Merge branch 'master' of https://gitlab.cern.ch/jalien/jalien-docs

docs/alienpy_commands.md

-# alien.py Commands
+# alien.py Command reference guide
 
-Soon to come...
+### access
+```
+usage: access   [options] <read|write> <lfn> [<specs>]
+-s :  for write requests, size of the file to be uploaded, when known
+-m :  for write requests, MD5 checksum of the file to be uploaded, when known
+-j :  for write requests, the job ID that created these files, when applicable
+-f :  for read requests, filter the SEs based on the given specs list
+-u :  for read requests, print http(s) URLs where available, and the envelopes in urlencoded format
+```
+
+---
+
+### cat
+```
+usage: cat   [-options] [<filename>]
+options:
+-o :  outputfilename
+-n :  number all output lines
+-b :  number nonblank output lines
+-E :  shows ends - display $ at end of each line number
+-T :  show tabs -display TAB characters as ^I
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### cd
+```
+usage: cd   [dir]
+```
+
+---
+
+### cert-info
+```
+Print user certificate information
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### cert-verify
+```
+Verify the user cert against the found CA stores (file or directory)
+X509_CERT_FILE/X509_CERT_DIR apply if set
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### certkey-match
+```
+Check private key against the public key
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### changeDiff
+```
+Show changes between the current version of the file and the previous one (same file name with a '~' suffix)
+usage: changeDiff   [<filename>]
+
+options:
+```
+
+---
+
+### chmod
+```
+Usage: chmod -R <octal mode> <path> [<path>...]
+
+Changes the access mode for a catalogue path
+-R : do a recursive chmod starting from the given path
+```
+
+---
+
+### chown
+```
+Usage: chown -R <user>[.<group>] <file>
+
+Changes an owner or a group for a file
+-R : do a recursive chown
+```
+
+---
+
+### commandlist
+```
+usage: commandlist
+Print the server-side (as opposed to client-side) known commands
+```
+
+---
+
+### commit
+```
+usage: commit   API command only, you should not need to call this directly
+```
+
+---
+
+### cp
+```
+Command format is of the form of (with the strict order of arguments):
+    cp <options> src dst
+    or
+    cp <options> -input input_file
+where src|dst are local files if prefixed with file:// or file: or grid files otherwise
+and -input argument is a file with >src dst< pairs
+after each src,dst can be added comma separated specifiers in the form of: @disk:N,SE1,SE2,!SE3
+where disk selects the number of replicas and the following specifiers add (or remove) storage endpoints from the received list
+options are the following :
+-h : print help
+-f : replace destination file (if destination is local it will be replaced only if integrity check fails)
+-P : enable persist on successful close semantic
+-cksum : check hash sum of the file; for downloads the central catalogue md5 will be verified;
+         for uploads (for xrootd client > 4.12.0) a hash type will be negociated with remote and transfer will be validated
+-y <nr_sources> : use up to the number of sources specified in parallel (N.B. Ignored as it breaks download of files stored in archives)
+-S <aditional TPC streams> : uses num additional parallel streams to do the transfer. (max = 15)
+-chunks <nr chunks> : number of chunks that should be requested in parallel
+-chunksz <bytes> : chunk size (bytes)
+-T <nr_copy_jobs> : number of parralel copy jobs from a set (for recursive copy); defaults to 8 for downloads
+
+for the recursive copy of directories the following options (of the find command) can be used:
+-glob <globbing pattern> : this is the usual AliEn globbing format; N.B. this is NOT a REGEX!!! defaults to all "*"
+-select <pattern> : select only these files to be copied; N.B. this is a REGEX applied to full path!!!
+-name <pattern> : select only these files to be copied; N.B. this is a REGEX applied to a directory or file name!!!
+-name <verb>_string : where verb = begin|contain|ends|ext and string is the text selection criteria.
+verbs are aditive : -name begin_myf_contain_run1_ends_bla_ext_root
+N.B. the text to be filtered cannont have underline <_> within!!!
+-parent <parent depth> : in destination use this <parent depth> to add to destination ; defaults to 0
+-a : copy also the hidden files .* (for recursive copy)
+-j <queue_id> : select only the files created by the job with <queue_id>  (for recursive copy)
+-l <count> : copy only <count> nr of files (for recursive copy)
+-o <offset> : skip first <offset> files found in the src directory (for recursive copy)
+```
+
+!!! warning "client-side implementation"
+
+---
+
+
+### deleteMirror
+```
+Removes a replica of a file from the catalogue
+Usage:
+        deleteMirror [-g] <lfn> <se> [<pfn>]
+
+Options:
+   -g: the lfn is a guid
+```
+
+---
+
+### df
+```
+Shows free disk space
+Usage: df
+```
+
+---
+
+### dirs
+```
+It provides the mechanics of Directory Stack Builtins of bash
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### du
+
+Gives the disk space usge of one or more directories  
+Usage: `du [-ncs] <path> ...`  
+Options:  
+`-n`: Print raw numbers in machine readable format  
+`-c`: Include collections in the summary information  
+`-s`: Print a summary of all parameters  
+
+---
+
+### edit
+```
+Command format: edit lfn
+After editor termination the file will be uploaded if md5 differs
+-datebck : the backup filename will be date based
+N.B. EDITOR env var must be set or fallback will be mcedit (not checking if exists)
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### error OR `$?err`
+```
+Return latest recorded error message.
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### exec
+```
+Command format: exec lfn list_of_arguments
+N.B.! The output and error streams will be captured and printed at the end of execution!
+for working within application use <edit>
+```
+
+!!! warning "client-side implementation"
+
+---
+
+
+### exitcode OR $?
+```
+Return the last known exitcode
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### exit
+```
+Exit the shell
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### find2
+```
+Client-side implementation of find; it will use as default the regex option of server's find.
+Command formant: find2 <options> <directory>
+-select <pattern> : select only these files; N.B. this is a REGEX applied to full path!!! defaults to all ".*"
+-name <pattern> : select only these files; N.B. this is a REGEX applied to a directory or file name!!! defaults to all ".*"
+-name <verb>_string : where verb = begin|contain|ends|ext and string is the text selection criteria. verbs are aditive e.g.:
+-name begin_myf_contain_run1_ends_bla_ext_root
+N.B. the text to be filtered cannont have underline <_> within!!!
+-d  : return also the directories
+-w[h] : long format, optionally human readable file sizes
+-a : show hidden .* files
+-j <queue_id> : filter files created by a certain job
+-l <count> : limit the number of returned entries to at most the indicated value
+-o <offset> : skip over the first <offset> results
+        
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### find
+```
+usage: find   [flags] <path> <pattern>
+options:
+-a :  show hidden .* files
+-s :  no sorting
+-x <target LFN>        :  create the indicated XML collection with the results of the find operation
+-d :  return also the directories
+-w[h]                  :  long format, optionally human readable file sizes
+-j <queueid>           :  filter files created by a certain job ID
+-l <count>             :  limit the number of returned entries to at most the indicated value
+-o <offset>            :  skip over the first /offset/ results
+-r :  pattern is a regular expression
+-f :  return all LFN data as JSON fields (API flag only)
+-y :  (FOR THE OCDB) return only the biggest version of each file
+```
+
+---
+
+### getSE
+```
+Command format: getSE <-id | -name | -srv> identifier_string
+Return the specified property for the SE specified label
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### grep
+```
+usage: grep   [-linux grep options] <pattern> [<filename>]+
+options:
+```
+
+---
+
+### groups
+```
+groups [<username>]
+shows the groups current user is a member of.
+```
+
+---
+
+### guid2lfn
+```
+usage: guid2lfn   <GUID>
+```
+
+---
+
+### help
+```
+usage: help [command]  or ?
+When command is provided, it will return the output of <command -h>
+When no argument, it will provide links to documentation and a list of available commands.  
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### kill
+```
+usage: kill   <jobId> [<jobId>[,<jobId>]]
+```
+
+---
+
+### la
+```
+alias of ls -a
+see ls
+```
+
+---
+
+### lfn2guid
+```
+usage: lfn2guid   <filename>
+```
+
+---
+
+### lfnexpiretime
+```
+usage: lfnexpiretime   [-options] [<file>]
+options:
+-r :  removes the expire time set for an LFN
+-a :  add a new expire time for the given LFN
+-e :  extends the current expire time for the given LFN
+-d <number>            :  specifies the number of days in the expire time
+-w <number>            :  specifies the number of weeks in the expire time
+-m <number>            :  specifies the number of months in the expire time
+-y <number>            :  specifies the number of years in the expire time
+```
+
+---
+
+### listFilesFromCollection
+```
+usage: listFilesFromCollection   [-options] collection
+options:
+-z :  show size and other file details
+-s :  silent (API only)
+```
+
+---
+
+### listSEDistance
+```
+listSEDistance: Returns the closest working SE for a particular site. Usage
+options:
+-site  :  site to base the results to, instead of using the default mapping of this client to a site
+-read  :  use the read metrics, optionally with an LFN for which to sort the replicas. Default is to print the write metrics.
+-qos   :  restrict the returned SEs to this particular tag
+```
+
+---
+
+### listSEs
+```
+listSEs: print all (or a subset) of the defined SEs with their details
+usage: listSEs   [-qos filter,by,qos] [-s] [SE name] [SE name] ...
+
+options:
+-qos                   :  filter the SEs by the given QoS classes. Comma separate entries for 'AND', pass multiple -qos options for an 'OR'
+-s :  print summary information
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### listTransfer
+```
+listTransfer: returns all the transfers that are waiting in the system
+Usage:
+listTransfer [-status <status>] [-user <user>] [-id <queueId>] [-verbose] [-master] [-summary] [-all_status] [-jdl] [-destination <site>]  [-list=<number(all transfers by default)>] [-desc]
+```
+
+---
+
+### lla
+```
+alias of ls -a -l
+see ls
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### ll
+```
+alias of ls -l
+see ls
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### logout
+alias of `exit`
+
+!!! warning "client-side implementation"
+
+---
+
+### ls
+usage: `ls   [-options] [<directory>]`  
+options:  
+`-l`   :  long format  
+`-a`   :  show hidden .\* files  
+`-F`   :  add trailing / to directory names  
+`-b`   :  print in guid format  
+`-c`   :  print canonical paths  
+`-H`   :  human readable file sizes (1024-based); implies '-l'  
+the `alien.py` client will use `-F` as default
+
+---
+
+### masterjob
+```
+usage: masterjob   <jobId> [-options] [merge|kill|resubmit|expunge]
+options:
+-status <status>       :  display only the subjobs with that status
+-id <id>               :  display only the subjobs with that id
+-site <id>             :  display only the subjobs on that site
+-printid               :  print also the id of all the subjobs
+-printsite             :  split the number of jobs according to the execution site
+
+merge                  :  collect the output of all the subjobs that have already finished
+kill                   :  kill all the subjobs
+resubmit               :  resubmit all the subjobs selected
+expunge                :  delete completely the subjobs
+
+You can combine kill and resubmit with '-status <status>' and '-id <id>'.
+For instance, if you do something like 'masterjob <jobId> -status ERROR_IB resubmit',
+ all the subjobs with status ERROR_IB will be resubmitted
+```
+
+---
+
+### mcedit
+```
+Command format: mcedit lfn
+After editor termination the file will be uploaded if md5 differs
+-datebck : the backup filename will be date based
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### md5sum
+```
+usage: md5sum   <filename1> [<or guid>] ...
+```
+
+---
+
+### mirror
+```
+mirror Copies a file into another SE
+Usage:
+mirror [-g] [-try <number>] [-S [se[,se2[,!se3[,qos:count]]]]] <lfn> [<SE>]
+ -g:      Use the lfn as a guid
+ -S:     specifies the destination SEs to be used
+ -try <NumOfAttempts>     Specifies the number of attempts to try and mirror the file
+```
+
+---
+
+### mkdir
+```
+usage: mkdir   [-options] <directory> [<directory>[,<directory>]]
+options:
+-p :  create parents as needed
+-silent                :  execute command silently
+```
+
+---
+
+### motd
+```
+usage: motd   Message of the day
+```
+
+---
+
+### mv
+```
+usage: mv    <LFN>  <newLFN>
+```
+
+---
+
+### nano
+```
+Command format: nano lfn
+After editor termination the file will be uploaded if md5 differs
+-datebck : the backup filename will be date based
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### packages
+```
+usage: packages
+list available packages
+```
+
+---
+
+### pfn
+```
+Command format : pfn [lfn]
+It will print only the list of associtated pfns (simplified form of whereis)
+```
+
+!!! warning "client-side implementation"
+
+
+---
+
+### pfn-status
+```
+Command format: pfn_status <pfn>
+It will return all flags reported by the xrootd server - this is direct access to XRootD server
+```
+
+!!! warning "client-side implementation"
+
+!!! note "No connection to central servers needed"
+
+---
+
+### ping
+```
+ping <count>
+where count is integer
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### popd
+```
+It provides the mechanics of Directory Stack Builtins of bash
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### prompt
+```
+Shell only function
+Toggle the following in the command prompt : <date> for date information and <pwd> for local directory
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### ps
+```
+usage: ps   [-options]
+options:
+-F l | -Fl | -L        :  long output format
+-f <flags|status>      :  any number of (long or short) upper case job states, or 'a' for all, 'r' for running states, 'f' for failed, 'd' for done, 's' for queued
+-u <userlist>        
+-s <sitelist>        
+-n <nodelist>        
+-m <masterjoblist>   
+-o <sortkey>         
+-j <jobidlist>       
+-l <query-limit>     
+
+-M :  show only masterjobs
+-X :  active jobs in extended format
+-A :  select all owned jobs of you
+-W :  select all jobs which are waiting for execution of you
+-E :  select all jobs which are in error state of you
+-a :  select jobs of all users
+-b :  do only black-white output
+-jdl <jobid>           :  display the job jdl
+-trace <jobid> <tag>*  :  display the job trace information
+-id:  only list the matching job IDs, for batch processing (implies -b)
+```
+
+---
+
+### pushd
+```
+It provides the mechanics of Directory Stack Builtins of bash
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### pwd
+```
+Print current work directory
+```
+
+---
+
+### queryML
+```
+usage: queryML <ML node>
+time range can be specified for a parameter:
+/[starting time spec]/[ending time spec]/parameter
+where the two time specs can be given in absolute epoch timestamp (in milliseconds), as positive values,
+or relative timestamp to `now`, when they are negative.
+For example `-60000` would be "1 minute ago" and effectively `-1` means "now".
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### quota
+```
+Client-side implementation that make use of server's jquota and fquota (hidden by this implementation)
+Command format: quota [user]
+if [user] is not provided, it will be assumed the current user
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### registerOutput
+```
+usage: registerOutput   <job ID>
+options:
+```
+
+---
+
+### resubmit
+```
+resubmit: resubmits a job or a group of jobs by IDs
+Usage:
+resubmit <jobid1> [<jobid2>....]
+```
+
+---
+
+### rmdir
+```
+usage: rmdir    [<option>] <directory>
+options:
+--ignore-fail-on-non-empty  :    ignore each failure that is solely because a directory is non-empty
+-p :  --parents   Remove DIRECTORY and its ancestors.  E.g., 'rmdir -p a/b/c' is similar to 'rmdir a/b/c a/b a'.
+-v :  --verbose  output a diagnostic for every directory processed
+   :  --help      display this help and exit
+   :  --version  output version information and exit
+-silent                :  execute command silently
+```
+
+---
+
+### rm
+```
+usage: rm    <LFN> [<LFN>[,<LFN>]]
+options:
+-f :  ignore nonexistent files, never prompt
+-r, -R                 :  remove directories and their contents recursively
+-i :  prompt before every removal (for JSh clients)
+```
+
+---
+
+### run
+```
+Command format: run shell_command arguments lfn
+the lfn must be the last element of the command
+N.B.! The output and error streams will be captured and printed at the end of execution!
+for working within application use <edit>
+additiona arguments recognized independent of the shell command:
+-force : will re-download the lfn even if already present
+-noout : will not capture output, the actual application can be used
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### SEqos
+```
+Command format: SEqos <SE name>
+Return the QOS tags for the specified SE (ALICE:: can be ommited and capitalization does not matter)
+```
+
+!!! warning "(partial) client-side implementation"
+
+---
+
+### setSite
+```
+usage: setSite   [site name]
+options:
+```
+
+---
+
+### showTagValue
+```
+usage: showtagValue   [flags] <filename> [<filename>...]
+options:
+-t :  restrict to this (comma separated) tag list only (default is to return all available tags)
+-c :  restrict to these (comma separated) list of attributes
+-l :  list available tags only
+```
+
+---
+
+### stat
+```
+usage: stat   [-v] <filename1> [<or uuid>] ...
+-v :  More details on the status.
+```
+
+---
+
+### submit
+```
+usage: submit   <URL>
+<URL> => <LFN>
+<URL> => file:///<local path>
+```
+
+---
+
+### testSE
+```
+Test the functional status of Grid storage elements
+Usage: testSE [options] <some SE names, numbers or @tags>
+-v :  verbose error messages even when the operation is expected to fail
+-c :  show full command line for each test
+-t :  time each operation
+-a :  test all SEs (obviously a very long operation)
+```
+
+---
+
+### time
+```
+Command format: time command arguments
+Print local (client side) command execution time (it includes the network delay, tomcat frontend and database backend)
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### timing
+```
+usage: timing   [on|off]
+options:
+enable printing of server side command execution time
+```
+
+---
+
+### token-destroy
+```
+Delete the token{cert,key}.pem files
+```
+
+!!! warning "client-side implementation"
+
+!!! note "No connection to central servers needed"
+
+---
+
+### token-info
+```
+Print token certificate information
+```
+
+!!! warning "client-side implementation"
+
+!!! note "No connection to central servers needed"
+
+---
+
+### token-init
+```
+usage: token-init   [-options]
+options:
+-u <username>          :  switch to another role of yours
+-v <validity (days)>   :  default depends on token type
+-t <tokentype>         :  can be one of: job, jobagent, host, user (default)
+-jobid <job DN extension>  :  expected to be present in a job token
+-hostname <FQDN>       :  required for a host certificate
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### token
+```
+Print only command!!! Use >token-init< for token (re)generation, see below the arguments
+usage: token   [-options]
+
+options:
+-u <username>          :  switch to another role of yours
+-v <validity (days)>   :  default depends on token type
+-t <tokentype>         :  can be one of: job, jobagent, host, user (default)
+-jobid <job DN extension>  :  expected to be present in a job token
+-hostname <FQDN>       :  required for a host certificate
+```
+
+---
+
+### token-verify
+```
+Verify the token cert against the found CA stores (file or directory)
+```
+
+!!! warning "client-side implementation"
+
+!!! note "No connection to central servers needed"
+
+---
+
+### tokenkey-match
+```
+Check token private key againts token public cert
+```
+
+!!! warning "client-side implementation"
+
+!!! note "No connection to central servers needed"
+
+---
+
+### top
+```
+usage: top
+```
+
+### touch
+```
+usage: touch    <LFN> [<LFN>[,<LFN>]]
+```
+
+### toXml
+```
+usage: toXml   [-i] [-x xml_file_name] [-a] [-l list_from] [lfns]
+options:
+-i :  ignore missing entries, continue even if some paths are not/no longer available
+-x :  write the XML content directly in this target AliEn file
+-a :  (requires -x) append to the respective collection
+-l :  read the list of LFNs from this file, one path per line
+```
+
+---
+
+### type
+```
+usage: type   <lfn> 
+Print the LFN type (file / directory / collection)
+```
+
+---
+
+### uptime
+```
+usage: uptime       
+options:
+```
+
+---
+
+### user
+```
+usage: user   <user name>
+Change effective role as specified.
+```
+
+---
+
+### uuid
+```
+usage: uuid   <uuid|filename> [<uuid|filename> ...]
+Decode v1 UUIDs and display the interesting bits
+```
+
+---
+
+### version
+```
+usage: version      
+Get information about the JAliEn version that answers your requests
+```
+
+!!! warning "client-side implementation"
+
+!!! note "No connection to central servers needed"
+
+---
+
+### vi
+```
+Command format: vi lfn
+After editor termination the file will be uploaded if md5 differs
+-datebck : the backup filename will be date based
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### vim
+```
+Command format: vim lfn
+After editor termination the file will be uploaded if md5 differs
+-datebck : the backup filename will be date based
+```
+
+!!! warning "client-side implementation"
+
+---
+
+### whereis
+```
+usage: whereis   [-options] [<filename>]
+options:
+-g :  use the lfn as guid
+-r :  resolve links (do not give back pointers to zip archives)
+-l :  lookup the LFN of the ZIP archive (slow and expensive IO operation, only use it sparingly!)
+```
+
+---
+
+### whoami
+```
+usage: whoami       
+options:
+-v :  verbose details of the current identity
+```
+
+---
+
+### whois
+```
+usage: whois   [account name]
+options:
+-s :  search for the given string(s) in usernames
+-f :  also search in full names
+-e :  search in email addresses too
+-d :  search in X509 DN (subject) fields
+-a :  search for the given string in all the above fields
+```
+
+---
+
+### w
+```
+usage: w   Show currently active users on the Grid
+```
+
+### xrdstat
+```
+usage: xrdstat   [-d [-i]] [-v] [-p PID,PID,...] [-s SE1,SE2,...] [-c] <filename1> [<or UUID>] ...
+options:
+-d :  Check by physically downloading each replica and checking its content. Without this a stat (metadata) check is done only.
+-i :  When downloading each replica, ignore `stat` calls and directly try to fetch the content.
+-s :  Comma-separated list of SE names to restrict the checking to. Default is to check all replicas.
+-c :  Print the full command line in case of errors.
+-v :  More details on the status.
+-p :  Comma-separated list of job IDs to check the input data of
+-o :  Only show the online status (for files with tape replicas in particular)
+-O :  Request the file to be brought online
+-4 :  Force IPv4 usage on all commands
+-6 :  Force IPv6 usage on all commands
+```
+
+---

docs/site/ce_guide.md

@@ -22,7 +22,7 @@ This approach only requires CVMFS and a valid Grid certificate or a user/host to
 3. Run the CE:
 
     ```console
-    ~$ jalien ComputingElement
+    ~$ jalien alien.site.ComputingElement
     ```
 
 This will start a JAliEn CE with default configuration options.
@@ -133,4 +133,4 @@ The JAliEn CE log directory is defined in LDAP, the same way as for legacy AliEn
 
 When using option 1 (CE in CVMFS), the CE can be updated by simply reloading the CE and alienv, activating the latest tag. For option 2 (CE from git), the latest version can be obtained by doing a ```git pull``` and ```compile.sh all```, before restarting.
 
-No action is needed for the JobAgents, as these are always started using the latest tag in CVMFS.
+No action is needed for the JobAgents, as these are always started using the same (or closest available) tag as the CE through CVMFS.

docs/site/vobox_container.md

@@ -71,7 +71,7 @@ Create a new MACVLAN bridge with both IPv4 and IPv6 support, named __docknet__,
         __--ip/ip6__ sets the desired network IPs for the container
 
     !!! info
-        Docker gives containers limited access to the host kernel, which __may prevent some tools from working properly__.
+        Docker gives containers limited access to the host kernel, which __will prevent some tools from working properly__.
         A possible workaround is to give the container additional privileges (see [advanced topics](#privileged-mode) for details).<br><br>
         As opposed to mounting CVMFS from the host, it is also possible to have it installed normally within the container.
         However, this will only work on a container with full access privileges.
@@ -153,5 +153,5 @@ This is known as an _autofs bug_, and can be avoided by disabling autofs on the
 If you prefer to leave autofs enabled, you can remove the error by accessing a directory within CVMFS on the host (e.g ```/cvmfs/alice.cern.ch```), and then restarting the container. 
 
 !!! warning
-    Be aware that this error will likely return on the next reboot.
+    Be aware that this error will likely return on the next reboot if autofs is left enabled.
 

docs/site/xrootd_rpms.md

+# XRootD Installation (RPMs)
+
+The following documentation describes how to install XRootD using RPMs.
+<br>The old page (with legacy instructions) can be found [here](https://alien.web.cern.ch/content/documentation/howto/site/xrootdbyrpms)
+
+!!! question ""
+    For questions and support, please contact [Adrian Sevcenco](../../user/help/#contact-us).
+
+## Packages Installation
+
+!!! info "Prerequisites"
+    These instructions assume EL7/CC7 x86_64 platform that is supported and tested. 
+    <br>__Redirector on disk server configuration is not supported nor foreseen.__
+
+
+!!! danger "Preparation of storage locations"
+    It is assumed that the server is already prepared with the necessary directories and correct rights and ownership.
+
+
+1. Install required tools (__root user is assumed__):
+
+    ```bash
+    ~# yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
+    ```
+
+2. Install the WLCG repository, for example for CC7:
+
+    ```bash
+    ~# rpm --import http://linuxsoft.cern.ch/wlcg/RPM-GPG-KEY-wlcg
+
+    ~# yum -y install http://linuxsoft.cern.ch/wlcg/centos7/x86_64/wlcg-repo-1.0.0-1.el7.noarch.rpm
+    ```
+
+!!! info "Updating from XRootD v4 to v5 case"
+    Because of configuration fixes and not only the minimum version recommended is 5.1  
+    See upgrading below
+
+
+3. Install the required packages  
+    3.1 If fresh install, install the metapackage that will pull XRootD as a dependency (when present in epel):
+
+    ```bash
+    ~# yum -y install alicexrdplugins
+    ```
+
+    3.2 For upgrade case it's best to remove all XRootD packages
+
+    ```bash
+    ~# yum remove -y xrootd*
+    ```
+
+    Then one can install either the epel version or the upstream XRootD version
+    <br>(see Yum repositories section from [XRootD downloads](https://xrootd.slac.stanford.edu/dload.html))
+    ```bash
+    ~# yum install -y xrootd-client xrootd-server
+    ```
+
+    The ALICE XRootD plugins are:  
+        - `tokenauthz` (not dependent on XRootD, to be found in WLCG repository)  
+        - `xrootd-alicetokenacc` (dependent on XRootD and `tokenauthz`)  
+        - `xrootd-aggregatingname2name` (dependent on XRootD)  
+        - `alicexrdplugins` (metapackage, will pull all required dependencies)  
+
+    In special cases (when a test/preview is desired), `xrootd-alicetokenacc`, `xrootd-aggregatingname2name`, `alicexrdplugins` can be downloaded from [here](https://asevcenc.web.cern.ch/asevcenc/xrootd5alice/)
+    otherwise they are usually found in WLCG repository.
+
+
+## XRootD Management Script
+
+!!! warning "Change of management tools!!! (and configuration template)"
+    The former `xrd.sh` was re-wrote and splited in `xrdctl` service management script and `xrd_mk_config` configuration generation script
+    <br>See the github repository [alicexrd](https://github.com/adriansev/alicexrd)
+    <br>When upgrading recreate `system.cnf` file (it has new content/organization) and run `xrd_mk_config` for XRootD configuration generation.
+
+
+!!! warning ""
+    Tested: __Running of XRootD as non-privileged user__
+    <br>Not yet tested: use of `xrd_mk_config` generated systemd service files.
+
+1. Deployment and setting up the environment:
+    <br>`xrdctl` and `xrd_mk_config` scripts and configuration files can be automatically deployed from github as follows:
+
+    ```bash
+    ~$ bash <(curl -fsSLk https://raw.githubusercontent.com/adriansev/alicexrd/master/deploy_alicexrd)
+    ```
+    The script will place the scripts within `${XRDCTLDIR:=~/alicexrd}` and configurations in `${XRDCONFDIR:=~/alicexrdconf}`
+
+    Within `XRDCONFDIR`:
+    <br>```~$ cp system.cnf_CHANGEME system.cnf```
+    <br> Then set `SE_NAME, LOCALROOT, OSS_SPACE_DIRS` as all former others are detected automatically.
+
+
+2. After completing the [configuration](#script-configuration) run the script: ```$XRDCTLDIR/xrdctl -c```.
+    <br>(one can symlink `xrdctl` into `$HOME/bin/`)
+    <br>Usage: ```xrdctl arg [configuration_file]```, where argument is _one_ of :
+
+    | Argument | Description |
+    |----------|-------------|
+    | `-l | --l | -list | --list` | list found configuration files
+    | `-s | --s | -status | --status` | show status of services
+    | `-c | --c | -check | --check` | check and restart if not running
+    | `-k | --k | -kill | --kill` | kill running processes
+    | `-f | --f | -restart | --restart` | force restart
+    | `-logs | --logs` | manage the logs
+    | `-addcron | --addcron` | add/refresh cron line
+    | `-removecron | --removecron` | remove the cron line
+
+    optionaly the configuration file can be explicitly declared.
+
+    !!! note
+        The operations will be applied on  
+            - specified configuration file  
+            __OR__  
+            - on *ALL* `.xrdcfg` files from `$XRDCONFDIR`  
+
+    Environment variables for `xrdctl`:
+
+    | Argument | Description |
+    |----------|-------------|
+    | XRD_READONLY | checked by xrootd configuration; if set the export (__for ALL found configurations__) will be declared as notwritable
+    | XRDCTL_CMD_XRD/XRDCTL_CMD_CMSD | xrootd and cmsd executables (other than the defaults from /usr/bin)
+    | XRDCTL_PRELOAD | use LD_PRELOAD for xrootd/cmsd processes
+    | XRDRUNDIR | location of admin,core,logs,logsbackup dirs; if not set it will be XRDCTLDIR/run/
+    | XRDCONFDIR | location (directory) of .xrdcfg configuration file(s); if not set it wll be XRDCTLDIR/xrootd.conf/
+    | XRDCTL_DEBUG | if set (any value) it will enable various printouts of xrdctl
+    | XRDCTL_DEBUG_SETX | bash enable -x
+    | XRDCTL_DEBUG_XRD | if set enable debug flag for xrootd process
+    | XRDCTL_DEBUG_CMSD | if set enable debug flag for cmsd process
+
+
+## Script Configuration
+
+The following table highlights environment variables that influence how ```xrd_mk_config``` works:
+<br>Usage: ```xrd_mk_config [template_configuration_file]```
+<br>where the specified argument is a custom path for template configuration (otherwise the `${XRDCONFDIR}/xrootd.xrootd.cf.tmp` is used)
+<br>It will parse/source `${XRDCONFDIR}/system.cnf` and generate the xrootd configuration.
+
+!!! warning "`${XRD_MULTISRV}` usage"
+    If "`${XRD_MULTISRV}`" is set, it will enable the spawning of an xrootd/cmsd process __FOR EACH `OSS_SPACE_DIRS`__
+    <br>In this mode, `oss.space` declaration will be commented/omitted,
+    and a distinct xrootd configuration file will be generated for each directory specified by `OSS_SPACE_DIRS`
+
+!!! note ""
+    `OSS_SPACE_DIRS` will be explicitly listed, so globbing will be expanded to all possible directories.
+    <br>Example: `/storage*/xrddata` will be expanded by `ls` to all __existing__ directories
+
+
+| Environment Variable | Description |
+|----------------------|-------------|
+| XRDRUNDIR | location of admin,core,logs,logsbackup dirs; if not set it will be XRDCTLDIR/run/
+| XRDCONFDIR | location (directory) of .xrdcfg configuration file(s); if not set it wll be XRDCTLDIR/xrootd.conf/
+
+
+
+## XRootD MonaLisa monitoring
+
+The monitoring of XRootD is done by MonaLisa agent - MLSensor  
+This is deployed as a distinct service, found within WLCG repository.
+
+```bash
+~# yum -y install mlsensor
+```
+
+There is a required configuration of service (as root):
+```bash
+~# cd /etc/mlsensor
+~# mlsensor_config mlsensor.properties.tmp <name of ALICE storage name>
+```
+
+!!! warning
+    if multiple XRootD services are used, make sure to modify `mlsensor.properties` file
+    <br>and update `lia.Monitor.modules.monXrdSpace.args` variable to a space separrated list of XRootD ports
+
+
+then the normal system enablement procedure can take place
+```
+systemctl enable mlsensor
+systemctl start mlsensor
+```

mkdocs.yml

@@ -36,12 +36,14 @@ nav:
       - Migration to JAliEn: user/migration.md
       - Troubleshooting:     user/help.md
     - Site:
-      - VOBox:                 site/vobox.md
-      - VOBox (Container):     site/vobox_container.md
-      - VOBox (HTCondor/ARC):  site/vobox_htc_arc.md
-      - Manage VOBox Proxy:       site/vobox_proxy.md
-      - "Monitoring: MonALISA":   site/monalisa.md
-      - Computing Element Guide:  site/ce_guide.md
+      - "VOBox":                 site/vobox.md
+      - "VOBox (Container)":     site/vobox_container.md
+      - "VOBox (HTCondor/ARC)":  site/vobox_htc_arc.md
+      - "Manage VOBox Proxy":    site/vobox_proxy.md
+      - "Monitoring: MonALISA":  site/monalisa.md
+      - "Computing Element Guide":  site/ce_guide.md
+      - "XRootD Install (RPMs)":    site/xrootd_rpms.md
+      - "XRootD Decommissioning":   http://lcg.in2p3.fr/wiki/index.php?title=ALICE_native_xrootd
     - Reference:
       - alien.py: alienpy_commands.md
       - JAliEn:   jalien_commands.md