For Users of the Previous System

This information is for users to migrate the previous system to the new system replaced in fiscal 2016.

There are no changes from the previous system in the host name (round robin) and how to log in. If you want to log in to the login node directly without going through the round robin, please refer to how to connect to the system because the specific host name has been changed ( IP address is not changed).

If you use the Portforwarder or PuTTY terminal and cannot connect to the supercomputer with the following message, you must delete the known_hosts information.

@@@  WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!   @@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
c0:30:d6:93:b2:d8:06:4a:6f:9c:d5:00:cc:c5:69:58.
Please contact your system administrator.
Add correct host key in /home/xxx/.ssh/known_hosts to get rid of this
message.
Offending RSA key in /home/xxx/.ssh/known_hosts:3
RSA host key for laurel.kudpc.kyoto-u.ac.jp has changed and you have
requested strict checking.
Host key verification failed.

Please delete the known_host information with the following instruction.

if you use Portforwarder

The known_hosts file exists in the directory the Portforwarder has been installed. All you have to do is to delete the known_hosts file.

if you use PuTTY

The known_hosts information is in the registry. You can delete the known_hosts information by the accessory tool of PuTTY.

  • Open a command prompt window, then use cd command to move to the directory PuTTY has been installed.
  • Type "putty -cleanup", then the known_hosts is deleted.

You can delete the known_hosts information with one of the following methods.

  • ssh-keygen command: type the following commands on the terminal

        ssh-keygen -R camphor.kudpc.kyoto-u.ac.jp
        ssh-keygen -R laurel.kudpc.kyoto-u.ac.jp
  • edit known_hosts file

    Open /Users/(user name)/.ssh/known_hosts by an editor app, then delete the content.

You can delete the known_hosts information with one of the following methods.

  • ssh-keygen command: type the following commands one the terminal

        ssh-keygen -R camphor.kudpc.kyoto-u.ac.jp
        ssh-keygen -R laurel.kudpc.kyoto-u.ac.jp
  • edit known_hosts file

    Open the known_hosts file by an editor app. Usually the file exists on /home/(user name)/.ssh directory. Then, delete the content.

When logging in to the system with Exceed onDemand, port number of port forwarding has been changed.

For how to log in with Exceed onDemand, see Logging In With Exceed onDemand

System Previous port number New port number
A 5500 5501
B,C 5500 5500 (Not changed)
Private Cluster 5500 5509

User data that had been saved in the previous system was migrated automatically and the absolute path was not changed.

In accordance with the system replacement, the capacity of the home directory and the large volume disk (LARGE) of the system E is increased.

Directory Capacity of the previous system Capacity of new system
Home directory 30GB 100GB
Large volume disk(Personal Course) 1TB 2TB

The capacity of the large volume disk follows the following formula.

System A,B

Type Capacity of the previous system Capacity of new system
Third priority 1.2TB x contract number of nodes 3.6TB x contract number of nodes
Second priority 2.0TB x contract number of nodes 6.0TB x contract number of nodes
Top priority 2.0TB x contract number of nodes 6.0TB x contract number of nodes

System C

Type Capacity of the previous system Capacity of new system
Third priority 1.2TB x contract number of nodes 14.4TB x contract number of nodes
Second priority 2.0TB x contract number of nodes 24TB x contract number of nodes

For the configuration of the file system of the new system, see Using File System.

The limit of CPU time and memory amount in the login nodes are extended to reduce a possibility of unintentional abortion of file transaction, etc.

System CPU Time(normal) CPU Time(maximum) Memory(normal)
Previous system 1 hour 20 hours 2GB
New system 4 hour 24 hours 4GB

  • The compiler continue to provide Cray, Intel, PGI and GNU.

  • In the new system, ACML library is not available.

  • Since the new system does not support GPU, GPU-related CUDA C, CUDA Fortran and OpenACC are not available.

Purpose LSF PBS
Specify the queue for submitting a job. -q QUEUENAME Not changed 
Specify the execution group. -ug GROUPNAME Not changed
Specify running elapse time for batch-requests -W HOUR : MIN Not changed
* Establish per-request Vnodes limits
* Establish per-vnode thread limit
* Establish per-vnode CPUS limit
* Establish per-vnode/per-cpu normal_page memory limits
-A p=X:t=X:c=X:m=X Not changed
Direct stdout output to the stated destination -o FILENAME Not changed
Direct stderr output to the stdout destination -e FILENAME Not changed
Merge stderr output and stdout output -o -j oe(output to STDOUT) / eo(output to STDERR)
Send mail -B/-N -m a(in job abortion) / b(in beginning job) / e(in ending job)
Send mail for the batch request to the stated user -u MAILADDR -M MAILADDR
Declare that batch request is not re-runnable -rn -r n (A space character is needed between r and n.)

Purpose LSF PBS
Check available queues qstat qstat -q
Submit a job qsub Not changed
Check job status qjobs qstat
Cancel a submitted job qkill qdel
View a user’s own Job qs Not changed

Purpose LSF PBS
Job request identifier LSB_JOBID QSUB_JOBID
Batch queue name LSB_QUEUE QSUB_QUEUE
Current directory of job submission LSB_SUBCWD QSUB_WORKDIR
Number of assigned processes when submitting a job LSB_PROCS QSUB_PROCS
Number of threads per assigned process when submitting a job LSB_THREADS QSUB_THREADS
Number of CPUs per assigned process when submitting a job LSB_CPUS QSUB_CPUS
Memory limit per assigned process LSB_MEMORY QSUB_MEMORY
Number of processes per node when executing jobs LSB_PPN QSUB_PPN


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