Difference between revisions of "Sandbox Home"

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= Welcome to ETH High Performance Computing Cluster Wiki =
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__NOTOC__
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<table style="width: 100%;">
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=Welcome to the scientific computing wiki=
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<td style="width: 30%; background: white; text-align: left;">
 
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[[Image:NvidiaDGX1_cropped1.jpg| 420px]]
 
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<td style="width: 2%; background: white; text-align: left;>
 
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<div style="width: 100%; background: #BFE5D9; height: 35px; border-radius: 10px; padding: 5px; margin:5px">
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<table style="width: 95%; border-spacing: 20px;">
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Sandbox Accessing the clusters| 1. Accessing the clusters]]
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<td style="width: 22%; text-align: left;">
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=== Quick guide ===
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<div style="background: #BFE5D9;" class="button">
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[[Accessing the cluster| '''Accessing the cluster''']]
 
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<div style="width: 100%; background: #BFE5D9; height: 35px; border-radius: 10px; padding: 5px; margin:5px">
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[[Storage and data transfer| '''Storage and data transfer''']]
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Storage and data transfer|2. Storage and data transfer]]
 
 
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<div style="width: 100%; background: #BFE5D9; height: 35px; border-radius: 10px; padding: 5px; margin:5px">
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[[Modules and applications | '''Modules and applications''']]
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Modules and applications | 3. Modules and applications]]
 
 
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<div style="width: 100%; background: #BFE5D9; height: 35px; border-radius: 10px; padding: 5px; margin:5px">
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[[Job management with LSF| '''Job management with LSF''' ]]
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[Job management with LSF| 4. Job management with LSF ]]
 
 
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<div style="width: 100%; background: #BFE5D9; height: 35px; border-radius: 10px; padding: 5px; margin:5px">
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[[running applications| '''Examples''']]
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[running applications|5. Tutorials]]
 
 
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== [[News]] ==
 
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[[New account request process for HPC clusters|'''New account request process for Euler and Leonhard Open''']]
 
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14.01.2021
 
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We are introducing a new automated process for obtaining an account for the HPC clusters of ETH, starting with Leonhard Open and later we also implement the same process on Euler. [[New account request process for HPC clusters|Read more...]]
 
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[[Upcoming Euler VII expansion|'''Upcoming Euler VII expansion''']]
 
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14.04.2020
 
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The next major expansion of the Euler cluster — Euler VII — will be based on the same kind of compute nodes as Euler VI
 
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[[Upcoming Euler VII expansion|Read more...]]
 
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[[COVID-19|'''COVID-19 — Cluster operation during state of emergency at ETH''']]
 
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17.03.2020
 
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As announced by President Joël Mesot in the evening of March 16 (see email), ETH will be operating in a state of emergency starting today. Most employees are required to work from home. [[COVID-19|Read more...]]
 
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[[Jupyter on Euler and Leonhard Open|'''Script to run a Jupyter notebook interactively in a batch job on Euler or Leonhard Open''']]
 
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27.09.2019
 
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Since Jupyter notebooks are becoming more widely used among the scientific community, the HPC group developed a script that you can run on your local computer. This shell script then starts a Jupyter notebook in a batch job on Euler/Leonhard Open (depending on which cluster you choose) and connects your local browser with it. [[Jupyter on Euler and Leonhard Open|Read more...]]
 
  
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=== Helpers and support ===
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<div style="background: #b2d9eac8;" class="button">
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[https://scicomp.ethz.ch/lsf_submission_line_advisor/ '''LSF Submission Line Advisor''']
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</div>
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<div style="background: #b2d9eac8;" class="button">
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[[FAQ|'''FAQ''']]
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</div>
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<div style="background: #b2d9eac8;" class="button">
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[[Euler_applications_and_libraries|'''Applications overview''']]
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<div style="background: #b2d9eac8;" class="button">
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[http://smartdesk.ethz.ch '''Smartdesk''']
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<div style="background: #b2d9eac8;" class="button">
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[mailto:cluster-support@id.ethz.ch '''Cluster support''']
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</div>
 
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<td style="width: 42%;" valign="middle" >[[Image:NvidiaDGX1_cropped1.jpg| 500px]]</td>
 
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== Clusters & Servers ==
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==News==
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{|class="wikitable" style="text-align: center; width: 45%;"
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{{:News}}
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! style="width:20%;"|[[Euler|Euler]]
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[[News|''More...'']]
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! style="width:20%;"|[[Leonhard|Leonhard Open]]
 
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! style="width:20%;"|[[Leonhard|Leonhard Med]]
 
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! style="width:20%;"|[[MATLAB_distributed_computing_server|MATLAB server]]
 
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! style="width:20%;"|[[CLC_genomics_server|CLC genomics server]]
 
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|-
 
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|<include nopre wikitext src="/cluster/wiki/auto/service_status/euler_status"/>
 
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|<include nopre wikitext src="/cluster/wiki/auto/service_status/leonhard_open_status"/>
 
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|<include nopre wikitext src="/cluster/wiki/auto/service_status/leonhard_med_status"/>
 
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|<include nopre wikitext src="/cluster/wiki/auto/service_status/calculus_status"/>
 
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|<include nopre wikitext src="/cluster/wiki/auto/service_status/clc_status"/>
 
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|}
 
  
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{|
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==Most recent software installations==
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| '''Green'''
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Twenty most recent software installation on each cluster. The list is based on the last modification time of the module files.
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|:  
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{| style="width: 100%; text-align:left;"
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|Service is '''fully operational'''
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! style="width: 50%"|Euler ('''new software stack''', [[Euler_applications_and_libraries|see complete list]]):
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|-
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! style="width: 50%"|
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|'''Orange'''
 
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|:  
 
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|Service is '''partially operational''' or still in '''beta testing phase'''
 
 
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|'''Red'''
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|<include nopre wikitext src="/cluster/wiki/auto/spack_module_tables/recent/euler" />
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|:
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|<include nopre wikitext src="/cluster/wiki/auto/spack_module_tables/recent/euler2" />
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|Service is '''unavailable'''
 
 
|}
 
|}
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<include nopre wikitext src="/cluster/wiki/auto/spack_module_tables/recent/etimestamp" />

Latest revision as of 07:11, 19 April 2022

Welcome to the scientific computing wiki

Quick guide

Accessing the cluster

Storage and data transfer

Modules and applications

Job management with LSF

Examples

Helpers and support

LSF Submission Line Advisor

FAQ

Applications overview

Smartdesk

Cluster support

NvidiaDGX1 cropped1.jpg

News

More...

Most recent software installations

Twenty most recent software installation on each cluster. The list is based on the last modification time of the module files.

Euler (new software stack, see complete list):
matlab/R2022a (Core)
spaceranger/2.0.0 (Core)
rosetta/3.13 (gcc 8.2.0, openmpi 4.1.4)
nextflow/22.04.4 (gcc 8.2.0)
nextflow/22.04.4 (gcc 6.3.0)
nextflow/22.04.4 (gcc 4.8.5)
nextflow/22.04.4 (intel 19.1.0)
virify/0.4.0 (Core)
atacprimertool/1.0 (gcc 4.8.5)
cudnn/8.4.0.27 (intel 19.1.0)
cudnn/8.4.0.27 (gcc 8.2.0)
cudnn/8.4.0.27 (gcc 6.3.0)
cudnn/8.4.0.27 (gcc 4.8.5)
kneaddata/0.10 (gcc 6.3.0)
kneaddata/0.10 (gcc 4.8.5)
trimmomatic/0.33 (gcc 8.2.0)
trimmomatic/0.33 (gcc 6.3.0)
trimmomatic/0.33 (gcc 4.8.5)
checkm/1.1.2 (gcc 6.3.0)
checkm/1.1.2 (gcc 4.8.5)

trf/4.09.1 (Core)
trimgalore/0.6.6 (intel 19.1.0)
trimgalore/0.6.6 (gcc 8.2.0)
trimgalore/0.6.6 (gcc 6.3.0)
trimgalore/0.6.6 (gcc 4.8.5)
hmmer/3.3.2 (intel 19.1.0, openmpi 4.1.4)
hmmer/3.3.2 (gcc 8.2.0, openmpi 4.1.4)
hmmer/3.3.2 (gcc 6.3.0, openmpi 4.1.4)
hmmer/3.3.2 (gcc 4.8.5, openmpi 4.1.4)
spectra/1.0.1 (intel 19.1.0)
spectra/1.0.1 (gcc 9.3.0)
spectra/1.0.1 (gcc 8.2.0)
spectra/1.0.1 (gcc 6.3.0)
spectra/1.0.1 (gcc 4.8.5)
adf/2022.103 (Core)
adf/2021.102 (Core)
blast-plus/2.12.0 (gcc 8.2.0)
blast-plus/2.12.0 (gcc 6.3.0)
freetype/2.11.1 (intel 19.1.0)
freetype/2.11.1 (gcc 8.2.0)

List of recently installed software has been updated on Thu Aug 11 16:24:34 CEST 2022

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