To receive notifications about scheduled maintenance, please subscribe to the mailing-list gitlab-operations@sympa.ethz.ch. You can subscribe to the mailing-list at https://sympa.ethz.ch

setup.md 17.3 KB
Newer Older
1
2
3
4
### **Setup**

#### Get permissions

5
6
Before setting up, you need permissions to access the codes and the input database. Email the following people to ask for the corresponding permissions.

Xuqian Yan's avatar
Xuqian Yan committed
7
```Note:: |:warning:| Currently, the codes are only accessible with an ETH account.
8
9
```

10
11
- Xuejiao Han (xuhan@eeh.ee.ethz.ch):
  - permission for the **DistIv** repository
12
  - access to the **PSL server** for the database (server name: itet-psl-s02)
13
- Jared Garrison (garrison@fen.ethz.ch):
14
15
  - permissions for the **eMark** repository
  - permissions for the **Shared** repository,
16
- Blazhe Gjorgiev (gblazhe@ethz.ch):
17
18
19
20
21
22
23
  - permission for the **Cascades** repository
  - permission for the **Run_Nexuse** repository
- Elena Raycheva (elena.raycheva@esc.ethz.ch):
  - permission for the **CentIv** repository
- Florian Landis  (landisf@ethz.ch):
  - permission for the **GemEl** repository
- Xuqian Yan (xuqian.yan@esc.ethz.ch):
Xuqian Yan's avatar
Xuqian Yan committed
24
  - permission for the overarching **Nexus-e** repository (<https://gitlab.ethz.ch/xyan/nexus-e.git>)
25

26
#### Local setup
27
Even though the current Nexus-e platform is **not** suitable to run locally because of high consumption of resources such as memory, we do recommend to at least get the codes and connect to the database locally in order to view, understand, and edit them easily.
28

Xuqian Yan's avatar
Xuqian Yan committed
29
30
31
Most the instructions below have been tested both on **Windows** and on **Mac**.

#####  1. Get the codes
32
Make sure you have installed [git](https://git-scm.com/).
Xuqian Yan's avatar
Xuqian Yan committed
33

34
The instructions here use **command lines**. If you have a GUI tool for git, you could use the corresponding operations in the GUI tool instead. An example using a GUI tool "GitKraken" can be found in section [Nexus-e repository instructions](nexuse_repo_instruction.html).
Xuqian Yan's avatar
Xuqian Yan committed
35
36
37
38
39
40
41
42
43

- Create a folder where you want to put the codes

- cd to that folder

- Clone the overarching repository with this command:

  ```git clone --recursive https://gitlab.ethz.ch/xyan/nexus-e.git```

Xuqian Yan's avatar
Xuqian Yan committed
44
  You will be asked for your username and password for the repository and its submodules.
Xuqian Yan's avatar
Xuqian Yan committed
45

Xuqian Yan's avatar
Xuqian Yan committed
46
In the end, the folder will look like the screenshot below. Note: You might not see the hidden files whose names start with a dot, and the `Results` folder will be automatically generated when you run Nexus-e.
Xuqian Yan's avatar
Xuqian Yan committed
47
48
49
50
51
52

![](images/nexus-e-folder.png)


##### 2. Connect with the input database

Xuqian Yan's avatar
Xuqian Yan committed
53
- Find information to connect with the database in `UserDBInfo.txt` in the repository. The file contains four lines (for confidentiality the username and password is not written here, but can be found in the file):
54
55
56
```
itet-psl-s02
3306
Xuqian Yan's avatar
Xuqian Yan committed
57
58
DATABASE_USERNAME
DATABASE_PASSWORD
59
60
61
62
63
64
```

- View the database
  - Install MySQL and MySQL Workbench
  - Connect to ETH VPN
  - Connect to the database with MySQL Workbench
65
    - Add a new MySQL connection
66
    ![](images/mysql-workbench-1.png)
67
    - Input connection information
68
    ![](images/mysql-workbench-2.png)
69
70
    - Click the button `Test Connection`. You will be asked to input your database password. Then you will see a seccess message:
    ![](images/mysql-workbench-3.png)
71
    ```eval_rst
72
73
    |:warning:| By default, everyone has write permission to the database. Therefore, to be safe, always make a local copy of the database before playing with it - i.e., first “Dump” it to a local folder, then import it to your personal MySQL account. These can be done in this window:
    ```
Xuqian Yan's avatar
Xuqian Yan committed
74
    ![](images/mysql-workbench-dump.png)
75

76
77
- (Optional) Work with a local copy of the database

78
79
    - Create a new text file to substitute `UserDBInfo.txt`.  
    For example, if you have dumped the common database to your local hosted database with IP address `127.0.0.1`, you could create a new text file as the following:
Xuqian Yan's avatar
Xuqian Yan committed
80
81
82
83
84
    ```
    127.0.0.1
    3306
    YOUR_LOCAL_USERNAME (e.g. "root")
    YOUR_LOCAL_PASSWORD
85
86
    ```  
    - Name the new file as  `UserDBInfo_xxx.txt`  (e.g., `UserDBInfo_local.txt`). An underscore "_" after "UserDBInfo" is needed to not synchronize it on git (see the file `.gitignore`).
Xuqian Yan's avatar
Xuqian Yan committed
87
    - Place the new file in the same folder as `UserDBInfo.txt`.
88
89
    - Point to the new file in the script.
      - Make a copy of `user_example_conf.m` in the folder `Run_Nexuse`. Name the copy as `user_conf.m`. (Note: You should only work with the local copy, because the original `xxx_example_conf.m` will be synchronized to git and it shouldn't be changed.)
Xuqian Yan's avatar
Xuqian Yan committed
90
      - Uncomment and adapt the variable `DB_INFO_FILE` in `user_conf.m` to be the new file name (e.g., `DB_INFO_FILE = 'UserDBInfo_local.txt';`).
91
92
93
94

    You might encounter the following problems when you run Nexus-e with a local database, follow the link for possible solutions:
    (1) [Error: "Access denied for user 'your_username'@'your_host_address' ..."](faq.html#access-denied-to-access-database)
    (2) [Error: "The server time zone value 'xxx' is unrecognized ..."](faq.html#database-server-timezone-issue)
Xuqian Yan's avatar
Xuqian Yan committed
95
    (3) [Error: "The user specified as a definer ('xxx'@'%') does not exist ..."](faq.html#database-definer-missing)
Xuqian Yan's avatar
Xuqian Yan committed
96
97

##### 3. Prepare software & license
98
You could skip this section if you don't plan to run the whole Nexus-e platform locally.
Xuqian Yan's avatar
Xuqian Yan committed
99

Xuqian Yan's avatar
Xuqian Yan committed
100
- **Matlab** (2018a or higher)
Xuqian Yan's avatar
Xuqian Yan committed
101
102
103

  - Set up database connector

104
    - Download the **MySQL connector** from [here](https://dev.mysql.com/downloads/connector/j/).
105
    Or, if you have access to the Nexus-e polybox, use the `mysql-connector-java-8.0.18.zip` provided in the folder `02_Model/02_Model_Setup_Instruction` (**Unzip** the file before the next step).
Xuqian Yan's avatar
Xuqian Yan committed
106

107
    - Copy the MySQL connector folder (e.g. mysql-connector-java-8.0.18) into a folder at your preference.
Xuqian Yan's avatar
Xuqian Yan committed
108
109
110
111
    We recommend to put it into the **Matlab preferences folder**, which you can find by typing in Matlab Command Window ```prefdir```.

    - Create a **javaclasspath.txt** file in the **Matlab preferences folder**.

112
    - In the **javaclasspath.txt** file, write the path to the connector .jar file that you just copied.
Xuqian Yan's avatar
Xuqian Yan committed
113
114
115
    E.g., On Blazhe's Windows computer the path is `C:\Users\gblazhe\AppData\Roaming\MathWorks\MATLAB\R2018a\mysql-connector-java-8.0.18\mysql-connector-java-8.0.18.jar`.

    - Reload Matlab
116
117

    - Test whether a database connector is set up successfully. Write the following commands in Matlab (substitue `YOUR_USERNAME` and `YOUR_PASSWORD` with your credentials for the database). If the second command returns `1`, it means success.
Xuqian Yan's avatar
Xuqian Yan committed
118
    ```
Xuqian Yan's avatar
Xuqian Yan committed
119
    conn = database("sys", YOUR_USERNAME, YOUR_PASSWORD, 'Vendor', 'MySQL', 'Server', "YOUR_HOST");
Xuqian Yan's avatar
Xuqian Yan committed
120
121
    isopen(conn)
    ```
122
123

- **Python** (3.x)
Xuqian Yan's avatar
Xuqian Yan committed
124
125
126
  ```eval_rst
  |:warning:| Note: we are now in the phase of transferring from python 2.x to python 3.x. Therefore, it is recommended to use python 3.x locally and identify potential issues for the transfer.

127
  ```
Xuqian Yan's avatar
Xuqian Yan committed
128
  - Python packages: install the required packages listed in `requirements.txt`.
129
  - Python path: If you use Mac or if you want to run Nexus-e in a python virtual environment, you need to configure Python path in Matlab. Otherwise, you could skip this step.
Xuqian Yan's avatar
Xuqian Yan committed
130
131
132
    - Make a copy of `user_example_conf.m` in the folder `Run_Nexuse`. Name the copy as `user_conf.m`. (Note: You should only work with the local copy, because the original `xxx_example_conf.m` will be synchronized to git and it shouldn't be changed.)
    - Find out your python path (it varies largely depending on your PC's operating system and how you installed python). Uncomment and adapt the variable `PATH_PYTHON` in `user_conf.m` accordingly.
    - If you have a python virtual environment, you could configure it following the instructions in `user_conf.m`.
Xuqian Yan's avatar
Xuqian Yan committed
133
134
135
136
137
138
139

- **GAMS**
  - Download from [here](https://www.gams.com/download/)
  - Set GAMS License
    - Use the `gamslice.txt` provided in polybox `02_Model/02_Model_Setup_Instruction`.
    - Install the license: [here](https://support.gams.com/installation:how_do_i_install_a_license_file) or [here](https://www.youtube.com/watch?v=vSe3YGkUVoc) or (for MacOS) [here](https://www.gams.com/latest/docs/UG_MAC_INSTALL.html).
  - GAMS path
Xuqian Yan's avatar
Xuqian Yan committed
140
141
    - If you haven't done so, make a copy of `user_example_conf.m` in the folder `Run_Nexuse`. Name the copy as `user_conf.m`. (Note: You should only work with the local copy, because the original `xxx_example_conf.m` will be synchronized to git and it shouldn't be changed.)
    - Find out your GAMS path (it varies largely depending on your PC's operating system and the version of GAMS). Uncomment and adapt the variable `PATH_GAMS` in `user_conf.m` accordingly.
142
143
144
145
    
- **Gurobi**(9.x)  
    - Download Gurobi and set up a free Gurobi academic license <https://www.gurobi.com/academia/academic-program-and-licenses>. 
    - Connect Gurobi with Matlab following [this instruction](https://www.gurobi.com/documentation/9.0/quickstart_mac/matlab_setting_up_grb_for_.html).
Xuqian Yan's avatar
Xuqian Yan committed
146
147

##### 4. Run Nexus-e
148

Xuqian Yan's avatar
Xuqian Yan committed
149
150
- Connect to ETH VPN (in order to connect with the database)
- Open Matlab
151
152
- Before running `run_Nexuse.m` for the first time, you need to run `bench_Nexuse.m`.
  It is recommended to repeat this step after major changes to the modules eMark and CentIv.
Xuqian Yan's avatar
Xuqian Yan committed
153
154
155
156
- Run the script `run_Nexuse.m` in the `Run_Nexuse` folder
  - You could change the variables `scen`, `tpRes`, and `limDifference` as instructed in the script
  - Consult Blazhe Gjorgiev (gblazhe@ethz.ch) if you want to run other scripts in the `Run_Nexuse` folder.

157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
#### Software for interacting with Euler from local machine ####

In our experience, it is usefull to have two tools available for
- transferring files between Euler and your local machine and
- interacting with the command prompt on Euler.

**GUIs for file transfer**

For transferring files between Euler and your personal computer, a graphical user interface (GUI) is useful.
We suggest [FileZilla](https://filezilla-project.org/) since it is available for "all" platforms.
The scicomp wiki also has [information](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters#Graphical_tools) on this.

**Command prompts for secure shell connections**

Unix systems (Linux/Mac) come with shells (command prompts) from which useful interactions with Euler are possible.
E.g., type `ssh <username>@euler.ethz.ch` to make a "secure shell" connection to Euler and issue commands to the Euler command prompt.
Windows users are less fortunate and have to install additional software to achieve this functionality.
Examples are
- putty.exe and
- [MobaXterm](https://mobaxterm.mobatek.net/).

We can highly recommend MobaXTerm.

<!-- ##### Install: putty.exe (not needed for Mac) ##### -->

<!-- Putty is command promt like interface from which you run your scripts on the cluster. -->
<!-- Use the commands below to run everything through putty. -->

<!-- ##### Install: WinSCP.exe/or Filezilla (for Mac) ##### -->

<!-- WinSCP is your GUI with your folder on the cluster, there you put your scripts and receive your results. -->
<!-- Results must be saved with a command in your script: -->
<!-- save (‘results’,’Var1’,’Var2’…). Var1, Var2, … denote the variables you want to save, while results denote the name of the file crated by Matlab (this is wat you see in WinSCP). -->

<!-- Remember to type in port 22 (default might be different) -->

**Login**

- Log-in with `ssh` on Unix-based operating systems:

  `ssh <ethz-username>@euler.ethz.ch`

  Lacking SSH keys, ssh will ask you for your ETH (LDAP) password and after that your following commands are issued to Euler.
  See [scicomp wiki](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters#SSH) for instructions for setting up SSH keys if desired.
- File transfers between local and Euler in FileZilla can be made through `sftp` (secure file transfer protocol).
  For this, enter `sftp://euler.ethz.ch` in the 'server' field and your ETH-user name and password in the respective fields, then hit 'connect'.
- Access to Euler: since May 2020, first time access to Euler is only granted upon request. ETH account holders just write an email to	cluster-support@id.ethz.ch;
   If you used the Euler cluster before the 15. May 2020, then you
   would need to change
   your LDAP password to get again access to the Euler cluster
   (wait for 1 day until the change takes effect).
   (see https://scicomp.ethz.ch/wiki/Getting_started_with_clusters
   for more info).

<!-- #### Starting steps #### -->

<!--  - login on putty (Hostname: euler.ethz.ch; than ethz username and pasword) -->
<!--  - login on the WinSCP (Hostname: euler.ethz.ch; than ethz username and	password) -->
<!--  - -->

<!-- NOTE: You can use windows Command Prompt to run your jobs on Euler instead of Putty. In this case, you can connect by typing: ssh username@euler.ethz.ch -->

<!-- #### Alternative to Putty #### -->

<!-- MobaXterm https://mobaxterm.mobatek.net/ -->

<!-- It offers more options and better interface looks then Putty.  In the same time, it can replace WinSCP. Strongly recommended. However for copying/transferring files from/to Euler -->
<!-- folders is slow. For this purpose WinSCP is better. [FileZilla](https://filezilla-project.org/) does the job well, too. -->

226
#### Euler setup
227
228
229
In order to run the full Nexus-e platform efficiently, we use [Euler](https://scicomp.ethz.ch/wiki/Euler), an ETH cluster for High Performance Computing. To set up the Nexus-e platform on Euler, you first need to access Euler. Instructions on accessing Euler and commands for Euler can be found [here](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters#Euler).

##### 1. Join the Nexus-e user group
230
We have a user group for access to Nexus-e specific licenses (e.g. GAMS) and the Euler pre-paid share. The user group is called: **MAVT-esc-nexus-e**, and is set and maintained by D-MAVT IT. To join the user group, ask Blazhe Gjorgiev (gblazhe@ethz.ch) to send an email to `servicedesk@mavt.ethz.ch`.
231
232

To check whether you are added to the user group, use command line ssh to Euler (type `ssh username@euler.ethz.ch`), then type `groups` to show a list of groups that your user account is linked to, which should contain “MAVT-esc-nexus-e”.
Xuqian Yan's avatar
Xuqian Yan committed
233
234

##### 2. Get the codes
235

236
237
238
239
- Create a folder where you want to put the codes
- cd to that folder
- Clone the overarching repository with this command:
  ```git clone --recursive https://gitlab.ethz.ch/xyan/nexus-e.git```
Xuqian Yan's avatar
Xuqian Yan committed
240
  You will be asked for your username and password for the repository and its submodules.
241

Xuqian Yan's avatar
Xuqian Yan committed
242
243
In the end, the folder will look like the screenshot below. Note: tThe `Results` folder will be automatically generated when you run Nexus-e.
![](images/euler-nexus-e-folder.png)
244
245

##### 3. Connect with the input database
246
- Download the **MySQL connector** from [here](https://dev.mysql.com/downloads/connector/j/).
247
248
Or, if you have access to the Nexus-e polybox, use the `mysql-connector-java-8.0.18.zip` provided in the folder `02_Model/02_Model_Setup_Instruction` (**Unzip** the file before the next step).

249
- Copy the MySQL folder in the hidden .matlab folder (e.g., .matlab/2019b)
250
251
252

- Create a **javaclasspath.txt** file in the same folder as above.

253
- In the **javaclasspath.txt** file, write the path to the connector .jar file that you just copied.
254
255
256
257
258
259
260
E.g., On Blazhe's Euler account the path is `/cluster/home/gblazhe/.matlab/R2018a/mysql-connector-java-8.0.18/mysql-connector-java-8.0.18.jar`.

- Logoff and re-login to Euler

##### 4. Prepare dependencies
Unlike setting up Nexue-s locally, we don't need to download any software or license on Euler. Instead, they are all prepared for all users in the user group **MAVT-esc-nexus-e**. You should already be a member of the group if you have followed the [first step](#join-the-nexus-e-user-group).

261
But still, we need to explicitely load all the dependencies, including modules (an Euler term for "software") and python packages.
262
263
264

- Load modules

265
  **Option 1**: Manually load modules every time before running Nexus-e
266

267
  Copy the following commands into Euler:
268
269
270
271
272
273
274
275
276
277
278
  ```
  module load new
  module load gams/28.2
  module load gurobi/8.1.1
  module load matlab/R2018a
  module load gcc/4.8.2
  module load python/3.7.1
  ```
    ```eval_rst
    |:warning:| Note: We used to load python/2.7.14. But we are now in the phase of transferring from python 2.x to python 3.x. Therefore, it is recommended to use python 3.x and identify potential issues for the transfer.
    ```
279
    Your Euler window should look similar to this:
280
281
282
    ```eval_rst
    .. image:: images/euler-module-load.png
      :width: 300px
283
    ```
284

285
  **Option 2**: Edit `.bash_profile` so that the modules are automatically loaded upon log in to Euler
286

287
  Write the same commands at the end of `.bash_profile`. This is a hidden file in your Euler's home directory. After adding these commands, your `.bash_profile` should look similar to this:
288
289
290
  ![](images/euler-bash-profile.png)

  **Test**: To test whether the modules have been successfully loaded, type `module list` in the commaand line. It should then list all loaded modules.
291

292
- Install python packages
293
294

  This you only need to do it **once**, i.e. you don't need to do it everytime when you run Nexus-e.
295
296
297
298
299
300

  In command line under your home directory, type
  ```
  pip install --user -r nexus-e/requirements.txt
  ```

Xuqian Yan's avatar
Xuqian Yan committed
301
##### 5. Run Nexus-e
302
- cd to the `Run_Nexuse` folder
303
304
- Before running `run_Nexuse.m` for the first time, you need to run `bench_Nexuse.m`.
  It is recommended to repeat this step after major changes to the modules eMark and CentIv.
305
306
307
308
- Submit the job with a command such as
```
bsub -n 36 -R "model==XeonGold_6150" -R "rusage[mem=5180]" -W "10:00" matlab -r run_Nexuse
```
309
The parameters in this command can be costomized. Details can be found [here](https://scicomp.ethz.ch/wiki/Getting_started_with_clusters).
310
311
312
313

Here we give a short explanation to the example command above:
![](images/euler-job-submission.png)

314
After submission, Euler will respond by telling you what the jobID is.