 ARCS System Support
What computer systems are available?
Windows users should use PuTTY. Faculty and staff can download PuTTY from Baylor's AppCenter page. Students can get PuTTY from the official site. PuTTY is also installed on many of the PCs in the Electronic Library Compute Facilities.
Mac OS X users should connect with the
Linux users should connect with the To connect to Kodiak with ssh, enter the following:
% ssh -l username kodiak.baylor.edu or % ssh username@kodiak.baylor.edu If your username on the ARCS system happens to be the same as that on your local system, you can omit the "-l username". Occasionally we update the operating system on the ARCS systems, so you may get the following message when you try to connect:
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY! To fix this, edit the file $HOME/.ssh/known_hosts and delete the line for the system and then reconnect. If you are concerned, you can contact us for assistance.
The first time you access your account you should change your password. To do so, type the command
To compile parallel MPI programs on the Cluster, use mpicc (for C/C++) and mpifort (for Fortran).
run_myprog.sh. This assumes that your program is named "myprog" and is in a directory, "/home/username/myprog/".
#!/bin/sh /home/username/myprog/myprog
To submit the job to the batch system, use the
% qsub -N myprog ./run_myprog 1234.rush.baylor.edu The qsub command will return with the job identifier assigned to the job by the batch system, e.g., 1234 above.
When the job finishes, you should find myprog.e1234 and myprog.o1234 in the myprog directory. These correspond to your program's stderr and stdout. If you want to see what is currently running in batch, use the
% qstat Job id Name User Time Use S Queue ------------------- ---------------- ---------------- -------- - ----- 1234.rush myprog me 0 R batch
If your program is running (or waiting in the batch queue) and you want to stop it, use the
% qdel 1234 Note for matlab users: The "matlab" command requires specific arguments in order to function correctly in batch. There's a sample shell script located in /usr/local/examples called run_matlab.sh that you may copy to your account and use to submit your matlab jobs to the batch system.
Here's an example of how to submit a matlab program to the batch system:
How do I run my program on the Cluster?
scasub command. scasub is a wrapper script for qsub. To submit a parallel (MPI) program, you will need to include the -mpimon option as well as specify the number of processes per node (-npn 2) and the number of processes you want to run (-np 8).
% scasub -mpimon -npn 2 -np 4 ./myprog 5678.el-hpc-cluster1a.baylor.edu The scasub command will return with the job identifier assigned to the job by the batch system, e.g., 5678 above.
When the job finishes, you should find myprog.e5678 and myprog.o5678 in the program's directory. These correspond to your program's stderr and stdout. Note that output from multiple MPI programs may be jumbled. If you want to see what is currently running in batch, uses the
% qstat Job id Name User Time Use S Queue ---------------- ---------------- ---------------- -------- - ----- 5677.el-hpc-clus someprog someuser 0 R scali_exec 5678.el-hpc-clus myprog me 0 R scali_exec
You can also use the
% scatop Node : PID USER PRI NI SZ RSS STAT %CPU %MEM TIME COMMAND n01 : 11613 someuser 14 0 330624 2660 R 94.0 0.0 0:02 someprog n01 : 11614 someuser 14 0 330624 2660 R 93.0 0.0 0:02 someprog n02 : 11537 someuser 14 0 330624 2660 R 93.6 0.0 0:02 someprog n02 : 11538 someuser 14 0 330624 2660 R 94.3 0.0 0:02 someprog n03 : 11202 someuser 14 0 330624 2660 R 75.0 0.0 0:03 someprog n03 : 11203 someuser 14 0 330624 2660 R 75.0 0.0 0:03 someprog n04 : 11361 someuser 14 0 330588 2440 R 72.2 0.0 0:02 someprog n04 : 11362 someuser 14 0 330624 2668 R 72.5 0.0 0:02 someprog n05 : 11351 someuser 14 0 330624 2660 R 79.7 0.0 0:03 someprog n05 : 11352 someuser 14 0 330624 2668 R 80.0 0.0 0:03 someprog n06 : 11479 someuser 14 0 330624 2660 R 78.0 0.0 0:03 someprog n06 : 11480 someuser 14 0 330624 2660 R 77.5 0.0 0:03 someprog n07 : 11415 someuser 14 0 330624 2660 R 77.7 0.0 0:03 someprog n07 : 11416 someuser 14 0 330624 2660 R 77.7 0.0 0:03 someprog n08 : 11468 someuser 14 0 330624 2660 R 80.2 0.0 0:03 someprog n08 : 11469 someuser 14 0 330624 2668 R 80.5 0.0 0:03 someprog n28 : 9554 me 16 0 1717 3452 R 79.0 0.0 0:00 myprog n28 : 9555 me 16 0 1764 3648 R 80.0 0.0 0:00 myprog n29 : 9449 me 17 0 1476 3648 R 75.0 0.0 0:00 myprog n29 : 9450 me 17 0 1734 3452 R 75.0 0.0 0:00 myprog
If your program is running (or waiting in the batch queue) and you want to stop it, use the
% qdel 5678How do I use MPICH (mpirun) instead of Scali MPI?
source command so that it executes in the current shell and not a sub-shell:
% source usempich Now using MPICH. If you want, you can check your $PATH variable to make sure it worked: % echo $PATH /usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin % source usempich Now using MPICH. % echo $PATH /usr/local/mpich/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin
Notice that the MPICH directory is now the first item in your PATH. Commands such as If your program has been compiled to use Scali MPI, you will need to recompile it to use MPICH instead, and vice versa. The compile commands are the same but are now located in the MPICH directory. Likewise, if your program has been compiled to use MPICH and you wish to switch back to Scali MPI, you need to recompile.
Unlike Scali, you don't use the
% scasub -r 180 -np 4 167.el-hpc-cluster1a.baylor.edu % qstat Job id Name User Time Use S Queue ---------------- ---------------- ---------------- -------- - ----- 167.el-hpc-clust RESERVED_180 me 0 R scali_execNote the R in the job status. This means your job is running (or in this case, nodes are reserved). If the status is Q, then there are currently not enough nodes available and your request is waiting in the queue. When the nodes are allocated to you, you will see a file in your directory named "reserved_nodes.jobid". This is a list of nodes that you should use as the "machinefile" for the mpirun command: % cat reserved_nodes.167 n04 n03 n02 n01Keep in mind that this is a list of reserved nodes and not processors. Because the nodes on the cluster have two processors each, you can run 8 jobs on these 4 nodes. If you would like, you can reserve the nodes specifying number of processors and processors per node, e.g., "scasub -np 8 -npn 2" as in a regular scasub command.
These nodes will be reserved for your use for the time requested. After the time expires the job is removed from the queue and the nodes will then be available for others to use. This does not mean that any programs you are running will automatically quit when time expires so you need to ensure that your programs don't continue to run by quitting them with the
Because the Scali batch system does not support MPICH programs, you will need to use
% mpirun -machinefile reserved_nodes.167 -np 8 -nolocal ./myprogThis runs the program interactively (although on the compute nodes). You can run mpirun in the background with a & after the command. Note that unlike the batch system, standard output (and stderr) is not redirected to a file and will still appear on the terminal. You will need to add "> outfile" if you wish to save stdout. You also need to redirect stdin or the program will stop.
% mpirun -machinefile reserved_nodes.167 -np 8 -nolocal ./myprog > outfile 2> errfile < /dev/null & [1] 18037 % tail -f outfile data ^C % [1]+ Done mpirun -machinefile reserved_nodes.167 -nolocal -np 8 ./myprog > outfile 2> errfile What are the runtime limits, quotas, etc.?
Note: We reserve the right to add or modify runtime limits and quotas at any time.
sftp (Secure FTP). You can also use scp (secure copy) but sftp is recommended. "Classic" FTP is not enabled on the ARCS systems.
To transfer files between a Windows system and an ARCS system, you should use WinSCP. Faculty and staff can download WinSCP from Baylor's AppCenter page. Students can get WinSCP from the official site. WinSCP is also installed on many of the PCs in the Electronic Library Compute Facilities. Mac OS X and Linux users should use the sftp (or scp) command from a Terminal window or console. How can I get the Tivoli backup client installed on my Linux system? I need help with some other Linux/Unix/VMS issue.
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