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Commit c4d9d230 authored by Lukáš Krupčík's avatar Lukáš Krupčík
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edit tranfer script

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scripts/preklopeni_dokumentace/html_md.sh
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......@@ -5,73 +5,12 @@
# version: 1.00
###
if [ "$1" = "-d" ]; then
# remove pdf, md and epub files
STARTTIME=$(date +%s)
if [ "$2" = "pdf" ]; then
echo "$(tput setaf 9)*.pdf deleted$(tput setaf 15)"
if [ -d ./pdf ]; then
rm -rf ./pdf
fi
elif [ "$2" = "epub" ]; then
echo "$(tput setaf 9)*.epub deleted$(tput setaf 15)"
if [ -d ./epub ]; then
rm -rf ./epub
fi
elif [ "$2" = "md" ]; then
echo "$(tput setaf 9)*.md deleted$(tput setaf 15)"
if [ -d ./converted ]; then
rm -rf ./converted
fi
elif [ "$2" = "all" ]; then
echo "$(tput setaf 9)all files deleted$(tput setaf 15)"
if [ -d ./docs.it4i ]; then
rm -rf ./converted
fi
if [ -d ./epub ]; then
rm -rf ./epub
fi
if [ -d ./pdf ]; then
rm -rf ./pdf
fi
if [ -d ./info ]; then
rm -rf ./info
fi
if [ -d ./docs.it4i.cz ]; then
rm -rf ./docs.it4i.cz
fi
fi
ENDTIME=$(date +%s)
echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
fi
if [ "$1" = "-w" ]; then
# download html pages
STARTTIME=$(date +%s)
rm -rf docs-old.it4i.cz
wget -X pbspro-documentation,changelog,whats-new,portal_css,portal_javascripts,++resource++jquery-ui-themes,anselm-cluster-documentation/icon.jpg -R favicon.ico,pdf.png,logo.png,background.png,application.png,search_icon.png,png.png,sh.png,touch_icon.png,anselm-cluster-documentation/icon.jpg,*js,robots.txt,*xml,RSS,download_icon.png,pdf,*zip,*rar,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs-old.it4i.cz;
# download images
wget --directory-prefix=./docs-old.it4i.cz/ http://verif.cs.vsb.cz/aislinn/doc/report.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig8.png
wget --directory-prefix=./docs-old.it4i.cz/ https://docs-old.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig9.png
ENDTIME=$(date +%s)
echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
wget -X portal_css,portal_javascripts,++resource++jquery-ui-themes,anselm-cluster-documentation/icon.jpg -R favicon.ico,pdf.png,logo.png,background.png,application.png,search_icon.png,png.png,sh.png,touch_icon.png,anselm-cluster-documentation/icon.jpg,*js,robots.txt,*xml,RSS,download_icon.png,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs-old.it4i.cz;
fi
if [ "$1" = "-c" ]; then
### convert html to md
STARTTIME=$(date +%s)
if [ -d ./docs.it4i.cz ]; then
# erasing the previous transfer
if [ -d ./docs.it4i ]; then
rm -rf ./docs.it4i
......@@ -80,16 +19,6 @@ if [ "$1" = "-c" ]; then
rm -rf ./info;
fi
# erasing duplicate files and unwanted files
(while read i;
do
if [ -f "$i" ];
then
echo "$(tput setaf 9)$i deleted";
rm "$i";
fi
done) < ./source/list_rm
# counter for html and md files
counter=1
count=$(find . -name "*.html" -type f | wc -l)
......@@ -113,44 +42,7 @@ if [ "$1" = "-c" ]; then
printf "\t\t.html => $(tput setaf 13).md\n$(tput setaf 15)"
pandoc -f html -t markdown+pipe_tables-grid_tables "${i%.*}TMP.html" -o "${i%.*}.md";
rm "${i%.*}TMP.html";
# filtering html and css elements...
printf "\t\tFiltering html and css elements in md files...\n"
sed -e 's/``` /```/' "${i%.*}.md" | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed -e 's/<\/span>//' | sed -e 's/^\*\*//' | sed -e 's/\\//g' | sed -e 's/^: //g' | sed -e 's/^Obsah//g' > "${i%.*}TMP.md";
while read x ; do
arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}TMP.TEST.md";
cat -s "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
done < ./source/replace
# repair formatting...
printf "\t\tFix formatting text...\n"
while read x ; do
arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" | sed -e 's/^``//g' > "${i%.*}TMP.TEST.md";
cat -s "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
done < ./source/formatting
# last repair formatting...
printf "\t\tLatest fix formatting text...\n"
while read x ; do
arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}TMP.TEST.md";
cat -s "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
done < ./source/lastFilter
cat "${i%.*}TMP.md" > "${i%.*}.md";
# delete temporary files
rm "${i%.*}TMP.md";
rm "${i%.*}TMP.TEST.md";
rm "${i%.*}TMP.html"
done
# delete empty files
......@@ -160,64 +52,4 @@ if [ "$1" = "-c" ]; then
rm "$i";
echo "$(tput setaf 9)$i deleted";
done
### create new folder and move converted files
# create folder info and list all files and folders
mkdir info;
echo "$(tput setaf 11)Create folder info and lists od files...";
find ./docs.it4i.cz -name "*.png" -type f > ./info/list_image;
find ./docs.it4i.cz -name "*.jpg" -type f >> ./info/list_image;
find ./docs.it4i.cz -name "*.jpeg" -type f >> ./info/list_image;
find ./docs.it4i.cz -name "*.md" -type f> ./info/list_md;
find ./docs.it4i.cz -type d | sort > ./info/list_folder;
count=$(find ./docs.it4i.cz -name "*.md" -type f | wc -l)
echo "$count"
if [ $count -eq 150 ]; then
mkdir docs.it4i;
(while read i;
do
mkdir "./docs.it4i/$i";
done) < ./source/list_folder
# move md files to folder converted
echo "$(tput setaf 11)Moved md files...";
while read a b ; do
mv "$a" "./docs.it4i/$b";
done < <(paste ./info/list_md ./source/list_md_mv)
# copy jpg, jpeg and png to folder converted
echo "$(tput setaf 11)Copy image files...";
while read a b ; do
cp "$a" "./docs.it4i/$b";
done < <(paste ./info/list_image ./source/list_image_mv)
cp ./docs.it4i.cz/salomon/salomon ./docs.it4i/salomon/salomon
cp ./docs.it4i.cz/salomon/salomon-2 ./docs.it4i/salomon/salomon-2
cp ./docs.it4i/salomon/resource-allocation-and-job-execution/fairshare_formula.png ./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
cp ./docs.it4i/salomon/resource-allocation-and-job-execution/job_sort_formula.png ./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
cp ./docs.it4i/salomon/software/debuggers/vtune-amplifier.png ./docs.it4i/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
cp ./docs.it4i/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./docs.it4i/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
cp ./docs.it4i.cz/virtualization-job-workflow ./docs.it4i/anselm-cluster-documentation/software/
cp ./docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg ./docs.it4i/salomon/accessing-the-cluster/anyconnecticon.jpg
cp ./docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg ./docs.it4i/salomon/accessing-the-cluster/anyconnectcontextmenu.jpg
cp ./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png ./docs.it4i/salomon/software/debuggers/TightVNC_login.png
# list all files and folder converted
find ./docs.it4i -name "*.png" -type f > ./info/list_image_converted;
find ./docs.it4i -name "*.jpg" -type f >> ./info/list_image_converted;
find ./docs.it4i -name "*.jpeg" -type f >> ./info/list_image_converted;
find ./docs.it4i -name "*.md" -type f> ./info/list_md_converted;
find ./docs.it4i -type d | sort > ./info/list_folder_converted;
echo "$(tput setaf 13)COMPLETED...$(tput setaf 15)";
else
printf "\n\n$(tput setaf 9)Can not create a folder docs.it4i, because the number of MD files disagrees. The converted files remain in the folder docs.it4i.cz !!!!...$(tput setaf 15)\n\n";
fi
else
printf "\n\n$(tput setaf 9)Folder docs.it4i.cz not exists!!!!...$(tput setaf 15)\n\nRun html_md.sh -w\n\n";
fi
ENDTIME=$(date +%s)
echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
fi
scripts/preklopeni_dokumentace/source/formatting deleted 100644 → 0
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[]()&
**[]()&**
- - &
.[]()&.
<!-- -->&
### []()[]()&###
### []()&###
### **&###
### 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/preklopeni_dokumentace/source/lastFilter deleted 100644 → 0
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>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/preklopeni_dokumentace/source/list_folder deleted 100644 → 0
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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/preklopeni_dokumentace/source/list_image_mv deleted 100644 → 0
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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
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![Anselm profile](../Anselmprofile.jpg "Anselm profile")&![](Anselmprofile.jpg)
![Login with&
profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")&![](loginwithprofile.jpeg)
![successful&
login](../successfullconnection.jpg "successful login")&![](successfullconnection.jpg)
![](bullxB510.png)**&![](bullxB510.png)&![](bullxB510.png.jpeg)
![CUBE&
Screenshot](Snmekobrazovky20141204v12.56.36.png "CUBE Screenshot")&![](Snmekobrazovky20141204v12.56.36.png)
![Vampir screenshot](../../../salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png "Vampir screenshot")&![](Snmekobrazovky20160708v12.33.35.png)
![Virtualization Job&
increases.](images/fig5.png.1 "fig5.png")&increases.](fig5.png.1 "fig5.png")
out.](fig1.png "Fig 1")&out.](fig1.png "Fig 1")
![FASTQ file.](images/fig2.png "fig2.png")&![FASTQ file.](fig2.png "fig2.png")
operation.](images/fig3.png "fig3.png")&operation.](fig3.png "fig3.png")&
where the position is ambiguous.](images/fig4.png)&where the position is ambiguous.](fig4.png)
genomic coordinates.](images/fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png.1 "fig6.png")
[![](cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png)](cygwin-and-x11-forwarding.html)&![](cygwinX11forwarding.png)
[![PuTTY - Create&
tunnel](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png "PuTTY Tunnel")](putty-tunnel.png)&![](putty-tunnel.png)
![TigerVNC&
vncviewer](../../../../anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png "Vncviewer")&![](vncviewer.png)
[**![](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png)**](TightVNC_login.png)&![](TightVNC_login.png)
[![Default Gnome&
session](../../../../salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png "Default Gnome session")](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)&![](gnome_screen.png)
[![Disable lock screen and&
screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/0259b284-18eb-402c-a55c-584562e26b47.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&![](gdmdisablescreensaver.png)
[![Screensaver&
Preferences](gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)&![](gdmscreensaver.png)
[![gnome-terminal.png](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/dc0f0207-c614-49be-9cfb-905a523c5a39.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/90ca3609-a3ff-4867-9019-954c74224961.png "gnome-compute-nodes-over-vnc.png")](gnome-compute-nodes-over-vnc.png)&![](gnome-compute-nodes-over-vnc.png)
[![Pageant](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png/@@images/b82926bc-3890-49b9-b5be-a673975e442b.png "Pageant")](PageantV.png)&![](PageantV.png)
[![](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png/@@images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png)](PuTTY_host_Salomon.png)&![](PuTTY_host_Salomon.png)
[![PuttyKey](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png/@@images/9f161548-31a6-42a7-ad61-4e885e4b4664.png "PuttyKey")](PuTTY_keyV.png)&![](PuTTY_keyV.png)
[![](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png/@@images/0eeeb971-b295-4780-88e7-7557da05a1cb.png)](PuTTY_save_Salomon.png)&![](PuTTY_save_Salomon.png)
[![](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png/@@images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png)](PuTTY_open_Salomon.png)&![](PuTTY_open_Salomon.png)
[![PuttyKeygenerator](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygeneratorV.png/@@images/22954eec-6127-4d42-b159-9bebacb3223d.png "PuttyKeygenerator")](PuttyKeygeneratorV.png)&![](PuttyKeygeneratorV.png)
[![PuttyKeygenerator_001](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_001V.png/@@images/f7c1889f-605f-4c5c-8904-d962ec4531a2.png "PuttyKeygenerator_001")](PuttyKeygenerator_001V.png)&![](PuttyKeygenerator_001V.png)
[![PuttyKeygenerator_002](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_002V.png/@@images/13b88922-8c1d-47b2-b3e6-043c18b11d86.png "PuttyKeygenerator_002")](PuttyKeygenerator_002V.png)&![](PuttyKeygenerator_002V.png)
[![PuttyKeygenerator_003](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png/@@images/29ff0f89-8203-4777-9a00-c068d3188fd0.png "PuttyKeygenerator_003")](20150312_143443.png)&![](PuttyKeygenerator_003V.png)
[![PuttyKeygenerator_004](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_004V.png/@@images/8ef00e6b-0155-4dc2-82e6-7141a15f282c.png "PuttyKeygenerator_004")](PuttyKeygenerator_004V.png)&![](PuttyKeygenerator_004V.png)
[![PuttyKeygenerator_005](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_005V.png/@@images/929621fe-45f7-45c8-9ed0-c34d430d65f4.png "PuttyKeygenerator_005")](PuttyKeygenerator_005V.png)&![](PuttyKeygenerator_005V.png)
[![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&
Install](https://docs.it4i.cz/salomon/vpn_web_login.png/@@images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png "VPN Install")](../vpn_web_login.png)&![](vpn_web_login.png)
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)
Install](https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png "VPN Install")](../vpn_web_download.png)&![](vpn_web_download.png)
Install](https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png "VPN Install")](../vpn_web_download_2.png)&![](vpn_web_download_2.png)
![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&
menu](https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg/@@images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpeg "Context menu")](../../anselm-cluster-documentation/anyconnectcontextmenu.jpg)&![](anyconnectcontextmenu.jpg)
[![VPN Contacting&
Cluster](https://docs.it4i.cz/salomon/vpn_contacting.png/@@images/9ccabccf-581a-476a-8c24-ce9842c3e657.png "VPN Contacting Cluster")](../vpn_contacting.png)&![](vpn_contacting.png)
login](https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png "VPN login")](../vpn_login.png)&![](vpn_login.png)
Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png "VPN Succesfull Connection")](../vpn_successfull_connection.png)&![](vpn_successfull_connection.png)
[![Salomon](https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg "Salomon")](../salomon-2)&![Salomon](../salomon-2)&![](salomon-2)
![UV&
2000](../uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")&![](uv-2000.jpeg)
[![Salomon](https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg "Salomon")](salomon)&![](salomon)
![Salomon](salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg "Salomon")&![](salomon-1.jpeg)
![Salomon](salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg "Salomon")&![](salomon-3.jpeg)
![Salomon](salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg "Salomon")&![](salomon-4.jpeg)
[![7D_Enhanced_hypercube.png](https://docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png "7D_Enhanced_hypercube.png")](7D_Enhanced_hypercube.png)&![](7D_Enhanced_hypercube.png)
[![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)
[![Fluent_Licence_1.jpg](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_1.jpg/@@images/0203aca4-d4f8-4372-ab71-432fcf15df43.jpeg "Fluent_Licence_1.jpg")](Fluent_Licence_1.jpg)&![](Fluent_Licence_1.jpg)
[![Fluent_Licence_2.jpg](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_2.jpg/@@images/5a50330d-afcf-4266-ba1b-1ab70c9ed1b1.jpeg "Fluent_Licence_2.jpg")](Fluent_Licence_2.jpg)&![](Fluent_Licence_2.jpg)
[![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)
[![Fluent_Licence_4.jpg](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_4.jpg/@@images/6f6f84e5-5012-42f3-88d6-1ab1c1bfee8f.jpeg "Fluent_Licence_4.jpg")](Fluent_Licence_4.jpg)&![](Fluent_Licence_4.jpg)
![](AMsetPar1.png/@@images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png)&![](AMsetPar1.png)
![Part of report.html](http://verif.cs.vsb.cz/aislinn/doc/report.png)&![](report.png)
[![](ddt1.png){.image-inline width="451"&![](ddt1.png)
height="513"}](ddt1.png)&
![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)
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tumor.](images/fig9.png "fig9.png")**&tumor.](fig9.png)
increases.](fig5.png.1 "fig5.png")&increases.](fig5.png)
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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|
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