Difference between revisions of "Biocluster2"

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__TOC__
 
__TOC__
 +
==Quick Links==
  
 +
* Main Site - [http://biocluster2.igb.illinois.edu http://biocluster2.igb.illinois.edu]
 +
* Request Account - [http://www.igb.illinois.edu/content/biocluster-account-form http://www.igb.illinois.edu/content/biocluster-account-form]
 +
* Cluster Accounting - [https://biocluster2.igb.illinois.edu/accounting/ https://biocluster2.igb.illinois.edu/accounting/]
 +
* Cluster Monitoring - [http://biocluster2.igb.illinois.edu/ganglia/ http://biocluster2.igb.illinois.edu/ganglia/]
 +
* SLURM Script Generator - [http://www-app.igb.illinois.edu/tools/slurm/ http://www-app.igb.illinois.edu/tools/slurm/]
 +
* Biocluster Applications - [https://help.igb.illinois.edu/Biocluster_Applications https://help.igb.illinois.edu/Biocluster_Applications]
  
 +
==Description==
 +
Biocluster is the High Performance Computing (HPC) resource for the Carl R Woese Institute for Genomic Biology (IGB) at the University of Illinois at Urbana-Champaign (UIUC). Containing 2824 cores and over 27.7 TB of RAM, Biocluster has a mix of various RAM and CPU configurations on nodes to best serve the various computation needs of the IGB and the Bioinformatics community at UIUC. For storage, Biocluster has 1.3 Petabytes of storage on its GPFS filesystem for reliable high speed data transfers within the cluster. Networking in Biocluster is either 1, 10 or 40 Gigibit ethernet depending on the class of node and its data transfer needs.
  
 +
==Cluster Specifications==
  
This document is new and under development.  If you find any mistakes please email help@igb.uiuc.edu and we will resolve them.
+
{| border="1" class='wikitable' width="1200" cellspacing="1" cellpadding="0" align="center"
 +
|-
 +
!|Queue Name
 +
!|Nodes
 +
!|Cores (CPUs) per Node
 +
!|Memory
 +
!|Networking
 +
!|Scratch Space /scatch
 +
!|GPUs
 +
|-
 +
||normal (default)
 +
||5 Supermicro SYS-2049U-TR4
 +
||72 Intel Xeon Gold 6150 @2.7 GHz
 +
||1.2TB
 +
||40GB Ethernet
 +
||7TB SSD
 +
|| 
 +
|-
 +
||lowmem
 +
||8 Supermicro SYS-F618R2-RTN+
 +
||12 Intel Xeon E5-2603 v4 @ 1.70Ghz
 +
||64GB RAM
 +
||10GB Ethernet
 +
||192GB
 +
|| 
  
== Quick Links ==
+
|-
 +
||gpu
 +
||1 Supermicro
 +
||28 Intel Xeon E5-2680 @ 2.4Ghz
 +
||128GB
 +
||1GB Ethernet
 +
||1TB
 +
||4 NVIDIA GeForce GTX 1080 Ti
 +
|-
 +
||classroom
 +
||10 Dell Poweredge R620
 +
||24 Intel Xeon E5-2697 v2 @ 2.7Ghz
 +
||384GB
 +
||10GB Ethernet
 +
||750GB
 +
|| 
  
*Main Site - [http://biocluster2.igb.illinois.edu http://biocluster2.igb.illinois.edu]
+
|}
*Request Account - [http://www.igb.illinois.edu/content/biocluster-account-form http://www.igb.illinois.edu/content/biocluster-account-form]
 
*Cluster Accounting - [https://biocluster2.igb.illinois.edu/accounting/ https://biocluster2.igb.illinois.edu/accounting/]
 
*Cluster Monitoring - [http://biocluster2.igb.illinois.edu/ganglia/ http://biocluster2.igb.illinois.edu/ganglia/]
 
*SLURM Script Generator - [http://www-app2.igb.illinois.edu/tools/slurm/ http://www-app2.igb.illinois.edu/tools/slurm/]
 
  
== Description ==
+
== Storage ==
 +
=== Information ===
  
Biocluster is the High Performance Computing (HPC) resource for the Carl R Wose Institute for Genomic Biology (IGB) at the University of Illinois at Urbana-Champaign (UIUC).  Containing 2824 cores and over 27.7 TB of RAM, Biocluster has a mix of various RAM and CPU configurations on nodes to best serve the various computation needs of the IGB and the Bioinformatics community at UIUC.  For storage, Biocluster has 2619 TB of storage on its Ceph filesystem for reliable high speed data transfers within the cluster.   Networking in Biocluster is either 1 or 10 Gigibit ethernet depending on the class of node and its data transfer needs.
+
* The storage system is a GPFS filesystem with 1.3 Petabytes of total disk space with 2 copies of the data. This data is '''NOT''' backed up.
 +
* The data is spread across 8 GPFS storage nodes.
  
== Cluster Specifications ==
+
===Cost===
  
'''Default Queue'''
+
{| border="1" width="624" cellspacing="1" cellpadding="0" align="center"
 +
|-
 +
!|Cost (Per Terabyte Per Month)
 +
|-
 +
||$8.75
 +
|}
  
*20 Dell PowerEdge R620 Servers
+
=== Calculate Usage (/home) ===
**24 Intel Xeon E5-2697 @ 2.7GHz CPU Cores per node
+
* Each Month, you will receive a bill on your monthly usage.  We take a snapspot of usage daily.  Then we average out the 95 percentile of daily snapspots to get an average usage for the month.
**384 Gigabytes of RAM per Node
+
* You can calculate your usage using the du command.  An example is below.  The result will be double what you are billed as their is 2 copies of the data.  Make sure to divide by 2.
 +
<pre>du -h /home/a-m/username</pre>
  
'''High Memory Queue'''
+
== Calculate Usage (/private_stores) ==
*2 Supermicro Servers
+
* These are private data storage nodes.  They do not get billed monthly.
**28 Intel Xeon E5-2690 v4 @ 2.60GHz CPU Cores per node
+
* The filesystems are XFS shared over NFS.
**768 Gigabytes of RAM per Node
+
* To calculate usage, use the du command
 +
<pre>du -h /private_stores/shared/directory</pre>
  
'''Large Memory Queue'''
+
==Queue Costs==
*1 Node - Dell R910
+
The cost for each job is dependent on which queue it is submitted to. Listed below are the different queues on the cluster with their cost.
**24 Intel Xeon E7540 @ 2.0GHz CPUs per node
 
**1024 Gigabytes (1TB) of RAM
 
  
'''Blacklight Queue'''
+
Usage is charge by the second. The CPU cost and memory cost are compared and the largest is what is billed.
*4 SGI UV1000 Nodes
+
{| border="1" width="624" cellspacing="1" cellpadding="0" align="center"
**384 Intel Xeon X7542 @ 2.67 CPUs per node
+
|-
**2 TB of Ram per node
+
!|Queue Name
 
+
!|CPU Cost ($ per CPU per day)
'''Budget Queue'''
+
!|Memory Cost ($ per GB per day)
*10 Dell Poweredge R410
+
!|GPU Cost ($ per GPU per day)
**8 Intel Xeon E5530 @ 2.4Ghz CPU Cores per node
 
**32 or 48 Gigabytes of RAM per Node
 
 
 
== Storage ==
 
  
=== Information ===
 
*The storage system is a CEPH filesystem with 2.4 Petabytes of disk space.  This data is '''NOT''' backed up.
 
*The data is spread across 15 CEPH storage nodes.
 
  
=== Cost ===
 
{| class="wikitable" width="624" align="center" border="1" cellpadding="0" cellspacing="1"
 
 
|-
 
|-
! Cost (Per Terabyte Per Month)
+
||normal (default)
 +
||$1.19
 +
||$0.07
 +
||NA
 
|-
 
|-
| $10
+
||lowmem
|}
+
||$0.50
 +
||$0.10
 +
||NA
  
== Queue Costs ==
 
  
The cost for each job is dependent on which queue it is submitted to. Listed below are the different queues on the cluster with their cost.
 
 
Usage is charge by the second.&nbsp; The CPU cost and memory cost are compared and the largest is what is billed.
 
 
{| class="wikitable" width="624" align="center" border="1" cellpadding="0" cellspacing="1"
 
|-
 
! Queue Name
 
! CPU Cost ($ per CPU per day)
 
! Memory Cost ($ per GB per day)
 
|-
 
| default
 
| $1.00
 
| $0.50
 
|-
 
| himemeory
 
| $2.00
 
| $1.00
 
 
|-
 
|-
| highthroughput
+
||GPU
| $1.00
+
||$2.00
| $0.50
+
||$0.44
|-
+
||$2.00
| largememory
 
| $8.50
 
| $0.20<br/>
 
|-
 
| blacklight<br/>
 
| $1.10
 
| $0.25
 
|-
 
| budget<br/>
 
| $0.50
 
| $0.25
 
 
|}
 
|}
  
== How To Get Biocluster ==
+
==Gaining Access==
 +
 
 +
* Please fill out the form at [http://www.igb.illinois.edu/content/biocluster-account-form http://www.igb.illinois.edu/content/biocluster-account-form] to request access to the Biocluster.
  
*Please fill out the form at [http://www.igb.illinois.edu/content/biocluster-account-form http://www.igb.illinois.edu/content/biocluster-account-form] to request access to the Biocluster.
+
==Cluster Rules==
  
== Cluster Rules ==
+
* '''Running jobs on the head node or login nodes are strictly prohibited.''' Running jobs on the head node could cause the entire cluster to crash and affect everyone's jobs on the cluster. Any program found to be running on the headnode will be stopped immediately and your account could be locked. You can start an interactive session to login to a node to manual run programs.
 +
* '''Installing Software''' Please email help@igb.illinois.edu for any software requests. Compiled software will be installed in /home/apps. If its a standard RedHat package (rpm), it will be installed in their default locations on the nodes.
 +
* '''Creating or Moving over Programs:''' Programs you create or move to the cluster should be first tested by you outside the cluster for stability. Once your program is stable, then it can be moved over to the cluster for use. Unstable programs that cause problems with the cluster can result in your account being locked. Programs should only be added by CNRG personnel and not compiled in your home directory.
 +
* '''Reserving Memory:''' SLURM allows the user to specify the amount of memory they want their program to use.. If your job tries to use more memory than you have reserved, the job will run out of memory and die. Make sure to specify the correct amount of memory.
 +
* '''Reserving Nodes and Processors:''' For each job, you must reserve the correct number of nodes and processors. By default you are reserved 1 processor on 1 node. If you are running a multiple processor job or a MPI job you need to reserve the appropriate amount. If you do not reserve the correct amount, the cluster will confine your job to that limit, increasing its runtime.
  
*'''Running jobs on the head node or login nodes are strictly prohibited.''' Running jobs on the head node could cause the entire cluster to crash and affect everyone's jobs on the cluster. Any program found to be running on the headnode will be stopped immediately and your account could be locked. You can start an interactive session to login to a node to manual run programs.
+
==How To Log Into The Cluster==
*'''Installing Software''' Please email help@igb.illinois.edu for any software requests. Compiled software will be installed in /home/apps. If its a standard RedHat package (rpm), it will be installed in their default locations on the nodes.
 
*'''Creating or Moving over Programs:''' Programs you create or move to the cluster should be first tested by you outside the cluster for stability. Once your program is stable, then it can be moved over to the cluster for use. Unstable programs that cause problems with the cluster can result in your account being locked.&nbsp; Programs should only be added by CNRG personnel and not compiled in your home directory.
 
*'''Reserving Memory:''' SLURM allows the user to specify the amount of memory they want their program to use.. If your job tries to use more memory than you have reserved, the job will run out of memory and die. Make sure to specify the correct amount of memory.
 
*'''Reserving Nodes and Processors:''' For each job, you must reserve the correct number of nodes and processors. By default you are reserved 1 processor on 1 node. If you are running a multiple processor job or a MPI job you need to reserve the appropriate amount. If you do not reserve the correct amount, the cluster will confine your job to that limit, increasing its runtime.
 
  
== How To Log Into The Cluster ==
+
* You will need to use an SSH client to connect.
  
*You will need to use an SSH client to connect.
+
===On Windows===
  
=== On Windows ===
+
* You can download Putty from [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html]
 +
* Install Putty and run it, in the Host Name input box enter '''biologin.igb.illinois.edu'''
  
*You can download Putty from [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html]
+
[[File:PUTTYbiologin.PNG|400px]]
*Install Putty and run it, in the Host Name input box enter '''biologin.igb.illinois.edu'''
 
  
[[File:PUTTYbiologin.PNG]]
+
* Hit Open and login using your IGB account credentials.
  
*Hit Open and login using your IGB account credentials.
+
===On Mac OS X===
  
=== On Mac OS X ===
+
* Simply open the terminal under Go >> Utilities >> Terminal
 +
* Type in '''ssh username@biologin.igb.illinois.edu''' where username is your NetID.
 +
* Hit the Enter key and type in your IGB password.
  
*Simply open the terminal under Go >> Utilities >> Terminal
+
==How To Submit A Cluster Job==
*Type in '''ssh username@biologin.igb.illinois.edu''' where username is your NetID.
 
*Hit the Enter key and type in your IGB password.
 
  
== How To Submit A Cluster Job ==
+
* The cluster runs the '''SLURM ''' queuing and resource mangement program.
 +
* All jobs are submitted to SLURM which distributes them automatically to the Nodes.
 +
* You can find all of the parameters that SLURM uses at [https://slurm.schedmd.com/quickstart.html https://slurm.schedmd.com/quickstart.html]
 +
* You can use our SLURM Generation Utility to help you learn to generate job scripts [http://www-app.igb.illinois.edu/tools/slurm/ http://www-app.igb.illinois.edu/tools/slurm/]
  
*The cluster runs the '''SLURM ''' queuing and resource mangement program.
+
===Create a Job Script===
*All jobs are submitted to SLURM which distributes them automatically to the Nodes.
 
*You can find all of the parameters that SLURM uses at [https://slurm.schedmd.com/quickstart.html https://slurm.schedmd.com/quickstart.html]
 
*You can use our SLURM Generation Utility to help you learn to generate job scripts [http://www-app2.igb.illinois.edu/tools/slurm/ http://www-app2.igb.illinois.edu/tools/slurm/]
 
  
=== Create a Job Script ===
+
* You must first create a SLURM job script file in order to tell SLURM how and what to execute on the nodes.
 +
* Type the following into a text editor and save the file '''test.sh''' ( [[Linux text editing]] )
  
*You must first create a SLURM job script file in order to tell SLURM how and what to execute on the nodes.
 
*Type the following into a text editor and save the file '''test.sh''' ( [[Linux text editing]] )
 
 
<pre>#!/bin/bash
 
<pre>#!/bin/bash
 
#SBATCH -p normal
 
#SBATCH -p normal
#SBATCH -c 1
 
 
#SBATCH --mem=1g
 
#SBATCH --mem=1g
 
#SBATCH -N 1
 
#SBATCH -N 1
 +
#SBATCH -n 1
  
 
sleep 20
 
sleep 20
 
echo "Test Script"  
 
echo "Test Script"  
 
</pre>
 
</pre>
*Change the permissions on the script to allow execution.
+
* You just created a simple SLURM Job Script.
<pre>chmod 775 test.sh</pre>
+
* To submit the script to the cluster, you will use the sbatch command.
*You just created a simple SLURM Job Script.
+
 
*To submit the script to the cluster, you will use the sbatch command.
 
 
<pre>sbatch test.sh</pre>
 
<pre>sbatch test.sh</pre>
*Line by line explanation
+
* Line by line explanation
**'''#!/bin/bash''' - tells linux this is a bash program and it should use a bash interpreter to execute it.
+
** '''#!/bin/bash''' - tells linux this is a bash program and it should use a bash interpreter to execute it.
**'''#SBATCH''' - are SLURM parameters, for explanations of these please scroll down to SLURM Parameters Explanations section.
+
** '''#SBATCH''' - are SLURM parameters, for explanations of these please scroll down to SLURM Parameters Explanations section.
**'''sleep 20''' - Sleep 20 seconds (only used to simulate processing time for this example)
+
** '''sleep 20''' - Sleep 20 seconds (only used to simulate processing time for this example)
**'''echo "Test Script"''' - Output some text to the screen when job completes ( simulate output for this example)
+
** '''echo "Test Script"''' - Output some text to the screen when job completes ( simulate output for this example)
*For example if you would like to run a blast job you may simply replace the last two line with the following
+
* For example if you would like to run a blast job you may simply replace the last two line with the following
<pre>module load blast
+
 
 +
<pre>module load BLAST
 
blastall -p blastn -d nt -i input.fasta -e 10 -o output.result -v 10 -b 5 -a 5
 
blastall -p blastn -d nt -i input.fasta -e 10 -o output.result -v 10 -b 5 -a 5
 
</pre>
 
</pre>
*Note: the module commands are explained under the '''Environment Modules''' section.
+
* Note: the module commands are explained under the '''Environment Modules''' section.
  
==== SLURM Parameters Explanations: ====
+
====SLURM Parameters Explanations:====
  
These are just a few parameter options, for more type '''man sbatch''' while logged into the cluster.
+
* To view all possible parameters
 +
** Run '''man sbatch''' at the command line
 +
** Go to [https://slurm.schedmd.com/sbatch.html https://slurm.schedmd.com/sbatch.html] to view the man page online
  
{| class="wikitable" border="1"
+
{| border="1" class='wikitable'
 
|-
 
|-
! Command
+
!|Command
! Description
+
!|Description
 
|-
 
|-
| #SBATCH -p PARTITION
+
||#SBATCH -p PARTITION
| Run the job on a specific queue/partition. This defaults to the "normal" queue
+
||Run the job on a specific queue/partition. This defaults to the "normal" queue
 
|-
 
|-
| #SBATCH -D /tmp/working_dir
+
||#SBATCH -D /tmp/working_dir
| Run the script from the /tmp/working_dir directory. This defaults to the current directory you are in.
+
||Run the script from the /tmp/working_dir directory. This defaults to the current directory you are in.
 
|-
 
|-
| #SBATCH -J ExampleJobName
+
||#SBATCH -J ExampleJobName
| Name of the job will be ExampleJobName
+
||Name of the job will be ExampleJobName
 
|-
 
|-
| #SBATCH -e /path/to/errorfile
+
||#SBATCH -e /path/to/errorfile
| Split off the error stream to this file. By default output and error streams are placed in the same file.
+
||Split off the error stream to this file. By default output and error streams are placed in the same file.
 
|-
 
|-
| #SBATCH -e /path/to/ouputfile
+
||#SBATCH -o /path/to/ouputfile
| Split off the output stream to this file. By default output and error streams are placed in the same file.
+
||Split off the output stream to this file. By default output and error streams are placed in the same file.
 
|-
 
|-
| #SBATCH --mail-user username@illinois.edu
+
||#SBATCH --mail-user username@illinois.edu
| Send an e-mail to specified email to receive job information.
+
||Send an e-mail to specified email to receive job information.
 
|-
 
|-
| #SBATCH --mail-type BEGIN, END, FAIL
+
||#SBATCH --mail-type BEGIN, END, FAIL
| Specifies when to send a message to email. You can select multiple of these with a comma separated list. Many other options exist.
+
||Specifies when to send a message to email. You can select multiple of these with a comma separated list. Many other options exist.
 
|-
 
|-
| #SBATCH -N X
+
||#SBATCH -N X
| Reserve X number of nodes.
+
||Reserve X number of nodes.
 
|-
 
|-
| #SBATCH -n X
+
||#SBATCH -n X
| Reserve X number of cpus.
+
||Reserve X number of cpus.
 
|-
 
|-
| #SBATCH --mem=XG  
+
||#SBATCH --mem=XG
| Reserve X gigabytes of RAM for the job.
+
||Reserve X gigabytes of RAM for the job.
 
|-
 
|-
 +
||#SBATCH --gres=gpu:X
 +
||Reserve X NVIDIA GPUs. (Only on GPU queues)
 
|}
 
|}
  
=== Create a Job Array Script ===
+
===Create a Job Array Script===
 +
Making a new copy of the script and then submitting each one for every input data file is time consuming. An alternative is to make a job array using the -t option in your submission script. The ---aray option allows many copies of the same script to be queued all at once. You can use the $SLURM_ARRAY_TASK_ID to differentiate between the different jobs in the array. A detailed example on how to do this is available at [[Job Arrays]]
  
Making a new copy of the script and then submitting each one for every input data file is time consuming. An alternative is to make a job array using the -t option in your submission script. The -t option allows many copies of the same script to be queued all at once. You can use the $SLURM_ARRAY_TASK_ID to differentiate between the different jobs in the array. A brief example on how to do this is available at [[Job Array Example]]
+
===Start An Interactive Session ===
  
=== Start An Interactive Login Session On A Compute Node ===
+
* Use the '''srun''' commsnf if you would like to run a job interactively.
  
*Use interactive srun if you would like to run a job interactively such as running a quick perl script or run a quick test interactively on your data.
 
 
<pre>srun --pty /bin/bash
 
<pre>srun --pty /bin/bash
 
</pre>
 
</pre>
*This will automatically reserve you a slot on one of the compute nodes and will start a terminal session on it.
+
* This will automatically reserve you a slot on one of the compute nodes and will start a terminal session on it.
*Closing your terminal window will also kill your processes running in your interactive srun session, therefor it's better to submit large jobs via non-interactive sbatch.
+
* Closing your terminal window will also kill your processes running in your interactive srun session, therefore it's better to submit large jobs via non-interactive sbatch.
*To run an application with a user interface you will need to setup xserver on your computer [[Xserver Setup]]
 
  
== View/Delete Submitted Jobs ==
+
=== X11 Graphical Applications ===
 +
* To run an application with a user interface you will need to setup an Xserver on your computer [[Xserver Setup]]
 +
*Then add the '''--x11''' parameter to your srun command
 +
<pre>
 +
srun --x11 --pty /bin/bash
 +
</pre>
  
=== Viewing Job Status ===
+
==View/Delete Submitted Jobs==
 +
===Viewing Job Status===
 +
 
 +
* To get a simple view of your current running jobs you may type:
  
*To get a simple view of your current running jobs you may type:
 
 
<pre>squeue -u userid
 
<pre>squeue -u userid
 
</pre>
 
</pre>
*This command brings up a list of your current running jobs.
+
* This command brings up a list of your current running jobs.
*The first number represents the job's ID number.
+
* The first number represents the job's ID number.
*Jobs may have different status flags:
+
* Jobs may have different status flags:
**'''R''' = job is currently running
+
** '''R''' = job is currently running
  
  
*For more detailed view type:
+
* For more detailed view type:
 +
 
 
<pre>squeue -l</pre>
 
<pre>squeue -l</pre>
*This will return a list of all nodes, their slot availability, and your current jobs.
+
* This will return a list of all nodes, their slot availability, and your current jobs.
  
=== List Queues ===
+
===List Queues===
 +
 
 +
* Simple view
 +
 
 +
<pre>sinfo</pre>This will show all queues as well as which nodes in those queues are fully used (alloc), partially used (mix), unused (idle), or unavailable (down).
  
*Simple view
 
<pre>sinfo
 
</pre>
 
This will show all queues as well as which nodes in those queues are fully used (alloc), partially used (mix), unused (idle), or unavailable (down).
 
</pre>
 
  
=== List All Jobs on Cluster With Nodes ===
+
===List All Jobs on Cluster With Nodes===
<pre>squeue
+
<pre>squeue</pre>
</pre>
+
===Deleting Jobs===
  
=== Deleting Jobs ===
+
* Note: You can only delete jobs which are owned by you.
 +
* To delete a job by job-ID number:
 +
* You will need to use '''scancel''', for example to delete a job with ID number 5523 you would type:
  
*Note: You can only delete jobs which are owned by you.
 
*To delete a job by job-ID number:
 
*You will need to use '''scancel''', for example to delete a job with ID number 5523 you would type:
 
 
<pre>scancel 5523
 
<pre>scancel 5523
 
</pre>
 
</pre>
*Delete all of your jobs
+
* Delete all of your jobs
 +
 
 
<pre>scancel -u userid
 
<pre>scancel -u userid
 
</pre>
 
</pre>
 +
===Troubleshooting job errors===
  
=== Troubleshooting job errors ===
+
* To view job errors in case job status shows '''Eqw''' or any other error in the status column use '''qstat -j''', for example if job # 23451 failed you would type:
  
*To view job errors in case job status shows '''Eqw''' or any other error in the status column use '''qstat -j''', for example if job # 23451 failed you would type:
 
 
<pre>scontrol show job 23451
 
<pre>scontrol show job 23451
 
</pre>
 
</pre>
 +
==Applications==
 +
===Application Lists===
  
== Applications ==
+
* View a list of installed applications at [https://help.igb.illinois.edu/Biocluster_Applications https://help.igb.illinois.edu/Biocluster_Applications]
 +
* List of currently installed applications from the commmand line, run '''module avail'''
  
=== Application Lists ===
+
===Application Installation===
  
*List of currently installed applications from the commmand line, run '''module avail'''
+
* Please email '''help@igb.illinois.edu''' to request new application or version upgrades
 +
* The Biocluster uses EasyBuild to build and install software.  You can read more about EasyBuild at [https://github.com/easybuilders/easybuild https://github.com/easybuilders/easybuild]
 +
* The Biocluster EasyBuild scripts are located at [https://github.com/IGB-UIUC/easybuild https://github.com/IGB-UIUC/easybuild]
  
=== Application Installation ===
+
===Environment Modules===
 +
* The Biocluster uses the Lmod modules package to manage the software that is installed.  You can read more about Lmod at [https://lmod.readthedocs.io/en/latest/ https://lmod.readthedocs.io/en/latest/]
 +
* To use an application, you need to use the '''module''' command to load the settings for an application
 +
* To load a particular environment for example QIIME/1.9.1, simply run this command:
  
*Please email '''help@igb.illinois.edu''' to request new application or version upgrades
+
<pre>module load QIIME/1.9.1
 +
</pre>
 +
* If you would like to simply load the latest version, run the the command without the /1.9.1 (version number):
 +
 
 +
<pre>module load QIIME
 +
</pre>
 +
* To view which environments you have loaded simply run '''module list''':
  
=== Environment Modules ===
+
<pre>bash-4.1$ module list
 +
Currently Loaded Modules:
 +
  1) BLAST/2.2.26-Linux_x86_64  2) QIIME/1.9.1
 +
</pre>
 +
* When submitting a job using a sbatch script you will have to add the '''module load qiime/1.5.0''' line before running qiime in the script.
 +
* To unload a module simply run '''module unload''':
  
*To use an application, you need to use the '''module''' command to load the settings for an application
+
<pre>module unload QIIME
 +
</pre>
 +
* Unload all modules
  
 +
<pre>module purge
 +
</pre>
  
 +
=== Containers ===
 +
*The Biocluster cluster supports Singularity to run containers.
 +
*The guide on how to use them is at [[Biocluster Singularity]]
  
*To load a particular environment for example qiime/1.5.0, simply run this command:
+
=== R Packages ===
<pre>module load qiime/1.5.0
+
*We have a local mirror of the [https://cran.r-project.org/ CRAN] and [https://www.bioconductor.org/ Bioconductor]. This allows you to install packages through an interactive session into your home folder.
 +
*To install a package, run an interactive
 +
<pre>
 +
srun --pty /bin/bash
 
</pre>
 
</pre>
*If you would like to simply load the latest version, run the the command without the /1.50 (version number):
+
*Load the R module
<pre>module load qiime
+
<pre>
 +
module load R/3.6.0-IGB-gcc-8.2.0
 
</pre>
 
</pre>
*To view which environments you have loaded simply run '''module list''':
+
*Run R
<pre>bash-4.1$ module list
+
<pre>
Currently Loaded Modulefiles:
+
R
  1) qiime
 
 
</pre>
 
</pre>
*When submitting a job using a qsub script you will have to add the '''module load qiime/1.5.0''' line before running qiime in the script.
+
*For CRAN packages, run install.packages()
*To unload a module simply run '''module unload''':
+
<pre>
<pre>module unload qiime
+
install.packages('shape');
 
</pre>
 
</pre>
*Unload all modules
+
*For Bioconductor packages, the BiocManager package is already installed.  You just need to run BiocManager::install to install a package
<pre>module purge
+
<pre>
 +
BiocManager::install('dada2')
 
</pre>
 
</pre>
 +
*If the package requires an external dependencies, you should email us to get it install centrally.
  
== Transferring data files ==
+
== Mirror Service - Genomic Databases ==
 +
* [[Biocluster Mirrors]]
  
=== Transferring using SFTP/SCP ===
+
==Transferring data files==
 +
===Transferring using SFTP/SCP===
 +
====Using WinSCP====
 +
*Download WinSCP installation package from http://winscp.net/eng/download.php#download2 and install it.
 +
*Once installed Run WinSCP >> enter biologin.igb.illinois.edu for the Host name >> Enter your IGB user name and password and click Login
 +
[[File:Bioclustertransfer.png|400px]]
 +
*Once you hit "Login, you should be connected to your Biocluster home folder, as shown below.
 +
[[File:Bioclustertransfer2.png|400px]]
 +
*From here you should be able to download or transfer your files.
  
*In order to transfer files to the cluster from a personal Desktop/Laptop you may use [[File Server Access|WinSCP]] the same way you would use it to transfer files to the [[File Server Access|File Server]].
+
====Using CyberDuck====
  
=== Transferring using Globus (NOT ACTIVE) ===
+
*To download cyberduck go to [http://cyberduck.ch http://cyberduck.c] and click on the large Zip icon to download.
 +
*Once cyberduck is installed on OSX you may start the program.
 +
*Click on '''Open Connection.'''
 +
*From the drop down menu at the top of the opopup window select '''SFTP(SSH File Transfer Protocol)'''
 +
[[File:Cyberduck screenshot sftp.png|400px]]
  
*The biocluster has a Globus endpoint setup. Then end point name is '''igb#biocluster.igb.illinois.edu'''
+
*Now in the '''Server:''' input box enter '''biologin.igb.illinois.edu''' and for Username and password enter your IGB credentials.
*Globus allows the transferring of very large files reliably.
 
*A guide on how to use Globus is [[Globus|here]]
 
  
=== Transferring from Biotech FTP Server ===
+
[[File:Cyberduckbiologin.png|400px]]
  
*One option to transfer data from the Biotech FTP server is to use a program called wget.
+
*Click '''Connect.'''
*It can download 1 file or an entire directory.
+
*You may now download or transfer your files.
*Replace USERNAME with the username provided by the Biotech Center.
+
*'''NOTICE:'''  Cyberduck by default wants to open multiple connections for transferring files.  The biocluster firewall limits you to 4 connections a minute.  This can cause transfers to timeout.  You can change Cyberduck to only use 1 connection by going to '''Preferences->Transfers->Transfer Files'''.  Select '''Open Single Connection'''.
  
The below example will download the file '''test_file.tar.gz'''
+
===Transferring using Globus===
<pre>wget --user=USERNAME --ask-password ftp://ftp.biotech.illinois.edu/test_file.tar.gz</pre>
+
 
*If you want to download an entire directory, you need to have the '''-r''' parameter set. This will recursively go through an entire directory and download it.
+
* The biocluster has a Globus endpoint setup. Then end point name is '''igb#biocluster.igb.illinois.edu'''
<pre>wget -r --user=USERNAME --ask-password ftp://ftp.biotech.illinois.edu/test_dir/</pre>
+
* Globus allows the transferring of very large files reliably.
 +
* A guide on how to use Globus is [[Globus|here]]
  
 
== References ==
 
== References ==
*OpenHPC [https://openhpc.community/ https://openhpc.community/]
+
 
*SLURM Job Scheduler Documentation - [https://slurm.schedmd.com/ https://slurm.schedmd.com/]
+
* OpenHPC [https://openhpc.community/ https://openhpc.community/]
*Rosetta Stone of Schedulers - [https://slurm.schedmd.com/rosetta.pdf https://slurm.schedmd.com/rosetta.pdf]
+
* SLURM Job Scheduler Documentation - [https://slurm.schedmd.com/ https://slurm.schedmd.com/]
*SLURM Quick Refernece - [https://slurm.schedmd.com/pdfs/summary.pdf https://slurm.schedmd.com/pdfs/summary.pdf]
+
* Rosetta Stone of Schedulers - [https://slurm.schedmd.com/rosetta.pdf https://slurm.schedmd.com/rosetta.pdf]
*CEPH Filesystem 0 [http://ceph.com/ceph-storage/file-system/ http://ceph.com/ceph-storage/file-system/]
+
* SLURM Quick Refernece - [https://slurm.schedmd.com/pdfs/summary.pdf https://slurm.schedmd.com/pdfs/summary.pdf]
*Lmod Module Homepage - [https://www.tacc.utexas.edu/research-development/tacc-projects/lmod https://www.tacc.utexas.edu/research-development/tacc-projects/lmod]
+
* CEPH Filesystem [http://ceph.com/ceph-storage/file-system/ http://ceph.com/ceph-storage/file-system/]
*Lmod Documentation - [https://lmod.readthedocs.io/en/latest/ https://lmod.readthedocs.io/en/latest/]
+
* GPFS Filesystem [https://en.wikipedia.org/wiki/IBM_Spectrum_Scale https://en.wikipedia.org/wiki/IBM_Spectrum_Scale]
 +
* Lmod Module Homepage - [https://www.tacc.utexas.edu/research-development/tacc-projects/lmod https://www.tacc.utexas.edu/research-development/tacc-projects/lmod]
 +
* Lmod Documentation - [https://lmod.readthedocs.io/en/latest/ https://lmod.readthedocs.io/en/latest/]

Revision as of 14:41, 14 January 2021

Quick Links[edit]

Description[edit]

Biocluster is the High Performance Computing (HPC) resource for the Carl R Woese Institute for Genomic Biology (IGB) at the University of Illinois at Urbana-Champaign (UIUC). Containing 2824 cores and over 27.7 TB of RAM, Biocluster has a mix of various RAM and CPU configurations on nodes to best serve the various computation needs of the IGB and the Bioinformatics community at UIUC. For storage, Biocluster has 1.3 Petabytes of storage on its GPFS filesystem for reliable high speed data transfers within the cluster. Networking in Biocluster is either 1, 10 or 40 Gigibit ethernet depending on the class of node and its data transfer needs.

Cluster Specifications[edit]

Queue Name Nodes Cores (CPUs) per Node Memory Networking Scratch Space /scatch GPUs
normal (default) 5 Supermicro SYS-2049U-TR4 72 Intel Xeon Gold 6150 @2.7 GHz 1.2TB 40GB Ethernet 7TB SSD  
lowmem 8 Supermicro SYS-F618R2-RTN+ 12 Intel Xeon E5-2603 v4 @ 1.70Ghz 64GB RAM 10GB Ethernet 192GB  
gpu 1 Supermicro 28 Intel Xeon E5-2680 @ 2.4Ghz 128GB 1GB Ethernet 1TB 4 NVIDIA GeForce GTX 1080 Ti
classroom 10 Dell Poweredge R620 24 Intel Xeon E5-2697 v2 @ 2.7Ghz 384GB 10GB Ethernet 750GB  

Storage[edit]

Information[edit]

  • The storage system is a GPFS filesystem with 1.3 Petabytes of total disk space with 2 copies of the data. This data is NOT backed up.
  • The data is spread across 8 GPFS storage nodes.

Cost[edit]

Cost (Per Terabyte Per Month)
$8.75

Calculate Usage (/home)[edit]

  • Each Month, you will receive a bill on your monthly usage. We take a snapspot of usage daily. Then we average out the 95 percentile of daily snapspots to get an average usage for the month.
  • You can calculate your usage using the du command. An example is below. The result will be double what you are billed as their is 2 copies of the data. Make sure to divide by 2.
du -h /home/a-m/username

Calculate Usage (/private_stores)[edit]

  • These are private data storage nodes. They do not get billed monthly.
  • The filesystems are XFS shared over NFS.
  • To calculate usage, use the du command
du -h /private_stores/shared/directory

Queue Costs[edit]

The cost for each job is dependent on which queue it is submitted to. Listed below are the different queues on the cluster with their cost.

Usage is charge by the second. The CPU cost and memory cost are compared and the largest is what is billed.

Queue Name CPU Cost ($ per CPU per day) Memory Cost ($ per GB per day) GPU Cost ($ per GPU per day)


normal (default) $1.19 $0.07 NA
lowmem $0.50 $0.10 NA


GPU $2.00 $0.44 $2.00

Gaining Access[edit]

Cluster Rules[edit]

  • Running jobs on the head node or login nodes are strictly prohibited. Running jobs on the head node could cause the entire cluster to crash and affect everyone's jobs on the cluster. Any program found to be running on the headnode will be stopped immediately and your account could be locked. You can start an interactive session to login to a node to manual run programs.
  • Installing Software Please email help@igb.illinois.edu for any software requests. Compiled software will be installed in /home/apps. If its a standard RedHat package (rpm), it will be installed in their default locations on the nodes.
  • Creating or Moving over Programs: Programs you create or move to the cluster should be first tested by you outside the cluster for stability. Once your program is stable, then it can be moved over to the cluster for use. Unstable programs that cause problems with the cluster can result in your account being locked. Programs should only be added by CNRG personnel and not compiled in your home directory.
  • Reserving Memory: SLURM allows the user to specify the amount of memory they want their program to use.. If your job tries to use more memory than you have reserved, the job will run out of memory and die. Make sure to specify the correct amount of memory.
  • Reserving Nodes and Processors: For each job, you must reserve the correct number of nodes and processors. By default you are reserved 1 processor on 1 node. If you are running a multiple processor job or a MPI job you need to reserve the appropriate amount. If you do not reserve the correct amount, the cluster will confine your job to that limit, increasing its runtime.

How To Log Into The Cluster[edit]

  • You will need to use an SSH client to connect.

On Windows[edit]

PUTTYbiologin.PNG

  • Hit Open and login using your IGB account credentials.

On Mac OS X[edit]

  • Simply open the terminal under Go >> Utilities >> Terminal
  • Type in ssh username@biologin.igb.illinois.edu where username is your NetID.
  • Hit the Enter key and type in your IGB password.

How To Submit A Cluster Job[edit]

Create a Job Script[edit]

  • You must first create a SLURM job script file in order to tell SLURM how and what to execute on the nodes.
  • Type the following into a text editor and save the file test.sh ( Linux text editing )
#!/bin/bash
#SBATCH -p normal
#SBATCH --mem=1g
#SBATCH -N 1
#SBATCH -n 1

sleep 20
echo "Test Script" 
  • You just created a simple SLURM Job Script.
  • To submit the script to the cluster, you will use the sbatch command.
sbatch test.sh
  • Line by line explanation
    • #!/bin/bash - tells linux this is a bash program and it should use a bash interpreter to execute it.
    • #SBATCH - are SLURM parameters, for explanations of these please scroll down to SLURM Parameters Explanations section.
    • sleep 20 - Sleep 20 seconds (only used to simulate processing time for this example)
    • echo "Test Script" - Output some text to the screen when job completes ( simulate output for this example)
  • For example if you would like to run a blast job you may simply replace the last two line with the following
module load BLAST
blastall -p blastn -d nt -i input.fasta -e 10 -o output.result -v 10 -b 5 -a 5
  • Note: the module commands are explained under the Environment Modules section.

SLURM Parameters Explanations:[edit]

Command Description
#SBATCH -p PARTITION Run the job on a specific queue/partition. This defaults to the "normal" queue
#SBATCH -D /tmp/working_dir Run the script from the /tmp/working_dir directory. This defaults to the current directory you are in.
#SBATCH -J ExampleJobName Name of the job will be ExampleJobName
#SBATCH -e /path/to/errorfile Split off the error stream to this file. By default output and error streams are placed in the same file.
#SBATCH -o /path/to/ouputfile Split off the output stream to this file. By default output and error streams are placed in the same file.
#SBATCH --mail-user username@illinois.edu Send an e-mail to specified email to receive job information.
#SBATCH --mail-type BEGIN, END, FAIL Specifies when to send a message to email. You can select multiple of these with a comma separated list. Many other options exist.
#SBATCH -N X Reserve X number of nodes.
#SBATCH -n X Reserve X number of cpus.
#SBATCH --mem=XG Reserve X gigabytes of RAM for the job.
#SBATCH --gres=gpu:X Reserve X NVIDIA GPUs. (Only on GPU queues)

Create a Job Array Script[edit]

Making a new copy of the script and then submitting each one for every input data file is time consuming. An alternative is to make a job array using the -t option in your submission script. The ---aray option allows many copies of the same script to be queued all at once. You can use the $SLURM_ARRAY_TASK_ID to differentiate between the different jobs in the array. A detailed example on how to do this is available at Job Arrays

Start An Interactive Session[edit]

  • Use the srun commsnf if you would like to run a job interactively.
srun --pty /bin/bash
  • This will automatically reserve you a slot on one of the compute nodes and will start a terminal session on it.
  • Closing your terminal window will also kill your processes running in your interactive srun session, therefore it's better to submit large jobs via non-interactive sbatch.

X11 Graphical Applications[edit]

  • To run an application with a user interface you will need to setup an Xserver on your computer Xserver Setup
  • Then add the --x11 parameter to your srun command
srun --x11 --pty /bin/bash

View/Delete Submitted Jobs[edit]

Viewing Job Status[edit]

  • To get a simple view of your current running jobs you may type:
squeue -u userid
  • This command brings up a list of your current running jobs.
  • The first number represents the job's ID number.
  • Jobs may have different status flags:
    • R = job is currently running


  • For more detailed view type:
squeue -l
  • This will return a list of all nodes, their slot availability, and your current jobs.

List Queues[edit]

  • Simple view
sinfo

This will show all queues as well as which nodes in those queues are fully used (alloc), partially used (mix), unused (idle), or unavailable (down).


List All Jobs on Cluster With Nodes[edit]

squeue

Deleting Jobs[edit]

  • Note: You can only delete jobs which are owned by you.
  • To delete a job by job-ID number:
  • You will need to use scancel, for example to delete a job with ID number 5523 you would type:
scancel 5523
  • Delete all of your jobs
scancel -u userid

Troubleshooting job errors[edit]

  • To view job errors in case job status shows Eqw or any other error in the status column use qstat -j, for example if job # 23451 failed you would type:
scontrol show job 23451

Applications[edit]

Application Lists[edit]

Application Installation[edit]

Environment Modules[edit]

  • The Biocluster uses the Lmod modules package to manage the software that is installed. You can read more about Lmod at https://lmod.readthedocs.io/en/latest/
  • To use an application, you need to use the module command to load the settings for an application
  • To load a particular environment for example QIIME/1.9.1, simply run this command:
module load QIIME/1.9.1
  • If you would like to simply load the latest version, run the the command without the /1.9.1 (version number):
module load QIIME
  • To view which environments you have loaded simply run module list:
bash-4.1$ module list
Currently Loaded Modules:
  1) BLAST/2.2.26-Linux_x86_64   2) QIIME/1.9.1
  • When submitting a job using a sbatch script you will have to add the module load qiime/1.5.0 line before running qiime in the script.
  • To unload a module simply run module unload:
module unload QIIME
  • Unload all modules
module purge

Containers[edit]

  • The Biocluster cluster supports Singularity to run containers.
  • The guide on how to use them is at Biocluster Singularity

R Packages[edit]

  • We have a local mirror of the CRAN and Bioconductor. This allows you to install packages through an interactive session into your home folder.
  • To install a package, run an interactive
srun --pty /bin/bash
  • Load the R module
module load R/3.6.0-IGB-gcc-8.2.0
  • Run R
R
  • For CRAN packages, run install.packages()
install.packages('shape');
  • For Bioconductor packages, the BiocManager package is already installed. You just need to run BiocManager::install to install a package
BiocManager::install('dada2')
  • If the package requires an external dependencies, you should email us to get it install centrally.

Mirror Service - Genomic Databases[edit]

Transferring data files[edit]

Transferring using SFTP/SCP[edit]

Using WinSCP[edit]

  • Download WinSCP installation package from http://winscp.net/eng/download.php#download2 and install it.
  • Once installed Run WinSCP >> enter biologin.igb.illinois.edu for the Host name >> Enter your IGB user name and password and click Login

Bioclustertransfer.png

  • Once you hit "Login, you should be connected to your Biocluster home folder, as shown below.

Bioclustertransfer2.png

  • From here you should be able to download or transfer your files.

Using CyberDuck[edit]

  • To download cyberduck go to http://cyberduck.c and click on the large Zip icon to download.
  • Once cyberduck is installed on OSX you may start the program.
  • Click on Open Connection.
  • From the drop down menu at the top of the opopup window select SFTP(SSH File Transfer Protocol)

Cyberduck screenshot sftp.png

  • Now in the Server: input box enter biologin.igb.illinois.edu and for Username and password enter your IGB credentials.

Cyberduckbiologin.png

  • Click Connect.
  • You may now download or transfer your files.
  • NOTICE: Cyberduck by default wants to open multiple connections for transferring files. The biocluster firewall limits you to 4 connections a minute. This can cause transfers to timeout. You can change Cyberduck to only use 1 connection by going to Preferences->Transfers->Transfer Files. Select Open Single Connection.

Transferring using Globus[edit]

  • The biocluster has a Globus endpoint setup. Then end point name is igb#biocluster.igb.illinois.edu
  • Globus allows the transferring of very large files reliably.
  • A guide on how to use Globus is here

References[edit]