From 085f85f81460a6995f6a4e058bd834d4c666017d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pavel=20Gajdu=C5=A1ek?= <gajdusek.pavel@gmail.com>
Date: Wed, 13 Sep 2017 14:26:24 +0200
Subject: [PATCH] mdlint
---
README.md | 4 +-
.../anselm/software/debuggers/valgrind.md | 46 +++++++++----------
.../software/machine-learning/tensorflow.md | 26 +++++------
.../salomon/software/debuggers/valgrind.md | 46 +++++++++----------
.../software/machine-learning/tensorflow.md | 22 ++++-----
docs.it4i/snippets/modules_matrix_search.md | 2 +-
docs.it4i/software/easybuild.md | 8 ++--
docs.it4i/software/singularity.md | 2 +
docs.it4i/software/spack.md | 6 +--
9 files changed, 82 insertions(+), 80 deletions(-)
diff --git a/README.md b/README.md
index 78d4938ab..7ca5d57a1 100644
--- a/README.md
+++ b/README.md
@@ -29,8 +29,8 @@ Mellanox
### Formulas are made with:
-* https://facelessuser.github.io/pymdown-extensions/extensions/arithmatex/
-* https://www.mathjax.org/
+* [https://facelessuser.github.io/pymdown-extensions/extensions/arithmatex/](https://facelessuser.github.io/pymdown-extensions/extensions/arithmatex/)
+* [https://www.mathjax.org/](https://www.mathjax.org/)
You can add formula to page like this:
diff --git a/docs.it4i/anselm/software/debuggers/valgrind.md b/docs.it4i/anselm/software/debuggers/valgrind.md
index 0e381e945..f6c3f6aaf 100644
--- a/docs.it4i/anselm/software/debuggers/valgrind.md
+++ b/docs.it4i/anselm/software/debuggers/valgrind.md
@@ -31,19 +31,19 @@ Compile the application which you want to debug as usual. It is advisable to add
For example, lets look at this C code, which has two problems :
```cpp
- #include <stdlib.h>
-
- void f(void)
- {
- int* x = malloc(10 * sizeof(int));
- x[10] = 0; // problem 1: heap block overrun
- } // problem 2: memory leak -- x not freed
-
- int main(void)
- {
- f();
- return 0;
- }
+#include <stdlib.h>
+
+void f(void)
+{
+ int* x = malloc(10 * sizeof(int));
+ x[10] = 0; // problem 1: heap block overrun
+} // problem 2: memory leak -- x not freed
+
+int main(void)
+{
+ f();
+ return 0;
+}
```
Now, compile it with Intel compiler :
@@ -161,19 +161,19 @@ so it is better to use the MPI-enabled valgrind from module. The MPI version req
Lets look at this MPI example :
```cpp
- #include <stdlib.h>
- #include <mpi.h>
+#include <stdlib.h>
+#include <mpi.h>
- int main(int argc, char *argv[])
- {
- int *data = malloc(sizeof(int)*99);
+int main(int argc, char *argv[])
+{
+ int *data = malloc(sizeof(int)*99);
- MPI_Init(&argc, &argv);
- MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
- MPI_Finalize();
+ MPI_Init(&argc, &argv);
+ MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
+ MPI_Finalize();
- return 0;
- }
+ return 0;
+}
```
There are two errors - use of uninitialized memory and invalid length of the buffer. Lets debug it with valgrind :
diff --git a/docs.it4i/anselm/software/machine-learning/tensorflow.md b/docs.it4i/anselm/software/machine-learning/tensorflow.md
index a495c8982..d35b92fec 100644
--- a/docs.it4i/anselm/software/machine-learning/tensorflow.md
+++ b/docs.it4i/anselm/software/machine-learning/tensorflow.md
@@ -6,9 +6,9 @@ TensorFlow is an open-source software library for machine intelligence.
Anselm provides three different TensorFlow modules:
- * Tensorflow/1.1.0
- * Tensorflow/1.1.0-CUDA-7.5.18-Python-3.6.1
- * Tensorflow/1.1.0-CUDA-8.0.44-Python-3.6.1
+* Tensorflow/1.1.0
+* Tensorflow/1.1.0-CUDA-7.5.18-Python-3.6.1
+* Tensorflow/1.1.0-CUDA-8.0.44-Python-3.6.1
### Tensorflow/1.1.0 (CPU only)
@@ -20,8 +20,8 @@ $ ml Tensorflow/1.1.0
This module was built with:
- * GCC/4.9.3
- * Python/3.6.1
+* GCC/4.9.3
+* Python/3.6.1
### Tensorflow/1.1.0-CUDA-7.5.18-Python-3.6.1 (GPU enabled)
@@ -33,10 +33,10 @@ $ ml Tensorflow/1.1.0-CUDA-7.5.18-Python-3.6.1
This module was built with:
- * GCC/4.9.3
- * Python/3.6.1
- * CUDA/7.5.18
- * cuDNN/5.1-CUDA-7.5.18
+* GCC/4.9.3
+* Python/3.6.1
+* CUDA/7.5.18
+* cuDNN/5.1-CUDA-7.5.18
### Tensorflow/1.1.0-CUDA-8.0.44-Python-3.6.1 (GPU enabled)
@@ -48,10 +48,10 @@ $ ml Tensorflow/1.1.0-CUDA-8.0.44-Python-3.6.1
This module was built with:
- * GCC/4.9.3
- * Python/3.6.1
- * CUDA/8.0.44
- * cuDNN/5.1-CUDA-8.0.44
+* GCC/4.9.3
+* Python/3.6.1
+* CUDA/8.0.44
+* cuDNN/5.1-CUDA-8.0.44
## TensorFlow application example
diff --git a/docs.it4i/salomon/software/debuggers/valgrind.md b/docs.it4i/salomon/software/debuggers/valgrind.md
index 188f98502..6a897e39f 100644
--- a/docs.it4i/salomon/software/debuggers/valgrind.md
+++ b/docs.it4i/salomon/software/debuggers/valgrind.md
@@ -30,19 +30,19 @@ Compile the application which you want to debug as usual. It is advisable to add
For example, lets look at this C code, which has two problems:
```cpp
- #include <stdlib.h>
-
- void f(void)
- {
- int* x = malloc(10 * sizeof(int));
- x[10] = 0; // problem 1: heap block overrun
- } // problem 2: memory leak -- x not freed
-
- int main(void)
- {
- f();
- return 0;
- }
+#include <stdlib.h>
+
+void f(void)
+{
+ int* x = malloc(10 * sizeof(int));
+ x[10] = 0; // problem 1: heap block overrun
+} // problem 2: memory leak -- x not freed
+
+int main(void)
+{
+ f();
+ return 0;
+}
```
Now, compile it with Intel compiler:
@@ -164,19 +164,19 @@ which must be included in the LD_PRELOAD environment variable.
Lets look at this MPI example:
```cpp
- #include <stdlib.h>
- #include <mpi.h>
+#include <stdlib.h>
+#include <mpi.h>
- int main(int argc, char *argv[])
- {
- int *data = malloc(sizeof(int)*99);
+int main(int argc, char *argv[])
+{
+ int *data = malloc(sizeof(int)*99);
- MPI_Init(&argc, &argv);
- MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
- MPI_Finalize();
+ MPI_Init(&argc, &argv);
+ MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
+ MPI_Finalize();
- return 0;
- }
+ return 0;
+}
```
There are two errors - use of uninitialized memory and invalid length of the buffer. Lets debug it with valgrind :
diff --git a/docs.it4i/salomon/software/machine-learning/tensorflow.md b/docs.it4i/salomon/software/machine-learning/tensorflow.md
index c2f004b13..cad52480f 100644
--- a/docs.it4i/salomon/software/machine-learning/tensorflow.md
+++ b/docs.it4i/salomon/software/machine-learning/tensorflow.md
@@ -6,9 +6,9 @@ TensorFlow is an open-source software library for machine intelligence.
Salomon provides three different TensorFlow modules:
- * Tensorflow/1.1.0
- * Tensorflow/1.2.0-GCC-7.1.0-2.28
- * Tensorflow/1.2.0-intel-2017.05-mkl
+* Tensorflow/1.1.0
+* Tensorflow/1.2.0-GCC-7.1.0-2.28
+* Tensorflow/1.2.0-intel-2017.05-mkl
### Tensorflow/1.1.0 (not recommended)
@@ -21,8 +21,8 @@ $ ml Tensorflow/1.1.0
This module was built with:
- * GCC/4.9.3
- * Python/3.6.1
+* GCC/4.9.3
+* Python/3.6.1
### Tensorflow/1.2.0-GCC-7.1.0-2.28 (default, recommended)
@@ -35,9 +35,9 @@ $ ml Tensorflow/1.2.0-GCC-7.1.0-2.28
This module was built with:
- * GCC/7.1.0-2.28
- * Python/3.6.1
- * protobuf/3.2.0-GCC-7.1.0-2.28-Python-3.6.1
+* GCC/7.1.0-2.28
+* Python/3.6.1
+* protobuf/3.2.0-GCC-7.1.0-2.28-Python-3.6.1
### Tensorflow/1.2.0-intel-2017.05-mkl
@@ -50,9 +50,9 @@ $ ml Tensorflow/1.2.0-intel-2017.05-mkl
This module was built with:
- * icc/2017.4.196-GCC-7.1.0-2.28
- * Python/3.6.1
- * protobuf/3.2.0-GCC-7.1.0-2.28-Python-3.6.1
+* icc/2017.4.196-GCC-7.1.0-2.28
+* Python/3.6.1
+* protobuf/3.2.0-GCC-7.1.0-2.28-Python-3.6.1
## TensorFlow application example
diff --git a/docs.it4i/snippets/modules_matrix_search.md b/docs.it4i/snippets/modules_matrix_search.md
index b936364e1..4d91e6caf 100644
--- a/docs.it4i/snippets/modules_matrix_search.md
+++ b/docs.it4i/snippets/modules_matrix_search.md
@@ -36,6 +36,6 @@ $("#searchInput").keyup(function () {
"color": "black"
});
}).css({
- "color": "#C0C0C0"
+ "color": "#C0C0C0"
});
</script>
diff --git a/docs.it4i/software/easybuild.md b/docs.it4i/software/easybuild.md
index 25efb9121..df4ddd4cf 100644
--- a/docs.it4i/software/easybuild.md
+++ b/docs.it4i/software/easybuild.md
@@ -12,8 +12,8 @@ All builds and installations are performed at user level, so you don't need the
EasyBuild relies on two main concepts
- * Toolchains
- * EasyConfig file (our easyconfigs is [here](https://code.it4i.cz/sccs/easyconfigs-it4i))
+* Toolchains
+* EasyConfig file (our easyconfigs is [here](https://code.it4i.cz/sccs/easyconfigs-it4i))
Detailed documentations is available [here](http://easybuild.readthedocs.io).
@@ -21,8 +21,8 @@ Detailed documentations is available [here](http://easybuild.readthedocs.io).
A toolchain corresponds to a compiler and a set of libraries which are commonly used to build a software. The two main toolchains frequently used on the IT4Innovations clusters are the **foss** and **intel**.
- * **foss** is based on the GCC compiler and on open-source libraries (OpenMPI, OpenBLAS, etc.).
- * **intel** is based on the Intel compiler and on Intel libraries (Intel MPI, Intel Math Kernel Library, etc.).
+* **foss** is based on the GCC compiler and on open-source libraries (OpenMPI, OpenBLAS, etc.).
+* **intel** is based on the Intel compiler and on Intel libraries (Intel MPI, Intel Math Kernel Library, etc.).
Additional details are available on [here](https://github.com/hpcugent/easybuild/wiki/Compiler-toolchains).
diff --git a/docs.it4i/software/singularity.md b/docs.it4i/software/singularity.md
index 026c42059..ce285e19b 100644
--- a/docs.it4i/software/singularity.md
+++ b/docs.it4i/software/singularity.md
@@ -1,3 +1,5 @@
+# Singularity Container
+
[Singularity](http://singularity.lbl.gov/) enables users to have full control of their environment. A non-privileged user can "swap out" the operating system on the host for one they control. So if the host system is running RHEL6 but your application runs in Ubuntu/RHEL7, you can create an Ubuntu/RHEL7 image, install your applications into that image, copy the image to another host, and run your application on that host in it’s native Ubuntu/RHEL7 environment.
Singularity also allows you to leverage the resources of whatever host you are on. This includes HPC interconnects, resource managers, file systems, GPUs and/or accelerators, etc. Singularity does this by enabling several key facets:
diff --git a/docs.it4i/software/spack.md b/docs.it4i/software/spack.md
index 9ad379812..284283f7c 100644
--- a/docs.it4i/software/spack.md
+++ b/docs.it4i/software/spack.md
@@ -241,7 +241,7 @@ $ spack edit git
!!! note
To change source link (ftp:// to http://) use `spack create URL -f` to regenerates rules.
-**Example**
+#### **Example**
```console
$ spack install git
@@ -290,7 +290,7 @@ autoconf@2.69 cmake@3.7.1 expat@2.2.0 git@2.11.0 libsigsegv@2.10 m4
bzip2@1.0.6 curl@7.50.3 gettext@0.19.8.1 libiconv@1.14 libxml2@2.9.4 ncurses@6.0 pcre@8.41 pkg-config@0.29.1 xz@5.2.2
```
-**Spack colorizes output**
+Spack colorizes output.
```console
$ spack find | less -R
@@ -317,7 +317,7 @@ $ spack load git
source ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.csh
```
-**First usage**
+### First usage
```console
$ . ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.sh
--
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