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.gitlab-ci.yml 0 → 100644
View file @ f1cf74e0
docs:
stage: test
image: davidhrbac/docker-mdcheck:latest
allow_failure: true
script:
- mdl -r ~MD013 *.md
shellcheck:
stage: test
image: davidhrbac/docker-shellcheck:latest
script:
- which shellcheck || apt-get update && apt-get install -y shellcheck
- shellcheck *.sh
README.md 0 → 100755
View file @ f1cf74e0
Převod html dokumentace do md formátu (version 0.53) - BETA
===========================================================
Výsledkem projektu by měl být skript pro stažení a převod stávající dokumentace na docs.it4i.cz do md formátu
### Základní požadavky
- stažení celé adresářové struktury docs.it4i.cz
- konverze html souborů na md soubory
- zachování stejného formatování jako na webu
### Postup
Pro svou práci si naklonujete Gitem repozitář do svého pracovního adresáře.
| Úkon | Orientační čas |
|--------|--------|
|Stažení|~1m|
|Převod|~16m|
|Export pdf|~12m|
|Export epub|~16s|
### Vývoj
| Verze | čas | změny |
|--------|--------|---|
|0.3|34m56s|přidání filtru pro html a css|
|0.4|24m56s|oprava obrázků + optimalizace|
|0.45|7m56s|optimalizace|
|0.47|11m7s|přidání filtrů pro opravu a nahrazení tabulek, vylepšení filtrace, ...|
|0.51|16m37s|export do pdf, export do epub, filtry, ...|
|0.52|16m37s|oprava exportu do pdf, nový filtr pro poslední opravu formátování a chyb, ...|
>**Problémy**
> * interní a externí odkazy
> * formátování tabulek
> * formátování kódů
### Funkce skriptu
Stažení souborů:
```bash
html_md.sh -w
```
Konverze html do md
```bash
html_md.sh -c
```
Export do pdf
```bash
html_md.sh -e pdf
```
Export do epub
```bash
html_md.sh -e epub
```
Smazání souborů
```bash
html_md.sh -d md
html_md.sh -d pdf
html_md.sh -d epub
```
html_md.sh 0 → 100755
View file @ f1cf74e0
#!/bin/bash
### DOWNLOAD AND CONVERT DOCUMENTATION
# autor: kru0052
# version: 0.53
# change: repait bugs
# bugs: bad internal links
###
if [ "$1" = "-e" ]; then
# export to pdf/epub
STARTTIME=$(date +%s)
counter=1
count=$(find ./converted -name "*.md" -type f | wc -l)
if [ "$2" = "epub" ]; then
rm -rf ./epub
find ./converted -name "*.md" |
while read i;
do
a=$(basename "$i")
b=$(dirname "$i")
c=$(pwd)
echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$a => $(tput setaf 13)${a%.*}.epub$(tput setaf 15)"
counter=$((counter+1))
cd "$b"
pandoc ${a%.*}.md -o ${a%.*}.epub
cd "$c"
done
mkdir epub;
(while read i;
do
mkdir "./epub/$i";
done) < ./source/list_folder
# move epub files to new folders
echo "$(tput setaf 11)moved epub files$(tput setaf 15)";
while read a ; do
mv "./converted/${a%.*}.epub" "./epub/${a%.*}.epub";
done < ./source/list_md_mv
fi
if [ "$2" = "pdf" ]; then
rm -rf ./pdf
find ./converted -name "*.md" |
while read i;
do
a=$(basename "$i")
b=$(dirname "$i")
c=$(pwd)
echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$a => $(tput setaf 13)${a%.*}.pdf$(tput setaf 15)"
#echo "$b"
counter=$((counter+1))
cd "$b"
#!double subscripts problem !!!!!!
#ansys-fluent.md
#capacity-computing.md
#job-submission-and-execution.md
if [ $a = "job-submission-and-execution.md" ]; then
pandoc ${a%.*}.md -o ${a%.*}.epub
pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
rm "${a%.*}.epub"
elif [ $a = "ansys-fluent.md" ]; then
#wkhtmltopdf ansys-fluent.md ansys-fluent.pdf
pandoc ${a%.*}.md -o ${a%.*}.epub
pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
rm "${a%.*}.epub"
elif [ $a = "capacity-computing.md" ]; then
pandoc ${a%.*}.md -o ${a%.*}.epub
pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
rm "${a%.*}.epub"
else
pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf
fi
cd "$c"
done
mkdir pdf;
(while read i;
do
mkdir "./pdf/$i";
done) < ./source/list_folder
# move epub files to new folders
echo "$(tput setaf 11)moved epub files$(tput setaf 15)";
while read a ; do
mv "./converted/${a%.*}.pdf" "./pdf/${a%.*}.pdf";
done < ./source/list_md_mv
fi
ENDTIME=$(date +%s)
echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..."
fi
if [ "$1" = "-d" ]; then
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 ./converted ]; 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
fi
if [ "$1" = "-w" ]; then
# download html pages
STARTTIME=$(date +%s)
rm -rf docs.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.it4i.cz;
# download images
wget --directory-prefix=./docs.it4i.cz/ http://verif.cs.vsb.cz/aislinn/doc/report.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig8.png
wget --directory-prefix=./docs.it4i.cz/ https://docs.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..."
fi
if [ "$1" = "-c" ]; then
### convert html to md
STARTTIME=$(date +%s)
if [ -d ./docs.it4i.cz ]; then
# erasing the previous transfer
rm -rf converted;
rm -rf info;
# 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=1
count=$(find . -name "*.html" -type f | wc -l)
find . -name "*.ht*" |
while read i;
do
# first filtering html
echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$i";
counter=$((counter+1))
printf "$(tput setaf 15)\t\tfiltering html files...\n";
HEAD=$(grep -n -m1 '<h1' "$i" |cut -f1 -d: | tr --delete '\n')
END=$(grep -n -m1 '<!-- <div tal:content=' "$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' > "${i%.*}TMP.html"
# converted .html to .md
printf "\t\t.html -> .md\n"
pandoc -f html -t markdown+pipe_tables-grid_tables "${i%.*}TMP.html" -o "${i%.*}.md";
rm "${i%.*}TMP.html";
# filtering html and css elements...
printf "\t\tfiltering html and css elements...\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\trepair formatting...\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
# repair image...
printf "\t\trepair images...\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%.*}.md";
cat -s "${i%.*}.md" > "${i%.*}TMP.md";
done < ./source/repairIMG
# repair tables
printf "\t\trepair tables...\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%.*}.md";
sed -e :a -e '/\\$/N; s/\\\n//; ta' "${i%.*}.md" > "${i%.*}TMP.md";
done < ./source/tab
# replace tables
printf "\t\treplace tables...\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"'/' "${i%.*}TMP.md" | sed -e 's/^>//' > "${i%.*}.md";
cat -s "${i%.*}.md" > "${i%.*}TMP.md";
done < ./source/tabREPLACE
# last repair formatting...
printf "\t\tlast repair formatting...\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";
done
# delete empty files
find -type f -size -10c |
while read i;
do
rm "$i";
echo "$(tput setaf 9)$i deleted";
done
### create new folder and move converted files
# create folder info and list all files and folder
mkdir info;
echo "$(tput setaf 11)create folder info and file lists";
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)
if [ $count -eq 150 ]; then
rm -rf ./converted
mkdir converted;
(while read i;
do
mkdir "./converted/$i";
done) < ./source/list_folder
# move md files to new folders
echo "$(tput setaf 11)moved md files";
while read a b ; do
mv "$a" "./converted/$b";
done < <(paste ./info/list_md ./source/list_md_mv)
# copy jpg and jpeg to new folders
echo "$(tput setaf 11)copy image files";
while read a b ; do
cp "$a" "./converted/$b";
done < <(paste ./info/list_image ./source/list_image_mv)
cp ./docs.it4i.cz/salomon/salomon ./converted/docs.it4i.cz/salomon/salomon
cp ./docs.it4i.cz/salomon/salomon-2 ./converted/docs.it4i.cz/salomon/salomon-2
cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
cp ./converted/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
cp ./converted/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
cp ./docs.it4i.cz/virtualization-job-workflow ./converted/docs.it4i.cz/anselm-cluster-documentation/software/
cp ./docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg ./converted/docs.it4i.cz/salomon/accessing-the-cluster/anyconnecticon.jpg
cp ./docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg ./converted/docs.it4i.cz/salomon/accessing-the-cluster/anyconnectcontextmenu.jpg
cp ./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png ./converted/docs.it4i.cz/salomon/software/debuggers/TightVNC_login.png
# listall files and folder /converted
find ./converted -name "*.png" -type f > ./info/list_image_converted;
find ./converted -name "*.jpg" -type f >> ./info/list_image_converted;
find ./converted -name "*.jpeg" -type f >> ./info/list_image_converted;
find ./converted -name "*.md" -type f> ./info/list_md_converted;
find ./converted -type d | sort > ./info/list_folder_converted;
echo "$(tput setaf 11)COMPLETED...$(tput setaf 15)";
else
printf "\n\n$(tput setaf 9)Can not create a folder converted, because the number of MD files disagrees. The converted files remain in the folder docs.it4i.cz !!!!...$(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
source/formatting 0 → 100644
View file @ f1cf74e0
[]()&
**[]()&**
- - &
.[]()&.
<!-- -->&
### []()[]()&###
### []()&###
### **&###
### 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.**
source/lastFilter 0 → 100644
View file @ f1cf74e0
>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)
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HOME](storage.html#home)&
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>Disk usage and quota commands&Disk usage and quota commands
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Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS&**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
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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)
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)
![Vampir screenshot](Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png "Vampir screenshot")&![](Snmekobrazovky20160708v12.33.35.png)
![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)
source/replace 0 → 100644
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style="text-align: left; float: none; ">&
class="anchor-link">&
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class="internal-link">&
class="internal-link"><span id="result_box" class="short_text"><span&
class="monospace">&
class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE&LAPACKE modelu, which includes Intel's LAPACKE
class="n">&
class="n">&
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class="short_text"><span&
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</div>&
<div>&
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{.external&
</span>&
<span&
[<span class="anchor-link">&
<span class="discreet">&
<span class="discreet"></span>&
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<span class="hps">&
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(<span id="result_box">&
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</span> <span&
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</span> <span class="hps">&
</span> <span class="hps">who have a valid</span> <span&
<span><span class="monospace">&
<span><span>Introduction&###Introduction
</span></span><span><span>&
</span></span></span></span><span><span>&
</span></span><span><span><span><span>&
.<span style="text-align: left; "> </span>&
<span style="text-align: start; ">&
{.state-missing-value
style="text-align: left; float: none; ">&
style="text-align: left; float: none; ">&
style="text-align: left; float: none; ">change it&change it to
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style="text-align: left; float: none; ">Enable X11&Enable X11
style="text-align: left; float: none; "> &
style="text-align: start; ">&
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.text}.&
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ssh-connection style="text-alignstart; "}&
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{#putty---before-we-start-ssh-connection style="text-align: start; "}&
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{.screen}&
{#setup-and-start-your-own-turbovnc-server}&
{style="text-align: left; "}&
ssh-connection style="text-alignstart; "}&
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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|