Meiji University Center for Mathematical Modeling and Applications

Note:
The symbol "$" is the prompt symbol.

MIMS SMP consists of four computation servers, two computation servers for GPGPU and one login server.

Computing server (mims-smp)

HPE ProLiant DL580 Gen10 server

HPE ProLiant DL380 Gen10 server

• 1. Login to mims-gate by SSH, and then login to mims-smp by SSH.
• 2. Prepare execution files and a ".q" file on mims-smp.
• 3. Submit your computation job by qsub command on mims-smp.
• 4. Logout and wait for completing the job.

Login

Login to mims-gate by ssh, and then login to mims-smp by ssh.
For example, if you are working on a Unix-like environment, launch a terminal emulator and do the followings:

　　[user's PC ] $ ssh username@mims-gate.mind.meiji.ac.jp
　　[mims-gate] $ ssh mims-smp

Here username above should be replaced by your own username. The first command should be done on your server, and the second command should be done on mims-gate.

Note:

• 1. It is prohibited to login mims-smp from other than mims-gate.
• 2. It is prohibited to login mims-gate from abroad.
  
• 3. A Windows user may have to install an SSH client software since Microsoft Windows does not provide with it by default.
  
• 4. See here for details of installation.

PuTTY: How to use SSH client software

Logout

Enter the exit command.

　　[mims-smp] $ exit
　　[mims-gate] $ exit

You can change your password by the passwd command:

　　$ passwd

After entering the current password of yours, you will be required to enter the new password twice.

Note:

• 1. Passwords must be secure.
• 2. Especially, the password for mims-gate must be absolutely secure:
  　mims-gate is open to the world.

sftp and scp are available on both mims-gate and mims-smp. Note that conmutation servers share the home directory of mims-smp. So any file in mims-smp can be seen from other computation servers.

Copying a file from client to mims-smp

　　[user's PC ] $ scp filename username@mims-gate.mind.meiji.ac.jp:
　　[user's PC ] $ ssh username@mims-gate.mind.meiji.ac.jp
　　[mims-gate] $ scp filename mims-smp:

Replace filename and username by the name of file and the user ID, respectively.

The first line copies filename from client to the home directory of mims-gate. The second line lets you login to mims-gate. The third line copies filename to the home directory of mims-smp.

Copying a file from mims-smp to client

　　[mims-smp ] $ scp filename mims-gate:
　　[user's PC] $ scp username@mims-gate:filename .

The first line copies filename from mims-smp to mims-gate. The second line copies filename from mims-gate to client (Don't miss the period at the end of line).

Note:
When you do any computation by MIMS-SMP, please submit your job by using qsub command.
We would greatly appreciate your cooperation.　

Submission flow

• 1. Prepare your programme.
• 2. Prepare a batch file.
• 3. Do the following and wait (You may logout from mims-smp after entering the command):

　　　[mims-smp] $ qsub ＜ name-of-the-batch-file
(Substitute the name of your batch file to name-of-the-batch-file.)

You can check submnitted jobs by the qstat command.
　　　[mims-smp] $ qstat

Also, you can check the trace of your job by tracejob command.

　　　[mims-smp]$ tracejob jobid
(Substitute the job ID to jobid)

Sample

Suppose that we save the following C code as hello.c:
　　#include 　
　　main()
　　{
　　#pragma omp parallel
　　printf("Hello world\n");
　　}

Suppose the path to hello.c is: $HOME/work/hello.c

Compile it
　　$ cd $HOME/work
　　$ icc -fopenmp hello.c

Save the following script as hello.q
　　#!/bin/sh
　　#PBS -N helloworld
　　#PBS -j oe
　　#PBS -l ncpus=12
　　#PBS -q low
　　$HOME/work/a.out

Submit the job:
　　$ qsub < hello.q

After a while, the program will run. The output will be written in the file helloworld.o**, where ** is the job ID.

◆ Options of qsub

You can specify the options above in the batch file: The line starting by "#PBS" specifies the option of qsub.

See "man qsub" for details (see also "man qstat", "man tracejob" ).

◆ Type of queue

　We have introduced the computing servers for GPGPU (mims-smpgpu0) on July 2021.
　Specify the queue as "gpu2".

　
Samples :

mid

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