[email protected]: Reserved for file editing, compilation and job submission/management
[email protected] && [email protected]: Reserved for file transfer, file management and data analysis/visualization
ssh [email protected]
# jlkang@hpc2021-io1 Thu Dec 30 13:31:09 ~
pwd # /home/jlkang: $HOME
cd /lustre1/u/jlkang # /lustre1/u/jlkang: $WORK
cd /lustre1/g/sbs_schunter # /lustre1/g/sbs_schunter: PI Group Share
cd /tmp # /tmp/home/jlkang: Long term, small size, 50GB per user, No scheduled clean-up, Daily Backup
/lustre1/u/jlkang: Short term, high performance, 500GB per user, Files not accessed in the past 60 days are subject to clean-up by system
(Be reminded to move important data to $HOME), No Backup
/lustre1/g/sbs_schunter: Moderate term, high performance, 5TB (Default) per PI group, shared between members in a research group, No scheduled clean-up
# jlkang@hpc2021-io1 Thu Dec 30 13:52:49 /lustre1/g/sbs_schunter
mkdir Kang; cd Kang; pwd # /lustre1/g/sbs_schunter/Kang: all the files i will store here - Avoid using “-l” option in “ls” command inside /lustre1
- Avoid having a large number of files in a single directory inside /lustre1
- Avoid accessing small files inside /lustre1
- Keep your source code and executables under /home instead of /lustre1
- Avoid repetitive “stat” operations against files inside /lustre1
- Avoid repetitive open/close operations against files inside /lustre1
jlkang@hpc2021-io1 Thu Dec 30 13:58:26 /lustre1/g/sbs_schunter/Kang
$diskquota
Disk quotas for user jlkang at Thu Dec 30 14:09:56 HKT 2021
+--------------------+---------+------------------------------+---------------------------------+
| | Quota | Block limits | File limits |
| Filesystem | Usage | used quota limit grace | files quota limit grace |
+---------------------+--------+------------------------------+---------------------------------+
/home/jlkang 0.0% 0G 52G [ZFS DOES NOT PROVIDE SOFT QUOTA]
/lustre1/u/jlkang 0.0% 0G 500G 510G - 4 0G 0G -
/lustre1/g/sbs_schunter 0.0% 0G 5120G 5130G - 1 0G 0G -# jlkang@hpc2021-io1 Thu Dec 30 14:20:38 ~
module keyword raxml samtools # module keyword [word1] [word2]: Search for available modules matching the keyword(s)
module load raxml samtools # module load [modA] [modB] [modC]: Load the environment for the default version of modules named modA, modB and modC in corresponding order
module list # List any currently loaded module(s)
module load bcftools/1.14 # module load [mod]/[version]: Load the environment for the specified version of module- When one module is in conflict with another (e.g different MPI libraries), the conflicting module may have to be unloaded before a desired one is loaded.
- some modules may depend on one another and hence they may be loaded/unloaded as a consequence of a subsequent module command in a dynamic fashion.
- To achieve automatic loading of a set of commonly used modules upon system login, user may add the module command in the shell profile (.bashrc).
- When caching error occurs while listing/loading modules, a user may delete the cache file and run the module command again.
rm -f /home/jlkang/.lmod.d/.cache/*.lua# jlkang@hpc2021 Thu Dec 30 15:19:01 ~
vi script.cmdscript.cmd
#!/bin/bash
#SBATCH --job-name=jmodeltest # 1. Job name
#SBATCH --mail-type=BEGIN,END,FAIL # 2. Send email upon events (Options: NONE, BEGIN, END, FAIL, ALL)
#SBATCH [email protected] # Email address to receive notification
#SBATCH --partition=amd # 3. Request a partition
#SBATCH --qos=normal # 4. Request a QoS
#SBATCH --nodes=1 # Request number of node(s)
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=128
#SBATCH --mem-per-cpu=1G
#SBATCH --time=1-10:00:00 # 7. Job execution duration limit day-hour:min:sec
#SBATCH --output=%x_%j.out # 8. Standard output log as $job_name_$job_id.out
#SBATCH --error=%x_%j.err # Standard error log as $job_name_$job_id.err
# print the start time
date
java -jar /home/jlkang/jmodeltest-2.1.10/jModelTest.jar -d single_copy.cds.concatenated.fasta -g 4 -i -f -AIC -BIC -a -tr 128
# print the end time
dateSubmit:
# jlkang@hpc2021 Thu Dec 30 15:19:32 ~
sbatch script.cmd
# Submitted batch job 112667
# jlkang@hpc2021 Thu Dec 30 15:26:08 ~
scancel 112667 # scancel <JobID>: cancel
# jlkang@hpc2021 Mon Apr 24 10:45:46 /lustre1/g/sbs_schunter/Kang/sea_urchin
sbatch --test-only script1.cmd # Check the waiting time
# sbatch: Job 1118951 to start at 2023-04-24T10:45:50 using 32 processors on nodes GPA-2-9 in partition amdCheck job status:
# jlkang@hpc2021 Thu Dec 30 15:22:35 ~
sq
# JOBID PARTITION NAME ST USER QOS NODES CPUS TRES_PER_NODE TIME_LIMIT TIME_LEFT NODELIST(REASON)
# 112667 amd jmodeltest PD jlkang normal 1 1 N/A 1-10:00:00 1-10:00:00 (Resources)
sj # sj -j 1468368 : check the queue time for your submitted job
# Job ID: 1468368 Account: sbs_schunter 2023-10-20 16:50:35
#╒═════════════════╤════════════════════════════════════════╤══════════════════╕
#│ User: jlkang │ Name: diamond │ State: PENDING │
#│ QoS: normal │ Partition: amd │ Priority: 41180 │
#╞═════════════════╪════════════════════════════════════════╧══════════════════╡
#│ Submit │ 2023-10-20 16:48:21 │
#│ Start │ 2023-10-21 14:26:25 │
#│ End By │ 2023-10-28 14:26:25 │
#╞═════════════════╪════════════════════╤══════════════════════════════════════╡
#│ Resource │ Requests │ Current usage │
#├─────────────────┼────────────────────┼──────────────────────────────────────┤
#│ Node │ 1 │ Pending for (Priority)... │
#│ CPU │ 32 │ Nil% │
#│ RAM │ 32GB │ Nil% │
#│ Wall time │ 7-00:00:00 │ 0:00 │
#│ GPU │ N/A │ Nil │
#└─────────────────┴────────────────────┴──────────────────────────────────────┘