* -> *

docs.it4i/anselm-cluster-documentation/compute-nodes.md

@@ -69,8 +69,8 @@ Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes
 * speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
 * peak performance:  19.2 GFLOP/s per core
 * caches:
-   * L2: 256 KB per core
-   * L3: 20 MB per processor
+  * L2: 256 KB per core
+  * L3: 20 MB per processor
 * memory bandwidth at the level of the processor: 51.2 GB/s
 
 ### Intel Sandy Bridge E5-2470 Processor
@@ -79,8 +79,8 @@ Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes
 * speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
 * peak performance:  18.4 GFLOP/s per core
 * caches:
-   * L2: 256 KB per core
-   * L3: 20 MB per processor
+  * L2: 256 KB per core
+  * L3: 20 MB per processor
 * memory bandwidth at the level of the processor: 38.4 GB/s
 
 Nodes equipped with Intel Xeon E5-2665 CPU have set PBS resource attribute cpu_freq = 24, nodes equipped with Intel Xeon E5-2470 CPU have set PBS resource attribute cpu_freq = 23.
@@ -103,28 +103,28 @@ Intel Turbo Boost Technology is used by default,  you can disable it for all nod
 
 * 2 sockets
 * Memory Controllers are integrated into processors.
-   * 8 DDR3 DIMMs per node
-   * 4 DDR3 DIMMs per CPU
-   * 1 DDR3 DIMMs per channel
-   * Data rate support: up to 1600MT/s
+  * 8 DDR3 DIMMs per node
+  * 4 DDR3 DIMMs per CPU
+  * 1 DDR3 DIMMs per channel
+  * Data rate support: up to 1600MT/s
 * Populated memory: 8 x 8 GB DDR3 DIMM 1600 MHz
 
 ### Compute Node With GPU or MIC Accelerator
 
 * 2 sockets
 * Memory Controllers are integrated into processors.
-   * 6 DDR3 DIMMs per node
-   * 3 DDR3 DIMMs per CPU
-   * 1 DDR3 DIMMs per channel
-   * Data rate support: up to 1600MT/s
+  * 6 DDR3 DIMMs per node
+  * 3 DDR3 DIMMs per CPU
+  * 1 DDR3 DIMMs per channel
+  * Data rate support: up to 1600MT/s
 * Populated memory: 6 x 16 GB DDR3 DIMM 1600 MHz
 
 ### Fat Compute Node
 
 * 2 sockets
 * Memory Controllers are integrated into processors.
-   * 16 DDR3 DIMMs per node
-   * 8 DDR3 DIMMs per CPU
-   * 2 DDR3 DIMMs per channel
-   * Data rate support: up to 1600MT/s
+  * 16 DDR3 DIMMs per node
+  * 8 DDR3 DIMMs per CPU
+  * 2 DDR3 DIMMs per channel
+  * Data rate support: up to 1600MT/s
 * Populated memory: 16 x 32 GB DDR3 DIMM 1600 MHz

docs.it4i/anselm-cluster-documentation/software/kvirtualization.md

@@ -99,7 +99,7 @@ We recommend, that startup script
 
 * maps Job Directory from host (from compute node)
 * runs script (we call it "run script") from Job Directory and waits for application's exit
-   * for management purposes if run script does not exist wait for some time period (few minutes)
+  * for management purposes if run script does not exist wait for some time period (few minutes)
 * shutdowns/quits OS
 
 For Windows operating systems we suggest using Local Group Policy Startup script, for Linux operating systems rc.local, runlevel init script or similar service.

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md

@@ -10,8 +10,8 @@ PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of bu
 
 * [project webpage](http://www.mcs.anl.gov/petsc/)
 * [documentation](http://www.mcs.anl.gov/petsc/documentation/)
-   * [PETSc Users Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
-   * [index of all manual pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
+  * [PETSc Users Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
+  * [index of all manual pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
 * PRACE Video Tutorial [part1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
 
 ## Modules
@@ -37,24 +37,24 @@ All these libraries can be used also alone, without PETSc. Their static or share
 ### Libraries Linked to PETSc on Anselm (As of 11 April 2015)
 
 * dense linear algebra
-   * [Elemental](http://libelemental.org/)
+  * [Elemental](http://libelemental.org/)
 * sparse linear system solvers
-   * [Intel MKL Pardiso](https://software.intel.com/en-us/node/470282)
-   * [MUMPS](http://mumps.enseeiht.fr/)
-   * [PaStiX](http://pastix.gforge.inria.fr/)
-   * [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
-   * [SuperLU](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu)
-   * [SuperLU_Dist](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
+  * [Intel MKL Pardiso](https://software.intel.com/en-us/node/470282)
+  * [MUMPS](http://mumps.enseeiht.fr/)
+  * [PaStiX](http://pastix.gforge.inria.fr/)
+  * [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
+  * [SuperLU](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu)
+  * [SuperLU_Dist](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
 * input/output
-   * [ExodusII](http://sourceforge.net/projects/exodusii/)
-   * [HDF5](http://www.hdfgroup.org/HDF5/)
-   * [NetCDF](http://www.unidata.ucar.edu/software/netcdf/)
+  * [ExodusII](http://sourceforge.net/projects/exodusii/)
+  * [HDF5](http://www.hdfgroup.org/HDF5/)
+  * [NetCDF](http://www.unidata.ucar.edu/software/netcdf/)
 * partitioning
-   * [Chaco](http://www.cs.sandia.gov/CRF/chac.html)
-   * [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)
-   * [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
-   * [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
+  * [Chaco](http://www.cs.sandia.gov/CRF/chac.html)
+  * [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)
+  * [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
+  * [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
 * preconditioners & multigrid
-   * [Hypre](http://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/)
-   * [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
-   * [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
+  * [Hypre](http://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/)
+  * [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
+  * [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)

docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md

@@ -96,12 +96,12 @@ BAM is the binary representation of SAM and keeps exactly the same information a
 Some features
 
 * Quality control
-   * reads with N errors
-   * reads with multiple mappings
-   * strand bias
-   * paired-end insert
+  * reads with N errors
+  * reads with multiple mappings
+  * strand bias
+  * paired-end insert
 * Filtering: by number of errors, number of hits
-   * Comparator: stats, intersection, ...
+  * Comparator: stats, intersection, ...
 
 ** Input: ** BAM file.
 

docs.it4i/anselm-cluster-documentation/storage.md

@@ -81,22 +81,22 @@ The architecture of Lustre on Anselm is composed of two metadata servers (MDS) a
  Configuration of the storages
 
 * HOME Lustre object storage
-   * One disk array NetApp E5400
-   * 22 OSTs
-   * 227 2TB NL-SAS 7.2krpm disks
-   * 22 groups of 10 disks in RAID6 (8+2)
-   * 7 hot-spare disks
+  * One disk array NetApp E5400
+  * 22 OSTs
+  * 227 2TB NL-SAS 7.2krpm disks
+  * 22 groups of 10 disks in RAID6 (8+2)
+  * 7 hot-spare disks
 * SCRATCH Lustre object storage
-   * Two disk arrays NetApp E5400
-   * 10 OSTs
-   * 106 2TB NL-SAS 7.2krpm disks
-   * 10 groups of 10 disks in RAID6 (8+2)
-   * 6 hot-spare disks
+  * Two disk arrays NetApp E5400
+  * 10 OSTs
+  * 106 2TB NL-SAS 7.2krpm disks
+  * 10 groups of 10 disks in RAID6 (8+2)
+  * 6 hot-spare disks
 * Lustre metadata storage
-   * One disk array NetApp E2600
-   * 12 300GB SAS 15krpm disks
-   * 2 groups of 5 disks in RAID5
-   * 2 hot-spare disks
+  * One disk array NetApp E2600
+  * 12 300GB SAS 15krpm disks
+  * 2 groups of 5 disks in RAID5
+  * 2 hot-spare disks
 
 \###HOME
 

docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md

@@ -129,18 +129,18 @@ A FAQ about certificates can be found here: [Certificates FAQ](certificates-faq/
 Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, please attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for [login credentials](obtaining-login-credentials/#the-login-credentials).
 
 * Go to [CAcert](www.cacert.org).
-   * If there's a security warning, just acknowledge it.
+  * If there's a security warning, just acknowledge it.
 * Click _Join_.
 * Fill in the form and submit it by the _Next_ button.
-   * Type in the e-mail address which you use for communication with us.
-   * Don't forget your chosen _Pass Phrase_.
+  * Type in the e-mail address which you use for communication with us.
+  * Don't forget your chosen _Pass Phrase_.
 * You will receive an e-mail verification link. Follow it.
 * After verifying, go to the CAcert's homepage and login using     _Password Login_.
 * Go to _Client Certificates_ _New_.
 * Tick _Add_ for your e-mail address and click the _Next_ button.
 * Click the _Create Certificate Request_ button.
 * You'll be redirected to a page from where you can download/install your certificate.
-   * Simultaneously you'll get an e-mail with a link to the certificate.
+  * Simultaneously you'll get an e-mail with a link to the certificate.
 
 ## Installation of the Certificate Into Your Mail Client
 

docs.it4i/salomon/compute-nodes.md

@@ -61,7 +61,7 @@ Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors
 * speed: 2.5 GHz, up to 3.3 GHz using Turbo Boost Technology
 * peak performance:  19.2 GFLOP/s per core
 * caches:
-   * Intel® Smart Cache:  30 MB
+  * Intel® Smart Cache:  30 MB
 * memory bandwidth at the level of the processor: 68 GB/s
 
 ### MIC Accelerator Intel Xeon Phi 7120P Processor
@@ -71,7 +71,7 @@ Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors
     GHz, up to 1.333 GHz using Turbo Boost Technology
 * peak performance:  18.4 GFLOP/s per core
 * caches:
-   * L2:  30.5 MB
+  * L2:  30.5 MB
 * memory bandwidth at the level of the processor:  352 GB/s
 
 ## Memory Architecture
@@ -82,9 +82,9 @@ Memory is equally distributed across all CPUs and cores for optimal performance.
 
 * 2 sockets
 * Memory Controllers are integrated into processors.
-   * 8 DDR4 DIMMs per node
-   * 4 DDR4 DIMMs per CPU
-   * 1 DDR4 DIMMs per channel
+  * 8 DDR4 DIMMs per node
+  * 4 DDR4 DIMMs per CPU
+  * 1 DDR4 DIMMs per channel
 * Populated memory: 8 x 16 GB DDR4 DIMM >2133 MHz
 
 ### Compute Node With MIC Accelerator
@@ -102,6 +102,6 @@ MIC Accelerator Intel Xeon Phi 7120P Processor
 * 2 sockets
 * Memory Controllers are are connected via an
     Interprocessor Network (IPN) ring.
-   * 16 GDDR5 DIMMs per node
-   * 8 GDDR5 DIMMs per CPU
-   * 2 GDDR5 DIMMs per channel
+  * 16 GDDR5 DIMMs per node
+  * 8 GDDR5 DIMMs per CPU
+  * 2 GDDR5 DIMMs per channel

docs.it4i/salomon/storage.md

@@ -35,14 +35,14 @@ The architecture of Lustre on Salomon is composed of two metadata servers (MDS)
 Configuration of the SCRATCH Lustre storage
 
 * SCRATCH Lustre object storage
-   * Disk array SFA12KX
-   * 540 x 4 TB SAS 7.2krpm disk
-   * 54 x OST of 10 disks in RAID6 (8+2)
-   * 15 x hot-spare disk
-   * 4 x 400 GB SSD cache
+  * Disk array SFA12KX
+  * 540 x 4 TB SAS 7.2krpm disk
+  * 54 x OST of 10 disks in RAID6 (8+2)
+  * 15 x hot-spare disk
+  * 4 x 400 GB SSD cache
 * SCRATCH Lustre metadata storage
-   * Disk array EF3015
-   * 12 x 600 GB SAS 15 krpm disk
+  * Disk array EF3015
+  * 12 x 600 GB SAS 15 krpm disk
 
 ### Understanding the Lustre File Systems