Merge recipes and hints into one page

doc.zih.tu-dresden.de/docs/software/containers.md

@@ -34,8 +34,8 @@ execution. Follow the instructions for [locally install Singularity](#local-inst
 [container creation](#container-creation).  Moreover, existing Docker container can easily be
 converted, which is documented [here](#importing-a-docker-container).
 
-If you are already familar with Singularity, you might be more intressted in our [singularity recipe
-hints](singularity_recipe_hints.md).
+If you are already familar with Singularity, you might be more intressted in our [singularity
+recipes and hints](singularity_recipe_hints.md).
 
 <!--ZIH wiki sites:-->
 

doc.zih.tu-dresden.de/docs/software/singularity_example_definitions.md

-# Singularity Example Definitions
-
-## Basic example
-
-A usual workflow to create Singularity Definition consists of the
-following steps:
-
--   Start from base image
--   Install dependencies
-    -   Package manager
-    -   Other sources
--   Build & Install own binaries
--   Provide entrypoints & metadata
-
-An example doing all this:
-
-```Bash
-Bootstrap: docker
-From: alpine
-
-%post
-  . /.singularity.d/env/10-docker*.sh
-
-  apk add g++ gcc make wget cmake
-
-  wget https://github.com/fmtlib/fmt/archive/5.3.0.tar.gz
-  tar -xf 5.3.0.tar.gz
-  mkdir build && cd build
-  cmake ../fmt-5.3.0 -DFMT_TEST=OFF
-  make -j$(nproc) install
-  cd ..
-  rm -r fmt-5.3.0*
-
-  cat hello.cpp
-#include <fmt/format.h>
-
-int main(int argc, char** argv){
-  if(argc == 1) fmt::print("No arguments passed!\n");
-  else fmt::print("Hello {}!\n", argv[1]);
-}
-EOF
-
-  g++ hello.cpp -o hello -lfmt
-  mv hello /usr/bin/hello
-
-%runscript
-  hello "$@"
-
-%labels
-  Author Alexander Grund
-  Version 1.0.0
-
-%help
-  Display a greeting using the fmt library
-
-  Usage:
-    ./hello 
-```
-
-## CUDA + CuDNN + OpenMPI
-
-- Chosen CUDA version depends on installed driver of host
-- OpenMPI needs PMI for SLURM integration
-- OpenMPI needs CUDA for GPU copy-support
-- OpenMPI needs ibverbs libs for Infiniband
-- openmpi-mca-params.conf required to avoid warnings on fork (OK on
-  taurus)
-- Environment variables SLURM_VERSION, OPENMPI_VERSION can be set to
-  choose different version when building the container
-
-```
-Bootstrap: docker
-From: nvidia/cuda-ppc64le:10.1-cudnn7-devel-ubuntu18.04
-
-%labels
-    Author ZIH
-    Requires CUDA driver 418.39+.
-
-%post
-    . /.singularity.d/env/10-docker*.sh
-
-    apt-get update
-    apt-get install -y cuda-compat-10.1
-    apt-get install -y libibverbs-dev ibverbs-utils
-    # Install basic development tools
-    apt-get install -y gcc g++ make wget python
-    apt-get autoremove; apt-get clean
-
-    cd /tmp
-
-    : ${SLURM_VERSION:=17-02-11-1}
-    wget https://github.com/SchedMD/slurm/archive/slurm-${SLURM_VERSION}.tar.gz
-    tar -xf slurm-${SLURM_VERSION}.tar.gz
-        cd slurm-slurm-${SLURM_VERSION}
-        ./configure --prefix=/usr/ --sysconfdir=/etc/slurm --localstatedir=/var --disable-debug
-        make -C contribs/pmi2 -j$(nproc) install
-    cd ..
-    rm -rf slurm-*
-
-    : ${OPENMPI_VERSION:=3.1.4}
-    wget https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION%.*}/openmpi-${OPENMPI_VERSION}.tar.gz
-    tar -xf openmpi-${OPENMPI_VERSION}.tar.gz
-    cd openmpi-${OPENMPI_VERSION}/
-    ./configure --prefix=/usr/ --with-pmi --with-verbs --with-cuda
-    make -j$(nproc) install
-    echo "mpi_warn_on_fork = 0" >> /usr/etc/openmpi-mca-params.conf
-    echo "btl_openib_warn_default_gid_prefix = 0" >> /usr/etc/openmpi-mca-params.conf
-    cd ..
-    rm -rf openmpi-*
-```

doc.zih.tu-dresden.de/docs/software/singularity_recipe_hints.md

-# Singularity Recipe Hints
+# Singularity Recipes and Hints
 
-## GUI (X11) Applications
+## Example Definitions
+
+### Basic Example
+
+A usual workflow to create Singularity Definition consists of the following steps:
+
+* Start from base image
+* Install dependencies
+    * Package manager
+    * Other sources
+* Build and install own binaries
+* Provide entry points and metadata
+
+An example doing all this:
+
+```bash
+Bootstrap: docker
+From: alpine
+
+%post
+  . /.singularity.d/env/10-docker*.sh
+
+  apk add g++ gcc make wget cmake
+
+  wget https://github.com/fmtlib/fmt/archive/5.3.0.tar.gz
+  tar -xf 5.3.0.tar.gz
+  mkdir build && cd build
+  cmake ../fmt-5.3.0 -DFMT_TEST=OFF
+  make -j$(nproc) install
+  cd ..
+  rm -r fmt-5.3.0*
+
+  cat hello.cpp
+#include <fmt/format.h>
+
+int main(int argc, char** argv){
+  if(argc == 1) fmt::print("No arguments passed!\n");
+  else fmt::print("Hello {}!\n", argv[1]);
+}
+EOF
+
+  g++ hello.cpp -o hello -lfmt
+  mv hello /usr/bin/hello
+
+%runscript
+  hello "$@"
+
+%labels
+  Author Alexander Grund
+  Version 1.0.0
+
+%help
+  Display a greeting using the fmt library
+
+  Usage:
+    ./hello
+```
+
+### CUDA + CuDNN + OpenMPI
+
+* Chosen CUDA version depends on installed driver of host
+* OpenMPI needs PMI for Slurm integration
+* OpenMPI needs CUDA for GPU copy-support
+* OpenMPI needs `ibverbs` library for Infiniband
+* `openmpi-mca-params.conf` required to avoid warnings on fork (OK on ZIH systems)
+* Environment variables `SLURM_VERSION` and `OPENMPI_VERSION` can be set to  choose different
+  version when building the container
+
+```bash
+Bootstrap: docker
+From: nvidia/cuda-ppc64le:10.1-cudnn7-devel-ubuntu18.04
+
+%labels
+    Author ZIH
+    Requires CUDA driver 418.39+.
+
+%post
+    . /.singularity.d/env/10-docker*.sh
+
+    apt-get update
+    apt-get install -y cuda-compat-10.1
+    apt-get install -y libibverbs-dev ibverbs-utils
+    # Install basic development tools
+    apt-get install -y gcc g++ make wget python
+    apt-get autoremove; apt-get clean
+
+    cd /tmp
+
+    : ${SLURM_VERSION:=17-02-11-1}
+    wget https://github.com/SchedMD/slurm/archive/slurm-${SLURM_VERSION}.tar.gz
+    tar -xf slurm-${SLURM_VERSION}.tar.gz
+        cd slurm-slurm-${SLURM_VERSION}
+        ./configure --prefix=/usr/ --sysconfdir=/etc/slurm --localstatedir=/var --disable-debug
+        make -C contribs/pmi2 -j$(nproc) install
+    cd ..
+    rm -rf slurm-*
+
+    : ${OPENMPI_VERSION:=3.1.4}
+    wget https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION%.*}/openmpi-${OPENMPI_VERSION}.tar.gz
+    tar -xf openmpi-${OPENMPI_VERSION}.tar.gz
+    cd openmpi-${OPENMPI_VERSION}/
+    ./configure --prefix=/usr/ --with-pmi --with-verbs --with-cuda
+    make -j$(nproc) install
+    echo "mpi_warn_on_fork = 0" >> /usr/etc/openmpi-mca-params.conf
+    echo "btl_openib_warn_default_gid_prefix = 0" >> /usr/etc/openmpi-mca-params.conf
+    cd ..
+    rm -rf openmpi-*
+```
+
+## Hints
+
+### GUI (X11) Applications
 
 Running GUI applications inside a singularity container is possible out of the box. Check the
 following definition:

doc.zih.tu-dresden.de/mkdocs.yml

@@ -30,8 +30,7 @@ nav:
       - Python Virtual Environments: software/python_virtual_environments.md
     - Containers:
       - Singularity: software/containers.md
-      - Singularity Recipe Hints: software/singularity_recipe_hints.md
-      - Singularity Example Definitions: software/singularity_example_definitions.md
+      - Singularity Recipes and Hints: software/singularity_recipe_hints.md
       - VM tools: software/vm_tools.md
     - Applications:
       - Licenses: software/licenses.md

doc.zih.tu-dresden.de/wordlist.aspell

@@ -139,6 +139,7 @@ PiB
 Pika
 pipelining
 png
+PMI
 PowerAI
 ppc
 PSOCK