<p>You need to install GCC, or a newer version of Clang.</p>

<p>Your compiler — though the binary is called <code>gcc</code> — is actually Clang, and the Clang version that’s shipping with macOS/Xcode still does not support OpenMP.</p>

<p>The easiest course of action is probably to install GCC via Homebrew (<code>brew install gcc</code>) and then configure Sniffles to use Homebrew’s GCC (i.e. setting the <code>CMAKE_C*_COMPILER</code> paths to <code>/usr/local/bin/g{cc,++}-$version</code>).</p>

CC BY-SA 4.0
2018-06-13T21:28:38.073Z
I have tried what you said, unsuccessfully. I have updated my original question.
Biomagician
CC BY-SA 4.0
2018-06-13T12:42:05.560Z
2018-06-13T12:42:05.560Z
Konrad Rudolph
<p>I have followed the steps described <a href="https://github.com/fritzsedlazeck/Sniffles/wiki#how-to-build-sniffles" rel="nofollow noreferrer">here</a> to install Sniffles on my Mac Book Pro running macOS High Sierra.</p>

<p>However, I am struggling with this step:</p>

<pre><code>cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 .. 
</code></pre>

<p>I do not have an /opt folder, so I get the following output:</p>

<pre><code>-- The C compiler identification is unknown
-- The CXX compiler identification is unknown
CMake Error at CMakeLists.txt:2 (project):
  The CMAKE_C_COMPILER:

    /opt/local/bin/gcc-mp-4.7

  is not a full path to an existing compiler tool.

  Tell CMake where to find the compiler by setting either the environment
  variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
  the compiler, or to the compiler name if it is in the PATH.


CMake Error at CMakeLists.txt:2 (project):
  The CMAKE_CXX_COMPILER:

    /opt/local/bin/g++-mp-4.7

  is not a full path to an existing compiler tool.

  Tell CMake where to find the compiler by setting either the environment
  variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
  to the compiler, or to the compiler name if it is in the PATH.


-- Configuring incomplete, errors occurred!
See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeOutput.log".
See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeError.log".
</code></pre>

<p>Unsurprisingly, the error file says that /opt/local/bin/gcc-mp-4.7 does not exist.</p>

<p>So I tried:</p>

<pre><code>cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_CXX_COMPILER=/usr/bin/gcc ..
</code></pre>

<p>I get another long message but the most important bit is:</p>

<pre><code>CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
</code></pre>

<p>I do not know what to do to solve this error.</p>

<p>I do have gcc here: /usr/bin/gcc and cmake version 3.8.1.</p>

<p>I have created an issue on the <a href="https://github.com/fritzsedlazeck/Sniffles/issues/80" rel="nofollow noreferrer">Sniffles GitHub repository</a>.</p>

<h3>Update 13th June 2018</h3>

<p>I installed the latest version of gcc:</p>

<pre><code>brew install gcc
Warning: gcc 8.1.0 is already installed and up-to-date
To reinstall 8.1.0, run `brew reinstall gcc`
</code></pre>

<p>Then, I tried to make cmake use gcc and g++ in the /usr/local/bin folder. </p>

<pre><code>cmake -D CMAKE_C_COMPILER=/usr/local/bin/gcc-8 -D CMAKE_CXX_COMPILER=/usr/local/bin/g++-8 ..
</code></pre>

<p>This recreated the same problem:</p>

<pre><code>CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
</code></pre>

<p>Do I need to set the OpenMP_C*_FLAGS to something?</p>

CC BY-SA 4.0
2018-06-13T10:26:32.863Z
Do you have OpenMP installed? It's required.
Devon Ryan
CC BY-SA 4.0
2018-06-13T12:38:59.723Z
@DevonRyan OpenMP is installed as part of GCC. The problem is that OP isn’t using GCC.
Konrad Rudolph
<software-installation>
Problem installing last build of Sniffles
# Problem installing last build of Sniffles

(Asked by: username_0 on 2018-06-13)

I have followed the steps described here to install Sniffles on my Mac Book Pro running macOS High Sierra.
However, I am struggling with this step:
cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 .. 

I do not have an /opt folder, so I get the following output:
-- The C compiler identification is unknown
-- The CXX compiler identification is unknown
CMake Error at CMakeLists.txt:2 (project):
  The CMAKE_C_COMPILER:

    /opt/local/bin/gcc-mp-4.7

  is not a full path to an existing compiler tool.

  Tell CMake where to find the compiler by setting either the environment
  variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
  the compiler, or to the compiler name if it is in the PATH.


CMake Error at CMakeLists.txt:2 (project):
  The CMAKE_CXX_COMPILER:

    /opt/local/bin/g++-mp-4.7

  is not a full path to an existing compiler tool.

  Tell CMake where to find the compiler by setting either the environment
  variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
  to the compiler, or to the compiler name if it is in the PATH.


-- Configuring incomplete, errors occurred!
See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeOutput.log".
See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeError.log".

Unsurprisingly, the error file says that /opt/local/bin/gcc-mp-4.7 does not exist.
So I tried:
cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_CXX_COMPILER=/usr/bin/gcc ..

I get another long message but the most important bit is:
CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)

I do not know what to do to solve this error.
I do have gcc here: /usr/bin/gcc and cmake version 3.8.1.
I have created an issue on the Sniffles GitHub repository.
Update 13th June 2018
I installed the latest version of gcc:
brew install gcc
Warning: gcc 8.1.0 is already installed and up-to-date
To reinstall 8.1.0, run `brew reinstall gcc`

Then, I tried to make cmake use gcc and g++ in the /usr/local/bin folder. 
cmake -D CMAKE_C_COMPILER=/usr/local/bin/gcc-8 -D CMAKE_CXX_COMPILER=/usr/local/bin/g++-8 ..

This recreated the same problem:
CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)

Do I need to set the OpenMP_C*_FLAGS to something?

**Tags:** software-installation
> **Comments:**
> **username_1**: Do you have OpenMP installed? It's required.  
> **username_2**: @DevonRyan OpenMP is installed as part of GCC. The problem is that OP isn’t using GCC.  

---

## 1 answers

### Answer by username_2 on 2018-06-13. Score: 4

You need to install GCC, or a newer version of Clang.

Your compiler — though the binary is called `gcc` — is actually Clang, and the Clang version that’s shipping with macOS/Xcode still does not support OpenMP.

The easiest course of action is probably to install GCC via Homebrew (`brew install gcc`) and then configure Sniffles to use Homebrew’s GCC (i.e. setting the `CMAKE_C*_COMPILER` paths to `/usr/local/bin/g{cc,++}-$version`).

> **Comments:**
> **username_0**: I have tried what you said, unsuccessfully. I have updated my original question.  

---

