Difference between revisions of "IRODS iCommands installation on CentOS 7"

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Here is an example of iRODS iCommands installation on CentOS 7, from iRODS repository
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'''Back to [https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS Swestore-iRODS Documentation]'''
  
== Install the public key and add the repository: ==
+
 
 +
Here is an example of iRODS iCommands installation on CentOS 7, from iRODS repository.
 +
 
 +
== Install the public key and add the repository ==
 
  [vitlacil@localhost ~]$ sudo rpm --import https://packages.irods.org/irods-signing-key.asc
 
  [vitlacil@localhost ~]$ sudo rpm --import https://packages.irods.org/irods-signing-key.asc
 
  [sudo] password for vitlacil: *************************
 
  [sudo] password for vitlacil: *************************
Line 153: Line 156:
 
  Complete!
 
  Complete!
  
== And Python dependencies ==  
+
== ... and Python dependencies ==  
 
  [vitlacil@localhost ~]$ sudo yum install python-psutil python-jsonschema
 
  [vitlacil@localhost ~]$ sudo yum install python-psutil python-jsonschema
 
  Loaded plugins: fastestmirror, langpacks
 
  Loaded plugins: fastestmirror, langpacks
Line 228: Line 231:
 
  [vitlacil@localhost ~]$  
 
  [vitlacil@localhost ~]$  
  
 
+
== Install iRODS iCommands ==
 
+
[vitlacil@localhost ~]$ sudo yum install irods-icommands
[vitlacil@localhost ~]$  
+
Loaded plugins: fastestmirror, langpacks
[vitlacil@localhost ~]$
+
Loading mirror speeds from cached hostfile
[vitlacil@localhost ~]$
+
  * base: mirrors.glesys.net
[vitlacil@localhost ~]$
+
  * epel: mirrors.glesys.net
[vitlacil@localhost ~]$
+
  * extras: mirrors.glesys.net
[vitlacil@localhost ~]$
+
  * updates: mirrors.glesys.net
[vitlacil@localhost ~]$ sudo yum install irods-icommands
+
  Resolving Dependencies
Loaded plugins: fastestmirror, langpacks
+
  --> Running transaction check
Loading mirror speeds from cached hostfile
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---> Package irods-icommands.x86_64 0:4.2.7-1 will be installed
* base: mirrors.glesys.net
+
--> Processing Dependency: irods-runtime = 4.2.7 for package: irods-icommands-4.2.7-1.x86_64
  * epel: mirrors.glesys.net
+
--> Processing Dependency: irods-externals-avro1.7.7-0 for package: irods-icommands-4.2.7-1.x86_64
  * extras: mirrors.glesys.net
+
--> Processing Dependency: irods-externals-jansson2.7-0 for package: irods-icommands-4.2.7-1.x86_64
* updates: mirrors.glesys.net
+
--> Processing Dependency: irods-externals-clang-runtime3.8-0 for package: irods-icommands-4.2.7-1.x86_64
Resolving Dependencies
+
--> Processing Dependency: irods-externals-zeromq4-14.1.3-0 for package: irods-icommands-4.2.7-1.x86_64
--> Running transaction check
+
--> Processing Dependency: irods-externals-boost1.60.0-0 for package: irods-icommands-4.2.7-1.x86_64
---> Package irods-icommands.x86_64 0:4.2.7-1 will be installed
+
--> Processing Dependency: irods-externals-libarchive3.3.2-0 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-runtime = 4.2.7 for package: irods-icommands-4.2.7-1.x86_64
+
--> Running transaction check
--> Processing Dependency: irods-externals-avro1.7.7-0 for package: irods-icommands-4.2.7-1.x86_64
+
---> Package irods-externals-avro1.7.7-0.x86_64 0:1.0-1 will be installed
--> Processing Dependency: irods-externals-jansson2.7-0 for package: irods-icommands-4.2.7-1.x86_64
+
---> Package irods-externals-boost1.60.0-0.x86_64 0:1.0-1 will be installed
--> Processing Dependency: irods-externals-clang-runtime3.8-0 for package: irods-icommands-4.2.7-1.x86_64
+
---> Package irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 will be installed
--> Processing Dependency: irods-externals-zeromq4-14.1.3-0 for package: irods-icommands-4.2.7-1.x86_64
+
---> Package irods-externals-jansson2.7-0.x86_64 0:1.0-1 will be installed
--> Processing Dependency: irods-externals-boost1.60.0-0 for package: irods-icommands-4.2.7-1.x86_64
+
---> Package irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1 will be installed
--> Processing Dependency: irods-externals-libarchive3.3.2-0 for package: irods-icommands-4.2.7-1.x86_64
+
---> Package irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1 will be installed
--> Running transaction check
+
---> Package irods-runtime.x86_64 0:4.2.7-1 will be installed
---> Package irods-externals-avro1.7.7-0.x86_64 0:1.0-1 will be installed
+
--> Finished Dependency Resolution
---> Package irods-externals-boost1.60.0-0.x86_64 0:1.0-1 will be installed
+
---> Package irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 will be installed
+
Dependencies Resolved
---> Package irods-externals-jansson2.7-0.x86_64 0:1.0-1 will be installed
+
 
---> Package irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1 will be installed
+
====================================================================================================
---> Package irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1 will be installed
+
  Package                                  Arch          Version          Repository          Size
---> Package irods-runtime.x86_64 0:4.2.7-1 will be installed
+
====================================================================================================
--> Finished Dependency Resolution
+
Installing:
 
+
  irods-icommands                          x86_64        4.2.7-1          renci-irods        526 k
Dependencies Resolved
+
Installing for dependencies:
 
+
  irods-externals-avro1.7.7-0              x86_64        1.0-1            renci-irods        1.5 M
====================================================================================================
+
  irods-externals-boost1.60.0-0            x86_64        1.0-1            renci-irods        13 M
Package                                  Arch          Version          Repository          Size
+
  irods-externals-clang-runtime3.8-0        x86_64        1.0-1            renci-irods        347 k
====================================================================================================
+
  irods-externals-jansson2.7-0              x86_64        1.0-1            renci-irods        165 k
Installing:
+
  irods-externals-libarchive3.3.2-0        x86_64        1.0-1            renci-irods        1.7 M
irods-icommands                          x86_64        4.2.7-1          renci-irods        526 k
+
  irods-externals-zeromq4-14.1.3-0          x86_64        1.0-1            renci-irods        549 k
Installing for dependencies:
+
  irods-runtime                            x86_64        4.2.7-1          renci-irods        3.6 M  
irods-externals-avro1.7.7-0              x86_64        1.0-1            renci-irods        1.5 M
+
irods-externals-boost1.60.0-0            x86_64        1.0-1            renci-irods        13 M
+
Transaction Summary
irods-externals-clang-runtime3.8-0        x86_64        1.0-1            renci-irods        347 k
+
====================================================================================================
irods-externals-jansson2.7-0              x86_64        1.0-1            renci-irods        165 k
+
Install  1 Package (+7 Dependent packages)
irods-externals-libarchive3.3.2-0        x86_64        1.0-1            renci-irods        1.7 M
+
irods-externals-zeromq4-14.1.3-0          x86_64        1.0-1            renci-irods        549 k
+
Total download size: 21 M
irods-runtime                            x86_64        4.2.7-1          renci-irods        3.6 M
+
Installed size: 158 M
 
+
Is this ok [y/d/N]: y  
Transaction Summary
+
Downloading packages:
====================================================================================================
+
(1/8): irods-externals-avro1.7.7-0-1.0-1.x86_64.rpm                          | 1.5 MB  00:00:03     
Install  1 Package (+7 Dependent packages)
+
(2/8): irods-externals-clang-runtime3.8-0-1.0-1.x86_64.rpm                  | 347 kB  00:00:00     
 
+
(3/8): irods-externals-jansson2.7-0-1.0-1.x86_64.rpm                        | 165 kB  00:00:00     
Total download size: 21 M
+
(4/8): irods-externals-libarchive3.3.2-0-1.0-1.x86_64.rpm                    | 1.7 MB  00:00:03     
Installed size: 158 M
+
(5/8): irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64.rpm                    | 549 kB  00:00:01     
Is this ok [y/d/N]: y
+
(6/8): irods-icommands-4.2.7-1.x86_64.rpm                                    | 526 kB  00:00:01     
Downloading packages:
+
(7/8): irods-externals-boost1.60.0-0-1.0-1.x86_64.rpm                        |  13 MB  00:00:16     
(1/8): irods-externals-avro1.7.7-0-1.0-1.x86_64.rpm                          | 1.5 MB  00:00:03     
+
(8/8): irods-runtime-4.2.7-1.x86_64.rpm                                      | 3.6 MB  00:00:08     
(2/8): irods-externals-clang-runtime3.8-0-1.0-1.x86_64.rpm                  | 347 kB  00:00:00     
+
----------------------------------------------------------------------------------------------------
(3/8): irods-externals-jansson2.7-0-1.0-1.x86_64.rpm                        | 165 kB  00:00:00     
+
Total                                                              1.0 MB/s |  21 MB  00:00:20    
(4/8): irods-externals-libarchive3.3.2-0-1.0-1.x86_64.rpm                    | 1.7 MB  00:00:03     
+
Running transaction check  
(5/8): irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64.rpm                    | 549 kB  00:00:01     
+
Running transaction test
(6/8): irods-icommands-4.2.7-1.x86_64.rpm                                    | 526 kB  00:00:01     
+
Transaction test succeeded
(7/8): irods-externals-boost1.60.0-0-1.0-1.x86_64.rpm                        |  13 MB  00:00:16     
+
Running transaction
(8/8): irods-runtime-4.2.7-1.x86_64.rpm                                      | 3.6 MB  00:00:08     
 
----------------------------------------------------------------------------------------------------
 
Total                                                              1.0 MB/s |  21 MB  00:00:20    
 
Running transaction check
 
Running transaction test
 
Transaction test succeeded
 
Running transaction
 
 
   Installing : irods-externals-avro1.7.7-0-1.0-1.x86_64                                        1/8  
 
   Installing : irods-externals-avro1.7.7-0-1.0-1.x86_64                                        1/8  
  Installing : irods-externals-boost1.60.0-0-1.0-1.x86_64                                      2/8  
+
  Installing : irods-externals-boost1.60.0-0-1.0-1.x86_64                                      2/8  
  Installing : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64                                    3/8  
+
  Installing : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64                                    3/8  
  Installing : irods-externals-libarchive3.3.2-0-1.0-1.x86_64                                  4/8  
+
  Installing : irods-externals-libarchive3.3.2-0-1.0-1.x86_64                                  4/8  
  Installing : irods-externals-jansson2.7-0-1.0-1.x86_64                                        5/8  
+
  Installing : irods-externals-jansson2.7-0-1.0-1.x86_64                                        5/8  
  Installing : irods-externals-clang-runtime3.8-0-1.0-1.x86_64                                  6/8  
+
  Installing : irods-externals-clang-runtime3.8-0-1.0-1.x86_64                                  6/8  
  Installing : irods-runtime-4.2.7-1.x86_64                                                    7/8  
+
  Installing : irods-runtime-4.2.7-1.x86_64                                                    7/8  
  Installing : irods-icommands-4.2.7-1.x86_64                                                  8/8  
+
  Installing : irods-icommands-4.2.7-1.x86_64                                                  8/8  
  Verifying  : irods-externals-clang-runtime3.8-0-1.0-1.x86_64                                  1/8  
+
  Verifying  : irods-externals-clang-runtime3.8-0-1.0-1.x86_64                                  1/8  
  Verifying  : irods-externals-jansson2.7-0-1.0-1.x86_64                                        2/8  
+
  Verifying  : irods-externals-jansson2.7-0-1.0-1.x86_64                                        2/8  
  Verifying  : irods-externals-libarchive3.3.2-0-1.0-1.x86_64                                  3/8  
+
  Verifying  : irods-externals-libarchive3.3.2-0-1.0-1.x86_64                                  3/8  
  Verifying  : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64                                    4/8  
+
  Verifying  : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64                                    4/8  
  Verifying  : irods-externals-boost1.60.0-0-1.0-1.x86_64                                      5/8  
+
  Verifying  : irods-externals-boost1.60.0-0-1.0-1.x86_64                                      5/8  
  Verifying  : irods-icommands-4.2.7-1.x86_64                                                  6/8  
+
  Verifying  : irods-icommands-4.2.7-1.x86_64                                                  6/8  
  Verifying  : irods-externals-avro1.7.7-0-1.0-1.x86_64                                        7/8  
+
  Verifying  : irods-externals-avro1.7.7-0-1.0-1.x86_64                                        7/8  
  Verifying  : irods-runtime-4.2.7-1.x86_64                                                    8/8  
+
  Verifying  : irods-runtime-4.2.7-1.x86_64                                                    8/8  
 +
 +
Installed:
 +
  irods-icommands.x86_64 0:4.2.7-1                                                                 
 +
 +
Dependency Installed:
 +
  irods-externals-avro1.7.7-0.x86_64 0:1.0-1        irods-externals-boost1.60.0-0.x86_64 0:1.0-1 
 +
  irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 irods-externals-jansson2.7-0.x86_64 0:1.0-1   
 +
  irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1  irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1
 +
  irods-runtime.x86_64 0:4.2.7-1                 
 +
 +
Complete!
 +
[vitlacil@localhost ~]$
  
Installed:
+
== Configure the iRODS environment ==
  irods-icommands.x86_64 0:4.2.7-1                                                                 
+
NOTE: Create your own configuration file !!
 
 
Dependency Installed:
 
  irods-externals-avro1.7.7-0.x86_64 0:1.0-1        irods-externals-boost1.60.0-0.x86_64 0:1.0-1 
 
  irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 irods-externals-jansson2.7-0.x86_64 0:1.0-1   
 
  irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1  irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1
 
  irods-runtime.x86_64 0:4.2.7-1                 
 
 
 
Complete!
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ ils
 
ERROR: environment_properties::capture: missing environment file. should be at [/home/vitlacil/.irods/irods_environment.json]
 
ERROR: _rcConnect: setRhostInfo error, IRODS_HOST is probably not set correctly status = -302000 USER_RODS_HOST_EMPTY
 
[vitlacil@localhost ~]$ ls ~/.
 
Desktop  Documents  Downloads  Music  Pictures  Public  Templates  Videos
 
[vitlacil@localhost ~]$ ls ~/
 
Desktop  Documents  Downloads  Music  Pictures  Public  Templates  Videos
 
[vitlacil@localhost ~]$ ls ~/.
 
Desktop  Documents  Downloads  Music  Pictures  Public  Templates  Videos
 
[vitlacil@localhost ~]$ ls -a ~/.
 
.              .bash_logout  .cache  Desktop    .esd_auth      .mozilla  Public
 
..            .bash_profile  .config  Documents  .ICEauthority  Music    Templates
 
.bash_history  .bashrc        .dbus    Downloads  .local        Pictures  Videos
 
[vitlacil@localhost ~]$ i
 
Display all 152 possibilities? (y or n)
 
i386                      imsettings-info          iprsos
 
iadmin                    imsettings-list          iprupdate
 
iapitest                  imsettings-reload        ips
 
ibun                      imsettings-switch        ipsec
 
ibus                      imv                      ipset
 
ibus-daemon              in                        iptables
 
ibus-setup                indent                    iptables-restore
 
ibus-table-createdb      index_dump                iptables-save
 
icd                      info                      iptables-xml
 
iceauth                  infocmp                  iptc
 
icedax                    infokey                  iptunnel
 
ichksum                  infotocap                iput
 
ichmod                    init                      ipwd
 
iclienthints              insmod                    iqdel
 
iconv                    install                  iqmod
 
iconvconfig              install-info              iqstat
 
iconvconfig.x86_64        installkernel            iquest
 
icp                      install-printerdriver    iquota
 
id                        instperf                  ireg
 
ident                    intel-microcode2ucode    irepl
 
idiag-socket-details      interdiff                irm
 
idn                      intltool-extract          irmdir
 
iecset                    intltoolize              irmtrash
 
ienv                      intltool-merge            irods-grid
 
ierror                    intltool-prepare          irqbalance
 
iexecmd                  intltool-update          irsync
 
iexit                    ionice                    irule
 
if                        iostat                    iscan
 
ifcfg                    ip                        iscsiadm
 
ifconfig                  ip6tables                iscsid
 
ifdown                    ip6tables-restore        iscsi-iname
 
ifenslave                ip6tables-save            iscsistart
 
ifnames                  ipa                      iscsiuio
 
ifsck                    ipa-certupdate            isdv4-serial-inputattach
 
ifstat                    ipa-client-automount      isodebug
 
ifup                      ipa-client-install        isodump
 
igawk                    ipa-getcert              isoinfo
 
iget                      ipa-getkeytab            iso-info
 
igetwild                  ipa-join                  iso-read
 
igroupadmin              ipa-rmkeytab              isosize
 
ihelp                    ipasswd                  isovfy
 
iinit                    ipcalc                    isysmeta
 
ijsgutenprint.5.2        ipcmk                    iticket
 
ilocate                  ipcrm                    itrim
 
ils                      ipcs                      itweb-settings
 
ilsresc                  iphybun                  itweb-settings.itweb
 
imcoll                    iphymv                    iuserinfo
 
imeta                    ipmaddr                  iw
 
imiscsvrinfo              iprconfig                ixmsg
 
imkdir                    iprdump                  izonereport
 
implantisomd5            iprinit                 
 
[vitlacil@localhost ~]$ i
 
 
 
bash: i: command not found...
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ ienv
 
ERROR: environment_properties::capture: missing environment file. should be at [/home/vitlacil/.irods/irods_environment.json]
 
irods_version - 4.2.7
 
[vitlacil@localhost ~]$ iinit
 
ERROR: environment_properties::capture: missing environment file. should be at [/home/vitlacil/.irods/irods_environment.json]
 
One or more fields in your iRODS environment file (irods_environment.json) are
 
missing; please enter them.
 
Enter the host name (DNS) of the server to connect to:
 
Enter the port number:
 
Enter your irods user name:
 
Enter your irods zone:
 
Those values will be added to your environment file (for use by
 
other iCommands) if the login succeeds.
 
 
 
Enter your current iRODS password:
 
ERROR: Save Password failure status = -909000 NO_PASSWORD_ENTERED
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ ienv
 
ERROR: environment_properties::capture: missing environment file. should be at [/home/vitlacil/.irods/irods_environment.json]
 
irods_version - 4.2.7
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ iinit
 
ERROR: iRODS Exception:
 
    file: /irods/lib/core/src/irods_environment_properties.cpp
 
    function: void irods::environment_properties::capture_json(const std::string &)
 
    line: 113
 
    code: -1 (Unknown iRODS error)
 
    message:
 
        [-] /irods/lib/core/src/irods_configuration_parser.cpp:92:irods::error irods::configuration_parser::load_json_object(const std::string &) :  status [Unknown iRODS error]  errno [Operation not permitted] -- message [failed to load file [/home/vitlacil/.irods/irods_environment.json] json error [unexpected newline]]
 
 
 
 
 
stack trace:
 
--------------
 
 
 
Dumping stack trace
 
<0> Offset: 0x65 Address: 0x7f3ec8b55a25 irods::exception::exception(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<1> Offset: 0xf2 Address: 0x7f3ec8b526f2 irods::environment_properties::capture_json(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<2> Offset: 0xbb Address: 0x7f3ec8b5239b irods::environment_properties::capture()
 
<3> Offset: 0x33 Address: 0x7f3ec8b52253 irods::environment_properties::instance()
 
<4> Offset:    Address: 0x7f3ec8b3e690 /lib/libirods_common.so.4.2.7(+0x62690) [0x7f3ec8b3e690]
 
<5> Offset:    Address: 0x7f3ec8b3d81a /lib/libirods_common.so.4.2.7(getRodsEnvFromFile+0x5a) [0x7f3ec8b3d81a]
 
<6> Offset:    Address: 0x7f3ec8b3d70b /lib/libirods_common.so.4.2.7(_getRodsEnv+0x1b) [0x7f3ec8b3d70b]
 
<7> Offset:    Address: 0x7f3ec8b3d6e0 /lib/libirods_common.so.4.2.7(getRodsEnv+0x10) [0x7f3ec8b3d6e0]
 
<8> Offset:    Address: 0x40e3db iinit() [0x40e3db]
 
<9> Offset:    Address: 0x7f3ec7142555 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f3ec7142555]
 
<10> Offset:    Address: 0x40e1d8 iinit() [0x40e1d8]
 
 
 
 
 
One or more fields in your iRODS environment file (irods_environment.json) are
 
missing; please enter them.
 
Enter the host name (DNS) of the server to connect to: :q
 
Enter the port number:
 
Enter your irods user name:
 
Enter your irods zone:
 
Those values will be added to your environment file (for use by
 
other iCommands) if the login succeeds.
 
 
 
Enter your current iRODS password:
 
ERROR: Save Password failure status = -909000 NO_PASSWORD_ENTERED
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ iinit
 
ERROR: iRODS Exception:
 
    file: /irods/lib/core/src/irods_environment_properties.cpp
 
    function: void irods::environment_properties::capture_json(const std::string &)
 
    line: 113
 
    code: -1 (Unknown iRODS error)
 
    message:
 
        [-] /irods/lib/core/src/irods_configuration_parser.cpp:92:irods::error irods::configuration_parser::load_json_object(const std::string &) :  status [Unknown iRODS error]  errno [Operation not permitted] -- message [failed to load file [/home/vitlacil/.irods/irods_environment.json] json error [unexpected newline]]
 
 
 
 
 
stack trace:
 
--------------
 
 
 
Dumping stack trace
 
<0> Offset: 0x65 Address: 0x7fc3816dea25 irods::exception::exception(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<1> Offset: 0xf2 Address: 0x7fc3816db6f2 irods::environment_properties::capture_json(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<2> Offset: 0xbb Address: 0x7fc3816db39b irods::environment_properties::capture()
 
<3> Offset: 0x33 Address: 0x7fc3816db253 irods::environment_properties::instance()
 
<4> Offset:    Address: 0x7fc3816c7690 /lib/libirods_common.so.4.2.7(+0x62690) [0x7fc3816c7690]
 
<5> Offset:    Address: 0x7fc3816c681a /lib/libirods_common.so.4.2.7(getRodsEnvFromFile+0x5a) [0x7fc3816c681a]
 
<6> Offset:    Address: 0x7fc3816c670b /lib/libirods_common.so.4.2.7(_getRodsEnv+0x1b) [0x7fc3816c670b]
 
<7> Offset:    Address: 0x7fc3816c66e0 /lib/libirods_common.so.4.2.7(getRodsEnv+0x10) [0x7fc3816c66e0]
 
<8> Offset:    Address: 0x40e3db iinit() [0x40e3db]
 
<9> Offset:    Address: 0x7fc37fccb555 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fc37fccb555]
 
<10> Offset:    Address: 0x40e1d8 iinit() [0x40e1d8]
 
 
 
 
 
One or more fields in your iRODS environment file (irods_environment.json) are
 
missing; please enter them.
 
Enter the host name (DNS) of the server to connect to: irods-login.swestore.se
 
Enter the port number: 2432
 
Enter your irods user name: s_dejvi
 
Enter your irods zone: snic.se
 
Those values will be added to your environment file (for use by
 
other iCommands) if the login succeeds.
 
 
 
Enter your current iRODS password:
 
[-] /irods/plugins/auth/native/libnative.cpp:342:irods::error native_auth_client_response(irods::plugin_context &, rcComm_t *) :  status [CAT_INVALID_AUTHENTICATION]  errno [] -- message [Call to rcAuthResponseFailed.]
 
 
 
failed with error -826000 CAT_INVALID_AUTHENTICATION
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ ienv
 
ERROR: iRODS Exception:
 
    file: /irods/lib/core/src/irods_environment_properties.cpp
 
    function: void irods::environment_properties::capture_json(const std::string &)
 
    line: 113
 
    code: -1 (Unknown iRODS error)
 
    message:
 
        [-] /irods/lib/core/src/irods_configuration_parser.cpp:92:irods::error irods::configuration_parser::load_json_object(const std::string &) :  status [Unknown iRODS error]  errno [Operation not permitted] -- message [failed to load file [/home/vitlacil/.irods/irods_environment.json] json error [unexpected newline]]
 
 
 
 
 
stack trace:
 
--------------
 
 
 
Dumping stack trace
 
<0> Offset: 0x65 Address: 0x7fc5ae704a25 irods::exception::exception(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<1> Offset: 0xf2 Address: 0x7fc5ae7016f2 irods::environment_properties::capture_json(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<2> Offset: 0xbb Address: 0x7fc5ae70139b irods::environment_properties::capture()
 
<3> Offset: 0x33 Address: 0x7fc5ae701253 irods::environment_properties::instance()
 
<4> Offset:    Address: 0x7fc5ae6ed9df /lib/libirods_common.so.4.2.7(printRodsEnv+0x1f) [0x7fc5ae6ed9df]
 
<5> Offset:    Address: 0x400b39 ienv() [0x400b39]
 
<6> Offset:    Address: 0x7fc5accf1555 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fc5accf1555]
 
<7> Offset:    Address: 0x400969 ienv() [0x400969]
 
 
 
 
 
irods_version - 4.2.7
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ ienv
 
ERROR: iRODS Exception:
 
    file: /irods/lib/core/src/irods_environment_properties.cpp
 
    function: void irods::environment_properties::capture_json(const std::string &)
 
    line: 113
 
    code: -1 (Unknown iRODS error)
 
    message:
 
        [-] /irods/lib/core/src/irods_configuration_parser.cpp:92:irods::error irods::configuration_parser::load_json_object(const std::string &) :  status [Unknown iRODS error]  errno [Operation not permitted] -- message [failed to load file [/home/vitlacil/.irods/irods_environment.json] json error [unexpected newline]]
 
 
 
 
 
stack trace:
 
--------------
 
 
 
Dumping stack trace
 
<0> Offset: 0x65 Address: 0x7fae752d9a25 irods::exception::exception(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<1> Offset: 0xf2 Address: 0x7fae752d66f2 irods::environment_properties::capture_json(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<2> Offset: 0xbb Address: 0x7fae752d639b irods::environment_properties::capture()
 
<3> Offset: 0x33 Address: 0x7fae752d6253 irods::environment_properties::instance()
 
<4> Offset:    Address: 0x7fae752c29df /lib/libirods_common.so.4.2.7(printRodsEnv+0x1f) [0x7fae752c29df]
 
<5> Offset:    Address: 0x400b39 ienv() [0x400b39]
 
<6> Offset:    Address: 0x7fae738c6555 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fae738c6555]
 
<7> Offset:    Address: 0x400969 ienv() [0x400969]
 
 
 
 
 
irods_version - 4.2.7
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ ienv
 
ERROR: iRODS Exception:
 
    file: /irods/lib/core/src/irods_environment_properties.cpp
 
    function: void irods::environment_properties::capture_json(const std::string &)
 
    line: 113
 
    code: -1 (Unknown iRODS error)
 
    message:
 
        [-] /irods/lib/core/src/irods_configuration_parser.cpp:92:irods::error irods::configuration_parser::load_json_object(const std::string &) :  status [Unknown iRODS error]  errno [Operation not permitted] -- message [failed to load file [/home/vitlacil/.irods/irods_environment.json] json error [unexpected newline]]
 
  
 +
[vitlacil@localhost ~]$ cat /home/vitlacil/.irods/irods_environment.json
 +
{
 +
  "irods_host": "irods-login.swestore.se",
 +
  "irods_port": 2432,
 +
  "irods_default_resource": "pdc-gpfs",
 +
  "irods_home": "/snic.se/home/s_dejvi",
 +
  "irods_cwd": "/snic.se/home/s_dejvi",
 +
  "irods_user_name": "s_dejvi",
 +
  "irods_zone_name": "snic.se",
 +
  "irods_client_server_negotiation": "request_server_negotiation",
 +
  "irods_client_server_policy": "CS_NEG_REFUSE",
 +
  "irods_default_hash_scheme": "SHA256",
 +
  "irods_encryption_algorithm": "AES-256-CBC",
 +
  "irods_encryption_key_size": 32,
 +
  "irods_encryption_num_hash_rounds": 16,
 +
  "irods_encryption_salt_size": 8,
 +
  "irods_match_hash_policy": "compatible",
 +
  "irods_authentication_scheme" : "PAM"
 +
}
 +
 +
[vitlacil@localhost ~]$
  
stack trace:
+
== Authenticate and test iRODS iCommands client ==
--------------
+
  [vitlacil@localhost ~]$ iinit
 
+
Enter your current PAM password: *************************
Dumping stack trace
+
  [vitlacil@localhost ~]$ ils
<0> Offset: 0x65 Address: 0x7f41b7ac6a25 irods::exception::exception(long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
+
/snic.se/home/s_dejvi:
<1> Offset: 0xf2 Address: 0x7f41b7ac36f2 irods::environment_properties::capture_json(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
 
<2> Offset: 0xbb Address: 0x7f41b7ac339b irods::environment_properties::capture()
 
<3> Offset: 0x33 Address: 0x7f41b7ac3253 irods::environment_properties::instance()
 
<4> Offset:    Address: 0x7f41b7aaf9df /lib/libirods_common.so.4.2.7(printRodsEnv+0x1f) [0x7f41b7aaf9df]
 
<5> Offset:    Address: 0x400b39 ienv() [0x400b39]
 
<6> Offset:    Address: 0x7f41b60b3555 /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f41b60b3555]
 
<7> Offset:    Address: 0x400969 ienv() [0x400969]
 
 
 
 
 
irods_version - 4.2.7
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ ienv
 
irods_version - 4.2.7
 
irods_server_control_plane_encryption_num_hash_rounds - 16
 
irods_host - irods-login.swestore.se
 
irods_user_name - s_dejvi
 
irods_zone_name - snic.se
 
irods_transfer_buffer_size_for_parallel_transfer_in_megabytes - 4
 
schema_name - irods_environment
 
irods_server_control_plane_encryption_algorithm - AES-256-CBC
 
irods_match_hash_policy - compatible
 
irods_encryption_num_hash_rounds - 16
 
irods_default_resource - pdc-gpfs
 
irods_home - /snic.se/home/s_dejvi
 
schema_version - v3
 
irods_encryption_salt_size - 8
 
irods_environment_file - /home/vitlacil/.irods/irods_environment.json
 
irods_default_number_of_transfer_threads - 4
 
irods_cwd - /snic.se/home/s_dejvi
 
irods_session_environment_file - /home/vitlacil/.irods/irods_environment.json.4792
 
irods_port - 2432
 
irods_encryption_algorithm - AES-256-CBC
 
irods_server_control_plane_port - 1248
 
irods_server_control_plane_key - 32_byte_server_control_plane_key
 
irods_client_server_negotiation - request_server_negotiation
 
irods_encryption_key_size - 32
 
irods_client_server_policy - CS_NEG_REFUSE
 
irods_default_hash_scheme - SHA256
 
irods_maximum_size_for_single_buffer_in_megabytes - 32
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ iinit
 
Enter your current iRODS password:
 
[-] /irods/plugins/auth/native/libnative.cpp:342:irods::error native_auth_client_response(irods::plugin_context &, rcComm_t *) : status [CAT_INVALID_AUTHENTICATION]  errno [] -- message [Call to rcAuthResponseFailed.]
 
 
 
  failed with error -826000 CAT_INVALID_AUTHENTICATION
 
[vitlacil@localhost ~]$ iinit
 
Enter your current iRODS password:
 
[-] /irods/plugins/auth/native/libnative.cpp:342:irods::error native_auth_client_response(irods::plugin_context &, rcComm_t *) :  status [CAT_INVALID_AUTHENTICATION]  errno [] -- message [Call to rcAuthResponseFailed.]
 
 
 
failed with error -826000 CAT_INVALID_AUTHENTICATION
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$
 
[vitlacil@localhost ~]$ iinit
 
Enter your current iRODS password:
 
[-] /irods/plugins/auth/native/libnative.cpp:342:irods::error native_auth_client_response(irods::plugin_context &, rcComm_t *) :  status [CAT_INVALID_AUTHENTICATION]  errno [] -- message [Call to rcAuthResponseFailed.]
 
 
 
failed with error -826000 CAT_INVALID_AUTHENTICATION
 
[vitlacil@localhost ~]$ iinit
 
Enter your current iRODS password:
 
[-] /irods/plugins/auth/native/libnative.cpp:342:irods::error native_auth_client_response(irods::plugin_context &, rcComm_t *) :  status [CAT_INVALID_AUTHENTICATION]  errno [] -- message [Call to rcAuthResponseFailed.]
 
 
 
  failed with error -826000 CAT_INVALID_AUTHENTICATION
 
[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json
 
[vitlacil@localhost ~]$ iinit
 
Enter your current PAM password:
 
[vitlacil@localhost ~]$ ils
 
/snic.se/home/s_dejvi:
 
 
   .DS_Store
 
   .DS_Store
 
   ._.DS_Store
 
   ._.DS_Store
Line 694: Line 363:
 
   C- /snic.se/home/s_dejvi/0 TiddlyWiki
 
   C- /snic.se/home/s_dejvi/0 TiddlyWiki
 
   C- /snic.se/home/s_dejvi/0 reading
 
   C- /snic.se/home/s_dejvi/0 reading
  C- /snic.se/home/s_dejvi/Dropbox
 
 
   C- /snic.se/home/s_dejvi/EOSC
 
   C- /snic.se/home/s_dejvi/EOSC
  C- /snic.se/home/s_dejvi/EOSC-Hub Reporting
 
 
   C- /snic.se/home/s_dejvi/EUDAT
 
   C- /snic.se/home/s_dejvi/EUDAT
 
   C- /snic.se/home/s_dejvi/FAIR
 
   C- /snic.se/home/s_dejvi/FAIR
 
   C- /snic.se/home/s_dejvi/FitSM
 
   C- /snic.se/home/s_dejvi/FitSM
   C- /snic.se/home/s_dejvi/Googletakeout
+
   .....
  C- /snic.se/home/s_dejvi/Magazines
+
 
  C- /snic.se/home/s_dejvi/PIDs
+
[vitlacil@localhost ~]$
  C- /snic.se/home/s_dejvi/Private
+
 
  C- /snic.se/home/s_dejvi/Public
+
'''Back to [https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS Swestore-iRODS Documentation]'''
  C- /snic.se/home/s_dejvi/SNIC ALL HANDS 2019
 
  C- /snic.se/home/s_dejvi/SNIC Storage
 
  C- /snic.se/home/s_dejvi/Security
 
  C- /snic.se/home/s_dejvi/WebDAV test
 
  C- /snic.se/home/s_dejvi/iRODS
 
  C- /snic.se/home/s_dejvi/nordic data services workshop da aggiungere in AFS
 
  C- /snic.se/home/s_dejvi/test.from.klemming
 
[vitlacil@localhost ~]$
 

Revision as of 13:32, 6 May 2020

Back to Swestore-iRODS Documentation


Here is an example of iRODS iCommands installation on CentOS 7, from iRODS repository.

Install the public key and add the repository

[vitlacil@localhost ~]$ sudo rpm --import https://packages.irods.org/irods-signing-key.asc
[sudo] password for vitlacil: *************************
[vitlacil@localhost ~]$ wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo
   [renci-irods]
    name=RENCI iRODS Repository
    baseurl=https://packages.irods.org/yum/pool/centos$releasever/$basearch
    enabled=1
    gpgcheck=1
    repo_gpgcheck=1
    gpgkey=https://packages.irods.org/irods-signing-key.asc
[vitlacil@localhost ~]$ 

List available packages

[vitlacil@localhost ~]$ sudo yum search irods 
Loaded plugins: fastestmirror, langpacks 
Loading mirror speeds from cached hostfile
 * base: mirror.hosthink.net
 * extras: mirror.hosthink.net
 * updates: mirror.hosthink.net
renci-irods/7/x86_64/signature                                               |  819 B  00:00:00      
Retrieving key from https://packages.irods.org/irods-signing-key.asc
Importing GPG key 0xACF9B42B:
 Userid     : "iRODS Consortium <info@irods.org>"
 Fingerprint: 9014 ff9f 75c6 6c77 1f1c b574 bd92 5dbd acf9 b42b
 From       : https://packages.irods.org/irods-signing-key.asc
Is this ok [y/N]: y
renci-irods/7/x86_64/signature                                               | 2.9 kB  00:00:04 !!! 
renci-irods/7/x86_64/primary_db                                              |  63 kB  00:00:01      
======================================== N/S matched: irods ========================================
irods-externals-autoconf5ad3567c-0.x86_64 : iRODS Build Dependency
irods-externals-avro1.7.7-0.x86_64 : iRODS Build Dependency
irods-externals-avro1.8.2-0.x86_64 : iRODS Build Dependency
irods-externals-avro1.9.0-0.x86_64 : iRODS Build Dependency
irods-externals-aws-sdk-cpp1.4.89-0.x86_64 : iRODS Build Dependency
irods-externals-aws-sdk-cpp1.4.89-1.x86_64 : iRODS Build Dependency
irods-externals-boost1.60.0-0.x86_64 : iRODS Build Dependency
irods-externals-boost1.67.0-0.x86_64 : iRODS Build Dependency
irods-externals-catch22.3.0-0.x86_64 : iRODS Build Dependency
irods-externals-clang-runtime3.8-0.x86_64 : iRODS Build Dependency
irods-externals-clang-runtime6.0-0.x86_64 : iRODS Build Dependency
irods-externals-clang3.8-0.x86_64 : iRODS Build Dependency
irods-externals-clang6.0-0.x86_64 : iRODS Build Dependency 
irods-externals-cmake3.11.4-0.x86_64 : iRODS Build Dependency
irods-externals-cmake3.5.2-0.x86_64 : iRODS Build Dependency
irods-externals-cppzmq4.1-0.x86_64 : iRODS Build Dependency
irods-externals-cppzmq4.2.3-0.x86_64 : iRODS Build Dependency
irods-externals-cpr1.3.0-0.x86_64 : iRODS Build Dependency
irods-externals-cpr1.3.0-1.x86_64 : iRODS Build Dependency
irods-externals-elasticlient0.1.0-0.x86_64 : iRODS Build Dependency
irods-externals-elasticlient0.1.0-1.x86_64 : iRODS Build Dependency
irods-externals-epm4.2-0.x86_64 : iRODS Build Dependency
irods-externals-fmt6.1.2-0.x86_64 : iRODS Build Dependency
irods-externals-fmt6.1.2-1.x86_64 : iRODS Build Dependency
irods-externals-imagemagick7.0.3-0.x86_64 : iRODS Build Dependency
irods-externals-imagemagick7.0.8-0.x86_64 : iRODS Build Dependency
irods-externals-jansson2.7-0.x86_64 : iRODS Build Dependency
irods-externals-json3.0.1-0.x86_64 : iRODS Build Dependency
irods-externals-json3.1.2-0.x86_64 : iRODS Build Dependency
irods-externals-json3.7.3-0.x86_64 : iRODS Build Dependency 
irods-externals-libarchive3.1.2-0.x86_64 : iRODS Build Dependency
irods-externals-libarchive3.3.2-0.x86_64 : iRODS Build Dependency
irods-externals-libarchive3.3.2-1.x86_64 : iRODS Build Dependency
irods-externals-libs359b62371-0.x86_64 : iRODS Build Dependency 
irods-externals-libs3a30e55e8-0.x86_64 : iRODS Build Dependency
irods-externals-libs3a30e55e8-1.x86_64 : iRODS Build Dependency
irods-externals-libs3f6a2098e-0.x86_64 : iRODS Build Dependency
irods-externals-mungefs1.0.2-0.x86_64 : iRODS Build Dependency 
irods-externals-mungefs1.0.3-0.x86_64 : iRODS Build Dependency
irods-externals-nanodbc2.13.0-0.x86_64 : iRODS Build Dependency
irods-externals-qpid-with-proton0.34-0.x86_64 : iRODS Build Dependency 
irods-externals-qpid-with-proton0.34-1.x86_64 : iRODS Build Dependency
irods-externals-redis4.0.10-0.x86_64 : iRODS Build Dependency 
irods-externals-redis4.0.8-0.x86_64 : iRODS Build Dependency
irods-externals-spdlog0.17.0-0.x86_64 : iRODS Build Dependency 
irods-externals-spdlog1.5.0-0.x86_64 : iRODS Build Dependency
irods-externals-spdlog1.5.0-1.x86_64 : iRODS Build Dependency
irods-externals-zeromq4-14.1.3-0.x86_64 : iRODS Build Dependency
irods-externals-zeromq4-14.1.6-0.x86_64 : iRODS Build Dependency
irods-auth-plugin-gsi.x86_64 : The integrated Rule-Oriented Data System 
irods-auth-plugin-krb.x86_64 : The integrated Rule-Oriented Data System
irods-database-plugin-mysql.x86_64 : The integrated Rule-Oriented Data System 
irods-database-plugin-oracle.x86_64 : The integrated Rule-Oriented Data System 
irods-database-plugin-postgres.x86_64 : The integrated Rule-Oriented Data System
irods-devel.x86_64 : The integrated Rule-Oriented Data System
irods-icommands.x86_64 : The integrated Rule-Oriented Data System
irods-microservice-plugins-curl.x86_64 : The integrated Rule-Oriented Data System
irods-resource-plugin-s3.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-apply-access-time.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-audit-amqp.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-data-movement.x86_64 : The integrated Rule-Oriented Data System 
irods-rule-engine-plugin-data-replication.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-data-verification.x86_64 : The integrated Rule-Oriented Data System 
irods-rule-engine-plugin-python.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-storage-tiering.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-tiered-storage.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-unified-storage-tiering.x86_64 : The integrated Rule-Oriented Data System
irods-rule-engine-plugin-update-collection-mtime.x86_64 : The integrated Rule-Oriented Data System
irods-runtime.x86_64 : The integrated Rule-Oriented Data System
irods-server.x86_64 : The integrated Rule-Oriented Data System
irods_rule_engine_plugin-apply_access_time.x86_64 : The integrated Rule-Oriented Data System
irods_rule_engine_plugin-data_movement.x86_64 : The integrated Rule-Oriented Data System
irods_rule_engine_plugin-data_replication.x86_64 : The integrated Rule-Oriented Data System
irods_rule_engine_plugin-data_verification.x86_64 : The integrated Rule-Oriented Data System
irods_rule_engine_plugin-storage_tiering.x86_64 : The integrated Rule-Oriented Data System
irods_rule_engine_plugin-unified_storage_tiering.x86_64 : The integrated Rule-Oriented Data System

  Name and summary matches only, use "search all" for everything.

[vitlacil@localhost ~]$ 

Install additional repositories needed for Python dependencies

[vitlacil@localhost ~]$ sudo yum install epel-release
   Loaded plugins: fastestmirror, langpacks
   Loading mirror speeds from cached hostfile
 * base: mirror.hosthink.net
 * extras: mirror.hosthink.net
 * updates: mirror.hosthink.net 
Resolving Dependencies 
--> Running transaction check
---> Package epel-release.noarch 0:7-11 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

====================================================================================================
 Package                     Arch                  Version              Repository             Size
====================================================================================================
Installing:
 epel-release                noarch                7-11                 extras                 15 k

Transaction Summary
====================================================================================================
Install  1 Package

Total download size: 15 k
Installed size: 24 k
Is this ok [y/d/N]: y
Downloading packages:
epel-release-7-11.noarch.rpm                                                 |  15 kB  00:00:00     
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Installing : epel-release-7-11.noarch                                                         1/1 
  Verifying  : epel-release-7-11.noarch                                                         1/1 

Installed:
  epel-release.noarch 0:7-11                                                                        

Complete!

... and Python dependencies

[vitlacil@localhost ~]$ sudo yum install python-psutil python-jsonschema
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
epel/x86_64/metalink                                                         |  24 kB  00:00:00     
 * base: mirror.zetup.net
 * epel: mirror.zetup.net
 * extras: mirror.zetup.net
 * updates: mirror.zetup.net
epel                                                                         | 4.7 kB  00:00:00     
(1/3): epel/x86_64/group_gz                                                  |  95 kB  00:00:00     
(2/3): epel/x86_64/updateinfo                                                | 1.0 MB  00:00:00     
(3/3): epel/x86_64/primary_db                                                | 6.8 MB  00:00:00     
Resolving Dependencies
--> Running transaction check
---> Package python2-jsonschema.noarch 0:2.5.1-4.el7 will be installed
--> Processing Dependency: python-repoze-lru for package: python2-jsonschema-2.5.1-4.el7.noarch
---> Package python2-psutil.x86_64 0:5.6.7-1.el7 will be installed
--> Running transaction check
---> Package python-repoze-lru.noarch 0:0.4-3.el7 will be installed
--> Finished Dependency Resolution

Dependencies Resolved
 
====================================================================================================
 Package                        Arch               Version                   Repository        Size
====================================================================================================
Installing:
 python2-jsonschema             noarch             2.5.1-4.el7               epel              75 k
 python2-psutil                 x86_64             5.6.7-1.el7               epel             399 k
Installing for dependencies:
 python-repoze-lru              noarch             0.4-3.el7                 epel              13 k

Transaction Summary
====================================================================================================
Install  2 Packages (+1 Dependent package)

Total download size: 487 k
Installed size: 2.6 M
Is this ok [y/d/N]: y
Downloading packages:
warning: /var/cache/yum/x86_64/7/epel/packages/python-repoze-lru-0.4-3.el7.noarch.rpm: Header V3 RSA/SHA256 Signature, key ID 352c64e5: NOKEY
Public key for python-repoze-lru-0.4-3.el7.noarch.rpm is not installed
(1/3): python-repoze-lru-0.4-3.el7.noarch.rpm                                |  13 kB  00:00:00     
(2/3): python2-jsonschema-2.5.1-4.el7.noarch.rpm                             |  75 kB  00:00:00     
(3/3): python2-psutil-5.6.7-1.el7.x86_64.rpm                                 | 399 kB  00:00:00     
----------------------------------------------------------------------------------------------------
Total                                                               1.3 MB/s | 487 kB  00:00:00     
Retrieving key from file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-7
Importing GPG key 0x352C64E5:
 Userid     : "Fedora EPEL (7) <epel@fedoraproject.org>"
 Fingerprint: 91e9 7d7c 4a5e 96f1 7f3e 888f 6a2f aea2 352c 64e5
 Package    : epel-release-7-11.noarch (@extras)
 From       : /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-7
Is this ok [y/N]: y
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Installing : python-repoze-lru-0.4-3.el7.noarch                                               1/3 
  Installing : python2-jsonschema-2.5.1-4.el7.noarch                                            2/3 
  Installing : python2-psutil-5.6.7-1.el7.x86_64                                                3/3 
  Verifying  : python2-jsonschema-2.5.1-4.el7.noarch                                            1/3 
  Verifying  : python2-psutil-5.6.7-1.el7.x86_64                                                2/3 
  Verifying  : python-repoze-lru-0.4-3.el7.noarch                                               3/3 

Installed:
  python2-jsonschema.noarch 0:2.5.1-4.el7            python2-psutil.x86_64 0:5.6.7-1.el7           

Dependency Installed:
  python-repoze-lru.noarch 0:0.4-3.el7                                                              

Complete!
[vitlacil@localhost ~]$ 

Install iRODS iCommands

[vitlacil@localhost ~]$ sudo yum install irods-icommands
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: mirrors.glesys.net
 * epel: mirrors.glesys.net
 * extras: mirrors.glesys.net
 * updates: mirrors.glesys.net
Resolving Dependencies
--> Running transaction check
---> Package irods-icommands.x86_64 0:4.2.7-1 will be installed
--> Processing Dependency: irods-runtime = 4.2.7 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-externals-avro1.7.7-0 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-externals-jansson2.7-0 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-externals-clang-runtime3.8-0 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-externals-zeromq4-14.1.3-0 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-externals-boost1.60.0-0 for package: irods-icommands-4.2.7-1.x86_64
--> Processing Dependency: irods-externals-libarchive3.3.2-0 for package: irods-icommands-4.2.7-1.x86_64
--> Running transaction check
---> Package irods-externals-avro1.7.7-0.x86_64 0:1.0-1 will be installed
---> Package irods-externals-boost1.60.0-0.x86_64 0:1.0-1 will be installed
---> Package irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 will be installed
---> Package irods-externals-jansson2.7-0.x86_64 0:1.0-1 will be installed
---> Package irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1 will be installed
---> Package irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1 will be installed
---> Package irods-runtime.x86_64 0:4.2.7-1 will be installed
--> Finished Dependency Resolution

Dependencies Resolved
 
====================================================================================================
 Package                                   Arch          Version           Repository          Size
====================================================================================================
Installing:
 irods-icommands                           x86_64        4.2.7-1           renci-irods        526 k
Installing for dependencies:
 irods-externals-avro1.7.7-0               x86_64        1.0-1             renci-irods        1.5 M
 irods-externals-boost1.60.0-0             x86_64        1.0-1             renci-irods         13 M
 irods-externals-clang-runtime3.8-0        x86_64        1.0-1             renci-irods        347 k
 irods-externals-jansson2.7-0              x86_64        1.0-1             renci-irods        165 k
 irods-externals-libarchive3.3.2-0         x86_64        1.0-1             renci-irods        1.7 M
 irods-externals-zeromq4-14.1.3-0          x86_64        1.0-1             renci-irods        549 k
 irods-runtime                             x86_64        4.2.7-1           renci-irods        3.6 M 

Transaction Summary
====================================================================================================
Install  1 Package (+7 Dependent packages)

Total download size: 21 M
Installed size: 158 M
Is this ok [y/d/N]: y 
Downloading packages:
(1/8): irods-externals-avro1.7.7-0-1.0-1.x86_64.rpm                          | 1.5 MB  00:00:03     
(2/8): irods-externals-clang-runtime3.8-0-1.0-1.x86_64.rpm                   | 347 kB  00:00:00     
(3/8): irods-externals-jansson2.7-0-1.0-1.x86_64.rpm                         | 165 kB  00:00:00     
(4/8): irods-externals-libarchive3.3.2-0-1.0-1.x86_64.rpm                    | 1.7 MB  00:00:03     
(5/8): irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64.rpm                     | 549 kB  00:00:01     
(6/8): irods-icommands-4.2.7-1.x86_64.rpm                                    | 526 kB  00:00:01     
(7/8): irods-externals-boost1.60.0-0-1.0-1.x86_64.rpm                        |  13 MB  00:00:16     
(8/8): irods-runtime-4.2.7-1.x86_64.rpm                                      | 3.6 MB  00:00:08     
----------------------------------------------------------------------------------------------------
Total                                                               1.0 MB/s |  21 MB  00:00:20      
Running transaction check 
Running transaction test
Transaction test succeeded
Running transaction
 Installing : irods-externals-avro1.7.7-0-1.0-1.x86_64                                         1/8 
  Installing : irods-externals-boost1.60.0-0-1.0-1.x86_64                                       2/8 
  Installing : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64                                    3/8 
  Installing : irods-externals-libarchive3.3.2-0-1.0-1.x86_64                                   4/8 
  Installing : irods-externals-jansson2.7-0-1.0-1.x86_64                                        5/8 
  Installing : irods-externals-clang-runtime3.8-0-1.0-1.x86_64                                  6/8 
  Installing : irods-runtime-4.2.7-1.x86_64                                                     7/8 
  Installing : irods-icommands-4.2.7-1.x86_64                                                   8/8 
  Verifying  : irods-externals-clang-runtime3.8-0-1.0-1.x86_64                                  1/8 
  Verifying  : irods-externals-jansson2.7-0-1.0-1.x86_64                                        2/8 
  Verifying  : irods-externals-libarchive3.3.2-0-1.0-1.x86_64                                   3/8 
  Verifying  : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64                                    4/8 
  Verifying  : irods-externals-boost1.60.0-0-1.0-1.x86_64                                       5/8 
  Verifying  : irods-icommands-4.2.7-1.x86_64                                                   6/8 
  Verifying  : irods-externals-avro1.7.7-0-1.0-1.x86_64                                         7/8 
  Verifying  : irods-runtime-4.2.7-1.x86_64                                                     8/8 

Installed:
  irods-icommands.x86_64 0:4.2.7-1                                                                  

Dependency Installed:
  irods-externals-avro1.7.7-0.x86_64 0:1.0-1        irods-externals-boost1.60.0-0.x86_64 0:1.0-1   
  irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 irods-externals-jansson2.7-0.x86_64 0:1.0-1    
  irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1  irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1
  irods-runtime.x86_64 0:4.2.7-1                   

Complete!
[vitlacil@localhost ~]$ 

Configure the iRODS environment

NOTE: Create your own configuration file !!

[vitlacil@localhost ~]$ cat /home/vitlacil/.irods/irods_environment.json
{
  "irods_host": "irods-login.swestore.se", 
  "irods_port": 2432,
  "irods_default_resource": "pdc-gpfs",
  "irods_home": "/snic.se/home/s_dejvi",
  "irods_cwd": "/snic.se/home/s_dejvi",
  "irods_user_name": "s_dejvi",
  "irods_zone_name": "snic.se", 
  "irods_client_server_negotiation": "request_server_negotiation",
  "irods_client_server_policy": "CS_NEG_REFUSE",
  "irods_default_hash_scheme": "SHA256",
  "irods_encryption_algorithm": "AES-256-CBC",
  "irods_encryption_key_size": 32,
  "irods_encryption_num_hash_rounds": 16,
  "irods_encryption_salt_size": 8,
  "irods_match_hash_policy": "compatible",
  "irods_authentication_scheme" : "PAM"
}

[vitlacil@localhost ~]$

Authenticate and test iRODS iCommands client

[vitlacil@localhost ~]$ iinit
Enter your current PAM password: *************************
[vitlacil@localhost ~]$ ils
/snic.se/home/s_dejvi:
 .DS_Store
 ._.DS_Store
 SISO.Certificate.pdf
 project_role_descriptions.docx
 worst-day-fosdem-2014.pdf
 C- /snic.se/home/s_dejvi/0 TiddlyWiki
 C- /snic.se/home/s_dejvi/0 reading
 C- /snic.se/home/s_dejvi/EOSC
 C- /snic.se/home/s_dejvi/EUDAT
 C- /snic.se/home/s_dejvi/FAIR
 C- /snic.se/home/s_dejvi/FitSM
 .....
  
[vitlacil@localhost ~]$

Back to Swestore-iRODS Documentation