Wiki source code of ComputingResourcesUserGuide

Version 1.1 by sendels on 2019/05/15 09:16
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1 = Brief User Guide to Computing Resources at FLASH =
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5 * [[Brief User Guide to Computing Resources at FLASH>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide#Brief_User_Guide_to_Computing_Re||shape="rect"]]
6 ** [[CAMP at BL1: hasfumidaq>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide#CAMP_at_BL1_hasfumidaq||shape="rect"]]
7 ** [[Maxwell HPC Cluster>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide#Maxwell_HPC_Cluster||shape="rect"]]
8 ** [[Gamma Portal>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide#Gamma_Portal||shape="rect"]]
9 ** [[Flash Control System>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide#Flash_Control_System||shape="rect"]]
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15 == CAMP at BL1: hasfumidaq ==
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17 **TL;DR:** Use the [[Maxwell cluster~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/IS/Maxwell||shape="rect"]] instead.
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19 The [[CAMP~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://photon-science.desy.de/facilities/flash/beamlines/bl_beamlines_flash1/camp/index_eng.html||shape="rect"]] cooperation used to operate a server for data acquisition and online analysis named **hasfumidaq**{{code language="none"}}{{/code}} (HASylab Flash Ultra fast Molecular Imaging DAQ). Currently the server runs as a backup only. It is going to be decommissioned, most probably early 2020.
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23 === Hardware and Operating System ===
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25 The machine {{code language="none"}}hasfumidaq{{/code}} is a 12 core Dell Precision T5500 with 12 GByte RAM and more than 80 TByte disk space running a GNU/Linux, Ubuntu 16.04, operating system.
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27 The local disk space of {{code language="none"}}hasfumidaq{{/code}} is **not** under any backup regime, ie. what is deleted or overwritten here is gone for good. The storage layout is as follows:
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31 |=(((
32 [[mount point>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide?sortcol=0;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
33 )))|=(((
34 [[type>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide?sortcol=1;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
35 )))|=(((
36 [[purpose>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide?sortcol=2;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
37 )))
38 |(((
39 {{code language="none"}}
40 ~/
41 {{/code}}
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43 AFS network
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45 programs and precious data needing backup
46 )))
47 |(((
48 {{code language="none"}}
49 /var/acqu/
50 {{/code}}
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52 local disk
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54 short term data acquisition files
55 )))
56 |(((
57 {{code language="none"}}
58 /var/data/
59 {{/code}}
60 )))|(((
61 local disk
62 )))|(((
63 midterm data storage and reproducible analysis
64 )))
65 |(((
66 [[desy.de/flash1/disk/>>url:http://desy.de/flash1/disk/||shape="rect"]]
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68 {{code language="none"}}
69 /pnfs/
70 {{/code}}
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72 NFS network
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74 longer term data storage for off line analysis
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77 For data acquisition {{code language="none"}}/var/acqu/{{/code}} is exported via NFS to {{code language="none"}}hasfcamppnccd1{{/code}} and {{code language="none"}}hasfcamppnccd2{{/code}}. There also is a CIFS (SAMBA) export of {{code language="none"}}/var/acqu/{{/code}} for user bl1acqus. Yet the latter is supposed to be used for MS Windows data acquisition nodes only.
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79 Note, there is a caveat with the PNFS (perfectly normal file system) disk: Files are not modifiable on this file system, once they are created.
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83 === User Login ===
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85 {{code language="none"}}Hasfumidaq{{/code}} provides logins to AFS account owners, who are members of the groups {{code language="none"}}hasylab{{/code}} or {{code language="none"}}cfel{{/code}}. Accordingly, you have access to your DESY AFS home directory on {{code language="none"}}hasfumidaq{{/code}}.
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87 If you use {{code language="none"}}hasfumidaq{{/code}} make sure you do not interfere with data acquisition at BL1, i.e. do not occupy many processor cores at full load and do not incur heavy network traffic. Mind, a single Matlab GUI creates a lot of network traffic already. For offline data analysis use the Petra III workgroup cluster instead. Please, do use your **personal account** working on {{code language="none"}}hasfumidaq{{/code}}. The functional account "bl1user" here should be restricted to data acquisition and the account "vuvfuser" to online data analysis for guests, who do not have a DESY AFS account.
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91 === Software and Administration ===
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93 For online or quasi online data analysis the usual set of scientific **software** is installed on hasfumidaq: Python with all the number crunching libraries, Java, HDFView in a current version, h5tools, Matlab R2013b and the DOOCS tools and libraries. If you need more, talk to the admins.
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95 **Administrators** of {{code language="none"}}hasfumidaq{{/code}} are the staff at FS-EC (Blume, Fleck, Rothkirch), the staff at IT (Flemming et al.), the CAMP staff (Passow, Erk) and the IT people at FS-FL (Düsterer, Grunewald, Sendel).
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99 == Maxwell HPC Cluster ==
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101 The Maxwell HPC cluster consists of a set of 64 core servers with 512 GByte of RAM each. They run a GNU/Linux of (% class="twikiNewLink" %)[[CentOS>>url:http://hasfweb.desy.de/bin/edit/Setup/CentOS?topicparent=Setup.ComputingResourcesUserGuide;nowysiwyg=0||rel="nofollow" shape="rect"]](%%) Linux 7 (Core) flavour. You login to **max-fsc**{{code language="none"}}{{/code}} and are connected to the server with lowest load. Please see [[the docs on confluence for details~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/IS/Maxwell||shape="rect"]].
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103 Your AFS home directory should be available as a link at ~~/afs/. You have an ASAP3 home directory common to all Maxwell nodes.
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105 On all {{code language="none"}}max-fsc{{/code}} nodes you have access to [[desy.de/flash1/disk/>>url:http://desy.de/flash1/disk/||shape="rect"]]{{code language="none"}}/pnfs/{{/code}} just as on {{code language="none"}}hasfumidaq{{/code}}. For intermediate storage of large files use the {{code language="none"}}/scratch{{/code}} space local to each node.
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107 Also the ASAP3 Core File System is mounted on all Maxwell nodes. It is accessible at /asap3/flash/gpfs~/~//data~/~/. Please refer to the [[documentation on confluence~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3||shape="rect"]].
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109 The cluster also is the location your files will be staged to, if you access them through the Gamma Portal.
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113 == Gamma Portal ==
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115 The [[Gamma Portal~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://gamma-portal.desy.de||shape="rect"]] is a web front end to DESY's dCache tape archive.
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117 Your data are migrated upon request to the responsible beam line scientist to the tape archive. The archive is organised along beamtime application numbers and provides elaborate access control.
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119 You access your data using your DOOR account. The web front end allows you to download your data. Also, if you have a DESY AFS account, it permits you to stage the data. That means a copy of your data is created on the PNFS disk for analysis on the Petra III workgroup cluster.
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123 == Flash Control System ==
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125 In addition to the services outlined above, DESY's group MCS-4 provides data acquisition services related to accelerator operations and beam diagnostics. For details you are referred to Stefan's [[Information about the FLASH DAQ system>>url:http://hasfweb.desy.de/bin/view/Setup/DAQmain||shape="rect" class="twikiLink"]] pages.
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127 For online DAQ access and analysis you login at {{code language="none"}}flashlxuser1{{/code}} or {{code language="none"}}flashlxuser2{{/code}}, using one of the functional accounts.