diff --git a/docs.it4i/all.pdf b/docs.it4i/all.pdf new file mode 100644 index 0000000000000000000000000000000000000000..ba5bfdb3092f987cc00956c33005b8897ffbb203 Binary files /dev/null and b/docs.it4i/all.pdf differ diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md similarity index 99% rename from docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md rename to docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md index f5b62facdb304d30c8cfdeb2b806872f8c4b527c..4334ee786f01d339f86925adbfc3cbc1900b3b12 100644 --- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md +++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md @@ -205,4 +205,4 @@ Starting Matlab workers is an expensive process that requires certain amount of |16|256|1008| |8|128|534| |4|64|333| - |2|32|210| + |2|32|210| \ No newline at end of file diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/parallel.pdf b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/parallel.pdf deleted file mode 100644 index d33d5a99c6e37258bec707a3d2f0aa4e20f5f4a5..0000000000000000000000000000000000000000 Binary files a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/parallel.pdf and /dev/null differ diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md index c10bb716f91c891e34a7b041e4e85ffb9adfa384..22abd458949c52b652915bbf6ac5160ff86ead59 100644 --- a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md +++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md @@ -335,7 +335,7 @@ Interpretation The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team.html) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality. - + **Figure 7**. *TEAM upload panel.* *Once the file has been uploaded, a panel must be chosen from the Panel* list. Then, pressing the Run button the diagnostic process starts. @@ -347,7 +347,7 @@ Once the file has been uploaded, a panel must be chosen from the Panel list. The For variant discovering/filtering we should upload the VCF file into BierApp by using the following form: -** +** **Figure 8.** *BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.** diff --git a/docs.it4i/pbspro-documentation/pbspro-programmers-guide.pdf b/docs.it4i/pbspro-documentation/pbspro-programmers-guide.pdf deleted file mode 100644 index 0dedf4abdd8383d57404efbae0943baab3185d91..0000000000000000000000000000000000000000 Binary files a/docs.it4i/pbspro-documentation/pbspro-programmers-guide.pdf and /dev/null differ diff --git a/docs.it4i/pbspro-documentation/pbspro-quick-start-guide.pdf b/docs.it4i/pbspro-documentation/pbspro-quick-start-guide.pdf deleted file mode 100644 index 19748e9c286e4ab83e6d8ec872bb4d20958189ac..0000000000000000000000000000000000000000 Binary files a/docs.it4i/pbspro-documentation/pbspro-quick-start-guide.pdf and /dev/null differ diff --git a/docs.it4i/pbspro-documentation/pbspro-reference-guide.pdf b/docs.it4i/pbspro-documentation/pbspro-reference-guide.pdf deleted file mode 100644 index 10f4b7f116a69f53e188686b109172dba13ba6f1..0000000000000000000000000000000000000000 Binary files a/docs.it4i/pbspro-documentation/pbspro-reference-guide.pdf and /dev/null differ diff --git a/docs.it4i/pbspro-documentation/pbspro-users-guide.pdf b/docs.it4i/pbspro-documentation/pbspro-users-guide.pdf deleted file mode 100644 index 8c933ce03e23ee4df154ebec358c17f2b7becd2e..0000000000000000000000000000000000000000 Binary files a/docs.it4i/pbspro-documentation/pbspro-users-guide.pdf and /dev/null differ diff --git a/docs.it4i/salomon/software/numerical-languages/parallel.pdf b/docs.it4i/salomon/software/numerical-languages/parallel.pdf deleted file mode 100644 index d33d5a99c6e37258bec707a3d2f0aa4e20f5f4a5..0000000000000000000000000000000000000000 Binary files a/docs.it4i/salomon/software/numerical-languages/parallel.pdf and /dev/null differ diff --git a/html_md.sh b/html_md.sh index 94e24a319a664fc4e56649a51cf2cdaf11e19ee7..e627da04740e054ccc40ee4d254bb6968ff35e03 100755 --- a/html_md.sh +++ b/html_md.sh @@ -7,6 +7,19 @@ # bugs: bad internal links ### +if [ "$1" = "-t" ]; then + test="pdfunite" + while read a ; do + test+=" $a" + done < seznam.txt + test+=" test.pdf" + $test + + while read a ; do + rm "$i" + done < seznam.txt + +fi if [ "$1" = "-d" ]; then # remove pdf, md and epub files STARTTIME=$(date +%s) @@ -27,7 +40,7 @@ if [ "$1" = "-d" ]; then fi elif [ "$2" = "all" ]; then echo "$(tput setaf 9)all files deleted$(tput setaf 15)" - if [ -d ./converted ]; then + if [ -d ./docs.it4i ]; then rm -rf ./converted fi if [ -d ./epub ]; then @@ -50,12 +63,12 @@ if [ "$1" = "-e" ]; then # export to pdf/epub STARTTIME=$(date +%s) counter=1 - count=$(find ./converted -name "*.md" -type f | wc -l) + count=$(find ./docs.it4i -name "*.md" -type f | wc -l) if [ "$2" = "epub" ]; then if [ -d ./epub ]; then rm -rf ./epub fi - find ./converted -name "*.md" | + find ./docs.it4i -name -name "*.md" | while read i; do a=$(basename "$i") @@ -87,7 +100,7 @@ if [ "$1" = "-e" ]; then if [ -d ./pdf ]; then rm -rf ./pdf fi - find ./converted -name "*.md" | + find ./docs.it4i -name "*.md" | while read i; do a=$(basename "$i") @@ -104,34 +117,31 @@ if [ "$1" = "-e" ]; then #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 + pandoc ${a%.*}.epub -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf rm "${a%.*}.epub" elif [ $a = "ansys-fluent.md" ]; then pandoc ${a%.*}.md -o ${a%.*}.epub - pandoc ${a%.*}.epub -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf + pandoc ${a%.*}.epub -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -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 + pandoc ${a%.*}.epub -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf rm "${a%.*}.epub" + elif [ $a = "list_of_modules.md" ]; then + echo "big files..." else - pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf + #pandoc ${a%.*}.md -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf + pandoc -V "geometry:paperwidth=8.26387in" -V "geometry:paperheight=29.7cm" -V "geometry:vmargin=1.4cm" -V "geometry:hmargin=1.6cm" -V "fontsize:12pt" -t latex --latex-engine=xelatex --mathml -o ${a%.*}.pdf ${a%.*}.md fi cd "$c" done - # new folder for pdf - mkdir pdf; - (while read i; - do - mkdir "./pdf/$i"; - done) < ./source/list_folder - - # move pdf files to folder pdf - echo "$(tput setaf 11)moved pdf files$(tput setaf 15)"; - while read a ; do - mv "./converted/${a%.*}.pdf" "./pdf/${a%.*}.pdf"; - done < ./source/list_md_mv + find ./docs.it4i -name "*.pdf" | + while read i; + do + echo "$i" >> seznam.txt + rm "$i" + done fi ENDTIME=$(date +%s) echo "It takes $(($ENDTIME - $STARTTIME)) seconds to complete this task..." diff --git a/it4i_theme/drawer.html b/it4i_theme/drawer.html index 0186b8b79ab8c731e3d2eba18c5231d3baafdc6e..7ae38474105000fc3443c355f5179f4c946b3919 100644 --- a/it4i_theme/drawer.html +++ b/it4i_theme/drawer.html @@ -14,7 +14,7 @@ <ul class="repo"> <li class="repo-download"> {% set version = config.extra.version | default("master") %} - <a href="pbspro-documentation/pbspro-programmers-guide.pdf" target="_blank" title="DOWNLOAD PDF VERSION" data-action="download"> + <a href="all.pdf" target="_blank" title="DOWNLOAD PDF VERSION" data-action="download"> <i class="icon icon-download"></i> DOWNLOAD PDF VERSION </a> </li> diff --git a/mkdocs.yml b/mkdocs.yml index f2f24ef9f12320aefdcf5e8d5fd8354585cbb239..7284593c68aa6fa59cdd8d2508e2bce494b93d57 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -101,7 +101,7 @@ pages: - Anselm Cluster Documentation-Software-Numerical Languages: - Introduction: anselm-cluster-documentation/software/numerical-languages/introduction.md - R: anselm-cluster-documentation/software/numerical-languages/r.md - - Matlab 2013-2014: anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md + - Matlab 2013-2014: anselm-cluster-documentation/software/numerical-languages/matlab_1314.md - Matlab: anselm-cluster-documentation/software/numerical-languages/matlab.md - Octave: anselm-cluster-documentation/software/numerical-languages/octave.md - Anselm Cluster Documentation-Software-Chemistry: diff --git a/seznam.txt b/seznam.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ca9601326c161ba0233694772b5bc77a6b1d4a4 --- /dev/null +++ b/seznam.txt @@ -0,0 +1,153 @@ +./docs.it4i/index.pdf +./docs.it4i/get-started-with-it4innovations/applying-for-resources.pdf +./docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.pdf +./docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/introduction.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.pdf +./docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.pdf +./docs.it4i/anselm-cluster-documentation/compute-nodes.pdf +./docs.it4i/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.pdf +./docs.it4i/anselm-cluster-documentation/accessing-the-cluster/vpn-access.pdf +./docs.it4i/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.pdf +./docs.it4i/anselm-cluster-documentation/introduction.pdf +./docs.it4i/anselm-cluster-documentation/software/compilers.pdf +./docs.it4i/anselm-cluster-documentation/software/gpi2.pdf +./docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.pdf +./docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.pdf +./docs.it4i/anselm-cluster-documentation/software/omics-master/overview.pdf +./docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.pdf +./docs.it4i/anselm-cluster-documentation/software/operating-system.pdf +./docs.it4i/anselm-cluster-documentation/software/kvirtualization.pdf +./docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-debugger.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-tbb.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-suite/introduction.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.pdf +./docs.it4i/anselm-cluster-documentation/software/mpi/mpi.pdf +./docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.pdf +./docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.pdf +./docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-languages/parallel.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-languages/introduction.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.pdf +./docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.pdf +./docs.it4i/anselm-cluster-documentation/software/isv_licenses.pdf +./docs.it4i/anselm-cluster-documentation/software/openfoam.pdf +./docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.pdf +./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.pdf +./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.pdf +./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.pdf +./docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.pdf +./docs.it4i/anselm-cluster-documentation/software/ansys/ansys.pdf +./docs.it4i/anselm-cluster-documentation/software/java.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/papi.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/cube.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/debuggers.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.pdf +./docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.pdf +./docs.it4i/anselm-cluster-documentation/software/chemistry/molpro.pdf +./docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.pdf +./docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.pdf +./docs.it4i/anselm-cluster-documentation/software/paraview.pdf +./docs.it4i/anselm-cluster-documentation/remote-visualization.pdf +./docs.it4i/anselm-cluster-documentation/environment-and-modules.pdf +./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.pdf +./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.pdf +./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.pdf +./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.pdf +./docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.pdf +./docs.it4i/anselm-cluster-documentation/network.pdf +./docs.it4i/anselm-cluster-documentation/storage/cesnet-data-storage.pdf +./docs.it4i/anselm-cluster-documentation/storage/storage.pdf +./docs.it4i/anselm-cluster-documentation/prace.pdf +./docs.it4i/anselm-cluster-documentation/hardware-overview.pdf +./docs.it4i/salomon/compute-nodes.pdf +./docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.pdf +./docs.it4i/salomon/accessing-the-cluster/outgoing-connections.pdf +./docs.it4i/salomon/accessing-the-cluster/vpn-access.pdf +./docs.it4i/salomon/introduction.pdf +./docs.it4i/salomon/software/compilers.pdf +./docs.it4i/salomon/software/operating-system.pdf +./docs.it4i/salomon/software/intel-suite/intel-advisor.pdf +./docs.it4i/salomon/software/intel-suite/intel-mkl.pdf +./docs.it4i/salomon/software/intel-suite/intel-debugger.pdf +./docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.pdf +./docs.it4i/salomon/software/intel-suite/intel-tbb.pdf +./docs.it4i/salomon/software/intel-suite/intel-inspector.pdf +./docs.it4i/salomon/software/intel-suite/intel-compilers.pdf +./docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.pdf +./docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.pdf +./docs.it4i/salomon/software/mpi/mpi.pdf +./docs.it4i/salomon/software/mpi/Running_OpenMPI.pdf +./docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.pdf +./docs.it4i/salomon/software/numerical-languages/parallel.pdf +./docs.it4i/salomon/software/numerical-languages/octave.pdf +./docs.it4i/salomon/software/numerical-languages/r.pdf +./docs.it4i/salomon/software/numerical-languages/introduction.pdf +./docs.it4i/salomon/software/numerical-languages/matlab.pdf +./docs.it4i/salomon/software/ansys/setting-license-preferences.pdf +./docs.it4i/salomon/software/ansys/licensing.pdf +./docs.it4i/salomon/software/ansys/ansys-fluent.pdf +./docs.it4i/salomon/software/ansys/ansys-ls-dyna.pdf +./docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.pdf +./docs.it4i/salomon/software/ansys/ansys-cfx.pdf +./docs.it4i/salomon/software/ansys/workbench.pdf +./docs.it4i/salomon/software/ansys/ansys.pdf +./docs.it4i/salomon/software/comsol/comsol-multiphysics.pdf +./docs.it4i/salomon/software/comsol/licensing-and-available-versions.pdf +./docs.it4i/salomon/software/java.pdf +./docs.it4i/salomon/software/debuggers/allinea-ddt.pdf +./docs.it4i/salomon/software/debuggers/allinea-performance-reports.pdf +./docs.it4i/salomon/software/debuggers/aislinn.pdf +./docs.it4i/salomon/software/debuggers/vampir.pdf +./docs.it4i/salomon/software/debuggers/Introduction.pdf +./docs.it4i/salomon/software/debuggers/valgrind.pdf +./docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.pdf +./docs.it4i/salomon/software/debuggers/total-view.pdf +./docs.it4i/salomon/software/chemistry/phono3py.pdf +./docs.it4i/salomon/software/chemistry/molpro.pdf +./docs.it4i/salomon/software/chemistry/nwchem.pdf +./docs.it4i/salomon/software/intel-xeon-phi.pdf +./docs.it4i/salomon/environment-and-modules.pdf +./docs.it4i/salomon/network/7d-enhanced-hypercube.pdf +./docs.it4i/salomon/network/ib-single-plane-topology.pdf +./docs.it4i/salomon/network/network.pdf +./docs.it4i/salomon/resource-allocation-and-job-execution/introduction.pdf +./docs.it4i/salomon/resource-allocation-and-job-execution/capacity-computing.pdf +./docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.pdf +./docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.pdf +./docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.pdf +./docs.it4i/salomon/storage/cesnet-data-storage.pdf +./docs.it4i/salomon/storage/storage.pdf +./docs.it4i/salomon/prace.pdf +./docs.it4i/salomon/hardware-overview.pdf +./docs.it4i/pbspro-documentation/pbspro-reference-guide.pdf +./docs.it4i/pbspro-documentation/pbspro-programmers-guide.pdf +./docs.it4i/pbspro-documentation/pbspro-users-guide.pdf +./docs.it4i/pbspro-documentation/sitemap.pdf +./docs.it4i/pbspro-documentation/pbspro-quick-start-guide.pdf