diff --git a/docs.it4i/anselm-cluster-documentation/compute-nodes.md b/docs.it4i/anselm-cluster-documentation/compute-nodes.md
index 0c7fba51abd9e749cbd9f7205fade151f31b951f..440201ed024b87d101ea4a28ffd9ad393df83e37 100644
--- a/docs.it4i/anselm-cluster-documentation/compute-nodes.md
+++ b/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
diff --git a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md b/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
index c97525397ffc063e0a8b82b64aff22ee1ba017ec..8ecfd71d5e62637b80eebd54f1cc32dedb818f5e 100644
--- a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
+++ b/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.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index 61e999f0017a80891c21a08aa36995f39452e01c..6d0b8fb58fae24e98cf4fe1f682e119890a12d67 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/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)
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 015cc71f2575911bd2c21e5aecc8494108402bf8..c968fb56351fc78cfbcfb0576ccc0ef8063a898c 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
+++ b/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.
diff --git a/docs.it4i/anselm-cluster-documentation/storage.md b/docs.it4i/anselm-cluster-documentation/storage.md
index 8ee81fee683c20874f93df2197d93689bcacbf0f..436e6141781c3d7d207e7a30718be58db8995316 100644
--- a/docs.it4i/anselm-cluster-documentation/storage.md
+++ b/docs.it4i/anselm-cluster-documentation/storage.md
@@ -81,22 +81,22 @@ The architecture of Lustre on Anselm is composed of two metadata servers (MDS)
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
diff --git a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index a20112ad4b31fd27468f5b975763557dee0a3f7a..7213ec31c1fc03b7cd770cb35c4cd77070ecdbb8 100644
--- a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/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
diff --git a/docs.it4i/salomon/compute-nodes.md b/docs.it4i/salomon/compute-nodes.md
index 239029f583014d5ce115d3fc64df04b0aa350073..83bca5c4045e93800fe922accb9882508f0aa0b1 100644
--- a/docs.it4i/salomon/compute-nodes.md
+++ b/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
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index 3828b77a373c636fce8f6454be656d6d59d0746a..0edbcd5db799a8517bbe8ffff128f9c552d70832 100644
--- a/docs.it4i/salomon/storage.md
+++ b/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