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1 -00 - How to login to Maxwell
1 +How to start the RecoGUI
Content
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1 -The DESY has a quite powerful compute cluster called the Maxwell cluster. The documentation can be found here [[https:~~/~~/confluence.desy.de/display/MXW/Maxwell+Cluster>>doc:MXW.Maxwell Cluster.WebHome||shape="rect"]], however as this can be confusing sometimes, we will try to condensate this to a step by step manual.
1 += {{id name="00-HowtologintoMaxwell-ShortVersion:"/}}**Short Version: ** =
2 2  
3 +Terminal:
3 3  
5 +(% class="code" %)
6 +(((
7 +salloc ~-~-partition=all ~-~-nodes=1 –time=06:00:00
8 +\\ssh max-bla123
9 +\\module load anaconda
10 +\\source activate ~~/envs/tomopy
11 +\\spyder&
12 +)))
4 4  
5 -{{toc/}}
14 +\\
6 6  
7 -= {{id name="00-HowtologintoMaxwell-GettingaDESYAccount"/}}Getting a DESY Account =
16 +Spyder:
8 8  
9 -During you beamtime you will encounter multiple systems, where you will need two different types of accounts:
18 +Open RecoGUI,
10 10  
11 -== {{id name="00-HowtologintoMaxwell-TheDOORAccount"/}}The DOOR Account ==
20 +(Right click on tab: "Set console working directory") (to be removed)
12 12  
13 -Before you arrive you have to create a DOOR account and do all the safety trainings. This account is also being used for the gamma-portal, where you can manage you beamtime data, grant access to other users and manage FTP access. However this account does not work with other resources. For this you will have to request a second account:
22 +Green Arrow to start program
14 14  
15 -== {{id name="00-HowtologintoMaxwell-ThePSXAccount"/}}The PSX Account ==
24 +\\
16 16  
17 -If you decide during a beamtime, you want to have access to the cluster, tell your local contact so, and they will request a PSX account for you. With this you will get access to the Kerberos, Windows and afs resources at DESY, which includes the cluster.
26 += {{id name="00-HowtologintoMaxwell-LongVersion:"/}}**Long Version: ** =
18 18  
28 +\\
19 19  
20 -After you got the account, you have to change the initial password within 6 days. For this, go to [[https:~~/~~/passwd.desy.de/>>url:https://passwd.desy.de/||shape="rect"]] and log in with your user name and initial password (you do not need any OTP when you sign in for the first time). Then agree to the terms and change your password.
30 +**Login to max-nova**: E.g. from browser [[https:~~/~~/max-nova.desy.de:3443/>>url:https://max-nova.desy.de:3443/auth/ssh||shape="rect"]]
21 21  
22 -= {{id name="00-HowtologintoMaxwell-UsingtheCluster"/}}Using the Cluster =
32 +\\
23 23  
24 -== {{id name="00-HowtologintoMaxwell-StructureoftheCluster"/}}Structure of the Cluster ==
34 +Click on "**Launch Session**" and "**XFCE**" Icon
25 25  
26 -=== {{id name="00-HowtologintoMaxwell-Overview"/}}Overview ===
36 +[[image:attach:image2021-4-27_13-55-52.png||height="250"]]
27 27  
28 -The Maxwell Cluster has (status 2021) more than 750 nodes in it. To organize this, you cannot access any node directly, but you have to request compute resources at first. You then can connect form an entrance node to you compute node
38 +\\
29 29  
30 -=== {{id name="00-HowtologintoMaxwell-EntranceNodes"/}}Entrance Nodes ===
40 +**Open a Terminal**, e.g. from the icon at the bottom of your desktop. You can also open it via right click → "Open Terminal here" directly on your desktop or from any folder.
31 31  
32 -If you have successfully obtained an PSX account you can get started. The entrance node are:
33 -
42 +[[image:attach:image2021-4-27_13-58-35.png||height="250"]]
34 34  
35 -[[https:~~/~~/max-display.desy.de:3389/auth/ssh>>url:https://max-display.desy.de:3443/auth/ssh||shape="rect"]]  (in any case)
44 +\\
36 36  
37 -These nodes are **not **for processing, as you will share them with many other users. So please do not do anything computational intensive on them, like reconstruction or visualization. Viewing images is ok.
46 +Now you can **allocate a node** for yourself, so you will have enough memory and power for your reconstruction.
38 38  
39 -=== {{id name="00-HowtologintoMaxwell-FastX2"/}}Fast X3 ===
48 +(% class="code" %)
49 +(((
50 +salloc ~-~-partition=all ~-~-nodes=1 ~-~-time=06:00:00
51 +)))
40 40  
41 -The cluster uses the software FastX3 for connection and virtual desktop. To get the right version of this, use the web interface, log in, and in the bottom right corner is a download link for the desktop client. The version has to match exactly to work properly.
53 +\\
42 42  
43 -If you want to add a connection in the desktop client, click the plus, select web, use the address above (including the port), and your username and force ssh authentication. Then you can choose if you want a virtual desktop (XFCE) or a terminal.
55 +You will get a node for 6 hours, you can also choose longer or shorter times.
44 44  
45 -=== {{id name="00-HowtologintoMaxwell-Partitions"/}}Partitions ===
57 +It can take some time before you get a node, then it will tell you which node is reserved for you. (Example: max-exfl069)
46 46  
47 -Starting from an entrance node, you can connect to a compute node. As there are multiple levels of priorities etc. the nodes are organizes in partitions. You can only access some of these. To view which one, open a terminal and use the commad:
59 +\\
48 48  
49 -{{code}}
50 -my-partitions
51 -{{/code}}
61 +Now you can  **login via ssh** on this node:
52 52  
53 -Your result will look something like this:
63 +(% class="code" %)
64 +(((
65 +ssh max-exfl069
66 +)))
54 54  
55 -[[image:attach:P5I.User Guide\: NanoCT.4\. Reconstruction Guide.00 - How to login to Maxwell.WebHome@image2021-5-4_10-28-14.png||queryString="version=1&modificationDate=1620116894626&api=v2"]]
68 +Enter your password.
56 56  
57 -== {{id name="00-HowtologintoMaxwell-SLURM"/}}SLURM ==
70 +\\
58 58  
59 -The access to the resources of the cluster is managed via a scheduler, SLURM.
72 +EXAMPLE:
60 60  
61 -SLURM schedules the access to nodes and can revokes access if higher priority jobs come.
74 +[[image:attach:image2021-4-27_13-52-11.png||height="125"]]
62 62  
63 -=== {{id name="00-HowtologintoMaxwell-PSXPartition"/}}PSX Partition ===
76 +\\
64 64  
65 -Here you cannot be kicked out of your allocation. However, only few nodes are in this partition and you can also only allocate few in parallel (2021: 5). Some of them have GPUs available.
78 +\\
66 66  
67 -=== {{id name="00-HowtologintoMaxwell-AllPartition"/}}All Partition ===
80 +Now you are on a different node [[image:http://confluence.desy.de/s/de_DE/7901/4635873c8e185dc5df37b4e2487dfbef570b5e2c/_/images/icons/emoticons/smile.svg||title="(Lächeln)" border="0" class="emoticon emoticon-smile"]].
68 68  
69 -Very large number of nodes available and you can allocate many in parallel (2021: 100). However each allocation can be revoked without a warning if s.o. with higher priority comes. This is very common to happen. If you want to use this partition, be sure to design your job accordingly. Only CPU nodes.
82 +\\
70 70  
71 -=== {{id name="00-HowtologintoMaxwell-AllgpuPartition"/}}Allgpu Partition ===
84 +You first have to **load the anaconda module:**
72 72  
73 -Like all, but with GPUs
86 +(% class="code" %)
87 +(((
88 +module load anaconda/3
89 +\\
90 +)))
74 74  
75 -=== {{id name="00-HowtologintoMaxwell-JhubPartition"/}}Jhub Partition ===
92 +and **activate your virtual environment**, depending on where you installed it:
76 76  
77 -For Jupyter Hub
94 +(% class="code" %)
95 +(((
96 +source activate ~~/envs/tomopy
97 +)))
78 78  
99 +\\
79 79  
80 -== {{id name="00-HowtologintoMaxwell-ConnectingtotheCluster"/}}Connecting to the Cluster ==
101 +~~/ takes you back to your home directory. In this case, the environment "tomopy" was installed in the home directory in the folder "envs". 
81 81  
82 -Connect to an entrance node via FastX. You will automatically be assigned to a node when you start a session via a load balancer (max-display001-003, max-nova001-002)
103 +\\
83 83  
84 -[[image:attach:P5I.User Guide\: NanoCT.4\. Reconstruction Guide.00 - How to login to Maxwell.WebHome@image2021-4-27_13-55-52.png||queryString="version=1&modificationDate=1619524552546&api=v2"]]
105 +now you can **start spyder**:
85 85  
86 -Choose a graphic interface and look around.
87 -
88 -
89 -== {{id name="00-HowtologintoMaxwell-DataStorage"/}}Data Storage ==
90 -
91 -The Maxwell cluster knows many storage systems. The most important are:
92 -
93 -Your User Folder: This has a hard limit of 30 GB. Be sure not to exceed this.
94 -
95 -The GPFS: here all the beamtime data are stored.
96 -
97 -=== {{id name="00-HowtologintoMaxwell-GPFS"/}}GPFS ===
98 -
99 -Usually you can find you data at: /asap3/petra3/gpfs/<beamline>/<year>/data/<beamtime_id>
100 -
101 -In there you will find a substructure:
102 -
103 -* raw: raw measurement data. Only applicant and beamtime leader can write/delete there
104 -* processed: for all processed data
105 -* scratch_cc: scratch folder w/o backup
106 -* shared: for everything else
107 -
108 -The GPFS has regular snapshots. The whole capacity of this is huge (several PB)
109 -
110 -== {{id name="00-HowtologintoMaxwell-HowtoGetaComputeNode"/}}How to Get a Compute Node ==
111 -
112 -If you want to do some processing, there are two ways to start a job in SLURM:
113 -
114 -1. Interactive
115 -1. Batch
116 -
117 -In both cases you are the only person working on the node, so use it as much as you like.
118 -
119 -=== {{id name="00-HowtologintoMaxwell-StartinganInteractiveJob"/}}Starting an Interactive Job ===
120 -
121 -To get a node you have to allocate one via SLURM e.g. use:
122 -
123 -{{code}}
124 -salloc -N 1 -p psx -t 1-05:00:00
125 -{{/code}}
126 -
127 -Looking at the individual options:
128 -
129 -* salloc: specifies you want a live allocation
130 -* -N 1: for one node
131 -* -p psx: on the psx partition. You can also add multiple separated with a comma: -p psx,all
132 -* -t 1-05:00:00: for the duration of 1 day and 5h
133 -* (((
134 -Other options could be: ~-~-mem=500GB with at least 500GB of memory,
135 -
136 136  (% class="code" %)
137 137  (((
138 -if you need gpu: (% class="bash plain" %){{code language="none"}}--constraint=P100{{/code}}
109 +spyder&
139 139  )))
140 -)))
141 -* ... see the SLURM documentation for more options
142 142  
143 -If your job is scheduled you see your assigned node and can connect via ssh to it. (in the rare case where you do not see anything use my-jobs to find out the host name).
112 +\\
144 144  
145 -=== {{id name="00-HowtologintoMaxwell-Startingabatchjob"/}}Starting a batch job ===
114 +EXAMPLE: (virtual environment in "envs/p36"
146 146  
147 -For a batch job you need a small shell script describing what you want to do. You do not see the job directly, but the output is written to a log file (and results can be stored on disk)
116 +[[image:attach:image2021-4-27_13-53-35.png||height="71"]]
148 148  
149 -With a batch job, you can also start an array job, where the same task is executed on multiple servers in parallel.
118 +\\
150 150  
151 -An example for such a script:
120 +You can also start another terminal e.g. if you want to look at your data / reconstructions in fiji.
152 152  
153 -{{code}}
154 -#!/bin/bash
155 -#SBATCH --time 0-01:00:00
156 -#SBATCH --nodes 1
157 -#SBATCH --partition all,ps
158 -#SBATCH --array 1-80
159 -#SBATCH --mem 250GB
160 -#SBATCH --job-name ExampleScript
122 +\\
161 161  
124 +\\
162 162  
163 -source /etc/profile.d/modules.sh
164 -echo "SLURM_JOB_ID $SLURM_JOB_ID"
165 -echo "SLURM_ARRAY_JOB_ID $SLURM_ARRAY_JOB_ID"
166 -echo "SLURM_ARRAY_TASK_ID $SLURM_ARRAY_TASK_ID"
167 -echo "SLURM_ARRAY_TASK_COUNT $SLURM_ARRAY_TASK_COUNT"
168 -echo "SLURM_ARRAY_TASK_MAX $SLURM_ARRAY_TASK_MAX"
169 -echo "SLURM_ARRAY_TASK_MIN $SLURM_ARRAY_TASK_MIN"
126 +\\
170 170  
171 -module load maxwell gcc/8.2
172 -
173 -.local/bin/ipython3 --pylab=qt5 PathToYourScript/Script.py $SLURM_ARRAY_TASK_ID
174 -
175 -exit
176 -
177 -
178 -{{/code}}
179 -
180 -
181 -To run this use
182 -
183 -{{code}}
184 -sbatch ./your_script.sh
185 -{{/code}}
186 -
187 -
188 -=== {{id name="00-HowtologintoMaxwell-Viewingyouallocations"/}}Viewing you allocations ===
189 -
190 -To view your pending or running allocations you can use:
191 -
192 -{{code}}
193 -squeue -u <username>
194 -
195 -or
196 -
197 -my-jobs
198 -{{/code}}
199 -
200 -
201 -=== {{id name="00-HowtologintoMaxwell-Whatisrealisticintermsofresources"/}}What is realistic in terms of resources ===
202 -
203 -To be fair, you will not get 100 nodes every time you want them. Especially during a user run, the machines are often quite busy. But if you design your scripts to be tolerant to sudden cancellation, it is still worth trying if you profit from massive parallelization.
204 -
205 -If you want to do some small processing, use one of the psx nodes. This should work most of the time.
206 -
207 -
208 -== {{id name="00-HowtologintoMaxwell-GrantingDataAccesstootherBeamtimes"/}}Granting Data Access to other Beamtimes ==
209 -
210 -If you have to add other users to a past beamtime, this can be done via the gamma-portal (by PI, leader or beamline scientist). After adding the accounts, these people have to make sure to log off from **all **FastX sessions, etc. to update the permissions.
211 -
212 -
213 -
214 -
128 +\\
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1 -204941497
1 +204941724
Title
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1 -00 - How to login to Maxwell
1 +How to start the RecoGUI
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/204941497/00 - How to login to Maxwell
1 +https://confluence.desy.de/spaces/P5I/pages/204941724/How to start the RecoGUI