Submit a batch job via bglsub
An automated script has been written by SCV staff to enable a batch job to be submitted via the command line without first having to prepare a jcf. This automated script is called bglsub (right-click on link to download). Its usage is as follows:
lee % bglsub numprocs CWD executable optional-user-input-file "optional mpirun arguments"
where:
-
numprocs is the number of processors you need (as in "mpirun -np numprocs" or "poe -procs numprocs"); mandatory input
-
CWD is the current working directory from which the job is launched; mandatory input
-
executable is the name of your executable, including the full directory path; mandatory input
-
optional-user-input-file is the input file to your executable, and again you must provide the full path. Note also that by input file it is meant to be those used by the C programming language (argc, argv).
Input through stdin is not supported.
-
"optional mpirun arguments" is any number of additional mpirun arguments you wish also to pass on to bglsub. Be sure
to enter the double quotes (") as shown.
Here is an example that requests 9 processors. Note that "9" is provided for mpirun. The system assigns 32 nodes to the job following the rule stated above.
lee % bglsub 9 /usr7/xyz/kadin/tmp /usr7/xyz/kadin/bin/ppanel
llsubmit: The job "fe1.bgl.bu.edu.162" has been submitted.
More conveniently, to run the job from the current directory, the above could be entered as
lee % cd /usr7/xyz/kadin/tmp
lee % bglsub 9 $PWD $home/bin/ppanel
llsubmit: The job "fe1.bgl.bu.edu.162" has been submitted.
Here is an example on passing optional mpirun flags to bglsub:
lee:PMPI/tmp % bglsub 256 $PWD $PWD/example1_15 - "-mode VN"
llsubmit: The job "fe2.bgl.bu.edu.647" has been submitted.
In the above, the virtual node mode (VN) is passed on to mpirun as an
optional mpirun parameter. Even though the "optional-user-input-file" is not
required by the user, "-" is entered as a place-holder for that item.
lee:PMPI/tmp % llq
Id Owner Submitted ST PRI Class Running On
------------------------ ---------- ----------- -- --- ------------ ----------
fe2.bgl.bu.edu.647.0 kadin 9/26 08:44 R 50 bgl fe2.bgl.bu.edu
fe1.bgl.bu.edu.383.0 kadin 9/25 10:14 H 50 bgl
2 job step(s) in queue, 0 waiting, 0 pending, 1 running, 1 held, 0 preempted
lee:PMPI/tmp % llbglparts
Partition Id Owner Conn Status Small Shape
================= ========== ===== ====== ===== =========
RMP26Se084419791 kadin MESH CONFI T 128 node
Even though the above example requests 256 processors, because both processors of each node are used, the system only need to allocate 128 nodes.
Tips on bglsub usage:
-
lee % bglsub to print a help file on bglsub
- If your executable is in a location other than $PWD, you can add the line
setenv MYEXEC /project/XYZ/ABC/uvw/myexec
to your .cshrc file. Then, you can then pass $MYEXEC in place of $PWD as the input to bglsub to reduce typing.
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