Differences between revisions 5 and 36 (spanning 31 versions)

Contents

File systems available
Access Policy
Directories and filesystems
Important Disclaimer
Access your data by SSHFS

File systems available

The users have at there disposal three types of filesystem:
- A common NFS filesystem for homes not shared with workernodes
- A lustre filesystem for some groups shared filesystem with the workernodes
- A CVMFS read-only filesystem for software provision
Groups involved in WLCG transfer data using grid technologies can also use the Tier-3 storage areas and dedicated software areas (CVMFS) made available by there communities.

Access Policy

By default both lustre and nfs individual group areas can be accessed (read only) by users of the same group.

Directories and filesystems

The pauli machines provide a wide set of filesystems so that users can access their data and applications.

NFS Home directories

Users home mounts are not shared with workernodes, they can be found only on submission nodes:

FILESYSTEM            MOUNTED ON            SCOPE
se63:/user            /user                 LIP groups

NFS Data directories

Projects specific data NFS mounts are not shared with workernodes and are found only on submission nodes:

FILESYSTEM            MOUNTED ON            SCOPE
se34:/sno             /n/sno                SNO+ data
se51:/sno             /s/sno                SNO+ data
se27:/ams             /z/ams                AMS data
se27:/comp            /z/comp               COMPASS data

LUSTRE Data directories

Projects specific data LUSTRE mounts are shared with workernodes:

FILESYSTEM            MOUNTED ON            SCOPE
mdt02@tcp:/t3atlas    /gstore/t3atlas       ATLAS Tier-3
mdt02@tcp:/T3CMS      /gstore/t3cms         CMS Tier-3
mdt04@tcp:/auger      /lstore/auger         AUGER
mdt04@tcp:/calo       /lstore/calo          ATLAS Lisboa
mdt02@tcp:/cmslocal   /lstore/cms           CMS
mdt03@tcp:/comp       /lstore/comp          COMP
mdt04@tcp:/lattes     /lstore/lattes        LATTES
mdt04@tcp:/nucria     /lstore/nucria        NUCRIA
mdt04@tcp:/pet        /lstore/pet           PET
mdt10@tcp:/sno        /lstore/sno           SNO PLUS
mds22@tcp:/titan      /lstore/titan         ATLAS
mds-feno@tcp:/feno    /lstore/feno          Phenomenology
mds-share@tcp:/share  /share                Shared with Atlas, Auger, CMS, Compass, NUCRIA, SPAC and SWGO

CVMFS Software provision

The CVMFS is a read-only filesystem with cache local to clients optimal for software provision:

FILESYSTEM            MOUNTED ON            SCOPE
cvmfs2                /cvmfs/cms.cern.ch    CMS VO
cvmfs2                /cvmfs/atlas.cern.ch  ATLAS VO
cvmfs2                /cvmfs/sw.el7         LIP

Important Disclaimer

Manipulating huge sets of small files generates performance degradation issues in /lustre due to the lock management. Therefore, you should not
- Compile anything under /lustre
- Store and access databases under /lustre

Access your data by SSHFS

Install sshfs package

On Ubuntu/debian:

# sudo apt-get install sshfs

On RHEL/CentOS/Fedora:

# sudo yum install fuse-sshfs

Create a local directory

# mkdir ~/homeNCG

Mount your remote folder

# sshfs martinsj@fermi.ncg.ingrid.pt: ~/homeNCG

When you're done, you can unmount it

# fusermount -u ~/homeNCG

.bashrc tunning

In case you're dealing with very long paths, as a suggestion, you can add to your ~/.bashrc file the following:

alias mfermi='f(){ dir=$1 ; [ -n "$dir" ] || dir=homeNCG ; [ -d ~/$dir ] || mkdir -p ~/$dir ; sshfs fermi.ncg.ingrid.pt: ~/$dir ;  unset -f f; }; f'
alias ufermi='f(){ dir=$1 ; [ -n "$dir" ] || dir=homeNCG ; [ -d ~/$dir ] && fusermount -u ~/$dir ; [ -d ~/$dir ] && rmdir ~/$dir ;  unset -f f; }; f'

alias mncg='f(){ dir=$1 ; [ -n "$dir" ] && ldir=`basename $dir` ; [ -d ~/$ldir ] || mkdir -p ~/$ldir ; [ -n "$dir$ldir" ] && sshfs fermi.ncg.ingrid.pt:$dir ~/$ldir ;  unset -f f; }; f'
alias uncg='f(){ dir=$1 ; [ -n "$dir" ] && ldir=`basename $dir` ; ldir=`echo $ldir ; [ -d ~/$ldir ] && fusermount -u ~/$ldir ; [ -d ~/$ldir ] && rmdir ~/$ldir ;  unset -f f; }; f'

alias mcalo='f(){ [ -d lcalo ] || mkdir ~/lcalo ; sshfs fermi.ncg.ingrid.pt:/lstore/calo ~/lcalo ;  unset -f f; }; f'
alias ucalo='f(){ [ -d ~/lcalo ] && fusermount -u ~/lcalo ; [ -d ~/$ldir ] && rmdir ~/lcalo ;  unset -f f; }; f'

This is how you can use it:

$ mfermi homeNCG
$ df
Filesystem           1K-blocks    Used Available Use% Mounted on
fermi.ncg.ingrid.pt: 209612800 3504112 206108688   2%
/home/martinsj/homeNCG
$ ufermi homeNCG

$ mncg /lstore/calo
...
$ uncg /lstore/calo

-  ⇤ ← Revision 5 as of 2016-12-07 15:18:45 → 
  Size: 7932
  Editor: jpina
  Comment:
+   ← Revision 36 as of 2024-03-07 11:37:09 → ⇥
  Size: 4925
  Editor: martinsj
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+## page was renamed from Computing/LIP_Lisbon_Farm/Data_Management
-Line 4:
+Line 5:
-== Directories and filesystems ==
 * The fermi machines provide a wide set of filesystems so that users can access their data and applications.
+= File systems available =
 Line 7:
- * The available filesystems in login machines are:
+ * The users have at there disposal three types of filesystem:
  * A '''common NFS filesystem''' for homes not shared with workernodes
  * A '''lustre filesystem''' for some groups shared filesystem with the workernodes
  * A '''CVMFS read-only filesystem''' for software provision
 * Groups involved in WLCG transfer data using grid technologies can also use the Tier-3 storage areas and dedicated software areas (CVMFS) made available by there communities.

= Access Policy =

 * By default both lustre and nfs individual group areas can be accessed (read only) by users of the same group.  


= Directories and filesystems =

The '''pauli''' machines provide a wide set of filesystems so that users can access their data and applications.

== NFS Home directories ==

Users home mounts are not shared with workernodes, they can be found only on submission nodes:
-Line 10:
+Line 27:
-# df -h
Filesystem              Size  Used Avail Use% Mounted on
mdt02@tcp:/atlas         12T  8.4T  2.7T  76% /lustre/atlas   ---> Lustre FS for ATLAS Tier-2 and Tier-3 grid activities
mdt02@tcp:/auger         28T   24T  2.9T  90% /lustre/auger   ---> Lustre FS for AUGER local users
mdt02@tcp:/calor         72T   37T   32T  54% /lustre/calo    ---> Lustre FS for CALO local users
mdt02@tcp:/pem          186G  118G   60G  67% /lustre/pet     ---> Lustre FS for PET local users
mdt02@tcp:/sno           10T  1.1T  8.5T  12% /lustre/sno     ---> Lustre FS for SNO local users
st011:/exports/soft      20G   12G  7.3G  61% /soft           ---> NFS fs for local software
st011:/exports/lip-tmp  2.0T  126G  1.9T   7% /hometmp        ---> NFS fs for temporary / scratch storage
st011:/exports/home      20G   12G  7.3G  61% /v/home         ---> NFS fs LIP homes and data
st002:/exports/home      22G  6.2G   14G  31% /u/home         ---> NFS fs LIP homes and data
st002:/exports/data      22G  6.2G   14G  31% /u/data         ---> NFS fs LIP homes and data
st002:/exports/x         12T  9.7T  2.2T  82% /x              ---> NFS fs LIP homes and data
st012:/exports           20G  3.8G   15G  20% /z              ---> NFS fs LIP homes and data
+FILESYSTEM            MOUNTED ON            SCOPE
se63:/user            /user                 LIP groups
-Line 25:
+Line 30:
- * The available filesystems in LIP-Coimbra login machines are:
+== NFS Data directories ==

Projects specific data NFS mounts are not shared with workernodes and are found only on submission nodes:
-Line 28:
+Line 36:
-$ df -h
Filesystem                        Size  Used Avail Use% Mounted on
lustre@tcp:/gstore                101T   71T   25T  75% /gstore                     ---> Lustre fs dedicated for atlas tier2 grid activities
llustre@tcp:/lstore-1              34T  9.4T   23T  30% /lstore/atlaslocalgroupdisk ---> Lustre fs dedicated for atlas tier3 grid users
llustre@tcp:/lstore-2              43T   38T  2.9T  93% /lstore/atlas               ---> Lustre fs dedicated for atlas local users
llustre@tcp:/lstore-3              18T   12T  5.5T  68% /lstore/lip                 ---> Lustre fs dedicated for lip local users
192.168.2.44:/software            3.9T  882G  3.0T  23% /software                   ---> NFS fs for local software
192.168.2.30:/exports/home-atlas   13T   12T  1.5T  89% /home/local/atlas           ---> NFS fs for ATLAS local homes
192.168.2.30:/exports/home-lip     13T   12T  1.4T  90% /home/local/lip             ---> NFS fs for LIP local homes
+FILESYSTEM            MOUNTED ON            SCOPE
se34:/sno             /n/sno                SNO+ data
se51:/sno             /s/sno                SNO+ data
se27:/ams             /z/ams                AMS data
se27:/comp            /z/comp               COMPASS data
}}}

== LUSTRE Data directories ==

Projects specific data LUSTRE mounts are shared with workernodes:

{{{
FILESYSTEM            MOUNTED ON            SCOPE
mdt02@tcp:/t3atlas    /gstore/t3atlas       ATLAS Tier-3
mdt02@tcp:/T3CMS      /gstore/t3cms         CMS Tier-3
mdt04@tcp:/auger      /lstore/auger         AUGER
mdt04@tcp:/calo       /lstore/calo          ATLAS Lisboa
mdt02@tcp:/cmslocal   /lstore/cms           CMS
mdt03@tcp:/comp       /lstore/comp          COMP
mdt04@tcp:/lattes     /lstore/lattes        LATTES
mdt04@tcp:/nucria     /lstore/nucria        NUCRIA
mdt04@tcp:/pet        /lstore/pet           PET
mdt10@tcp:/sno        /lstore/sno           SNO PLUS
mds22@tcp:/titan      /lstore/titan         ATLAS
mds-feno@tcp:/feno    /lstore/feno          Phenomenology
mds-share@tcp:/share  /share                Shared with Atlas, Auger, CMS, Compass, NUCRIA, SPAC and SWGO
}}}

== CVMFS Software provision ==

The '''CVMFS''' is a read-only filesystem with cache local to clients optimal for software provision:

{{{
FILESYSTEM            MOUNTED ON            SCOPE
cvmfs2                /cvmfs/cms.cern.ch    CMS VO
cvmfs2                /cvmfs/atlas.cern.ch  ATLAS VO
cvmfs2                /cvmfs/sw.el7         LIP
-Line 40:
+Line 76:
-== Data Management ==
=== LIP-Lisbon use cases ===
 * At LIP-Lisbon, the home filesystem is not shared between the submission hosts and the execution hosts. As a result, it is the user responsibility to transfer data and applications to/from the execution machines.

 * There are several ways to manage data in LIP-Lisbon FARM:
  1. Automatic transfers via scp
  1. Data access via /hometmp (NFS)
  1. Data access via /lustre

==== Automatic transfers via scp ====
 * '''SCOPE: This is the most appropriate method to transfer a small number of small files.'''

 * The automatic transfer of data and application via scp is triggered by declaring files (or directories) to transfer in dedicated system variables defined in the submission script.
  * '''SGEIN{1...N}''': Define one variable for each file or directory to transfer from the submission machine to the execution machine
  * '''SGEOUT{1...N}''': Define one variable for each file or directory to transfer from the execution machine to the submission machine

{{{
# Transfer input file (MyMacro.c) to the execution machine
#$ -v SGEIN1=MyMacro.c

# Transfer output file (graph_with_law.pdf) from the execution machine
#$ -v SGEOUT1=graph_with_law.pdf
}}}
 * The full syntax for scp automatic transfers is described hereafter. Keep in mind that all paths should be relative to the current working directory (where you are submitting the job):

{{{
# My input file is called input_file1.txt and it will have the same name in the execution host
#$ -v SGEIN1=input_file1.txt

# My input file is called input_file2.txt but it will be called inputfile2.txt in the execution host
#$ -v SGEIN2=input_file2.txt:inputfile2.txt

# My input is a full directory (The directory INPUT3 must exist in the submission host)
#$ -v SGEIN3=INPUT3

# My input is the file INPUT4/input_file4.txt, and it will exist in the execution host in INPUT4/inputfile4.txt
#$ -v SGEIN4=INPUT4/input_file4.txt:INPUT4/inputfile4.txt

# My input is the directory INPUT5 and it will be called INPUT_AT_WORKERNODE1 in the execution host
#$ -v SGEIN5=INPUT5:INPUT_AT_WORKERNODE1

# My input is the file INPUT6/input_file6.txt, and it will exist in the execution host in INPUT_AT_WORKERNODE2/inputfile6.txt
#$ -v SGEIN6=INPUT6/input_file6.txt:INPUT_AT_WORKERNODE2/inputfile6.txt

# My input is the directory INPUT7 which will pass to the execution host as the tree of directories
#    INPUT_AT_WORKERNODE3/INPUT_AT_WORKERNODE4
#$ -v SGEIN7=INPUT7:INPUT_AT_WORKERNODE3/INPUT_AT_WORKERNODE4

# My input is the file INPUT8/input_file8.txt which will pass to the execution host
#    as INPUT_AT_WORKERNODE5/INPUT_AT_WORKERNODE6/inputfile8.txt
#$ -v SGEIN8=INPUT8/input_file8.txt:INPUT_AT_WORKERNODE5/INPUT_AT_WORKERNODE6/inputfile8.txt
}}}
==== Data access via /hometmp (NFS) ====
 * '''SCOPE: Same input files and applications are used by multiple jobs'''

 * If the same input files should serve multiple jobs, users should store those files under the '''/hometmp''' directory, shared between the submission hosts and the execution hosts. This is more efficient than copying the same files over and over again.

 * Simultaneously, users can use '''/hometmp''' to check the status of running jobs using, for example, dedicated logs. Check the following example:

{{{
# ! /bin/bash

MY_HOMETMP=/hometmp/csys/goncalo

OUTPUT_FILE=output_file1.txt
INPUT_FILE=input_file1.txt
OUTPUT_FILE=output_file1.txt
MyLOG=mylog.txt

echo "Starting second test on `date`"> $MY_HOMETMP/$MyLOG

tr -s 'a-z' 'A-Z' < $MY_HOMETMP/$INPUT_FILE >> $OUTPUT_FILE
mv -f $OUTPUT_FILE $MY_HOMETMP/$OUTPUT_FILE

echo "Finishing second test on `date`" >> $MY_HOMETMP/$MyLOG
}}}
 * While the job is running, the user can check the job status consulting the '''mylog.txt''' log in /hometmp

===== Important Disclaimer =====
 * Users should be aware of the following issues:
  1. Be cautious so that files are not squeezed when writing to the /hometmp, specially while sending arrays of jobs.
  1. It is preferable that users do not write OUTPUT results directly to /hometmp (due to performance degradation generated by lock management mechanisms). It is better to write OUTPUT results to the local disk (where the jobs is executing), and copy it at the end of your job to /hometmp
  1. Data in /hometmp will be deleted after 30 days.

==== Access data via '''/lustre''' ====
 * '''SCOPE: Store and access big/huge data files.'''

 * '''/lustre''' is a shared filesystem (present in the execution hosts and in the submission hosts) dedicated for the '''storage of big/huge files'''. The following directories are accessible for the local LIP groups:
  1. /lustre/lip.pt/data/calo
  1. /lustre/lip.pt/data/cosmo
  1. /lustre/lip.pt/data/pet
  1. /lustre/lip.pt/data/sno

 * Groups involved in WLCG transfer data using grid technologies to the following locations
  1. '''ATLAS''': /lustre/lip.pt/data/atlas/atlaslocalgroupdisk (calo group has read access to this filesystem)

===== Important Disclaimer =====
+= Important Disclaimer =
-Line 140:
+Line 80:
+= Access your data by SSHFS =

== Install sshfs package ==

On Ubuntu/debian:
{{{ 
# sudo apt-get install sshfs
}}}

On RHEL/CentOS/Fedora:
{{{
# sudo yum install fuse-sshfs
}}}


== Create a local directory ==
{{{ 
# mkdir ~/homeNCG
}}}

== Mount your remote folder ==
{{{
# sshfs martinsj@fermi.ncg.ingrid.pt: ~/homeNCG
}}}

== When you're done, you can unmount it ==
{{{
# fusermount -u ~/homeNCG
}}}

== .bashrc tunning ==

In case you're dealing with very long paths, as a suggestion, you can add to your ~/.bashrc file the following:

{{{ 
alias mfermi='f(){ dir=$1 ; [ -n "$dir" ] || dir=homeNCG ; [ -d ~/$dir ] || mkdir -p ~/$dir ; sshfs fermi.ncg.ingrid.pt: ~/$dir ;  unset -f f; }; f'
alias ufermi='f(){ dir=$1 ; [ -n "$dir" ] || dir=homeNCG ; [ -d ~/$dir ] && fusermount -u ~/$dir ; [ -d ~/$dir ] && rmdir ~/$dir ;  unset -f f; }; f'

alias mncg='f(){ dir=$1 ; [ -n "$dir" ] && ldir=`basename $dir` ; [ -d ~/$ldir ] || mkdir -p ~/$ldir ; [ -n "$dir$ldir" ] && sshfs fermi.ncg.ingrid.pt:$dir ~/$ldir ;  unset -f f; }; f'
alias uncg='f(){ dir=$1 ; [ -n "$dir" ] && ldir=`basename $dir` ; ldir=`echo $ldir ; [ -d ~/$ldir ] && fusermount -u ~/$ldir ; [ -d ~/$ldir ] && rmdir ~/$ldir ;  unset -f f; }; f'

alias mcalo='f(){ [ -d lcalo ] || mkdir ~/lcalo ; sshfs fermi.ncg.ingrid.pt:/lstore/calo ~/lcalo ;  unset -f f; }; f'
alias ucalo='f(){ [ -d ~/lcalo ] && fusermount -u ~/lcalo ; [ -d ~/$ldir ] && rmdir ~/lcalo ;  unset -f f; }; f'
}}}

This is how you can use it:

{{{
$ mfermi homeNCG
$ df
Filesystem           1K-blocks    Used Available Use% Mounted on
fermi.ncg.ingrid.pt: 209612800 3504112 206108688   2%
/home/martinsj/homeNCG
$ ufermi homeNCG

$ mncg /lstore/calo
...
$ uncg /lstore/calo

}}}

Diff for "Computing/LIP_Lisbon_Farm/3_Data_Management"

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