Sign upLogin

Ensembl/ensembl-hive

View on GitHub
Star
docs/MPI_howto.md

Summary

Maintainability
Test Coverage

Line length
Open

We won't discuss the inner parts of the modules, but real examples can be found in the [ensembl-compara](https://github.com/Ensembl/ensembl-compara) repository. It ships modules used for phylogenetic trees inference: [RAxML](https://github.com/Ensembl/ensembl-compara/blob/release/77/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/RAxML.pm) and [ExaML](https://github.com/Ensembl/ensembl-compara/blob/feature/update_pipeline/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/ExaML.pm). They look very light-weight (only command-line definitions) because most of the logic is in the base class (*GenericRunnable*), but nevertheless show the command lines used and the parametrization of multi-core and MPI runs.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

1. You need to setup a resource class that encodes those requirements e.g. *16 cores and 24Gb of RAM*:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

            '16Gb_64c_mpi' => {'LSF' => '-q mpi -a openmpi -n 64 -M16000 -R"select[mem>16000] rusage[mem=16000] same[model] span[ptile=4]"' },
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Code block style
Open

        module load openmpi-x86_64
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Trailing spaces
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Multiple consecutive blank lines
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD012 - Multiple consecutive blank lines

Tags: whitespace, blank_lines

Aliases: no-multiple-blanks

This rule is triggered when there are multiple consecutive blank lines in the document:

Some text here


Some more text here

To fix this, delete the offending lines:

Some text here

Some more text here

Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.

Line length
Open

MPI usually comes in two implementations: OpenMPI and mpich2. One of the most common source of problems is to compile the code with one MPI implementation and try to run it with another. You must compile and run your code with the **same** MPI implementation.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

  * `-q mpi -a openmpi` is needed to tell LSF you will run a job in the MPI/OpenMPI environment
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Code block style
Open

        sub resource_classes {
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Header style
Open

###The Hive bit
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

Header style
Open

###!!!Temporary files!!!
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

Line length
Open

With this tutorial, our goal is to give insights on how to set up the Hive to run jobs using Shared Memory Parallelism (threads) and Distributed Memory Parallelism (MPI).
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

  * `span[ptile=4]`, this option specifies the granularity in which LSF will split the jobs/per node. In this example we ask for at least 4 jobs to be executed in the same machine. This might affect queuing times.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Inconsistent indentation for list items at the same level
Open

  * `span[ptile=4]`, this option specifies the granularity in which LSF will split the jobs/per node. In this example we ask for at least 4 jobs to be executed in the same machine. This might affect queuing times.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD005 - Inconsistent indentation for list items at the same level

Tags: bullet, ul, indentation

Aliases: list-indent

This rule is triggered when list items are parsed as being at the same level, but don't have the same indentation:

* Item 1
    * Nested Item 1
    * Nested Item 2
   * A misaligned item

Usually this rule will be triggered because of a typo. Correct the indentation for the list to fix it:

* Item 1
  * Nested Item 1
  * Nested Item 2
  * Nested Item 3

Line length
Open

You should check the documentation of the code you want to run to find out how to define the number of threads it will use.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

            'cmd' => 'cmd 1 ; cmd  2 ; mpirun.lsf -np 64 -mca btl tcp,self #examl_exe# -examl_parameter_1 value1 -examl_parameter_2 value2',
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Ordered list item prefix
Open

2. You need to add the analysis to your pipeconfig:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Line length
Open

            '24Gb_16_core_job' => { 'LSF' => '-n 16 -M24000  -R"select[mem>24000] span[hosts=1] rusage[mem=24000]"' },
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

Here is an excerpt of Ensembl Compara's [ExaML](https://github.com/Ensembl/ensembl-compara/blob/feature/update_pipeline/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/ExaML.pm) MPI module. Note that LSF needs the MPI command to be run through mpirun.lsf
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Header style
Open

###Tips for compiling for MPI
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

Code block style
Open

        sub param_defaults {
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Line length
Open

>This case requires a bit more attention, so please be very careful in including / loading the right libraries / modules.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

No space after hash on atx style header
Open

###Tips for compiling for MPI
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

Trailing spaces
Open

---
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

            # ...
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Line length
Open

Here again, once the environment is properly set up, we only have to define the correct resource class and comand lines in Hive.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

The resource description is specific to our LSF environment, so adapt it to yours, but:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Header style
Open

####Otherwise, follow the recommended usage in your institute
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

Consider starting bulleted lists at the beginning of the line
Open

  * `-q mpi -a openmpi` is needed to tell LSF you will run a job in the MPI/OpenMPI environment
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD006 - Consider starting bulleted lists at the beginning of the line

Tags: bullet, ul, indentation

Aliases: ul-start-left

This rule is triggered when top level lists don't start at the beginning of a line:

Some text

  * List item
  * List item

To fix, ensure that top level list items are not indented:

Some test

* List item
* List item

Rationale: Starting lists at the beginning of the line means that nested list items can all be indented by the same amount when an editor's indent function or the tab key is used to indent. Starting a list 1 space in means that the indent of the first nested list is less than the indent of the second level (3 characters if you use 4 space tabs, or 1 character if you use 2 space tabs).

Inconsistent indentation for list items at the same level
Open

  * `same[model]` is needed to ensure that the selected compute nodes all have the same hardware. You may also need something like `select[avx]` to select the nodes that have the [AVX instruction set](http://en.wikipedia.org/wiki/Advanced_Vector_Extensions)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD005 - Inconsistent indentation for list items at the same level

Tags: bullet, ul, indentation

Aliases: list-indent

This rule is triggered when list items are parsed as being at the same level, but don't have the same indentation:

* Item 1
    * Nested Item 1
    * Nested Item 2
   * A misaligned item

Usually this rule will be triggered because of a typo. Correct the indentation for the list to fix it:

* Item 1
  * Nested Item 1
  * Nested Item 2
  * Nested Item 3

Trailing spaces
Open

            # ...
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Spaces inside link text
Open

####If your compute environment uses [Module ](http://modules.sourceforge.net/)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD039 - Spaces inside link text

Tags: whitespace, links

Aliases: no-space-in-links

This rule is triggered on links that have spaces surrounding the link text:

[ a link ](http://www.example.com/)

To fix this, remove the spaces surrounding the link text:

[a link](http://www.example.com/)

Line length
Open

  * `same[model]` is needed to ensure that the selected compute nodes all have the same hardware. You may also need something like `select[avx]` to select the nodes that have the [AVX instruction set](http://en.wikipedia.org/wiki/Advanced_Vector_Extensions)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Trailing punctuation in header
Open

###!!!Temporary files!!!
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD026 - Trailing punctuation in header

Tags: headers

Aliases: no-trailing-punctuation

Parameters: punctuation (string; default ".,;:!?")

This rule is triggered on any header that has a punctuation character as the last character in the line:

# This is a header.

To fix this, remove any trailing punctuation:

# This is a header

Note: The punctuation parameter can be used to specify what characters class as punctuation at the end of the header. For example, you can set it to '.,;:!' to allow headers with question marks in them, such as might be used in an FAQ.

Inconsistent indentation for list items at the same level
Open

  * `-q mpi -a openmpi` is needed to tell LSF you will run a job in the MPI/OpenMPI environment
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD005 - Inconsistent indentation for list items at the same level

Tags: bullet, ul, indentation

Aliases: list-indent

This rule is triggered when list items are parsed as being at the same level, but don't have the same indentation:

* Item 1
    * Nested Item 1
    * Nested Item 2
   * A misaligned item

Usually this rule will be triggered because of a typo. Correct the indentation for the list to fix it:

* Item 1
  * Nested Item 1
  * Nested Item 2
  * Nested Item 3

Line length
Open

First of all, your institution / compute-farm provider may have documentation on this topic. Please refer to them for implementation details (intranet-only links: [EBI](http://www.ebi.ac.uk/systems-srv/public-wiki/index.php/EBI_Good_Computing_Guide), [Sanger institute](http://mediawiki.internal.sanger.ac.uk/index.php/How_to_run_MPI_jobs_on_the_farm))
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

*Module* provides configuration files (module-files) for the dynamic modification of the user’s environment.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

No space after hash on atx style header
Open

###The Hive bit
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

Horizontal rule style
Open

---
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD035 - Horizontal rule style

Tags: hr

Aliases: hr-style

Parameters: style ("consistent", "---", "***", or other string specifying the horizontal rule; default "consistent")

This rule is triggered when inconsistent styles of horizontal rules are used in the document:

---

- - -

***

* * *

****

To fix this, ensure any horizontal rules used in the document are consistent, or match the given style if the rule is so configured:

---

---

Note: by default, this rule is configured to just require that all horizontal rules in the document are the same, and will trigger if any of the horizontal rules are different than the first one encountered in the document. If you want to configure the rule to match a specific style, the parameter given to the 'style' option is a string containing the exact horizontal rule text that is allowed.

Trailing spaces
Open

We would like to call your attention to the `cmd` parameter, where we define the command line used to run Thread_app. Note that the actual command line would vary between different programs, but in this case, the parameter `-T` is set to 16 cores.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Line length
Open

Just with this basic configuration, the Hive is able to run Thread_app in 16 cores.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Ordered list item prefix
Open

3. You need to add the analysis to your pipeconfig:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Code block style
Open

        sub resource_classes {
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Trailing spaces
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Line length
Open

If you have access to Intel compilers, we strongly recommend you to try compiling your code with it and checking for performance improvements.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

No space after hash on atx style header
Open

###!!!Temporary files!!!
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

Header style
Open

####If your compute environment uses [Module ](http://modules.sourceforge.net/)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

Multiple consecutive blank lines
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD012 - Multiple consecutive blank lines

Tags: whitespace, blank_lines

Aliases: no-multiple-blanks

This rule is triggered when there are multiple consecutive blank lines in the document:

Some text here


Some more text here

To fix this, delete the offending lines:

Some text here

Some more text here

Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.

Line length
Open

>If you have already compiled your code and know how to enable the use of multiple threads / cores, this case should be very straightforward. It basically consists in defining the proper resource class in your pipeline. We also include some tips on how to compile code under MPI environment, but be aware that will vary across systems.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

No space after hash on atx style header
Open

####Otherwise, follow the recommended usage in your institute
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

Code block style
Open

        {   -logic_name => 'MPI_app',
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Trailing spaces
Open

Just with this basic configuration, the Hive is able to run Thread_app in 16 cores.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Multiple consecutive blank lines
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD012 - Multiple consecutive blank lines

Tags: whitespace, blank_lines

Aliases: no-multiple-blanks

This rule is triggered when there are multiple consecutive blank lines in the document:

Some text here


Some more text here

To fix this, delete the offending lines:

Some text here

Some more text here

Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.

Line length
Open

We would like to call your attention to the `cmd` parameter, where we define the command line used to run Thread_app. Note that the actual command line would vary between different programs, but in this case, the parameter `-T` is set to 16 cores.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

This can be easily taken care by properly setting up your .bashrc to load the right modules.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

If you don't have modules for the MPI environment available on your system, please make sure you include the right libraries (PATH, and any other environment variables)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Code block style
Open

        module avail
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Multiple consecutive blank lines
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD012 - Multiple consecutive blank lines

Tags: whitespace, blank_lines

Aliases: no-multiple-blanks

This rule is triggered when there are multiple consecutive blank lines in the document:

Some text here


Some more text here

To fix this, delete the offending lines:

Some text here

Some more text here

Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.

Code block style
Open

        {   -logic_name => 'app_multi_core',
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Code block style
Open

        sub worker_temp_directory_name {
Severity: Info
Found in docs/MPI_howto.md by markdownlint

Trailing spaces
Open

  * `span[ptile=4]`, this option specifies the granularity in which LSF will split the jobs/per node. In this example we ask for at least 4 jobs to be executed in the same machine. This might affect queuing times.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

No space after hash on atx style header
Open

####If your compute environment uses [Module ](http://modules.sourceforge.net/)
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

There are no issues that match your filters.

Category
Status