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pandoc:introduction-to-vsc:06_node_access_job_control:node_access_job_control [2018/01/31 11:13] – Pandoc Auto-commit pandocpandoc:introduction-to-vsc:06_node_access_job_control:node_access_job_control [2020/10/20 09:13] (current) – Pandoc Auto-commit pandoc
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   * Article written by Jan Zabloudil (VSC Team) <html><br></html>(last update 2017-10-09 by jz).   * Article written by Jan Zabloudil (VSC Team) <html><br></html>(last update 2017-10-09 by jz).
  
- 
-===== Node access ===== 
- 
-  - ... after submitting a job script 
-  - ... in interactive sessions 
  
  
 ---- ----
  
-===== Job scripts: sbatch ===== 
  
-<code bash> 
-[jz@l31 somedirectory]$ sbatch job.sh 
-Submitted batch job 54321 
-[jz@l31 somedirectory]$ squeue -u jz 
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
-             54321  mem_0064     test       jz  R       0:04      1 n20-038 
-[jz@l31 somedirectory]$ ssh n20-038 
-Last login: Wed Mar 15 14:26:01 2017 from l31.cm.cluster 
-[jz@n20-038 ~]$ 
- 
-</code> 
  
 ---- ----
  
-===== Interactive jobs: salloc ===== +====== Node access ======
- +
-<HTML> +
-<!--<div class="incremental smaller"> +
-<div style="float:left;width:50%">--> +
-</HTML> +
-=== Option 1: === +
- +
-<code bash> +
-[jz@l31 somedirectory]$ salloc -N1 +
-salloc: Pending job allocation 5115879 +
-salloc: job 5115879 queued and waiting for resources +
-salloc: job 5115879 has been allocated resources +
-salloc: Granted job allocation 5115879 +
-[jz@l31 somedirectory]$ squeue -u jz +
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) +
-           5115879  mem_0064     bash       jz  R       0:18      1 n07-043 +
-</code> +
- +
-**NOTE:** the slurm prolog script is **not** automatically run in this case. The prolog performs basic tasks such as +
- +
-  * clean up from previous job, +
-  * checking basic node functionality, +
-  * adapting firewall settings to access license servers. +
  
 +{{.:folie_12_1_connect.png?0x600}}
  
  
 ---- ----
  
-===== Interactive jobs: salloc ===== +====== Node access ======
- +
-To trigger the execution of the prolog you need to run an **srun** command, e.g.: +
- +
-<code bash> +
-[jz@l31 somedirectory]$ srun hostname +
-</code> +
- +
-Then access the node: +
- +
-<code bash> +
-[jz@l31 somedirectory]$ ssh n07-043 +
-Warning: Permanently added 'n07-043,10.141.7.43' (ECDSA) to the list of known hosts. +
-[jz@n07-043 ~]$ +
-</code>+
  
 +{{.:folie_12_2_connect.png?0x600}}
  
  
 ---- ----
  
-===== Interactive jobs: salloc =====+====== Node access ======
  
-=== Option 2: === +{{.:folie_14_salloc.png?0x600}}
- +
-<code bash> +
-[jz@l31 somedirectory]$ salloc -N1 srun --pty --preserve-env $SHELL +
-salloc: Pending job allocation 5115908 +
-salloc: job 5115908 queued and waiting for resources +
-salloc: job 5115908 has been allocated resources +
-salloc: Granted job allocation 5115908 +
-[jz@n09-046 somedirectory]$ +
-</code> +
-<code bash> +
-[jz@l31 somedirectory]$ salloc srun -N1 --pty --preserve-env $SHELL +
-salloc: Pending job allocation 5115909 +
-salloc: job 5115909 queued and waiting for resources +
-salloc: job 5115909 has been allocated resources +
-salloc: Granted job allocation 5115909 +
-[jz@n15-062 somedirectory]$ +
-</code>+
  
  
 ---- ----
  
-===== No job on node =====+====== 1) Job scripts: sbatch ======
  
-<code bash> +(DEMO)
-[jz@l31 somedirectory]$ squeue -u jz +
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) +
- +
-[jz@l31 somedirectory]$ ssh n15-002 +
-Warning: Permanently added 'n15-002,10.141.15.2' (ECDSA) to the list of known hosts. +
-Access denied: user jz (uid=70497) has no active jobs on this node. +
-Connection closed by 10.141.15.2 +
-</code> +
- +
----- +
- +
-===== Exercise 1: interactive job ===== +
- +
-1.) login as user //training//:+
  
 <code bash> <code bash>
-[...]$ ssh training@vsc3.vsc.ac.at+[me@l31]$ sbatch job.sh     # submit batch job 
 +[me@l31]$ squeue -u me      # find out on which node(s) job is running 
 +[me@l31]$ ssh <nodename>    # connect to node 
 +[me@n320-038]$ ...          # connected to node named n320-038
 </code> </code>
-or +more about from Claudia
- +
-<code bash> +
-[...]$ su - training +
-</code> +
-create a directory and copy example: +
- +
-<code bash> +
-[training@l31]$ mkdir my_directory_name +
-[training@l31]$ cd my_directory_name +
-[training@l31 my_directory_name]$ cp -r ~/examples/06_node_access_job_control/linpack . +
-[training@l31 my_directory_name]$ ls +
-HPL.dat  job.sh  xhpl +
-</code> +
  
  
 ---- ----
  
-===== Exercise 1: interactive job, cont. =====+====== Interactive jobs: salloc ======
  
-2.) Allocate one node for an interactive session: +<HTML><ol start="2" style="list-style-type: decimal;"></HTML> 
- +<HTML><li></HTML>with salloc EXAMPLE: linpack (DEMO)<HTML></li></HTML><HTML></ol></HTML>
-(name the job in a useful way with the '-J' option)+
  
 <code bash> <code bash>
-[training@l31 linpack]$ salloc -J jz_hpl -N 1 +~/examples/06_node_access_job_control/linpack 
-salloc: Pending job allocation 5260456 +[me@l31 linpack]$ salloc -J me_hpl -N 1  # allocate "1" node(s) 
-salloc: job 5260456 queued and waiting for resources +[me@l31 linpack]$ squeue -u me      # find out which node(s) is(are) allocated 
-salloc: job 5260456 has been allocated resources +[me@l31 linpack]$ srun hostname     # clean & check functionality & licence 
-salloc: Granted job allocation 5260456 +[me@l31 linpack]$ ssh n3XX-YYY       # connect to node nXX-YYY 
-[training@l31 linpack]$ squeue -u training +[me@n3XX-YYY ~]$ module purge 
-             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) +[me@n3XX-YYY ~]$ module load intel/17 intel-mkl/2017 intel-mpi/2017 
-           5260456  mem_0064   jz_hpl training  R       0:11      1 n41-001+[me@n3XX-YYY ~]$ cd my_directory_name/linpack 
 +[me@n3XX-YYY linpack]$ mpirun -np 16 ./xhpl
 </code> </code>
- +stop the process (Ctlr+C or Strg+C)
-3.) Run an srun command:+
  
 <code bash> <code bash>
-[training@l31 linpack]$ srun hostname+[me@n3XX-YYY linpack]$ exit 
 +[me@l31 linpack]$ exit
 </code> </code>
- 
- 
  
 ---- ----
  
-===== Exercise 1: interactive job, cont. =====+====== Interactive jobs: salloc ======
  
-4.) Login to allocated node and execute a program:+===== notes: =====
  
 <code bash> <code bash>
-[training@l31 linpack]$ ssh n41-001 +[me@l31]$ srun hostname
-Last login: Thu Apr 20 15:38:33 2017 from l31.cm.cluster +
- +
-[training@n41-001 ~]$ cd my_directory_name/linpack +
- +
-[training@n41-001 linpack]$ module load intel/17 intel-mkl/2017 intel-mpi/2017 +
-  Loading intel/17 from: /cm/shared/apps/intel/compilers_and_libraries_2017.2.174/linux +
-  Loading intel-mkl/2017 from: /cm/shared/apps/intel/compilers_and_libraries_2017.2.174/linux/mkl +
-  Loading intel-mpi/2017 from: /cm/shared/apps/intel/compilers_and_libraries_2017.2.174/linux/mpi +
- +
-[training@n41-001 linpack]$ mpirun -np 16 ./xhpl +
- +
-Number of Intel(R) Xeon Phi(TM) coprocessors : 0 +
-================================================================================ +
-HPLinpack 2.1  --  High-Performance Linpack benchmark  --   October 26, 2012 +
-Written by A. Petitet and R. Clint Whaley,  Innovative Computing Laboratory, UTK +
-Modified by Piotr Luszczek, Innovative Computing Laboratory, UTK +
-Modified by Julien Langou, University of Colorado Denver +
-================================================================================ +
 </code> </code>
 +**NOTE:** the slurm prolog script is **not** automatically run in this case. The prolog performs basic tasks such as
  
- +  * clean up from previous job, 
- +  * checking basic node functionality, 
----- +  * adapting firewall settings to access license servers.
- +
-===== Exercise 1: interactive job, cont. ===== +
- +
-5.) stop the process (Ctlr+C or Strg+C), log out of the node and the delete job: +
- +
-<code bash> +
-[training@n41-001 linpack]$ exit +
-[training@l31 linpack]$ exit +
-exit +
-salloc: Relinquishing job allocation 5260456 +
-salloc: Job allocation 5260456 has been revoked. +
-</code> +
- +
- +
- +
----- +
- +
-===== Exercise 1: interactive job, summary ===== +
- +
-<code bash> +
-[training@l31 linpack]$ salloc -J jz_hpl -N 1  +
-[training@l31 linpack]$ squeue -u training +
-[training@l31 linpack]$ srun hostname +
-[training@l31 linpack]$ ssh nXX-YYY +
-[training@nXX-YYY ~]$ module load intel/17 intel-mkl/2017 intel-mpi/2017 +
-[training@nXX-YYY ~]$ cd my_directory_name/linpack +
-[training@nXX-YYY linpack]$ mpirun -np 16 ./xhpl +
-</code> +
-stop the process (Ctlr+C or Strg+C) +
- +
-<code bash> +
-[training@nXX-YYY linpack]$ exit +
-[training@l31 linpack]$ exit +
-</code>+
  
  
Line 245: Line 96:
 [training@l31 my_directory_name]$ squeue -u training [training@l31 my_directory_name]$ squeue -u training
              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-           5262833  mem_0064      hpl training R        0:04      1 n41-001+           5262833  mem_0064      hpl training R        0:04      1 n341-001
 </code> </code>
  
Line 251: Line 102:
  
 <code bash> <code bash>
-[training@l31 my_directory_name]$ ssh n41-001+[training@l31 my_directory_name]$ ssh n341-001
 Last login: Fri Apr 21 08:43:07 2017 from l31.cm.cluster Last login: Fri Apr 21 08:43:07 2017 from l31.cm.cluster
 </code> </code>
Line 262: Line 113:
  
 <code bash> <code bash>
-[training@n41-001 ~]$ top+[training@n341-001 ~]$ top
 </code> </code>
  
Line 281: Line 132:
 </code> </code>
  
-  * 1 ... show cpu core load +  * 1 … show cpu core load 
-  * Shift+H ... show threads+  * Shift+H … show threads
  
  
  
 ---- ----
- 
-===== Exercise 2: job script, cont. ===== 
- 
-<code bash> 
-[training@n41-001 ~]$ ps -U training u 
-</code> 
-<code bash> 
-[training@n41-001 ~]$ ps -U training f 
-</code> 
-<code bash> 
-[training@n41-001 ~]$ ps -U training e 
-</code> 
-<code bash> 
-[training@n41-001 ~]$ ps -U training eu 
-</code> 
-<code bash> 
-[training@n41-001 ~]$ ps -U training ef 
-</code> 
-<code bash> 
-[training@n41-001 ~]$ ps -U training euf 
-</code> 
  
 3.) Cancel the job: 3.) Cancel the job:
  
 <code bash> <code bash>
-[training@n41-001 ~]$ scancel <job ID>+[training@n341-001 ~]$ exit 
 +[training@l31 ~]$ scancel <job ID>
 </code> </code>
 +<HTML>
 +</div>
 +</div>
 +</HTML>
  
 +----
  
 +===== Prolog Failure =====
  
----- +If a check in the SLURM prolog script fails on one of the nodes assigned to your job, you will see a message like the following in your slurm-$JOBID.out file:
- +
-===== Exercise 3: interactive job with srun =====+
  
 <code bash> <code bash>
-[training@l31 linpack]$ salloc -J jz_hpl -N 1+Error running slurm prolog: 228
 </code> </code>
-<code bash> +The error code (228) tells you what kind of check has failed. A list of currently existing error codes is:
-[training@l31 linpack]$ squeue -u training +
-</code> +
-<code bash> +
-[training@l31 linpack]$ srun -n 2 hostname +
-</code> +
-<code bash> +
-[training@l31 linpack]$ module purge +
-</code> +
-<code bash> +
-[training@l31 linpack]$ module load intel/17 intel-mkl/2017 intel-mpi/2017 +
-</code> +
-<code bash> +
-[training@l31 linpack]$ export I_MPI_PMI_LIBRARY=/cm/shared/apps/slurm/current/lib/libpmi.so +
-</code> +
-<code bash> +
-[training@l31 linpack]$ srun -n 16 ./xhpl +
-</code> +
- +
-type Ctrl+C or Strg+C to stop the job and remove the job allocation:+
  
 <code bash> <code bash>
-[training@l31 linpack]$ exit +ERROR_MEMORY=200 
-exit +ERROR_INFINIBAND_HW=201 
-salloc: Relinquishing job allocation 5264616+ERROR_INFINIBAND_SW=202 
 +ERROR_IPOIB=203 
 +ERROR_BEEGFS_SERVICE=204 
 +ERROR_BEEGFS_USER=205 
 +ERROR_BEEGFS_SCRATCH=206 
 +ERROR_NFS=207 
 +ERROR_USER_GROUP=220 
 +ERROR_USER_HOME=221 
 +ERROR_GPFS_START=228 
 +ERROR_GPFS_MOUNT=229 
 +ERROR_GPFS_UNMOUNT=230
 </code> </code>
  
 +  * node will be //drained// (unavailable for subsequent jobs until fixed)
 +  * resubmit your job
  
  
Line 358: Line 186:
  
 <code bash> <code bash>
-[jz@l31 ~]$ squeue -u jz+VSC-4 >  squeue -u $user 
              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-           5115915  mem_0064     bash       jz  R      34:50      1 n05-071+            409879  mem_0096 training       sh  R    1:10:59      3 n407-030,n411-[007-008]
  
-[jz@l31 ~]$ alias squeue='squeue -o "%.18i %.10Q  %.12q %.8j %.8u %8U %.2t %.10M %.6D %R" -u jz' +VSC-4 >  squeue  -p mem_0096 | more 
-[jz@l31 ~]$ squeue +             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
-             JOBID   PRIORITY           QOS     NAME     USER USER     ST       TIME  NODES NODELIST(REASON) +             .......................................................................... 
-           5115915      30209         admin     bash       jz 70497     R      33:41      1 n05-071+            407141  mem_0096 interfac   mjech3 PD       0:00      4 (Priority) 
 +      409880_[1-6]  mem_0096 OP1_2_Fi wiesmann PD       0:00      1 (Resources,Priority) 
 +            409879  mem_0096 training       sh  R    1:30:16      3 n407-030,n411-[007-008] 
 +            402078  mem_0096      sim mboesenh  R 4-22:46:13      1 n403-007
 </code> </code>
  
-  * Formatting option: -o <output_format>, --format=<output_format> +  * optional reformatting via -o, for example,
-  * The format of each field is ''%%%[[.]size]type%%''. +
-  * "." means right justification. +
-  * "size" is the field width +
-  * "type" the field type (JOBID, PRIORITY, etc.) +
  
 <code bash> <code bash>
-[jz@l31 ~]$ man squeue+VSC-4 >  squeue -u $user -o "%.18i %.10Q  %.12q %.8j %.8u %8U %.2t %.10M %.6D %R" 
 +             JOBID   PRIORITY           QOS     NAME     USER UID      ST       TIME  NODES NODELIST(REASON) 
 +            409879    3000982         admin training       sh 71177     R    1:34:55      3 n407-030,n411-[007-008]
 </code> </code>
  
  
 +<HTML>
 +</div>
 +</HTML>
  
 ---- ----
Line 386: Line 217:
  
 <code bash> <code bash>
-[training@l31 linpack]$ scontrol show job 5264675 +VSC-4 >  scontrol show job 409879 
-JobId=5264675 JobName=hpl +JobId=409879 JobName=training 
-   UserId=training(72127) GroupId=p70824(70824) MCS_label=N/A +   UserId=sh(71177) GroupId=sysadmin(60000) MCS_label=N/A 
-   Priority=1861 Nice=0 Account=p70824 QOS=normal_0064+   Priority=3000982 Nice=0 Account=sysadmin QOS=admin
    JobState=RUNNING Reason=None Dependency=(null)    JobState=RUNNING Reason=None Dependency=(null)
-   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 +   Requeue=0 Restarts=0 BatchFlag=0 Reboot=0 ExitCode=0:0 
-   RunTime=00:00:36 TimeLimit=3-00:00:00 TimeMin=N/A +   RunTime=01:36:35 TimeLimit=10-00:00:00 TimeMin=N/A 
-   SubmitTime=2017-04-21T11:30:18 EligibleTime=2017-04-21T11:30:18 +   SubmitTime=2020-10-12T15:50:44 EligibleTime=2020-10-12T15:50:44 
-   StartTime=2017-04-21T11:30:49 EndTime=2017-04-24T11:30:56 Deadline=N/A+   AccrueTime=2020-10-12T15:50:44 
 +   StartTime=2020-10-12T15:51:07 EndTime=2020-10-22T15:51:07 Deadline=N/A
    PreemptTime=None SuspendTime=None SecsPreSuspend=0    PreemptTime=None SuspendTime=None SecsPreSuspend=0
-   Partition=mem_0064 AllocNode:Sid=l31:28554+   LastSchedEval=2020-10-12T15:51:07 
 +   Partition=mem_0096 AllocNode:Sid=l40:186217
    ReqNodeList=(null) ExcNodeList=(null)    ReqNodeList=(null) ExcNodeList=(null)
-   NodeList=n41-001 +   NodeList=n407-030,n411-[007-008] 
-   BatchHost=n41-001 +   BatchHost=n407-030 
-   NumNodes=1 NumCPUs=32 NumTasks=16 CPUs/Task=1 ReqB:S:C:T=0:0:*:* +   NumNodes=3 NumCPUs=288 NumTasks=3 CPUs/Task=1 ReqB:S:C:T=0:0:*:* 
-   TRES=cpu=32,node=1,gres/cpu_mem_0064=32 +   TRES=cpu=288,mem=288888M,node=3,billing=288,gres/cpu_mem_0096=288 
-   Socks/Node=* NtasksPerN:B:S:C=16:0:*:* CoreSpec=* +   Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=* 
-   MinCPUsNode=16 MinMemoryNode=0 MinTmpDiskNode=0 +   MinCPUsNode=1 MinMemoryNode=96296M MinTmpDiskNode=0 
-   Features=(null) Gres=cpu_mem_0064:32 Reservation=(null)+   Features=(null) DelayBoot=00:00:00
    OverSubscribe=NO Contiguous=0 Licenses=(null) Network=(null)    OverSubscribe=NO Contiguous=0 Licenses=(null) Network=(null)
-   Command=/home/lv70824/training/Examples/06_node_access_job_control/linpack/job.sh +   Command=(null) 
-   WorkDir=/home/lv70824/training/Examples/06_node_access_job_control/linpack +   WorkDir=/home/fs60000/sh
-   StdErr=/home/lv70824/training/Examples/06_node_access_job_control/linpack/slurm-5264675.out +
-   StdIn=/dev/null +
-   StdOut=/home/lv70824/training/Examples/06_node_access_job_control/linpack/slurm-5264675.out+
    Power=    Power=
 +   TresPerNode=cpu_mem_0096:96
 </code> </code>
 +
  
 ---- ----
Line 421: Line 253:
  
 <code bash> <code bash>
-[jz@l31 ~]$ sacct -j 5115879 
-       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode 
------------- ---------- ---------- ---------- ---------- ---------- -------- 
-5115879            bash   mem_0064   sysadmin         32  COMPLETED      0:0 
-</code> 
  
-specify options: +VSC-4 >  sacct -j 409878  
- +       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode  
-<code bash> +------------ ---------- ---------- ---------- ---------- ---------- --------  
-[jz@l31 ~]$ sacct -j 5115879 -o jobid,jobname,cluster,nodelist,Start,End,cputime,cputimeraw,ncpus,qos,account,ExitCode +409878         training   mem_0096   sysadmin        288  COMPLETED      0:0 
-       JobID    JobName    Cluster        NodeList               Start                 End    CPUTime CPUTimeRAW      NCPUS        QOS    Account ExitCode +
------------- ---------- ---------- --------------- ------------------- ------------------- ---------- ---------- ---------- ---------- ---------- -------- +
-5115879            bash       vsc3         n07-043 2017-03-15T14:31:39 2017-03-15T14:36:43   02:42:08       9728         32      admin   sysadmin      0:0+
 </code> </code>
  
-inspect man page for more options:+adjust output
  
 <code bash> <code bash>
-[jz@l31 ~]$ man sacct+VSC-4 >  sacct -j 409878 -o jobid,jobname,cluster,nodelist,Start,End,cputime,cputimeraw,ncpus,qos,account,ExitCode 
 +       JobID    JobName    Cluster        NodeList               Start                 End    CPUTime CPUTimeRAW      NCPUS        QOS    Account ExitCode  
 +------------ ---------- ---------- --------------- ------------------- ------------------- ---------- ---------- ---------- ---------- ---------- --------  
 +409878         training       vsc4 n407-030,n411-+ 2020-10-12T15:49:42 2020-10-12T15:51:06   06:43:12      24192        288      admin   sysadmin      0:0 
 </code> </code>
  
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 <code bash> <code bash>
-[jz@l31 ~]$ vsc3CoreHours.py -h+VSC-3 >  vsc3CoreHours.py -h
 usage: vsc3CoreHours.py [-h] [-S STARTTIME] [-E ENDTIME] [-D DURATION] usage: vsc3CoreHours.py [-h] [-S STARTTIME] [-E ENDTIME] [-D DURATION]
                         [-A ACCOUNTLIST] [-u USERNAMES] [-uni UNI]                         [-A ACCOUNTLIST] [-u USERNAMES] [-uni UNI]
Line 478: Line 305:
  
 <code bash> <code bash>
-[jz@l31 ~]$ vsc3CoreHours.py -S 2017-01-01 -E 2017-03-31 -u jz+VSC-3 >  vsc3CoreHours.py -S 2020-01-01 -E 2020-10-01 -u sh
 =================================================== ===================================================
 Accounting data time range Accounting data time range
-From: 2017-01-01 00:00:00 +From: 2020-01-01 00:00:00 
-To:   2017-03-31 00:00:00+To:   2020-10-01 00:00:00
 =================================================== ===================================================
 Getting accounting information for the following account/user combinations: Getting accounting information for the following account/user combinations:
-account:   sysadmin users: jz+account:   sysadmin users: sh
 getting data, excluding these qos: goodluck, gpu_vis, gpu_compute getting data, excluding these qos: goodluck, gpu_vis, gpu_compute
 =============================== ===============================
              account     core_h              account     core_h
 _______________________________ _______________________________
-            sysadmin   56844.87+            sysadmin   25775.15
 _______________________________ _______________________________
-               total   56844.87+               total   25775.15
 </code> </code>
  
Line 512: Line 339:
  
 ---- ----
 +
  
  • pandoc/introduction-to-vsc/06_node_access_job_control/node_access_job_control.1517397227.txt.gz
  • Last modified: 2018/01/31 11:13
  • by pandoc