From cc35d49d629788c6f1d8cc951221d245b93e84dc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pavel=20Jir=C3=A1sek?= <pavel.jirasek@vsb.cz>
Date: Tue, 31 Jan 2017 10:23:42 +0100
Subject: [PATCH] Fix resource-allocation-and-job-execution

---
 docs.it4i/anselm/software/ansys/ansys-ls-dyna.md              | 2 +-
 docs.it4i/anselm/software/ansys/ls-dyna.md                    | 2 +-
 .../anselm/software/debuggers/allinea-performance-reports.md  | 2 +-
 docs.it4i/anselm/software/kvirtualization.md                  | 4 ++--
 docs.it4i/anselm/software/numerical-languages/octave.md       | 2 +-
 docs.it4i/anselm/software/numerical-languages/r.md            | 4 ++--
 docs.it4i/anselm/software/omics-master/overview.md            | 4 ++--
 docs.it4i/anselm/software/openfoam.md                         | 4 ++--
 docs.it4i/anselm/software/paraview.md                         | 2 +-
 .../accessing-the-clusters/graphical-user-interface/vnc.md    | 2 +-
 docs.it4i/salomon/software/ansys/ansys-cfx.md                 | 2 +-
 docs.it4i/salomon/software/ansys/ansys-ls-dyna.md             | 2 +-
 .../salomon/software/debuggers/allinea-performance-reports.md | 2 +-
 docs.it4i/salomon/software/numerical-languages/octave.md      | 2 +-
 docs.it4i/salomon/software/numerical-languages/r.md           | 4 ++--
 15 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/docs.it4i/anselm/software/ansys/ansys-ls-dyna.md b/docs.it4i/anselm/software/ansys/ansys-ls-dyna.md
index 18a0193bc..af46af93a 100644
--- a/docs.it4i/anselm/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/anselm/software/ansys/ansys-ls-dyna.md
@@ -50,6 +50,6 @@ echo Machines: $hl
 /ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
 ```
 
-Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the PBS file (above) is common and description can be find on [this site](../../job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
 
 Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ANSYS solver via parameter i=
diff --git a/docs.it4i/anselm/software/ansys/ls-dyna.md b/docs.it4i/anselm/software/ansys/ls-dyna.md
index dd5682a25..063bcf245 100644
--- a/docs.it4i/anselm/software/ansys/ls-dyna.md
+++ b/docs.it4i/anselm/software/ansys/ls-dyna.md
@@ -30,6 +30,6 @@ module load lsdyna
 /apps/engineering/lsdyna/lsdyna700s i=input.k
 ```
 
-Header of the PBS file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.html). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the PBS file (above) is common and description can be find on [this site](../../job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
 
 Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA **.k** file which is attached to the LS-DYNA solver via parameter i=
diff --git a/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md b/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
index ad8d74d77..a05f8ad4e 100644
--- a/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
@@ -29,7 +29,7 @@ Instead of [running your MPI program the usual way](../mpi/), use the the perf r
     $ perf-report mpirun ./mympiprog.x
 ```
 
-The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../job-submission-and-execution/).
 
 ## Example
 
diff --git a/docs.it4i/anselm/software/kvirtualization.md b/docs.it4i/anselm/software/kvirtualization.md
index b838944b0..668a12ee7 100644
--- a/docs.it4i/anselm/software/kvirtualization.md
+++ b/docs.it4i/anselm/software/kvirtualization.md
@@ -12,7 +12,7 @@ There are situations when Anselm's environment is not suitable for user needs.
 * Application requires privileged access to operating system
 * ... and combinations of above cases
 
-We offer solution for these cases - **virtualization**. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of [Resource Allocation and Job Execution](../../resource-allocation-and-job-execution/introduction/).
+We offer solution for these cases - **virtualization**. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of [Resource Allocation and Job Execution](../job-submission-and-execution/).
 
 Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.
 
@@ -202,7 +202,7 @@ Run script runs application from shared job directory (mapped as drive z:), proc
 
 ### Run Jobs
 
-Run jobs as usual, see  [Resource Allocation and Job Execution](../../resource-allocation-and-job-execution/introduction/). Use only full node allocation for virtualization jobs.
+Run jobs as usual, see  [Resource Allocation and Job Execution](../job-submission-and-execution/). Use only full node allocation for virtualization jobs.
 
 ### Running Virtual Machines
 
diff --git a/docs.it4i/anselm/software/numerical-languages/octave.md b/docs.it4i/anselm/software/numerical-languages/octave.md
index 7624f95e5..19142eb0f 100644
--- a/docs.it4i/anselm/software/numerical-languages/octave.md
+++ b/docs.it4i/anselm/software/numerical-languages/octave.md
@@ -48,7 +48,7 @@ To run octave in batch mode, write an octave script, then write a bash jobscript
     exit
 ```
 
-This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the [Job execution section](http://support.it4i.cz/docs/anselm/resource-allocation-and-job-execution).
+This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the [Job execution section](../../job-submission-and-execution/).
 
 The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c code. This is very useful for running native c subroutines in octave environment.
 
diff --git a/docs.it4i/anselm/software/numerical-languages/r.md b/docs.it4i/anselm/software/numerical-languages/r.md
index f62cad83d..d70ea9026 100644
--- a/docs.it4i/anselm/software/numerical-languages/r.md
+++ b/docs.it4i/anselm/software/numerical-languages/r.md
@@ -66,7 +66,7 @@ Example jobscript:
     exit
 ```
 
-This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../job-submission-and-execution/).
 
 ## Parallel R
 
@@ -396,4 +396,4 @@ Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, runnin
     exit
 ```
 
-For more information about jobscript and MPI execution refer to the [Job submission](../../resource-allocation-and-job-execution/job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
+For more information about jobscript and MPI execution refer to the [Job submission](../../job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
diff --git a/docs.it4i/anselm/software/omics-master/overview.md b/docs.it4i/anselm/software/omics-master/overview.md
index 7c3876e23..072994e9e 100644
--- a/docs.it4i/anselm/software/omics-master/overview.md
+++ b/docs.it4i/anselm/software/omics-master/overview.md
@@ -231,7 +231,7 @@ second one.
 
       --project>. Project ID of your supercomputer allocation.
 
-      --queue. [Queue](../../resource-allocation-and-job-execution/introduction.html) to run the jobs in.
+      --queue. [Queue](../../introduction.html) to run the jobs in.
 ```
 
 Input, output and ped arguments are mandatory. If the output folder does not exist, the pipeline will create it.
@@ -278,7 +278,7 @@ Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID):
     $ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod
 ```
 
-This command submits the processing [jobs to the queue](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+This command submits the processing [jobs to the queue](../../job-submission-and-execution.html).
 
 If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:
 
diff --git a/docs.it4i/anselm/software/openfoam.md b/docs.it4i/anselm/software/openfoam.md
index d7394a6e9..a2c98e3f2 100644
--- a/docs.it4i/anselm/software/openfoam.md
+++ b/docs.it4i/anselm/software/openfoam.md
@@ -45,7 +45,7 @@ In /opt/modules/modulefiles/engineering you can see installed engineering softwa
     lsdyna/7.x.x               openfoam/2.2.1-gcc481-openmpi1.6.5-SP
 ```
 
-For information how to use modules please [look here](../environment-and-modules/ "Environment and Modules ").
+For information how to use modules please [look here](../environment-and-modules/).
 
 ## Getting Started
 
@@ -112,7 +112,7 @@ Job submission
     $ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
 ```
 
-For information about job submission please [look here](../resource-allocation-and-job-execution/job-submission-and-execution/ "Job submission").
+For information about job submission please [look here](../job-submission-and-execution/).
 
 ## Running Applications in Parallel
 
diff --git a/docs.it4i/anselm/software/paraview.md b/docs.it4i/anselm/software/paraview.md
index 8d7f0552f..700736980 100644
--- a/docs.it4i/anselm/software/paraview.md
+++ b/docs.it4i/anselm/software/paraview.md
@@ -26,7 +26,7 @@ To launch the server, you must first allocate compute nodes, for example
     $ qsub -I -q qprod -A OPEN-0-0 -l select=2
 ```
 
-to launch an interactive session on 2 nodes. Refer to [Resource Allocation and Job Execution](../resource-allocation-and-job-execution/introduction/) for details.
+to launch an interactive session on 2 nodes. Refer to [Resource Allocation and Job Execution](../job-submission-and-execution/) for details.
 
 After the interactive session is opened, load the ParaView module :
 
diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
index e516ab59c..f064b2e6a 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -198,7 +198,7 @@ Allow incoming X11 graphics from the compute nodes at the login node:
 $ xhost +
 ```
 
-Get an interactive session on a compute node (for more detailed info [look here](../../../anselm/resource-allocation-and-job-execution/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:
+Get an interactive session on a compute node (for more detailed info [look here](../../../anselm/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:
 
 ```bash
 $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=24
diff --git a/docs.it4i/salomon/software/ansys/ansys-cfx.md b/docs.it4i/salomon/software/ansys/ansys-cfx.md
index 0eb52d3e6..21ce8f93b 100644
--- a/docs.it4i/salomon/software/ansys/ansys-cfx.md
+++ b/docs.it4i/salomon/software/ansys/ansys-cfx.md
@@ -47,7 +47,7 @@ echo Machines: $hl
 /ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
 ```
 
-Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](../../job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
 
 Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def
 
diff --git a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
index 5d49022a7..8646c2666 100644
--- a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
@@ -50,6 +50,6 @@ echo Machines: $hl
 /ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
 ```
 
-Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](../../job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
 
 Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ansys solver via parameter i=
diff --git a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
index f79935222..3d0826e99 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
@@ -28,7 +28,7 @@ Instead of [running your MPI program the usual way](../mpi/mpi/), use the the pe
     $ perf-report mpirun ./mympiprog.x
 ```
 
-The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [the queue system](../../job-submission-and-execution/).
 
 ## Example
 
diff --git a/docs.it4i/salomon/software/numerical-languages/octave.md b/docs.it4i/salomon/software/numerical-languages/octave.md
index 1f96d0849..6461bc4cc 100644
--- a/docs.it4i/salomon/software/numerical-languages/octave.md
+++ b/docs.it4i/salomon/software/numerical-languages/octave.md
@@ -45,7 +45,7 @@ To run octave in batch mode, write an octave script, then write a bash jobscript
     exit
 ```
 
-This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/).
+This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the [Job execution section](../../).
 
 The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c code. This is very useful for running native c subroutines in octave environment.
 
diff --git a/docs.it4i/salomon/software/numerical-languages/r.md b/docs.it4i/salomon/software/numerical-languages/r.md
index e6f9a69b4..6a01926e1 100644
--- a/docs.it4i/salomon/software/numerical-languages/r.md
+++ b/docs.it4i/salomon/software/numerical-languages/r.md
@@ -66,7 +66,7 @@ Example jobscript:
     exit
 ```
 
-This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+This script may be submitted directly to the PBS workload manager via the qsub command.  The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../job-submission-and-execution/).
 
 ## Parallel R
 
@@ -392,7 +392,7 @@ Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, runnin
     exit
 ```
 
-For more information about jobscripts and MPI execution refer to the [Job submission](../../resource-allocation-and-job-execution/job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
+For more information about jobscripts and MPI execution refer to the [Job submission](../../job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
 
 ## Xeon Phi Offload
 
-- 
GitLab