Migrating from Zcluster to Sapelo
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- Berenice Turner
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1 GACRC User Quick Guide: Migrating from Zcluster to Sapelo The GACRC Staff Version 1.0 8/4/17 1
2 Discussion Points I. Request Sapelo User Account II. III. IV. Systems Transfer Files Configure Software Environment V. Job Submission Workflow VI. Job Submission Script VII. Appendices 8/4/17 2
3 Request Sapelo User Account Sapelo cluster user account: Note: A valid official UGA MyID is a MUST to create a user account! PI Request User Account PI Verification New User Training User Account Provisioning Welcome Letter 1. The UGA PI uses the GACRC online form to request a user account for a group member. 2. Once we received the request, we will verify it with the PI. 3. After verification by the PI, the new user will be required to attend a training session. 4. After the user attended training, we will provision a Sapelo account for the user. 5. A welcome letter is sent to the user once user account is ready. 8/4/17 3
4 Systems Overview Diagram ssh Login Node zcluster.rcc.uga.edu Accessing Line Zcluster qlogin /home/abclab/userid Interactive Node /escratch4/userid ssh/scp Transfer Node xfer.gacrc.uga.edu /project/abclab /home/myid Interactive Node /lustre1/myid qlogin ssh Login Node sapelo1.gacrc.uga.edu Sapelo 8/4/17 4
5 Systems Overview Log on to Zcluster Login Node: Open Zcluster Interactive Node: Zcluster Home Directory: Zcluster Global Scratch: Create Working Directory on Zcluster Global Scratch: ssh (using zcluster password) type qlogin command from login node /home/abclab/userid /escratch4/userid (4TB quota) type make_escratch command from login node Log on to Sapelo Login Node: Open Sapelo Interactive Node: Sapelo Home Directory: Sapelo Global Scratch: Create Working Directory on Sapelo Global Scratch: ssh (using UGA MyID password) type qlogin command from login node /home/myid (100GB quota) /lustre1/myid use mkdir command in /lustre1/myid from interactive node Log on to GACRC Transfer Node: Group Project Space: ssh (using UGA MyID password) /project/abclab ( abc are initials of the PI of the group) 8/4/17 5
6 Systems Storage Environment Name Role Purpose Zcluster Sapelo Home ssh landing spot static data, e.g., scripts, software /home/abclab/userid /home/myid (100GB quota) Global Scratch Job working space Current Job data being used by running jobs /escratch4/userid (4TB quota) /lustre1/myid (no quota limited by capacity) Project Active data storage Non-current active data for future analysis /project/abclab (1TBinitial quota) 8/4/17 6
7 Systems Computing Resources Overview 150x 8-core 16GB RAM nodes with Intel Xeon processors (total 1200 cores) 45x 12-core 48GB RAM nodes with Intel Xeon processors (total 540 cores) Zcluster 4x 8-core 192GB RAM nodes with Intel Xeon processors (total 32 cores) 10x 12-core 256GB RAM nodes with Intel Xeon processors (total 120 cores) 2x 32-core 512GB RAM nodes with Intel Xeon processors (total 64 cores) 6x 32-core 64GB RAM nodes with AMD Opteron processors (total 192 cores) 4x 12-core 96GB RAM nodes with Intel Xeon processors, 8 NVIDIA K20Xm GPU cards each 112x 48-core 128GB RAM nodes with AMD Opteron processors (total 5376 cores) 4x 48-core 256GB RAM nodes with AMD Opteron processors (total 192 cores) Sapelo 6x 48-core 512GB RAM nodes with AMD Opteron processors (total 288 cores) 1x 48-core 1TB RAM node with AMD Opteron processors (total 48 cores) 3x 28-core 1TB RAM node with Intel Xeon processors (total 84 cores) 2x 16-core 128GB RAM nodes with Intel Xeon processors, 8 NVIDIA K40m GPU cards each 85+ buy-in nodes with variable configurations 8/4/17 7
8 Transfer of Files All Sapelo and zcluster users, as well as all GACRC PIs, can access the GACRC transfer nodes (xfer.gacrc.uga.edu) and using UGA MyID and MyID password to authenticate. Note that a user's home directory on transfer node is the same as the user's Sapelo home directory, which is not the same as the user's Zcluster home directory. Transfer nodes can access the following file systems using their full paths: Sapelo Home Directory: Zcluster Home Directory: Zcluster Global Scratch: Sapelo Global Scratch: Group Project Folder cd /home/myid cd /panfs/pstor.storage/home/abclab/userid cd /escratch4/userid cd /lustre1/myid cd /project/abclab Detailed instructions can be found at the link above 8/4/17 8
9 File Transferring Tree /project/abclab /lustre1/myid /escratch4/userid /home/myid Transfer Node /panfs/pstor.storage/home/abclab/userid scp/ssh local ü ü scp: Remote file transferring between your local computer and your folders on file systems ssh: Logging on to transfer node. Once logged on, you can use cp or mv for file transfer between file systems. 8/4/17 9
10 Configure Software Environment Sapelo User issues module commands to configure various paths for software packages (in a job submission script or on the command line of an interactive session): 1. module avail : show all modules available on cluster 2. module load modulename/version : load the needed module modulename with a version 3. module list : list all modules you already loaded For example: Zcluster User manually exports various paths for software packages (in a job submission script or on the command line of an interactive session), for example: export PATH= :$PATH $ module load python/2.7.8 $ module load R/3.2.3 $ module list Currently Loaded Modules: 1) moab/ ) StdEnv 3) python/ ) R/ /4/17 10
11 Job Submission Workflow (general) Zcluster 1. Log on to zcluster login node: ssh 2. Create a working dir on global scratch: make_escratch 3. Change to working dir on global scratch: cd /escratch4/userid/userid_mmm_dd (mmm, dd: date abbreviations) 4. Create a zcluster job submission script: nano./sub.sh 5. Submit job: qsub -q rcc-30d./sub.sh Sapelo 1. Log on to Sapelo login node: ssh MyID@sapelo1.gacrc.uga.edu 2. Go to Sapelo Interactive node: qlogin 3. Change to Sapelo global scratch: cd /lustre1/myid 4. Create a working dir on global scratch: mkdir./workdir 5. Change to working dir on global scratch: cd./workdir 6. Create a Sapelo job submission script: nano./sub.sh 7. Submit job: qsub./sub.sh 8/4/17 11
12 Job Submission Script (NCBI Blast as example) sub.sh on Zcluster #!/bin/bash cd `pwd` export PATH=/usr/local/ncbiblast/latest/bin:$PATH sub.sh on Sapelo #PBS -S /bin/bash #PBS -q batch #PBS -N testblast #PBS -l nodes=1:ppn=4:amd #PBS -l mem=20gb #PBS -l walltime=480:00:00 blastall -p blastn -d /db/ncbiblast/latest/nt \ -a 4 -i QUERY \ -o out.query cd $PBS_O_WORKDIR module load ncbiblast+/ blastall -p blastn -d /db/ncbiblast/nrte/latest/nt \ -a 4 -i QUERY \ -o out.query > outputfile 2>&1 qsub -q rcc-30d -pe thread 4./sub.sh qsub./sub.sh 8/4/17 12
13 Appendix 1: 8/4/17 13
14 Appendix 2: Common Command Summary Tasks Zcluster Sapelo Common file/dir operations Transfer remote files Open interactive session ls, cd, pwd, file, cat, less, more, cp mv, mkdir, rm, rmdir, dos2unix, mac2unix, etc. scp,sftp or SSH Secure Client File Transfer, FileZilla, WinSCP qlogin Create working directory on global scratch make_escratch mkdir subdirectoryname Edit script files nano sub.sh or vim sub.sh Submit a batch job qsub q queuename l pe sub.sh qsub sub.sh check job status qstat Check detailed job info qsj jobid, qstat j jobid, qacct j jobid qstat f jobid, showjobs jobid Cancel a job from queue qdel jobid, qdel u userid qdel jobid 8/4/17 14
15 Appendix 3: Current process for a UGA PI to request (re)activation or creation of a MyID for an external collaborator To keep a user's MyID active after he/she leaves UGA, or to create a MyID for an external research collaborator: 1. The PI accesses the EITS helpdesk portal at 2. Click on "MyID Account Request on the right side of the page in Popular Services section. 3. Use MyID credentials to log on the service page. 4. In the MyID Request From, enter his/her information and select "GACRC Remote Collaborator" for the Account Type field. 5. After verification by the GACRC Director, EITS will generate collaborator s MyID 6. If collaborator is visiting UGA campus, MyID can be obtained through OVPR s Visiting Researcher & Scholar program 8/4/17 15
16 Appendix 4: Useful Links GACRC Website: GACRC Wiki: Systems: How to Transfer Files: Current Software List: How to Submit a Job: How to Get Help: GACRC Training Opportunities: How to register a new GACRC New Lab: How to register a new GACRC User: 8/4/17 16
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