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<!-- keep this as a security measure: #uncomment if the subject should only be modifiable by the listed groups * Set ALLOWTOPICCHANGE = Main.TWikiAdminGroup,Main.CMSAdminGroup * Set ALLOWTOPICRENAME = Main.TWikiAdminGroup,Main.CMSAdminGroup #uncomment this if you want the page only be viewable by the listed groups # * Set ALLOWTOPICVIEW = Main.TWikiAdminGroup,Main.CMSAdminGroup,Main.CMSAdminReaderGroup --> %TOC% ---+ Fast searching into /pnfs by dc_find %N% To search into =/pnfs= the T3 users can use =dc_find= with *the constraint that the information retrieved will be in the worst case 24h old* ; this limitation is absolutely indifferent in basically all the practical cases and =dc_find= will run faster than searching into =/pnfs= by the usual Linux commands =cd=, =ls=, =find= . ---++ dc_find =%ORANGE%dc_find%ENDCOLOR%= requests the T3 user password and it has many options because of its flexibility but most of them have a reasonable %BLUE%default%ENDCOLOR% %GREEN%value%ENDCOLOR% that can be left as it is. <pre>%BLUE%$%ENDCOLOR% %ORANGE%dc_find%ENDCOLOR% -h usage: %ORANGE%dc_find%ENDCOLOR% [-h] [-v] [-p PATH] [-s NAME] [-as ATIME_START] [-ae ATIME_END] [-cs CTIME_START] [-ce CTIME_END] [-min SIZE_MIN] [-max SIZE_MAX] [-d DEPTH] [-u UID] [-g GID] [-oat | -oct | -ou | -og | -os] [-oa] [-od] [-l LIMIT] [-f PNFS_FILE_OUTPUT] [--db DBNAME] [--dbuser DBUSER] [--dbhost DBHOST] [--dbport DBPORT] The tool partially replicates the 'find' command in a dCache environment optional arguments: -h, --help show this help message and exit -v, --verbose verbose -p PATH, --pnfspath PATH The /pnfs dir to be used to start the search; if not specified and the user is inside a /pnfs dir then the search will start from there. -s NAME, --string NAME A string to be searched among the /pnfs files and dirs names; %BLUE%default%ENDCOLOR% %GREEN%'*'%ENDCOLOR% -as ATIME_START, --access-time-start ATIME_START files or dirs accessed after this time; %BLUE%default%ENDCOLOR% %GREEN%"1999-01-01 00:00:00"%ENDCOLOR% -ae ATIME_END, --access-time-end ATIME_END files or dirs accessed before this time; %BLUE%default%ENDCOLOR% %GREEN%"2999-01-01 00:00:00"%ENDCOLOR% -cs CTIME_START, --creation-time-start CTIME_START files or dirs created after this time; %BLUE%default%ENDCOLOR% %GREEN%"1999-01-01 00:00:00"%ENDCOLOR% -ce CTIME_END, --creation-time-end CTIME_END files or dirs created before this time; %BLUE%default%ENDCOLOR% %GREEN%"2999-01-01 00:00:00"%ENDCOLOR% -min SIZE_MIN, --min-size-MB SIZE_MIN files bigger than this size; %BLUE%default%ENDCOLOR% %GREEN%0%ENDCOLOR% -max SIZE_MAX, --max-size-MB SIZE_MAX files smaller than this size; %BLUE%default%ENDCOLOR% %GREEN%1000000%ENDCOLOR% -d DEPTH, --max-depth DEPTH stop the search at this depth; %BLUE%default%ENDCOLOR% %GREEN%1000%ENDCOLOR% -u UID, --uid UID files or dirs that belong to this uid; %BLUE%default%ENDCOLOR% %GREEN%'*'%ENDCOLOR% -g GID, --gid GID files or dirs that belong to this gid; %BLUE%default%ENDCOLOR% %GREEN%'*'%ENDCOLOR% -oat, --order-by-access-time -oct, --order-by-creation-time -ou, --order-by-uid -og, --order-by-gid -os, --order-by-size -oa, --order-ascending -od, --order-descending -l LIMIT, --limit-result LIMIT -f PNFS_FILE_OUTPUT, --file PNFS_FILE_OUTPUT output file; %BLUE%default%ENDCOLOR% %GREEN%dc_find.pnfs.txt%ENDCOLOR% --db DBNAME the database name; %BLUE%default%ENDCOLOR% %GREEN%chimera%ENDCOLOR% --dbuser DBUSER the database user name used to authenticate; %BLUE%default%ENDCOLOR% %GREEN%your Linux account name%ENDCOLOR% --dbhost DBHOST the database host; %BLUE%default%ENDCOLOR% %GREEN%t3dcachedb03.psi.ch%ENDCOLOR% --dbport DBPORT the database port; %BLUE%default%ENDCOLOR% %GREEN%5432%ENDCOLOR% examples: %ORANGE%dc_find%ENDCOLOR% --file /tmp/dc_find.out -p /pnfs/psi.ch/cms/trivcat/store/user/bianchi/ --string t-channel_TuneZ2star --order-by-access-time %ORANGE%dc_find%ENDCOLOR% --string .root -p /pnfs/ --order-by-uid -l 100 %ORANGE%dc_find%ENDCOLOR% --string .root -p /pnfs/ --access-time-start "2014-01-01 00:00:00" -l 100 </pre> Follows a =%ORANGE%dc_find%ENDCOLOR%= example that involves an arbitrary =/pnfs= dir where the user entered by =cd=: <pre> %BLUE%$%ENDCOLOR% pwd /pnfs/psi.ch/cms/trivcat/store/user/ursl %BLUE%$%ENDCOLOR% %ORANGE%dc_find%ENDCOLOR% --string .root --order-by-size --order-desc --limit 1000 --file $HOME/dc_find.out %RED%Password:%ENDCOLOR% %BLUE%$%ENDCOLOR% head $HOME/dc_find.out +-------+-----+-----+-----+----------------------------------+----------------------------------+------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | depth | MB | uid | gid | ctime | atime | mode | adler32 | /pnfs | pools | +-------+-----+-----+-----+----------------------------------+----------------------------------+------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------+ | 11 | 422 | 584 | 538 | 2013-11-08 17:16:27.816000+01:00 | 2014-01-10 15:41:58.263000+01:00 | 644 | ce688b67 | /pnfs/psi.ch/cms/trivcat/store/user/yangyong/data/reco/v6/TTH_HToBB_M-125_8TeV-pythia6Summer12_DR53X-PU_S10_START53_V7A-v1AODSIM/analysis.TTH_HToBB_M-125_8TeV-pythia6Summer12_DR53X-PU_S10_START53_V7A-v1AODSIM_3_1_nxT.root | t3fs14_cms_8 | | 11 | 482 | 584 | 538 | 2013-11-08 17:16:27.695000+01:00 | 2014-01-13 10:49:45.009000+01:00 | 644 | f50c2466 | /pnfs/psi.ch/cms/trivcat/store/user/yangyong/data/reco/v6/TTH_HToBB_M-125_8TeV-pythia6Summer12_DR53X-PU_S10_START53_V7A-v1AODSIM/analysis.TTH_HToBB_M-125_8TeV-pythia6Summer12_DR53X-PU_S10_START53_V7A-v1AODSIM_13_1_HsS.root | t3fs14_cms_11 | ... </pre> ---++ View v_pnfs The advanced T3 users can directly use [[http://www.postgresql.org/docs/9.3/static/app-psql.html][psql]] to interact with the PostgreSQL view =v_pnfs= that reports each =/pnfs= file and dir; we highlighted the %ORANGE%columns%ENDCOLOR% that are interesting for these users: | *depth* | *ipnfsid* | *%ORANGE%path%ENDCOLOR%* | *iname* | *%ORANGE%isize%ENDCOLOR%* | *%ORANGE%iuid%ENDCOLOR%* | *%ORANGE%igid%ENDCOLOR%* | *%ORANGE%ictime%ENDCOLOR%* | *%ORANGE%iatime%ENDCOLOR%* | *imtime* | *imode* | *adler32* | *pools* | <br /> We list some common [[http://www.postgresql.org/docs/9.3/static/app-psql.html][psql]] queries, but *it's up to the T3 users to write, save and regularly run their specific queries*.<br /><br /> *Ho many GB am I globally using in =/pnfs= ?* <pre>BASH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where %ORANGE%iuid=$(id -u)%ENDCOLOR%;" TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where %ORANGE%iuid=`id -u`%ENDCOLOR%;" </pre> *Ho many GB is my group globally using in =/pnfs=?* <pre>BASH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where %ORANGE%igid=$(id -g)%ENDCOLOR%;" TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where %ORANGE%igid=`id -g`%ENDCOLOR%;" </pre> *Ho many GB is my group using in an arbitrary =/pnfs= dir, e.g. =/pnfs/psi.ch/cms/trivcat/store/%BLUE%*%ENDCOLOR%= ?* <pre>BASH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where igid=$(id -g) and %ORANGE%path like '/pnfs/psi.ch/cms/trivcat/store/%ENDCOLOR%%BLUE%%%ENDCOLOR%%ORANGE%'%ENDCOLOR%;" TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where igid=`id -g` and %ORANGE%path like '/pnfs/psi.ch/cms/trivcat/store/%ENDCOLOR%%BLUE%%%ENDCOLOR%%ORANGE%'%ENDCOLOR%;" </pre> *Ho many GB is my group using in =/pnfs/psi.ch/cms/trivcat/store/%BLUE%*%ENDCOLOR%= that weren't read since 2014-01-01 ?* <br /> You can specify whatever =iatime= date. <pre>BASH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where igid=$(id -g) and path like '/pnfs/psi.ch/cms/trivcat/store/%BLUE%%%ENDCOLOR%' and %ORANGE%iatime <= '2014-01-01'%ENDCOLOR%; " TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as GB from v_pnfs where igid=`id -g` and path like '/pnfs/psi.ch/cms/trivcat/store/%BLUE%%%ENDCOLOR%' and %ORANGE%iatime <= '2014-01-01'%ENDCOLOR%; " </pre> *How to save in a file all the =/pnfs= files involved in the previous query?* <br /> Here the files list is going to be saved in =$PWD/pnfsfiles=. <pre>BASH $ psql %ORANGE%-o $PWD/pnfsfiles%ENDCOLOR% -d chimera -h t3dcachedb03.psi.ch %ORANGE%-A -q%ENDCOLOR% --command="select %ORANGE%path,isize as bytes,iatime,iuid,igid%ENDCOLOR% from v_pnfs where igid=$(id -g) and path like '/pnfs/psi.ch/cms/trivcat/store/%BLUE%%%ENDCOLOR%' and iatime <= '2014-01-01'; " TCSH $ psql %ORANGE%-o $PWD/pnfsfiles%ENDCOLOR% -d chimera -h t3dcachedb03.psi.ch %ORANGE%-A -q%ENDCOLOR% --command="select %ORANGE%path,isize as bytes,iatime,iuid,igid%ENDCOLOR% from v_pnfs where igid=`id -g` and path like '/pnfs/psi.ch/cms/trivcat/store/%BLUE%%%ENDCOLOR%' and iatime <= '2014-01-01'; " $ head -1 pnfsfiles %ORANGE%path%ENDCOLOR%|%ORANGE%bytes%ENDCOLOR%|%ORANGE%iatime%ENDCOLOR%|%ORANGE%iuid%ENDCOLOR%|%ORANGE%igid%ENDCOLOR% </pre> *Ho many TB are the T3 groups using in =/pnfs/psi.ch/cms/trivcat/store/%BLUE%*%ENDCOLOR%= that weren't read since 2014-01-01 ?* <pre>BASH/TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000/1000) as %BLUE%TB%ENDCOLOR%,%ORANGE%igid%ENDCOLOR% from v_pnfs where path like '/pnfs/psi.ch/cms/trivcat/store/%ENDCOLOR%%BLUE%%%ENDCOLOR%' and %ORANGE%iatime < '2014-01-01' group by igid order by %ENDCOLOR%%BLUE%TB%ENDCOLOR%%ORANGE% desc %ENDCOLOR%;" %BLUE%TB%ENDCOLOR% | %ORANGE%igid%ENDCOLOR% -----+------ 176 | 500 # common data 129 | 533 # ethz-susy 23 | 536 # uniz-bphys 19 | 531 # ethz-ewk 17 | 534 # psi-bphys 8 | 538 # uniz-pixel 5 | 532 # ethz-higgs 3 | 530 # ethz-bphys 0 | 535 # psi-pixel 0 | 537 # uniz-higgs </pre> *Who did upload more GB during the last month ( without considering files that were deleted ) ?* <pre>BASH/TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select trunc(sum(isize)/1000/1000/1000) as %BLUE%GB%ENDCOLOR%,%ORANGE%iuid%ENDCOLOR% from v_pnfs where ictime > %ORANGE%date_trunc('day', NOW() - interval '1 month')%ENDCOLOR% group by iuid order by GB desc ;" Password: %BLUE%GB%ENDCOLOR% | %ORANGE%iuid%ENDCOLOR% ------+------ 7401 | 521 # ursl 4451 | 607 # mwang 3540 | 585 # ... 2587 | 584 2466 | 603 ... </pre> *How to list the =/pnfs= files such that ..* <br /> Here we retrieve a list of files satisfying many different constraints in parallel; a this stage the SQL code should be self-explanatory. <pre>BASH/TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select path,iatime,isize from v_pnfs where path like '/pnfs/psi.ch/cms/trivcat/store/user/ursl/%BLUE%%%ENDCOLOR%.gz' and iatime < '2014-03-01' and iatime > '2014-01-01' order by iatime limit 10 ;" Password: path | iatime | isize -------------------------------------------------------------------------------------+----------------------------+------------ /pnfs/psi.ch/cms/trivcat/store/user/ursl/strebeli/ggHyy/store/mcanlo_store_0.tar.gz | 2014-02-27 13:33:15.222+01 | 1127148238 /pnfs/psi.ch/cms/trivcat/store/user/ursl/strebeli/ggHyy/store/mcanlo_store_1.tar.gz | 2014-02-27 13:34:17.122+01 | 189441386 /pnfs/psi.ch/cms/trivcat/store/user/ursl/strebeli/ggHyy/store/mcanlo_store_3.tar.gz | 2014-02-27 13:35:12.52+01 | 950718190 /pnfs/psi.ch/cms/trivcat/store/user/ursl/strebeli/ggHyy/store/mcanlo_store_4.tar.gz | 2014-02-27 13:35:36.329+01 | 947247447 (4 rows) </pre> As the queries get complex and recurring is better to save them in a file: so here we prepare a %BLUE%query%ENDCOLOR% file and we run it: <pre>$ cat %BLUE%query%ENDCOLOR% %ORANGE%select%ENDCOLOR% trunc(sum(isize)/1000/1000/1000) %ORANGE%as%ENDCOLOR% GB, ictime::timestamp::date %ORANGE%as%ENDCOLOR% day %ORANGE%from%ENDCOLOR% v_pnfs %ORANGE%where%ENDCOLOR% path %ORANGE%like%ENDCOLOR% '%BLUE%%%ENDCOLOR%PU_S10_START53_V7D-v3%BLUE%%%ENDCOLOR%root' %ORANGE%and%ENDCOLOR% ictime > '2011-01-01' %ORANGE%group by%ENDCOLOR% day %ORANGE%order by%ENDCOLOR% day %ORANGE%asc%ENDCOLOR%; BASH/TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q -f %BLUE%query%ENDCOLOR% gb | day ------+------------ 1071 | 2013-02-01 4130 | 2013-02-02 3316 | 2013-02-03 1190 | 2013-02-04 43 | 2013-11-11 46 | 2013-11-12 63 | 2013-11-18 292 | 2013-11-19 28 | 2013-11-20 </pre> <strong>Which are the =/pnfs= dirs where have been uploaded more GB during the last month ?</strong><br /> Here we combine together the expressing power of SQL with the [[http://www.postgresql.org/docs/9.3/static/functions-matching.html#FUNCTIONS-POSIX-REGEXP][regular expressions]]; the metadata of a =/pnfs= dir is =512= bytes so by excluding the rows with isize = =512= we're basically considering only the =/pnfs= files. The expression %BLUE%[^\/]*$%ENDCOLOR% matches the file name that will be erased by the %BLUE%regexp_replace%ENDCOLOR%. <pre> $ cat %BLUE%query%ENDCOLOR% %ORANGE%select%ENDCOLOR% trunc(sum(isize)/1000/1000/1000) %ORANGE%as%ENDCOLOR% GB, %BLUE%regexp_replace%ENDCOLOR%(path, '%BLUE%[^\/]*$%ENDCOLOR%', '') %ORANGE%as%ENDCOLOR% dir %ORANGE%from%ENDCOLOR% v_pnfs %ORANGE%where%ENDCOLOR% ictime > date_trunc('day', NOW() - interval '1 month') %ORANGE%and%ENDCOLOR% isize != 512 %ORANGE%group by%ENDCOLOR% dir %ORANGE%order by%ENDCOLOR% GB %ORANGE%desc%ENDCOLOR%; BASH/TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q -f %BLUE%query%ENDCOLOR% gb | dir ------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1995 | /pnfs/psi.ch/cms/trivcat/store/user/yangyong/data/reco/tree/v5_13/ 1246 | /pnfs/psi.ch/cms/trivcat/store/user/jngadiub/Thea/QCD_defaultCones/ 1042 | /pnfs/psi.ch/cms/trivcat/store/user/mwang/data/SingleElectron/EDBR_PATtuple_edbr_wh_20140210_SingleElectron_Run2012%ORANGE%D%ENDCOLOR%-22Jan2013-v1/c2d529e1c78e50623ca40825abf53f99/ 902 | /pnfs/psi.ch/cms/trivcat/store/user/mwang/data/SingleElectron/EDBR_PATtuple_edbr_wh_20140210_SingleElectron_Run2012%ORANGE%C%ENDCOLOR%-22Jan2013-v1/c2d529e1c78e50623ca40825abf53f99/ </pre> <strong>Which are the =/pnfs= dirs where I/my group have/has uploaded more GB during the last month ?</strong><br /> Add to the previous query either this contraint <pre> %ORANGE%and %ENDCOLOR%iuid = YOUR_UID</pre> or this contraint:<pre> %ORANGE%and %ENDCOLOR%igid = YOUR_GID</pre> </br> ---++ View v_pnfs_top_dirs *NOTE* The simplest ways to consult the preordered =/pnfs= dirs list consists of: * downloading by =wget= http://t3mon.psi.ch/ganglia/PSIT3-custom/v_pnfs_top_dirs.txt and then run the =grep= command. * observing online http://t3mon.psi.ch/ganglia/PSIT3-custom/v_pnfs_top_dirs.html The view =v_pnfs_top_dirs= reports each =/pnfs= dirs ( not the files ) *preordered from the biggest dirs to the smallest dirs*: | *%ORANGE%totmb%ENDCOLOR%* | *depth* | *ipnfsid* | *%ORANGE%path%ENDCOLOR%* | *%ORANGE%iuid%ENDCOLOR%* | *%ORANGE%igid%ENDCOLOR%* | *ictime* | *%ORANGE%iatime%ENDCOLOR%* | *imtime* | typically a T3 user will extract from the view =v_pnfs_top_dirs= all the dirs involving his/her =uid=, or his/her =gid=, by: <pre>BASH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select totmb,path,ictime,iatime from v_pnfs_top_dirs where iuid=$(id -u) ;" TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select totmb,path,ictime,iatime from v_pnfs_top_dirs where iuid=`id -u` ;" totmb | path | ictime | iatime -----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------+---------------------------- 3979 | /pnfs/psi.ch/cms/trivcat/store/data/Run2012D/DoubleElectron/RAW-RECO/ZElectron-22Jan2013-v1/10000 | 2013-11-15 17:48:01.372+01 | 2013-11-14 11:13:55.999+01 3976 | /pnfs/psi.ch/cms/trivcat/store/data/Run2011A/MuOnia/AOD/08Nov2011-v1/0001 | 2012-12-07 21:24:37.456+01 | 2012-12-07 21:24:37.456+01 3964 | /pnfs/psi.ch/cms/trivcat/store/data/Run2011A/MuOnia/AOD/08Nov2011-v1/0000 | 2012-12-07 21:24:37.456+01 | 2012-12-07 21:24:37.456+01 3953 | /pnfs/psi.ch/cms/trivcat/store/data/Run2012C/DoubleElectron/RAW-RECO/ZElectron-22Jan2013-v1/20000 | 2013-06-01 13:56:01.777+02 | 2013-05-30 18:28:18.34+02 3935 | /pnfs/psi.ch/cms/trivcat/store/data/Run2012B/MuOnia/AOD/13Jul2012-v1/0000 | 2012-11-30 17:15:09.289+01 | 2012-11-12 19:55:24+01 3899 | /pnfs/psi.ch/cms/trivcat/store/data/Run2012B/MuOnia/AOD/13Jul2012-v1/0001 | 2012-11-30 17:15:21.191+01 | 2012-11-11 11:56:39+01 3877 | /pnfs/psi.ch/cms/trivcat/store/data/Run2011B/MuOnia/AOD/19Nov2011-v1/0000 | 2012-12-08 23:27:58.153+01 | 2012-12-08 23:27:58.153+01 </pre> or a query based on a string present in the dir name, e.g. %BLUE%*%ENDCOLOR%%ORANGE%Run2011A%ENDCOLOR%%BLUE%*%ENDCOLOR% : <pre>BASH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select totmb,path,ictime,iatime from v_pnfs_top_dirs where path like '%BLUE%%%ENDCOLOR%%ORANGE%Run2011A%ENDCOLOR%%BLUE%%%ENDCOLOR%' and iuid=$(id -u);" TCSH $ psql -d chimera -h t3dcachedb03.psi.ch -q --command="select totmb,path,ictime,iatime from v_pnfs_top_dirs where path like '%BLUE%%%ENDCOLOR%%ORANGE%Run2011A%ENDCOLOR%%BLUE%%%ENDCOLOR%' and iuid=`id -u`;" </pre> *By regularly paying attention the view =v_pnfs_top_dirs= all the T3 users are kindly invited to proactively delete their big and unnecessary =/pnfs= dirs by HowToAccessSe#gfalFS* ---++ PostgreSQL permissions *This is relevant and accessible only to the T3 admins* NodeTypeDBServerChimera#t3users
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Topic revision: r14 - 2014-12-09
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FabioMartinelli
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