4419-a523-7763e3642846&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F2d792816-b6ed-4c3a-b32c-03c6254e7c1d%2FUntitled.png?table=block&id=9994fdd1-cae1-45a4-b3de-7b427512fd3b&t=9994fdd1-cae1-45a4-b3de-7b427512fd3b&width=960&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fa753c3e9-30dd-4aba-a9c0-dddce9e763c4%2FUntitled.png?table=block&id=22b3c9be-cb20-47c1-9654-4e655eeae530&t=22b3c9be-cb20-47c1-9654-4e655eeae530&width=960&cache=v2)
3.4 编译
编译之前,
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F7583d59d-efad-4cdf-8c06-ed847d01bfb4%2FUntitled.png?table=block&id=24f7045c-ed29-485e-9812-01361dacca2e&t=24f7045c-ed29-485e-9812-01361dacca2e&width=912&cache=v2)
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F145d9471-9a46-4d8b-9808-861e81f50cae%2FUntitled.png?table=block&id=e3173baa-5051-4cc3-9463-61018d30cd62&t=e3173baa-5051-4cc3-9463-61018d30cd62&width=1248&cache=v2)
修改后之后然后编译
然后
最后
我这里是 64 ,64代表你的cpu的核数,这个过程比较久,慢慢等就行了,我们已经用了 tmux ,不用担心断连
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fd6a7c05f-ce18-4fc8-b32d-e63b70804734%2FUntitled.png?table=block&id=0f8a53e2-e2f3-4be1-95f3-665c48295234&t=0f8a53e2-e2f3-4be1-95f3-665c48295234&width=912&cache=v2)
得到这个说明成功了
3.5 增加最大共享内存
然后在最下面一行填入
注意这里的 N=你的内存*1024*1024*1024 需要自己手动计算
3.6 rumge 配置
先建立一个 restart 文件夹
先使用命令
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Ff9d74263-6800-4cd3-8759-1b09a488954f%2FUntitled.png?table=block&id=283060ba-36a3-4914-b1da-342966e317fd&t=283060ba-36a3-4914-b1da-342966e317fd&width=528&cache=v2)
得到你的机器名字,马上我们就要用,记住。
然后进入
$HOME/gamess
目录用文本编辑器打开![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Ff3230f97-7dac-46de-acc8-923cbf0acec6%2FUntitled.png?table=block&id=008edd5d-3dc7-4436-bafc-e478e193e96f&t=008edd5d-3dc7-4436-bafc-e478e193e96f&width=816&cache=v2)
修改第二行,加入
rm -rf $HOME/gamess/restart/*
代码![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fd54e28ec-13dc-4ae9-a134-f695090e2af7%2FUntitled.png?table=block&id=d5307b6b-9916-40ed-bd37-f5c800e42ab7&t=d5307b6b-9916-40ed-bd37-f5c800e42ab7&width=1344&cache=v2)
修改核数
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F716ed42f-41f0-4628-9192-d389b9dbed32%2FUntitled.png?table=block&id=9cd7f4b6-741a-4fd3-a8ad-cc82774b7d90&t=9cd7f4b6-741a-4fd3-a8ad-cc82774b7d90&width=816&cache=v2)
找到448行
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F049155c6-ddb7-4f8b-a69f-d1e8dce0905c%2FUntitled.png?table=block&id=e1149b9b-aad5-47b0-9caa-6dc137291d54&t=e1149b9b-aad5-47b0-9caa-6dc137291d54&width=816&cache=v2)
空一行加入这个代码
这里的 master 改成你的 hostname
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F045e65fa-00f8-4e05-a54e-6fb7e3c44908%2FUntitled.png?table=block&id=b10ac7a5-447a-436b-9d11-3eba5bae2592&t=b10ac7a5-447a-436b-9d11-3eba5bae2592&width=912&cache=v2)
3.7 运行测试
在运行测试之前,运气不好你会遇到这个错误
The GAMESS executable gamess.0.0.x
or else the DDIKICK executable ddikick.x
could not be found in directory /home/wxyhgk/src/gamess,
or else they did not properly link to executable permission.
所以你需要这样
开始运行测试
这里的测试项是做什么的可以到这里查看(点我打开)
等待他测试完,运行好之后,我们使用命令
看看48个任务是否全部通过测试
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fe51e7db7-d66b-4830-91a5-2ed17c7fa489%2FUntitled.png?table=block&id=479e3c4e-8a6c-4031-8c2b-78e05f562622&t=479e3c4e-8a6c-4031-8c2b-78e05f562622&width=480&cache=v2)
这里很多时候不通过会出现所谓的 901 错误,像这样
这个错误的原因有这么种情况
- 前面的没配置好
- 没有设置内存
- 核数配置错误了
- 提前设置了多核运行
3.8 配置多核运行
修改 runall 文件里面的设置,首先修改hostname
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2F38a8d343-3c36-4cf2-9c40-43544511d9db%2FUntitled.png?table=block&id=0b8f3f18-6196-485e-8fe2-b640d8f05e64&t=0b8f3f18-6196-485e-8fe2-b640d8f05e64&width=912&cache=v2)
然后修改核数
![notion image](https://www.notion.so/image/https%3A%2F%2Fs3-us-west-2.amazonaws.com%2Fsecure.notion-static.com%2Fe5b01801-0f67-4a52-bad9-6788cdd9bfe6%2FUntitled.png?table=block&id=2702dbe1-b382-45fc-918e-dcaf1a3e2cac&t=2702dbe1-b382-45fc-918e-dcaf1a3e2cac&width=912&cache=v2)
3.9 其他
配置环境变量
在最后一行加入以下代码
加入完成之后,保存,然后退出终端,重新进去就能使用 gms 命令了
运行 GAMESS :
这里 name 是你的输入文件名字
4. 参考文章
4.1 tumx
4.2 GMAESS 安装教程
4.3 GAMESS 测试项官方说明
- 作者:我心永恒
- 链接:https://wxyhgk.com/article/ubuntu-gamess
- 声明:本文采用 CC BY-NC-SA 4.0 许可协议,转载请注明出处。