Skip to content
B2STAGE service core code for EUDAT project: iRODS-DSI
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
DSI
external
images
.gitignore
CMakeLists.txt
ChangeLog.txt
README.md
setup.sh.template

README.md

B2STAGE-GridFTP (iRODS-DSI)

B2STAGE service core code for EUDAT project: DSI interface for iRODS (version > 4)

GridFTP is a high-performance, secure, reliable data transfer protocol which provides remote access to data stores. There are many different types of data storage systems from standard file systems to arrays of magnetic tape: to allow GridFTP to be used with as many data storage systems as possible, the GridFTP can be extended, implementing an interface called Data Storage Interface (DSI).

The GridFTP iRODS DSI consists of C functions which can interact with iRODS through the iRODS C API. The main supported operations are get, put, delete and list.

Alt text

Once installed and configured, users will be able to interact with iRODS through any GridFTP client passing to it a valid iRODS path; for instance:

$ globus-url-copy -list gsiftp://develvm.cluster.cineca.it:2811/tempZone/home/myuser/

will list the content of the /tempZone/home/myuser/ iRODS collection.

The module can be loaded by the GridFTP server at start-up time through a specific command line option. Therefore, no changes are required in the GridFTP server installation. The decoupling from the possible future changes to the server simplifies the maintenance of the software module.

Prerequisites

  • CMake 2.7 or higher (part of irods-externals in iRODS 4.2.X)

  • iRODS with the Development Tools and Runtime Libraries packages: follow the instructions at https://packages.irods.org/ to add the iRODS repository to your package manager. Installation instructions can be found at https://irods.org/download/

  • For 4.2, the iRODS external packages need to be installed. These provide a consistent build environment (cmake, clang, etc.) to build the GridFTP plugin:

    Ubuntu:

     sudo apt-get install 'irods-externals*
    

    Centos:

     sudo yum -y install irods-devel
     sudo yum install irods-externals-clang3.8-0.x86_64
    
  • Globus and other packages:

    Ubuntu:

     sudo apt-get install -y globus-gridftp-server-progs globus-gass-copy-progs libglobus-gss-assist-dev
     sudo apt-get install -y libglobus-common-dev libglobus-gridftp-server-dev libglobus-gridmap-callout-error-dev
     sudo apt-get install -y libcurl4-openssl-dev
     sudo apt-get install -y git
     sudo apt-get install -y g++
     sudo apt-get install -y dpkg-dev
     sudo apt-get install -y cdbs
     sudo apt-get install -y globus-gsi-cert-utils-progs
     sudo apt-get install -y globus-proxy-utils
    

    Centos:

     sudo yum install -y globus-gridftp-server-progs globus-gass-copy-progs
     sudo yum install -y globus-common-devel globus-gridftp-server-devel   globus-gridmap-callout-error-devel
     sudo yum install -y libcurl-devel
     sudo yum install -y git
     sudo yum install -y gcc-c++
     sudo yum install -y globus-gsi-cert-utils-progs
     sudo yum install -y globus-proxy-utils
    

Building iRODS DSI with CMake

  1. Clone this repository

    git clone https://github.com/EUDAT-B2STAGE/B2STAGE-GridFTP.git
    
  2. Create a deployment folder:

    mkdir /<preferred_path>/iRODS_DSI
    
  3. Set some environment variables that are used by the build process and the PATH so that the correct version of cmake will be found.

    export PATH=/opt/irods-externals/cmake3.5.2-0/bin:$PATH
    export GLOBUS_LOCATION="/usr"
    export IRODS_PATH="/usr"
    export DEST_LIB_DIR="/<preferred_path>/iRODS_DSI"
    export DEST_BIN_DIR="/<preferred_path>/iRODS_DSI"
    export DEST_ETC_DIR="/<preferred_path>/iRODS_DSI"
    export IRODS_EXTERNALS_PATH=/opt/irods-externals
    

    In Ubuntu you may need to set up C_INCLUDE_PATH so that the globus_config.h header can be found.

    export C_INCLUDE_PATH=/usr/include/x86_64-linux-gnu/globus
    

    or

    export C_INCLUDE_PATH=/usr/include/globus
    

    If you are building for iRODS 4.2, set the IRODS_42_COMPAT environment variable to true.

    export IRODS_42_COMPAT=true
    
  4. Build and install the iRODS-DSI:

    cd B2STAGE-GridFTP
    cmake .
    make install
    

Configuring the GridFTP server and run

  1. As the user who runs the GridFTP server, create the file ~/.irods/irods_environment.json (or ~/.irods/.irodsEnv for iRODS < 4.1.x) and populate it with the information related to a rodsadmin" user; for instance:

    {
       "irods_host" : "irods4", 
       "irods_port" : 1247,
       "irods_user_name" : "rods",
       "irods_zone_name" : "tempZone",
       "irods_default_resource" : "demoResc"
    }
    

    Note that the "irods_host" and "irods_port" identify the iRODS server that the DSI will contact during each request. Be sure to set the irods_default_resource, this variable is not set when you create the file with iinit or when you copy it over from another user.

  2. As the user who runs the GridFTP server, try an ils icommand to verify that the information set in the irods_environment.json are fine. If needed, perform an iinit to authenticate the iRODS user.

  3. Add the following lines to the GridFTP configuration file (typically $GLOBUS_LOCATION/etc/gridftp.conf*):

    $LD_LIBRARY_PATH "$LD_LIBRARY_PATH:/<preferred_path>/iRODS_DSI"
    $irodsConnectAsAdmin "rods"
    load_dsi_module iRODS 
    auth_level 4
    

    In case the GridFTP is run as a system service, also set the $HOME env variable pointing to the home folder of the user who runs the gridftp server:

    $HOME /path/to/user/home
    
  4. Add the following line at the beginning of the globus-gridftp-server (usually /etc/init.d/globus-gridftp-server) file:

    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/<preferred_path>/iRODS_DSI/"
    
  5. When deploying the DSI with iRODS 4.1, it is necessary to load the GridFTP server library alongside the DSI library by adding the following lines at the beginning of the globus-gridftp-server (usually /etc/init.d/globus-gridftp-server) file: Ubuntu:

    export LD_PRELOAD="$LD_PRELOAD:/usr/lib/x86_64-linux-gnu/libglobus_gridftp_server.so:/iRODS_DSI/libglobus_gridftp_server_iRODS.so"
    

    Centos:

    export LD_PRELOAD="$LD_PRELOAD:/usr/lib64/libglobus_gridftp_server.so:/iRODS_DSI/libglobus_gridftp_server_iRODS.so"
    
  6. To enable the GridFTP CKSM (checksum) command to interoperate with Globus.org, it is necessary to configure iRODS to use MD5 checksums (iRODS 4 otherwise defaults to SHA-256). Edit /etc/irods/server_config.json and set:

    "default_hash_scheme": "MD5",
    
  7. Run the server with:

    /etc/init.d/globus-gridftp-server restart
    

Additional configuration

  1. Optionally, it is possible to enable the DSI module to manage the input path as a PID: the DSI will try to resolve the PID and perform the requested operation using the URI returned by the Handle server (currently only listing and downloading is supported). For instance:

    globus-url-copy -list  gsiftp://develvm01.pico.cineca.it:2811/11100/da3dae0a-6371-11e5-ba64-a41f13eb32b2/
    

    will return the list of objects contained in the collection to which the PID "11100/da3dae0a-6371-11e5-ba64-a41f13eb32b2/" points, or:

    globus-url-copy gsiftp://develvm01.pico.cineca.it:2811/11100/xa3dae0a-6371-11e5-ba64-a41f13eb32b1 /test.txt
    

    will download the object pointed by the PID "11100/xa3dae0a-6371-11e5-ba64-a41f13eb32b1".

    If the PID resolution fails (either because the Handle server cannot resolve the PID or because the path passed as input is not a PID) the DSI will try to perform the requested operation anyway, using the original input path. This guarantees that the DSI can accept both PIDs and standard iRODS paths.

    To enable the PID resolution export the address of your handle-resolver to the GridFTP configuration file (typically $GLOBUS_LOCATION/etc/gridftp.conf):

    $pidHandleServer "http://hdl.handle.net/api/handles"
    

    If you are using a different resolver than the global handle resolver, replace hdl.handle.net with the correct address.

    Note: Once the PID is correctly resolved, the requested operation (listing or downloading) will be correctly performed only if the URI returned by the Handle server is a valid iRODS path pointing to the iRODS instance to which the DSI is connected to.

  2. If desired, change the default home directory by setting the homeDirPattern environment variable in

    $GLOBUS_LOCATION/etc/gridftp.conf
    

    The pattern can reference up to two strings with %s, first gets substituted with the zone name, second with the user name. The default alue is "/%s/home/%s", making the default directory /<zone>/home/<username>.

    Default configuration:

    $homeDirPattern "/%s/home/%s"
    

    Example alternative configuration (defaulting to /<zone>/home):

    $homeDirPattern "/%s/home"
    
  3. It is possible to specify a policy to manage more than one iRODS resource setting the irodsResourceMap environment variable in $GLOBUS_LOCATION/etc/gridftp.conf.

    $irodsResourceMap "path/to/mapResourcefile"
    

    The irodsResourceMap variable must point to a file which specifies which iRODS resource has to be used when uploading or downloading a file in a particular iRODS path. For example:

    $cat path/to/mapResourcefile
    
    /CINECA01/home/cin_staff/rmucci00;resc-repl
    /CINECA01/home/cin_staff/mrossi;resc-repl
    

    If none of the listed paths is matched, the iRODS default resource is used.

  4. Optionally, use a Globus gridmap callout module to map subject DNs to iRODS user names based on the existing mappings in iRODS (in r_user_auth table). Configuring this feature eliminates the need for a local grid map file - all user mappings can be done through the callout function.

    The gridmap callout configuration file gets already created as '/preferred_path/iRODS_DSI/gridmap_iRODS_callout.conf'.

    To activate the module, set the '$GSI_AUTHZ_CONF' environment variable in $GLOBUS_LOCATION/etc/gridftp.conf to point to the configuration file already created as '/preferred_path/iRODS_DSI/gridmap_iRODS_callout.conf'.

    $GSI_AUTHZ_CONF /preferred_path/iRODS_DSI/gridmap_iRODS_callout.conf
    

    Note that in order for this module to work, the server certificate DN must be authorized to connect as a rodsAdmin user (e.g., the 'rods' user).

Additional notes

This module also supports invoking an iRODS server-side command with iexec in case the DN does not have a mapping yet. The command would receive the DN being mapped as a single argument and may for example add a mapping to an existing account, or create a new account. To enable this feature, set the $irodsDnCommand environment variable in '/etc/gridftp.conf' to the name of the command to execute. On the iRODS server, the command should be installed in '$IRODS_HOME/server/bin/cmd/'. For example, to invoke a script called 'createUser', add:

$irodsDnCommand "createUser"

There is also a command line utility to test the mapping lookups (and script execution) that would otherwise be done by the gridmap module. This utility command gets installed into '$DEST_BIN_DIR/testirodsmap' and should be invoked with the DN as a single argument. The command would need to see the same environment variables as the gridmap module loaded into the GridFTP server - specifically, $irodsEnvFile pointing to the iRODS environment and '$irodsDnCommand' setting the command to invoke if no mapping is found. The 'testirodsmap' command also needs to have access to the server host certificate - and find it either through the default mechanisms used by Globus GSI or by explicitly setting the 'X509_USER_CERT' and 'X509_USER_KEY' environment variables. (The easiest way is to run the command in the same environment as the Globus GridFTP server, i.e., under the root account). For example, invoke the command with:

export irodsDnCommand=createUser 
export irodsEnvFile=/path/to/.irodsEnv
$DEST_BIN_DIR/testirodsmap "/C=XX/O=YYY/CN=Example User"

Licence

Copyright 2011-2017 EUDAT CDI - www.eudat.eu.

Copyright (c) 1999-2006 University of Chicago

Globus DSI to manage data on iRODS.

Author: Roberto Mucci - SCAI - CINECA Email: hpc-service@cineca.it

Globus gridmap iRODS callout to map subject DNs to iRODS accounts.

Author: Vladimir Mencl, University of Canterbury Email: vladimir.mencl@canterbury.ac.n

You can’t perform that action at this time.