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scripts/motd.sh 0 → 100755
View file @ eab09266
#!/bin/bash
### MOTD and Downtime history
# autor: kru0052
# 2016 IT4Innovations
# version 1.0
###
printf "update"
wget -q http://www.it4i.cz/support/?lang=en
printf " ... OK\n"
i="index.html?lang=en"
HEAD=$(grep -n -m1 'class="matrix light-grey' "$i" |cut -f1 -d: | tr --delete '\n')
END=$(grep -n -m1 '<h3>Other</h3>' "$i" |cut -f1 -d: | tr --delete '\n')
LAST=$(wc -l "$i" | cut -f1 -d' ')
DOWN=$((LAST-END+2))
sed '1,'"$((HEAD-1))"'d' "$i" | sed -n -e :a -e '1,'"$DOWN"'!{P;N;D;};N;ba' | sed '/<div/d' > "TMP.html"
rm "/srv/downtime/$i"
title="Message of the day"
head=$(cat TMP.html | grep "rss-item-title" | cut -d ">" -f 2 | cut -d "<" -f 1)
date=$(cat TMP.html | grep "<i>" | cut -d ">" -f 2 | cut -d "<" -f 1 | cut -d " " -f 1)
info=$(cat TMP.html | grep "<p>" | cut -d ">" -f 2 | cut -d "<" -f 1)
rm /srv/downtime/TMP.html
echo ""
echo "$title"
echo "$date - $head"
echo "$info"
echo ""
# poovolene stavy - Salomon Maintenance, Anselm Maintenance, Back in Production, Infrastructure Maintenance, PBS Maintenance, SCRATCH Maintenance, HOME Maintenance, Salomon and Anselm Maintenance
if [ "$head" = "Salomon Maintenance" ] || [ "$head" = "Anselm Maintenance" ] || [ "$head" = "Back in Production" ] || [ "$head" = "Infrastructure Maintenance" ] || [ "$head" = "PBS Maintenance" ] || [ "$head" = "SCRATCH Maintenance" ] || [ "$head" = "HOME Maintenance" ] || [ "$head" = "Salomon and Anselm Maintenance" ]; then
dateDown=$(cat /srv/downtime/docs/index.md | sed -n '/---/{n;p;}' | cut -d "|" -f 2 | cut -d " " -f 1)
headDown=$(cat /srv/downtime/docs/index.md | sed -n '/---/{n;p;}' | cut -d "|" -f 3 | cut -d "*" -f 3)
echo "$date - $dateDown"
if [ "$date" = "$dateDown" ] && [ "$head" = "$headDown" ]; then
echo "Everything up-to-date..."
else
echo "Updating Downtime History..."
test=" |$date 00:00:00|**$head** $info|"
sed '/---/a '"$test"'' /srv/downtime/docs/index.md > /srv/downtime/TMP.md
cat /srv/downtime/TMP.md > /srv/downtime/docs/index.md
# rm /srv/downtime/TMP.md
fi
# echo "### $title" > docs/index.md
# echo "**$head**" >> docs/index.md
# echo "$date - $info" >> docs/index.md
else
echo "Downtime History not updated..."
fi
echo "# $title" > docs/motd.md
echo "**$head**" >> docs/motd.md
echo "$date - $info" >> docs/motd.md
time=$(date)
sed '$d' /srv/downtime/docs/index.md > /srv/downtime/TMP.md
cat /srv/downtime/TMP.md > /srv/downtime/docs/index.md
rm /srv/downtime/TMP.md
echo "updating $time" >> /srv/downtime/docs/index.md
scripts/source/formatting 0 → 100644
View file @ eab09266
[]()&
**[]()&**
- - &
.[]()&.
<!-- -->&
### []()[]()&###
### []()&###
### **&###
### class="n">&###
### Gnome on Windows**&### Gnome on Windows
### Notes **&### Notes
**Summary&**Summary**
Tape Library T950B**&**Tape Library T950B**
****The R version 3.0.1 is available on Anselm, along with GUI interface&**The R version 3.0.1 is available on Anselm, along with GUI interface
^&
Input:** FASTQ file.&Input: FASTQ file.
Output:** FASTQ file plus an HTML file containing statistics on the&Output: FASTQ file plus an HTML file containing statistics on the
*Figure 2.****** FASTQ file.***&*Figure 2.**FASTQ file.**
Component:** Hpg-aligner.****&Component:** Hpg-aligner.**
Input:** VCF&Input:** VCF**
the corresponding QC and functional annotations.&the corresponding QC and functional annotations.**
Core features:**&**Core features:**
Regulatory:**&**Regulatory:**
Functional annotation**&**Functional annotation**
Variation**&**Variation**
Systems biology**&**Systems biology**
[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.&**[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
Workaround:**&**Workaround:**
-g** : Generates extra debugging information usable by GDB. -g3&-g** : Generates extra debugging information usable by GDB. -g3**
-O0** : Suppress all optimizations.&-O0** : Suppress all optimizations.**
nodes.****&nodes.
###Compute Nodes Without Accelerator**&###Compute Nodes Without Accelerator
###Compute Nodes With MIC Accelerator**&###Compute Nodes With MIC Accelerator
###Compute Nodes With GPU Accelerator**&###Compute Nodes With GPU Accelerator
###Fat Compute Nodes**&###Fat Compute Nodes
**Figure Anselm bullx B510 servers****&**Figure Anselm bullx B510 servers**
### Compute Nodes Summary********&### Compute Nodes Summary
<p><a href="x-window-system/cygwin-and-x11-forwarding.html" If no able to forward X11 using PuTTY to CygwinX</a>&[If no able to forward X11 using PuTTY to CygwinX](x-window-system/cygwin-and-x11-forwarding.html)
<p><a href="http://x.cygwin.com/" Install Cygwin</a>&[Install Cygwin](http://x.cygwin.com/)
Component:**> Hpg-Fastq & FastQC&Component:**> Hpg-Fastq & FastQC**
Input:** BAM file.&Input:** BAM file.**
Output:** BAM file plus an HTML file containing statistics. &Output:** BAM file plus an HTML file containing statistics.**
Component:** GATK.&Component:** GATK.**
Input:** BAM&Input:** BAM**
Output:** VCF&Output:** VCF**
Variant Call Format (VCF)**&**Variant Call Format (VCF)**
</span></span>&
/ansys_inc/shared_les/licensing/lic_admin/anslic_admin&/ansys_inc/shared_les/licensing/lic_admin/anslic_admin
<td align="left">& |
However, users need only manage User and CA certificates. Note that your&**However, users need only manage User and CA certificates. Note that your
X.509 PKI certificates for communication with us.&X.509 PKI certificates for communication with us.**
PuTTYgen**&**PuTTYgen**
key](../ssh-keys.html) file if Pageant ****SSH&key](../ssh-keys.html) file if Pageant **SSH
authentication agent is not used.&authentication agent is not used.**
scripts/source/lastFilter 0 → 100644
View file @ eab09266
>key.&key.
</span>&
`.ssh`&`.ssh` directory: 700 (drwx------)
Authorized_keys,&Authorized_keys, known_hosts and public key (`.pub` file): `644 (-rw-r--r--)`
Private key&Private key (`id_rsa/id_rsa.ppk` ): `600 (-rw-------)`
(gnome-session:23691): WARNING **: Cannot open display:& (gnome-session:23691): WARNING **: Cannot open display:**
![XWin-listen-tcp.png](XWinlistentcp.png "XWin-listen-tcp.png")&![XWin-listen-tcp.png](XWinlistentcp.png "XWin-listen-tcp.png")
![](cygwinX11forwarding.png)&![](cygwinX11forwarding.png)
Search for the localhost and port number (in this case&**Search for the localhost and port number (in this case
Preferences](gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)&![](gdmscreensaver.png)
maximum performance**&maximum performance
Better performance** is obtained by logging on the allocated compute&**Better performance** is obtained by logging on the allocated compute
class="discreet">&
id="result_box"&
class="hps alt-edited">stated &stated in the previous example.
Water-cooled Compute Nodes With MIC Accelerator**&**Water-cooled Compute Nodes With MIC Accelerator**
Access from PRACE network:**&**Access from PRACE network:**
Access from public Internet:**&**Access from public Internet:**
Access from PRACE network:**&**Access from PRACE network:**
Access from public Internet:**&**Access from public Internet:**
>VPN client installation&VPN client installation
Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)&![](vpn_web_install_2.png)
[![ Salomon IB&
topology](https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png/@@images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png " Salomon IB topology")](Salomon_IB_topology.png)&![](Salomon_IB_topology.png)
###IB single-plane topology - ICEX Mcell**&###IB single-plane topology - ICEX Mcell
As shown in a diagram [IB&As shown in a diagram ![IB
- - &
{.state-missing-value&
.contenttype-file}&
- **qprod**, the Production queue****&- **qprod**, the Production queue
HTML commented section #1 (removed Capacity computing section, this&
will be optimized for Salomon)&
pri>>ority.&priority.
>>Eligible time can be seen as eligible_time attribute of&Eligible time can be seen as eligible_time attribute of
HTML commented section #3 (Capacity computing need to be reworked)&
<col width="12%" />&
<th align="left">& |
### Notes**&### Notes
HOME](storage.html#home)&
and [ &
SCRATCH](storage.html#shared-filesystems).&
There are two main shared file systems on Salomon cluster, the [&There are two main shared file systems on Salomon cluster, the [HOME](storage.html#home)and [SCRATCH](storage.html#shared-filesystems).
>Disk usage and quota commands&Disk usage and quota commands
>OpenCL&### OpenCL
Execution on host**&**Execution on host**
Execution on host - MPI processes distributed over multiple&**Execution on host - MPI processes distributed over multiple
Host only node-file:**&**Host only node-file:**
MIC only node-file**:&MIC only node-file:
Host and MIC node-file**:&Host and MIC node-file:
interface Rstudio&interface Rstudio**
### >&###
3. >>&3. >
- >>&- >
>Usage with MPI&Usage with MPI
>>&>
id="result_box"> &
<span&
>Introduction&Introduction
>Options&Options
***[ANSYS&**[ANSYS
Channel partner](http://www.ansys.com/)***&Channel partner](http://www.ansys.com/)**
Multiphysics)-**Commercial.**&Multiphysics)-**Commercial.
>1. Common way to run Fluent over pbs file&1. Common way to run Fluent over pbs file
>2. Fast way to run Fluent from command line&2. Fast way to run Fluent from command line
**Academic**&**Academic
***&**
id="result_box"&
</span>&
[![Fluent_Licence_2.jpg](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_2.jpg/@@images/73f37ed4-3bd3-4dbd-818e-4f8d9ecd7524.jpeg "Fluent_Licence_2.jpg")](Fluent_Licence_2.jpg)&![](Fluent_Licence_2.jpg)
Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS&**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
scripts/source/list_folder 0 → 100644
View file @ eab09266
anselm-cluster-documentation
anselm-cluster-documentation/accessing-the-cluster
anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access
anselm-cluster-documentation/resource-allocation-and-job-execution
anselm-cluster-documentation/software
anselm-cluster-documentation/software/ansys
anselm-cluster-documentation/software/chemistry
anselm-cluster-documentation/software/comsol
anselm-cluster-documentation/software/debuggers
anselm-cluster-documentation/software/intel-suite
anselm-cluster-documentation/software/mpi-1
anselm-cluster-documentation/software/numerical-languages
anselm-cluster-documentation/software/numerical-libraries
anselm-cluster-documentation/software/omics-master-1
anselm-cluster-documentation/storage-1
get-started-with-it4innovations
get-started-with-it4innovations/accessing-the-clusters
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer
get-started-with-it4innovations/obtaining-login-credentials
salomon
salomon/accessing-the-cluster
salomon/hardware-overview-1
salomon/network-1
salomon/resource-allocation-and-job-execution
salomon/software
salomon/software/ansys
salomon/software/chemistry
salomon/software/comsol
salomon/software/debuggers
salomon/software/intel-suite
salomon/software/mpi-1
salomon/software/numerical-languages
salomon/storage
scripts/source/list_image_mv 0 → 100644
View file @ eab09266
anselm-cluster-documentation/software/omics-master-1/fig2.png
anselm-cluster-documentation/software/omics-master-1/fig5.png
anselm-cluster-documentation/software/omics-master-1/fig6.png
anselm-cluster-documentation/software/omics-master-1/fig3.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/TightVNC_login.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/putty-tunnel.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-terminal.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmscreensaver.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-compute-nodes-over-vnc.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmdisablescreensaver.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwinX11forwarding.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/XWinlistentcp.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_004V.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_003V.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PageantV.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_001V.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_host_Salomon.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_keyV.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_005V.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_save_Salomon.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygeneratorV.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_open_Salomon.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_002V.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_006V.png
salomon/accessing-the-cluster/copy_of_vpn_web_install_3.png
salomon/accessing-the-cluster/vpn_contacting.png
salomon/resource-allocation-and-job-execution/rswebsalomon.png
salomon/accessing-the-cluster/vpn_successfull_connection.png
salomon/accessing-the-cluster/vpn_web_install_2.png
salomon/accessing-the-cluster/vpn_web_login_2.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome_screen.png
salomon/network-1/IBsingleplanetopologyAcceleratednodessmall.png
salomon/network-1/IBsingleplanetopologyICEXMcellsmall.png
salomon/network-1/Salomon_IB_topology.png
salomon/network-1/7D_Enhanced_hypercube.png
salomon/accessing-the-cluster/vpn_web_login.png
salomon/accessing-the-cluster/vpn_login.png
salomon/software/debuggers/totalview2.png
salomon/software/debuggers/Snmekobrazovky20160211v14.27.45.png
salomon/software/debuggers/ddt1.png
salomon/software/debuggers/totalview1.png
salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png
salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png
salomon/software/ansys/AMsetPar1.png
salomon/accessing-the-cluster/vpn_contacting_https_cluster.png
salomon/accessing-the-cluster/vpn_web_download.png
salomon/accessing-the-cluster/vpn_web_download_2.png
salomon/accessing-the-cluster/vpn_contacting_https.png
salomon/accessing-the-cluster/vpn_web_install_4.png
anselm-cluster-documentation/software/omics-master-1/fig7.png
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vncviewer.png
salomon/resource-allocation-and-job-execution/job_sort_formula.png
salomon/resource-allocation-and-job-execution/fairshare_formula.png
anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png
anselm-cluster-documentation/quality2.png
anselm-cluster-documentation/turbovncclientsetting.png
get-started-with-it4innovations/obtaining-login-credentials/Authorization_chain.png
anselm-cluster-documentation/scheme.png
anselm-cluster-documentation/quality3.png
anselm-cluster-documentation/legend.png
anselm-cluster-documentation/bullxB510.png
salomon/software/debuggers/vtune-amplifier.png
anselm-cluster-documentation/software/debuggers/totalview2.png
anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png
anselm-cluster-documentation/software/debuggers/ddt1.png
anselm-cluster-documentation/software/debuggers/totalview1.png
anselm-cluster-documentation/software/numerical-languages/Matlab.png
anselm-cluster-documentation/quality1.png
anselm-cluster-documentation/software/omics-master-1/fig1.png
anselm-cluster-documentation/software/omics-master-1/fig8.png
salomon/software/debuggers/report.png
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpnuiV.png
anselm-cluster-documentation/software/omics-master-1/fig4.png
anselm-cluster-documentation/software/omics-master-1/fig7x.png
anselm-cluster-documentation/software/omics-master-1/fig9.png
salomon/software/ansys/Fluent_Licence_2.jpg
salomon/software/ansys/Fluent_Licence_4.jpg
salomon/software/ansys/Fluent_Licence_1.jpg
salomon/software/ansys/Fluent_Licence_3.jpg
anselm-cluster-documentation/accessing-the-cluster/Anselmprofile.jpg
anselm-cluster-documentation/accessing-the-cluster/anyconnecticon.jpg
anselm-cluster-documentation/accessing-the-cluster/anyconnectcontextmenu.jpg
anselm-cluster-documentation/accessing-the-cluster/logingui.jpg
anselm-cluster-documentation/software/ansys/Fluent_Licence_2.jpg
anselm-cluster-documentation/software/ansys/Fluent_Licence_4.jpg
anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg
anselm-cluster-documentation/software/ansys/Fluent_Licence_3.jpg
anselm-cluster-documentation/accessing-the-cluster/firstrun.jpg
anselm-cluster-documentation/accessing-the-cluster/successfullconnection.jpg
salomon/sgi-c1104-gp1.jpeg
salomon/salomon-1.jpeg
salomon/hardware-overview-1/uv-2000.jpeg
salomon/salomon-3.jpeg
salomon/salomon-4.jpeg
anselm-cluster-documentation/accessing-the-cluster/loginwithprofile.jpeg
anselm-cluster-documentation/accessing-the-cluster/instalationfile.jpeg
anselm-cluster-documentation/accessing-the-cluster/successfullinstalation.jpeg
anselm-cluster-documentation/accessing-the-cluster/java_detection.jpeg
anselm-cluster-documentation/accessing-the-cluster/executionaccess.jpeg
anselm-cluster-documentation/accessing-the-cluster/downloadfilesuccessfull.jpeg
anselm-cluster-documentation/accessing-the-cluster/executionaccess2.jpeg
anselm-cluster-documentation/accessing-the-cluster/login.jpeg
scripts/source/list_md_mv 0 → 100644
View file @ eab09266
get-started-with-it4innovations/accessing-the-clusters/introduction.md
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
get-started-with-it4innovations/applying-for-resources.md
salomon/introduction.md
salomon/resource-allocation-and-job-execution/introduction.md
salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
salomon/resource-allocation-and-job-execution/capacity-computing.md
salomon/resource-allocation-and-job-execution/job-priority.md
salomon/prace.md
salomon/environment-and-modules.md
salomon/network-1/7d-enhanced-hypercube.md
salomon/network-1/ib-single-plane-topology.md
salomon/network-1/network.md
salomon/accessing-the-cluster/outgoing-connections.md
salomon/accessing-the-cluster/vpn-access.md
salomon/software/debuggers/intel-vtune-amplifier.md
salomon/software/debuggers/summary.md
salomon/software/debuggers/allinea-performance-reports.md
salomon/software/debuggers/valgrind.md
salomon/software/debuggers/allinea-ddt.md
salomon/software/debuggers/aislinn.md
salomon/software/debuggers/vampir.md
salomon/software/debuggers/total-view.md
salomon/software/numerical-languages/introduction.md
salomon/software/numerical-languages/octave.md
salomon/software/numerical-languages/matlab.md
salomon/software/numerical-languages/r.md
salomon/software/operating-system.md
salomon/software/mpi-1/mpi.md
salomon/software/mpi-1/mpi4py-mpi-for-python.md
salomon/software/mpi-1/Running_OpenMPI.md
salomon/software/intel-xeon-phi.md
salomon/software/chemistry/phono3py.md
salomon/software/chemistry/molpro.md
salomon/software/chemistry/nwchem.md
salomon/software/ansys/ansys.md
salomon/software/compilers.md
salomon/software/intel-suite/intel-compilers.md
salomon/software/intel-suite/intel-inspector.md
salomon/software/intel-suite/intel-integrated-performance-primitives.md
salomon/software/intel-suite/intel-advisor.md
salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
salomon/software/intel-suite/intel-mkl.md
salomon/software/intel-suite/intel-parallel-studio-introduction.md
salomon/software/intel-suite/intel-tbb.md
salomon/software/intel-suite/intel-debugger.md
salomon/software/debuggers.md
salomon/software/java.md
salomon/software/comsol/comsol-multiphysics.md
salomon/software/comsol/licensing-and-available-versions.md
salomon/software/ansys/ansys-mechanical-apdl.md
salomon/software/ansys/setting-license-preferences.md
salomon/software/ansys/workbench.md
salomon/software/ansys/licensing.md
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[![PuttyKeygenerator_006](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_006V.png/@@images/de851079-6ed4-440a-b270-77dd6a0a950c.png "PuttyKeygenerator_006")](PuttyKeygenerator_006V.png)&![](PuttyKeygenerator_006V.png)
[![VPN&
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Install](https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png "VPN Install")](../vpn_web_login_2.png)&![](vpn_web_login_2.png)
Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)[![VPN&![](vpn_web_install_2.png)
Install](https://docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png/@@images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png "VPN Install")](../copy_of_vpn_web_install_3.png)&![](copy_of_vpn_web_install_3.png)
Install](https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png "VPN Install")](../vpn_web_install_4.png)&![](vpn_web_install_4.png)
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![Icon](https://docs.it4i.cz/anselm-cluster-documentation/icon.jpg/@@images/56ee3417-80b8-4988-b9d5-8cda3f894963.jpeg "Icon")&
[![VPN Contacting&
Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png/@@images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png "VPN Contacting Cluster")](../vpn_contacting_https_cluster.png)&![](vpn_contacting_https_cluster.png)
Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png "VPN Contacting Cluster")](../vpn_contacting_https.png)&![](vpn_contacting_https.png)
[![Successfull&
connection](https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpeg "Successfull connection")](../../anselm-cluster-documentation/anyconnecticon.jpg)&![](anyconnecticon.jpg)
[![Context&
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[![VPN Contacting&
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[![Salomon](https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg "Salomon")](../salomon-2)&![Salomon](../salomon-2)&![](salomon-2)
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[![Mcell](ib-single-plane-topology/IBsingleplanetopologyICEXMcellsmall.png "Mcell")](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)&![](IBsingleplanetopologyICEXMcellsmall.png)
[![Accelerated&
nodes](ib-single-plane-topology/IBsingleplanetopologyAcceleratednodessmall.png "Accelerated nodes")](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)&![](IBsingleplanetopologyAcceleratednodessmall.png)
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[![Fluent_Licence_3.jpg](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_3.jpg/@@images/5f65d83b-44e3-419c-96d2-8a4419227b1e.jpeg "Fluent_Licence_3.jpg")](Fluent_Licence_3.jpg)&![](Fluent_Licence_3.jpg)
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![Part of report.html](http://verif.cs.vsb.cz/aislinn/doc/report.png)&![](report.png)
[![](ddt1.png){.image-inline width="451"&![](ddt1.png)
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![Allinea Reverse&
Connect](Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")&![](Snmekobrazovky20160211v14.27.45.png)
[![screenshot](https://docs.it4i.cz/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png "VTune Amplifier")](vtune-amplifier)&![](vtune-amplifier.png)
[![](https://docs.it4i.cz/salomon/software/debuggers/totalview1.png/@@images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png)](totalview1.png)&![](totalview1.png)
[![](totalview2.png)](totalview2.png)&![](TightVNC_login.png)
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![Intel Trace&
Analyzer](Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png "Intel Trace Analyzer")&![](Snmekobrazovky20151204v15.35.12.png)
![The Authorization chain for access and utilization of computational&
resources on&
Anselm](../../anselm-cluster-documentation/Authorization_chain.png "Authorization chain")&![](Authorization_chain.png)
screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&![](gdmdisablescreensaver.png)
[![gnome-terminal.png](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/b44f5d8c-156d-4041-9bb0-973996413834.png "gnome-terminal.png")](gnome-terminal.png)&![](gnome-terminal.png)
[![gnome-compute-nodes-over-vnc.png](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png/@@images/d4c9b6b6-6e2c-48c0-84dd-26d291517355.png "gnome-compute-nodes-over-vnc.png")](gnome-compute-nodes-over-vnc.png)&![](gnome-compute-nodes-over-vnc.png)
![screenshot](vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png "VTune Amplifier")&![screenshot](vtune-amplifier.png)
genomic coordinates.](fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png)
out.](images/fig1.png "Fig 1")&out.](fig1.png)
operation.](fig3.png "fig3.png")&operation.](fig3.png)
starts.](images/fig7.png "fig7.png")&starts.](fig7.png)
H).](images/fig7x.png "fig7x.png")&H).](fig7x.png)
](images/fig8.png "fig8.png")*&](fig8.png)*
tumor.](images/fig9.png "fig9.png")**&tumor.](fig9.png)
increases.](fig5.png.1 "fig5.png")&increases.](fig5.png)
scripts/source/replace 0 → 100644
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<span><span>Introduction&###Introduction
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compute nodes number of workers start-up time[s]&|compute nodes|number of workers|start-up time[s]|
--------------- ------------------- --------------------&|---|---|---|
16 384 831&|16|384|831|
8 192 807&|8|192|807|
4 96 483&|4|96|483|
2 48 16&|2|48|16|
Node type Count Range Memory Cores [Access](resource-allocation-and-job-execution/resources-allocation-policy.html)&|Node type|Count|Range|Memory|Cores|[Access](resource-allocation-and-job-execution/resources-allocation-policy.html)|
---------------------------- ------- --------------- -------- ------------- --------------------------------------------------------------------------------------------------&|---|---|---|---|---|---|
Nodes without accelerator 180 cn[1-180] 64GB 16 @ 2.4Ghz qexp, qprod, qlong, qfree&|Nodes without accelerator|180|cn[1-180]|64GB|16 @ 2.4Ghz|qexp, qprod, qlong, qfree|
Nodes with GPU accelerator 23 cn[181-203] 96GB 16 @ 2.3Ghz qgpu, qprod&|Nodes with GPU accelerator|23|cn[181-203]|96GB|16 @ 2.3Ghz|qgpu, qprod|
Nodes with MIC accelerator 4 cn[204-207] 96GB 16 @ 2.3GHz qmic, qprod&|Nodes with MIC accelerator|4|cn[204-207]|96GB|16 @ 2.3GHz|qmic, qprod|
Fat compute nodes 2 cn[208-209] 512GB 16 @ 2.4GHz qfat, qprod&|Fat compute nodes|2|cn[208-209]|512GB|16 @ 2.4GHz|qfat, qprod|
Node Processor Memory Accelerator&|Node|Processor|Memory|Accelerator|
------------------ --------------------------------------- -------- ----------------------&|---|---|---|---|
w/o accelerator 2x Intel Sandy Bridge E5-2665, 2.4GHz 64GB -&|w/o accelerator|2x Intel Sandy Bridge E5-2665, 2.4GHz|64GB|-|
GPU accelerated 2x Intel Sandy Bridge E5-2470, 2.3GHz 96GB NVIDIA Kepler K20&|GPU accelerated|2x Intel Sandy Bridge E5-2470, 2.3GHz|96GB|NVIDIA Kepler K20|
MIC accelerated 2x Intel Sandy Bridge E5-2470, 2.3GHz 96GB Intel Xeon Phi P5110&|MIC accelerated|2x Intel Sandy Bridge E5-2470, 2.3GHz|96GB|Intel Xeon Phi P5110|
Fat compute node 2x Intel Sandy Bridge E5-2665, 2.4GHz 512GB -&|Fat compute node|2x Intel Sandy Bridge E5-2665, 2.4GHz|512GB|-|
Login address Port Protocol Login node&|Login address|Port|Protocol|Login node|
------------------------ ------ ---------- -----------------------------------------&|---|---|---|---|
salomon.it4i.cz 22 ssh round-robin DNS record for login[1-4]&|salomon.it4i.cz|22|ssh|round-robin DNS record for login[1-4]|
login1.salomon.it4i.cz 22 ssh login1&|login1.salomon.it4i.cz|22|ssh|login1|
login2.salomon.it4i.cz 22 ssh login2&|login1.salomon.it4i.cz|22|ssh|login1|
login3.salomon.it4i.cz 22 ssh login3&|login1.salomon.it4i.cz|22|ssh|login1|
login4.salomon.it4i.cz 22 ssh login4&|login1.salomon.it4i.cz|22|ssh|login1|
Toolchain Module(s)&|Toolchain|Module(s)|
-------------------- ------------------------------------------------&|---|----|
GCC GCC&|GCC|GCC|
ictce icc, ifort, imkl, impi&|ictce|icc, ifort, imkl, impi|
intel GCC, icc, ifort, imkl, impi&|intel|GCC, icc, ifort, imkl, impi|
gompi GCC, OpenMPI&|gompi|GCC, OpenMPI|
goolf BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK&|goolf|BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK|
>iompi OpenMPI, icc, ifort&|iompi|OpenMPI, icc, ifort|
iccifort icc, ifort&|iccifort|icc, ifort|
Login address Port Protocol Login node& |Login address|Port|Protocol|Login node|
------------------------------ ------ ---------- ----------------------------------& |---|---|
salomon-prace.it4i.cz 2222 gsissh login1, login2, login3 or login4& |salomon-prace.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
login1-prace.salomon.it4i.cz 2222 gsissh login1& |login1-prace.salomon.it4i.cz|2222|gsissh|login1|
login2-prace.salomon.it4i.cz 2222 gsissh login2& |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
login3-prace.salomon.it4i.cz 2222 gsissh login3& |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
login4-prace.salomon.it4i.cz 2222 gsissh login4& |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
|Login address|Port|Protocol|Login node|& |Login address|Port|Protocol|Login node|
------------------------ ------ ---------- ----------------------------------& |---|---|
salomon.it4i.cz 2222 gsissh login1, login2, login3 or login4& |salomon.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
login1.salomon.it4i.cz 2222 gsissh login1& |login1.salomon.it4i.cz|2222|gsissh|login1|
login2.salomon.it4i.cz 2222 gsissh login2& |login2-prace.salomon.it4i.cz|2222|gsissh|login2|
login3.salomon.it4i.cz 2222 gsissh login3& |login3-prace.salomon.it4i.cz|2222|gsissh|login3|
login4.salomon.it4i.cz 2222 gsissh login4& |login4-prace.salomon.it4i.cz|2222|gsissh|login4|
Login address Port Node role& |Login address|Port|Node role|
------------------------------- ------ -----------------------------& |---|---|
gridftp-prace.salomon.it4i.cz 2812 Front end /control server& |gridftp-prace.salomon.it4i.cz|2812|Front end /control server|
lgw1-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw1-prace.salomon.it4i.cz|2813|Backend / data mover server|
lgw2-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw2-prace.salomon.it4i.cz|2813|Backend / data mover server|
lgw3-prace.salomon.it4i.cz 2813 Backend / data mover server& |lgw3-prace.salomon.it4i.cz|2813|Backend / data mover server|
Login address Port Node role& |Login address|Port|Node role|
------------------------- ------ -----------------------------& |---|---|
gridftp.salomon.it4i.cz 2812 Front end /control server& |gridftp.salomon.it4i.cz|2812|Front end /control server|
lgw1.salomon.it4i.cz 2813 Backend / data mover server& |lgw1.salomon.it4i.cz|2813|Backend / data mover server|
lgw2.salomon.it4i.cz 2813 Backend / data mover server& |lgw2.salomon.it4i.cz|2813|Backend / data mover server|
lgw3.salomon.it4i.cz 2813 Backend / data mover server& |lgw3.salomon.it4i.cz|2813|Backend / data mover server|
File system mount point Filesystem Comment& |File system mount point|Filesystem|Comment|
------------------------- ------------ ----------------------------------------------------------------& |---|---|
/home Lustre Default HOME directories of users in format /home/prace/login/& |/home|Lustre|Default HOME directories of users in format /home/prace/login/|
/scratch Lustre Shared SCRATCH mounted on the whole cluster& |/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
Data type Default path& |Data type|Default path|
------------------------------ ---------------------------------& |---|---|
large project files /scratch/work/user/prace/login/& |large project files|/scratch/work/user/prace/login/|
large scratch/temporary data /scratch/temp/& |large scratch/temporary data|/scratch/temp/|
---------------------------------------------------------------------------------------------------------------------------------------------&
queue Active project Project resources Nodes priority authorization walltime&|queue|Active project|Project resources|Nodes|priority|authorization|walltime default/max|
default/max&
--------------------- -|---|---|---|--------------------- ---------- --------------- -------------&|---|---|
**qexp** no none required 32 nodes, max 8 per user 150 no 1 / 1h& |**qexp** Express queue|no|none required|32 nodes, max 8 per user|150|no|1 / 1h|
Express queue&\\
**qprace** yes &gt; 0 >1006 nodes, max 86 per job 0 no 24 / 48h&|**qprace** Production queue|yes|&gt; 0|1006 nodes, max 86 per job|0|no|24 / 48h|
Production queue&\\
**qfree** yes none required 752 nodes, max 86 per job -1024 no 12 / 12h&|**qfree** Free resource queue|yes|none required|752 nodes, max 86 per job|-1024|no|12 / 12h|
Free resource queue&\\
---------------------------------------------------------------------------------------------------------------------------------------------&
Port Protocol& |Port|Protocol|
------ ----------& |---|---|
22 ssh& |22|ssh|
80 http& |80|http|
443 https& |443|https|
9418 git& |9418|git|
Node Count Processor Cores Memory Accelerator& |Node|Count|Processor|Cores|Memory|Accelerator|
----------------- ------- ---------------------------------- ------- -------- --------------------------------------------& |---|---|
w/o accelerator 576 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB -& |w/o accelerator|576|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|-|
MIC accelerated 432 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB 2x Intel Xeon Phi 7120P, 61cores, 16GB RAM& |MIC accelerated|432|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|2x Intel Xeon Phi 7120P, 61cores, 16GB RAM|
Node Count Processor Cores Memory GPU Accelerator& |Node|Count|Processor|Cores|Memory|GPU Accelerator|
--------------- ------- --------------------------------- ------- -------- ------------------------------& |---|---|
visualization 2 2x Intel Xeon E5-2695v3, 2.3GHz 28 512GB NVIDIA QUADRO K5000, 4GB RAM& |visualization|2|2x Intel Xeon E5-2695v3, 2.3GHz|28|512GB|NVIDIA QUADRO K5000, 4GB RAM|
Hypercube dimension& |Hypercube|dimension|
--------------------- -------------------------------------------& |---|---|
1D ehc_1d& |1D|ehc_1d|
2D ehc_2d& |2D|ehc_2d|
3D ehc_3d& |3D|ehc_3d|
4D ehc_4d& |4D|ehc_4d|
5D ehc_5d& |5D|ehc_5d|
6D ehc_6d& |6D|ehc_6d|
7D ehc_7d& |7D|ehc_7d|
Node type Count Short name Long name Rack& |Node type|Count|Short name|Long name|Rack|
-------------------------------------- ------- ------------------ -------------------------- -------& |---|---|
M-Cell compute nodes w/o accelerator 576 cns1 -cns576 r1i0n0 - r4i7n17 1-4& |M-Cell compute nodes w/o accelerator|576|cns1 -cns576|r1i0n0 - r4i7n17|1-4|
compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r37u31n1008 21-38& |compute nodes MIC accelerated|432|cns577 - cns1008|r21u01n577 - r37u31n1008|21-38|
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------&
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services& |Mountpoint|Usage|Protocol|Net|Capacity|Throughput|Limitations|Access|
---------------------------------------------- -------------------------------- ------------- -------------- ------------ ------------- ------------------------- -----------------------------& |---|---|
/home home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up&| /home|home directory|NFS, 2-Tier|0.5 PB|6 GB/s|Quota 250GB|Compute and login nodes|backed up|
/scratch/work large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none& |/scratch/work|large project files|Lustre|1.69 PB|30 GB/s|Quota|Compute and login nodes|none|
1TB&
/scratch/temp job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed& |/scratch/temp|job temporary data|Lustre|1.69 PB|30 GB/s|Quota 100TB|Compute and login nodes|files older 90 days removed|
/ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends& |/ramdisk|job temporary data, node local|local|120GB|90 GB/s|none|Compute nodes|purged after job ends|
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------&
Application Version module& |Application|Version|module|
------------- -------------- ---------------------& |---|---|
**R** R 3.1.1 R/3.1.1-intel-2015b& |**R**|R 3.1.1|R/3.1.1-intel-2015b|
**Rstudio** Rstudio 0.97 Rstudio& |**Rstudio**|Rstudio 0.97|Rstudio|
24 MPI**&**24 MPI**
--------------- -----------------------& |**Version**|**Module**|
**Version** **Module**& |---|---|
2016 Update 2 Advisor/2016_update2& |2016 Update 2|Advisor/2016_update2|
2016 Update 1 Inspector/2016_update1& |2016 Update 1|Inspector/2016_update1|
Interface Integer type& |Interface|Integer type|
----------- -----------------------------------------------& |---|---|
LP64 32-bit, int, integer(kind=4), MPI_INT& |LP64|32-bit, int, integer(kind=4), MPI_INT|
ILP64 64-bit, long int, integer(kind=8), MPI_INT64 & |ILP64|64-bit, long int, integer(kind=8), MPI_INT64|
Parameter Value& |Parameter|Value|
------------------------------------------------- -----------------------------& |---|---|
>max number of atoms 200& |max number of atoms|200|
>max number of valence orbitals 300& |max number of valence orbitals|300|
>max number of basis functions 4095& |max number of basis functions|4095|
>max number of states per symmmetry 20& |max number of states per symmmetry|20|
>max number of state symmetries 16& |max number of state symmetries|16|
>max number of records 200& |max number of records|200|
>max number of primitives >maxbfn x [2]& |max number of primitives|maxbfn x [2]|
Address Port Protocol& |Address|Port|Protocol|
-------------------------------------------------- ---------------------------------- -----------------------------------------& |---|---|
anselm.it4i.cz 22 scp, sftp& |anselm.it4i.cz|22|scp, sftp|
login1.anselm.it4i.cz 22 scp, sftp& |login1.anselm.it4i.cz|22|scp, sftp|
login2.anselm.it4i.cz 22 scp, sftp& |login2.anselm.it4i.cz|22|scp, sftp|
class="discreet">dm1.anselm.it4i.cz 22 class="discreet">scp, sftp</span>& |dm1.anselm.it4i.cz|22|scp, sftp|
Login address Port Protocol Login node& |Login address|Port|Protocol|Login node|
----------------------- ------ ---------- ----------------------------------------------& |---|----|
anselm.it4i.cz 22 ssh round-robin DNS record for login1 and login2& |anselm.it4i.cz|22|ssh|round-robin DNS record for login1 and login2|
login1.anselm.it4i.cz 22 ssh login1& |login1.anselm.it4i.cz|22|ssh|login1|
login2.anselm.it4i.cz 22 ssh login2& |login2.anselm.it4i.cz|22|ssh|login2|
ver.sh 0 → 100755
View file @ eab09266
#!/bin/bash
VER=$(git log --pretty=format:'%h / %an / %ai' -n 1)
sed "s,__VERSION__,\<\/BR\>$VER," mkdocs.yml -i