The NIG Supercomputer
Other Commands
This document is a former NIG supercomputer (2019) document and is kept for reference purposes.
Please note that it does not work in the same way on the current NIG supercomputer (2025).
Using GPU
Check CUDA manual.
Checking the job execution status (qstat)
Checking the job submission status
qstate checks whether the submitted job by using qsub was submitted as a job. To check the status of the submitted job, use the qstat command. For example, when the job is submitted, qstate shows as follows.
[username@at027 ~]$ qstat
job-ID prior name user state submit/start at queue jclass slots ja-task-ID
------------------------------------------------------------------------------------------------------------------------------------------------
80312 0.50000 QLOGIN username r 02/27/2019 17:42:00 login.q@at027 1
80313 0.25000 jobname username r 02/27/2019 17:44:30 epyc.q@at040 1
80314 0.25000 jobname username r 02/27/2019 17:44:35 epyc.q@at040 1
80315 0.25000 jobname username r 02/27/2019 17:44:40 epyc.q@at040 1
The meanings of the characters in the "state" colum at this time are as follows.
| state | meaning |
|---|---|
| r | running |
| qw | queued, waiting |
| t | transferring to the execution host |
| E | error in the job |
| d | the job is in the process of being deleted |
The "qstat -f" command shows the queue usage status like this output result.
[username@at027 ~]$ qstat -f
queuename qtype resv/used/tot. np_load arch states
---------------------------------------------------------------------------------
medium.q@m01 BP 0/0/80 0.00 lx-amd64
---------------------------------------------------------------------------------
medium.q@m02 BP 0/0/80 0.00 lx-amd64
---------------------------------------------------------------------------------
medium.q@m03 BP 0/0/80 0.00 lx-amd64
---------------------------------------------------------------------------------
medium.q@m04 BP 0/0/80 0.00 lx-amd64
(中略)
---------------------------------------------------------------------------------
epyc.q@at033 BP 0/0/64 0.00 lx-amd64
---------------------------------------------------------------------------------
epyc.q@at034 BP 0/0/64 0.00 lx-amd64
---------------------------------------------------------------------------------
epyc.q@at035 BP 0/0/64 0.00 lx-amd64
(中略)
---------------------------------------------------------------------------------
intel.q@it003 BP 0/0/32 0.00 lx-amd64
---------------------------------------------------------------------------------
intel.q@it004 BP 0/0/32 0.00 lx-amd64
---------------------------------------------------------------------------------
intel.q@it005 BP 0/0/32 0.00 lx-amd64
---------------------------------------------------------------------------------
intel.q@it006 BP 0/0/32 0.00 lx-amd64
---------------------------------------------------------------------------------
(以下略)
This makes it possible to determine which node (queue) the job is submitted to.
"qstaus -j jobID" prints information about the job with a list.
[username@at027 ~]$ qstat -j 199666
==============================================================
job_number: 199666
jclass: NONE
submission_time: 02/27/2019 17:42:00.867
owner: username
uid: 9876
group: ddbj
gid: 9876
supplementary group: ddbj
sge_o_home: /home/username
sge_o_log_name: username
sge_o_path: /cm/local/apps/gcc/7.2.0/bin:/home/geadmin/UGER/bin/lx-amd64:/cm/local/apps/environment-modules/4.0.0//bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/4.0.0/bin:/home/username/.local/bin:/home/username/bin
sge_o_shell: /bin/bash
sge_o_workdir: /lustre8/home/username
sge_o_host: gw1
account: sge
stderr_path_list: NONE:NONE:/dev/null
hard resource_list: d_rt=259200,mem_req=8G,s_rt=259200,s_stack=10240K,s_vmem=8G
soft resource_list: epyc=TRUE,gpu=TRUE,intel=TRUE,login=TRUE
mail_list: username@gw1
notify: FALSE
job_name: QLOGIN
stdout_path_list: NONE:NONE:/dev/null
priority: 0
jobshare: 0
restart: n
env_list: TERM=xterm
department: defaultdepartment
binding: NONE
mbind: NONE
submit_cmd: qlogin
category_id: 4
request_dispatch_info: FALSE
start_time 1: 02/27/2019 17:42:00.884
job_state 1: r
exec_host_list 1: at027:1
granted_req. 1: mem_req=8.000G
usage 1: wallclock=01:00:01, cpu=00:00:00, mem=0.00000 GBs, io=0.00000 GB, iow=0.000 s, ioops=0, vmem=N/A, maxvmem=N/A
scheduling info: -
Checking the status of all cluster queues
To get a grasp on the job submission status of each queue, the queue load status, etc., type and execute "qstat -g c". You can also get the overall status with it.
[username@at027 ~]$ qstat -g c
CLUSTER QUEUE CQLOAD USED RES AVAIL TOTAL aoACDS cdsuE
--------------------------------------------------------------------------------
epyc.q 0.00 1 0 4159 4224 0 64
gpu.q 0.00 0 0 64 112 0 48
intel.q 0.00 0 0 1472 1472 0 0
login.q 0.00 4 0 380 384 0 0
login_gpu.q 0.00 0 0 48 48 0 0
medium.q 0.00 0 0 800 800 0 0
short.q 0.00 0 0 128 224 0 96
The meanings of the numbers are as follows
- USED: Number of slots currently in use
- RES: Number of Advance Reservation slots
- AVAIL: Number of available slots
- TOTAL: Total number of slots
- aoACDS: Number of slots which the compute node is in one of the aoACDS states
- cdsuE: Number of slots which the compute node is in one of the cdsuE states
You can find more details with man qstat.
Deleting jobs(qdel)
The qdel command is used to delete a job without waiting for the job to finish. Use "qdel jobID". "qdel -u username" enables to delete all jobs that you have submitted.
| Parameter Description | Description |
|---|---|
| -f *job_id(s)* | Forces the deletion a job even if the responsible execution host does not respond. |
| *job_id* -t range | Deletes specific tasks of an array job. It is also possible to delete a specific range of array jobs. |
| -u *user_list* | Deletes all job of the specified user. |
Changing the job execution condition(qalter)
The qalter can be used to change the amount of memory used by a batch job submitted to a queue. To change the memory requirement of a job from 200GB to 100GB, first check the hard_resource_list of the job with qstat command. Since the change of hard_resource_list by qalter overwrites the entire hard_resource_list, you should also specify and change the hard_resource_list other than the memory requirement and memory.
[username@at027 ~]$ qstat -j 25453855 |grep hard_resource_list
hard_resource_list: mem_req=100G,s_vmem=100G
[username@at027 ~]$ qalter -l d_rt=600,mem_req=100G,s_rt=600,s_stack=10240K,s_vmem=100G,short=TRUE 25453855
modified hard resource list of job 25453855
modified environment of job 25453855
[username@at027 ~]$ qstat -j 25453855 |grep hard_resource_list
hard_resource_list: d_rt=600,mem_req=100G,s_rt=600,s_stack=10240K,s_vmem=100G,short=TRUE
Checking the result of jobs
About the result, if you don't specify any options in the qsub command line, the standard output is output to the file named job name.o job ID and the standard error output is output with the following file name in the home directory.
job name.e jobID
You can use the qreport command to check detailed information such as how much resources the executed job used.
[username@at137 ~]$ qreport -j 110488
==============================================================
owner okishinya
jobnumber 110488
taskid undefined
slots 1
pe_taskid NONE
granted_pe NONE
exit_status 0
failed 0
qname epyc.q
hostname at116
jobname TEST_intel
qsub_time 20190307-22:30:33
start_time 20190307-22:31:31
end_time 20190307-22:31:35
ru_wallclock 4.249
cpu 3.0
mem 0.0
maxvmem 0.0G
r_mem 8.000G
r_q NONE
r_cpu NONE
Setup of environment variables required for running Grid Engine
To be able to execute commands such as qsub of Grid Engine, a series of environment variables must be set up. Normally, you do not need to set up these environment variables yourself because they are automatically set up when you login to the gateway node of the general analysis division.
Explicit setup may be required in special cases, such as when you use qsub from the Singularity container. In this case, execute the following command.
As in the User’s Manual, the necessary environment variables are set up by executing the shell script provided by Grid Engine as follows:
export SGE_ROOT=/home/geadmin/UGER
export SGE_CELL=uger
source $SGE_ROOT/$SGE_CELL/common/settings.sh