IMPORTANT: All users must first request an account on 'ivan'. The URL is : http://www.son.washington.edu/Informatics/MR_Lab/IVANAccess/IVANAccessform.asp
ivan is a stand-alone workstation that is our first test environment for general use by IBIC-affiliated investigators and collaborators as well as students who took Clark Johnson's fMRI class in the summer of 2010.
ivan is the preferred platform for converting Enhanced DICOM to NIFTI. See https://www.ibic.washington.edu/wiki/display/data/Enhanced+DICOM
(Was https://www.ibic.washington.edu/wiki/display/Edicom/Home for detailed procedures.)
The original "ivan" workstation was a Dell Precision T5400 with :
2 CPUs / 8 cores which are Intel Xeon E5405 running at 2.00GHz, bus speed 1333MHz, 12MB of L2 cache.
16GB of Quad-channel DDR2 SDRAM
NVIDIA FX4800 Quadro Graphics Card.
1.5TB Western Digital local disk drive
The current "ivan" workstation is a Dell Precision T1600 with :
1 CPU / 4 cores which are Intel Xeon E31225 running at 3.10GHz
8GB of Quad-channel DDR2 SDRAM
NVIDIA NVS 300 Graphics Card.
1.5TB Western Digital local disk drive
"ivan" runs the current version of Evolution software, 0.7 (24 June, 2011), under Ubuntu 10.04. A full description is at : https://www.ibic.washington.edu/wiki/display/ivan/Description+of+IVAN+Software
There is no connection to the NAS or any external data storage system. All user storage is on the local scratch disk, 1.5TB, mounted at /var/local/scratch.
/mnt/home/ibic/bin is a local copy, on the OS disk, of the executables on the NAS.
Because the NAS is not mounted, and to maintain only one LDAP home directory, we need to create a symbolic link from a user's normal home directory path /mnt/home/<user name> to local disk.
This is done,all as sudo, as follows:
mkdir /var/local/scratch/<user name>
chown <user name>:<user name> /var/local/scratch/<user name>
ln -s /var/local/scratch/<user name> /mnt/home/<user name>
( this can be run in /mnt/home with the script "./mklink <user name>" )
NOTE that you are not creating a <user name> subdirectory on /mnt/home/.
Now if you cd to /mnt/home, and ls -lart on <user name> you should see: <user name> -> /var/local/scratch/<user name>
Add the following lines to the .bashrc of each user :
IMPORTANT: Users must first request an account on 'ivan'. The request form URL is : http://www.son.washington.edu/Informatics/MR_Lab/IVANAccess/IVANAccessform.asp
Kerberos NetID is used to log on to ivan. First time users on the Unix workstations are added as follows:
sudo addgroup --system --gid <xxxx> <group_name>
sudo adduser --system --home /mnt/home/<user_name> --uid <xxxx> --gid <xxxx> --shell /bin/bash <user_name>
NOTE that when creating the new user account above, the user_name and group_name are the same. Also, the group ID (gid) and user ID (uid) will be the same number , and must be unique.;
Check /etc/passwd and an inventory of the LDAP user IDs so as not to duplicate.
The user's home directory for ivan will be on a local 1.5TB disk, /var/local/scratch/<user_name>. (See details about symbolic link in Home Directory paragraph above.)
Then, the user and user's group are added with ldapadd. See https://www.ibic.washington.edu/wiki/display/itdev/ldapadd%2C+ldapmodify%2C+ldapdelete
For both existing users (LDAP account already set up for IBIC workstations) and first time users:
vi Modify_attrStandAloneIVAN.ldif and insert the current <user name>. To add user 'pboord' for example:
ldapadd -x -W -D "cn=admin,dc=ibic,dc=washington,dc=edu" -f Modify_attrStandAloneIVAN.ldif
At this point the user is added to the standalone_ivan group.
You can confirm current members of this group with the LDAP command: ldapsearch -x "cn=standalone_ivan",
or for an individual you can use the Unix command : groups <user name>
You can confirm the user's attributes with : ldapsearch -x 'uid=<user name>'