fix mdl complaints

docs.it4i/salomon-upgrade.md

@@ -12,7 +12,7 @@ Salomon operating system has been upgraded to the latest CentOS 7.6 on 2018-12-0
 * glibc upgraded to 2.17 (2.12 now)
 * software modules/binaries should be recompiled or deleted
 
-## Discontinued Modules
+# Discontinued Modules
 
 A new tag has been introduced. Modules tagged with **C6** might be malfunctioning. These modules might be recompiled during transition period. Keep support@it4i.cz informed on malfunctioning modules.
 

docs.it4i/salomon/shell-and-data-access.md

@@ -22,7 +22,7 @@ The authentication is by the [private key][1] only.
 
     md5:
 
-    f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)
+    f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)<br />
     70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)
 
     sha256:

docs.it4i/software/chemistry/molpro.md

@@ -61,6 +61,7 @@ molpro -d /scratch/$USER/$PBS_JOBID caffeine_opt_diis.com
 # delete scratch directory
 rm -rf /scratch/$USER/$PBS_JOBID
 ```
+
 [1]: ../../salomon/storage.md
 
 [a]: http://www.molpro.net/

docs.it4i/software/chemistry/phono3py.md

@@ -166,6 +166,7 @@ Finally the thermal conductivity result is produced by grouping single conductiv
 ```console
 $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --br --read_gamma
 ```
+
 [1]: ./POSCAR.txt
 [2]: ./KPOINTS.txt
 [3]: ./POTCAR.txt

docs.it4i/software/isv_licenses.md

@@ -18,6 +18,7 @@ If an ISV application was purchased for educational (research) purposes and also
 For each license there is a [table][a], which provides the information about the name, number of available (purchased/licensed), number of used and number of free license features.
 
 ### Text Interface
+
 (Anselm only, obsolete)
 
 For each license there is a unique text file, which provides the information about the name, number of available (purchased/licensed), number of used and number of free license features. The text files are accessible from the Anselm command prompt.
@@ -54,6 +55,7 @@ $ cat /apps/user/licenses/matlab_features_state.txt
 ```
 
 ## License Aware Job Scheduling
+
 Anselm cluster and Salomon cluster provide license aware job scheduling.
 
 Selected licenses are accounted and checked by the scheduler of PBS Pro. If you ask for certain licenses, the scheduler won't start the job until the asked licenses are free (available). This prevents to crash batch jobs, just because of unavailability of the needed licenses.

docs.it4i/software/lang/julialang.md

@@ -46,7 +46,7 @@ end
 
 vol = sphere_vol(3)
 # @printf allows number formatting but does not automatically append the \n to statements, see below
-@printf "volume = %0.3f\n" vol 
+@printf "volume = %0.3f\n" vol
 #> volume = 113.097
 
 quad1, quad2 = quadratic2(2.0, -2.0, -12.0)
@@ -156,7 +156,7 @@ println("e_str1 == e_str2: $(e_str1 == e_str2)")
 #> e_str1 == e_str2: true
 
 # available number format characters are [f, e, g, c, s, p, d](https://github.com/JuliaLang/julia/blob/master/base/printf.jl#L15):
-# (pi is a predefined constant; however, since its type is 
+# (pi is a predefined constant; however, since its type is
 # "MathConst" it has to be converted to a float to be formatted)
 @printf "fix trailing precision: %0.3f\n" float(pi)
 #> fix trailing precision: 3.142
@@ -226,9 +226,9 @@ println(r)
 r = eachmatch(r"[\w]{4,}", s1)
 for i in r print("\"$(i.match)\" ") end
 println()
-#> "quick" "brown" "jumps" "over" "lazy" 
+#> "quick" "brown" "jumps" "over" "lazy"
 
-# a string can be repeated using the [repeat](http://julia.readthedocs.org/en/latest/manual/strings/#common-operations) function, 
+# a string can be repeated using the [repeat](http://julia.readthedocs.org/en/latest/manual/strings/#common-operations) function,
 # or more succinctly with the [^ syntax](http://julia.readthedocs.org/en/latest/stdlib/base/#Base.^):
 r = "hello "^3
 show(r); println() #> "hello hello hello "
@@ -487,7 +487,7 @@ println(1 in keys(a1)) #> true
 # where [keys](http://docs.julialang.org/en/latest/stdlib/base/#Base.keys) creates an iterator over the keys of the dictionary
 
 # similar to keys, [values](http://docs.julialang.org/en/latest/stdlib/base/#Base.values) get iterators over the dict's values:
-printsum(values(a1)) 
+printsum(values(a1))
 #> Base.ValueIterator for a Dict{Int64,String} with 3 entries: String["two","three","one"]
 
 # use [collect](http://docs.julialang.org/en/latest/stdlib/base/#Base.collect) to get an array:

docs.it4i/software/mpi/ompi-examples.md

@@ -8,7 +8,7 @@ There are two MPI examples, each using one of six different MPI interfaces:
 
 ### Hello World
 
-``` c tab="C"
+```c tab="C"
 /*
  * Copyright (c) 2004-2006 The Trustees of Indiana University and Indiana
  *                         University Research and Technology
@@ -18,6 +18,7 @@ There are two MPI examples, each using one of six different MPI interfaces:
  * Sample MPI "hello world" application in C
  */
 
+<!-- markdownlint-disable MD018 MD025 -->
 #include <stdio.h>
 #include "mpi.h"
 
@@ -38,7 +39,7 @@ int main(int argc, char* argv[])
 }
 ```
 
-``` c++ tab="C++"
+```c++ tab="C++"
 //
 // Copyright (c) 2004-2006 The Trustees of Indiana University and Indiana
 //                         University Research and Technology
@@ -55,7 +56,9 @@ int main(int argc, char* argv[])
 // bindings.
 //
 
+<!-- markdownlint-disable MD018 MD025 -->
 #include "mpi.h"
+<!-- markdownlint-disable MD022 -->
 #include <iostream>
 
 int main(int argc, char **argv)
@@ -75,7 +78,7 @@ int main(int argc, char **argv)
 }
 ```
 
-``` fortran tab="F mpi.h"
+```fortran tab="F mpi.h"
 C
 C Copyright (c) 2004-2006 The Trustees of Indiana University and Indiana
 C                         University Research and Technology
@@ -105,7 +108,7 @@ C
         end
 ```
 
-``` fortran tab="F use mpi"
+```fortran tab="F use mpi"
 !
 ! Copyright (c) 2004-2006 The Trustees of Indiana University and Indiana
 !                         University Research and Technology
@@ -136,7 +139,7 @@ program main
 end
 ```
 
-``` java tab="Java"
+```java tab="Java"
 /*
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.
@@ -166,7 +169,6 @@ import mpi.*;
 class Hello {
     static public void main(String[] args) throws MPIException {
 
-
 	MPI.Init(args);
 
 	int myrank = MPI.COMM_WORLD.getRank();
@@ -187,6 +189,7 @@ class Hello {
 * C shmem.h:           [hello_oshmem_c.c](../../src/ompi/hello_oshmem_c.c)
 * Fortran shmem.fh:    [hello_oshmemfh.f90](../../src/ompi/hello_oshmemfh.f90)
 
+<!-- markdownlint-disable MD001 -->
 ### Send a Trivial Message Around in a Ring
 
 * C:                   [ring_c.c](../../src/ompi/ring_c.c)
@@ -200,6 +203,7 @@ class Hello {
 
 Additionally, there's one further example application, but this one only uses the MPI C bindings:
 
+<!-- markdownlint-disable MD001 -->
 ### Test the Connectivity Between All Pross
 
 * C:   [connectivity_c.c](../../src/ompi/connectivity_c.c)

docs.it4i/software/numerical-languages/octave.md

@@ -106,6 +106,7 @@ $ ssh mic0                                               # login to the MIC card
 $ source /apps/tools/octave/3.8.2-mic/bin/octave-env.sh  # set up environment variables
 $ octave -q /apps/tools/octave/3.8.2-mic/example/test0.m # run an example
 ```
+
 [1]: ../../salomon/job-submission-and-execution.md
 [2]: ../intel/intel-xeon-phi-salomon.md
 [3]: ../../salomon/compute-nodes.md