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--- pandoc:introduction-to-vsc:04_module_environment:01_modules [2018/01/31 11:10] – Pandoc Auto-commit pandoc
+++ pandoc:introduction-to-vsc:04_module_environment:01_modules [2018/01/31 13:17] – Pandoc Auto-commit pandoc
@@ Line 1: / Line 1: @@
+====== Software management ======
+  * Article written by Markus Stöhr (VSC Team) <html><br></html>(last update 2017-10-09 by ms).
+===== Considerations =====
+  - Find a suitable **location and directory structure** for serveral versions of the same library/code
+  - Manage the **user environment** to be able to access the correct version automatically
+  - Manage different software stacks, e.g. use different compiler(-version) or different library versions to build another library (–> 1.)
+----
+===== Location of compiled software =====
+<code>
+mountpoint
+└── processor architecture
+    │
+    └── glibc (C-library) of OS
+        │
+        └── processor type
+            │
+            └──program name
+               │
+               └──program version
+</code>
+<code>
+/opt/sw
+└── x86_64
+    │
+    └── glibc-2.17
+        │
+        └── ivybridge-ep
+            │
+            └──hdf5
+               │
+               └──1.8.18-MPI
+</code>
+----
+==== Details of hdf5/1.8.18-MPI ====
+<code>
+tree -d -L 5 /opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5/1.8.18-MPI
+</code>
+<code>
+/opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5/1.8.18-MPI
+├── gcc
+│   └── 5.3
+│       └── intel-mpi
+│           └── 5
+│               ├── bin
+│               ├── include
+│               ├── lib
+│               └── share
+└── intel
+    ├── 15
+    │   └── intel-mpi
+    │       └── 5
+    │           ├── bin
+    │           ├── include
+    │           ├── lib
+    │           └── share
+    ├── 16
+    │   └── intel-mpi
+    │       └── 5
+    │           ├── bin
+    │           ├── include
+    │           ├── lib
+    │           └── share
+    └── 17
+        └── intel-mpi
+            └── 2017
+                ├── bin
+                ├── include
+                ├── lib
+                └── share
+</code>
+Software used for compiling is reflected in the directory structure
+===== Environment Modules =====
+  * **environment**: global variables available to current and all sub-shells (‘env’/ ‘set’ )
+  * http://modules.sourceforge.net/
+  * **module**: all modifications (set and prepend to variables) in the user environment necessary for using a piece of software
+  * handles additional software, which is not installed to default system paths
+  * makes different versions of one piece of software available
+  * **prerequisites**: loading a module may require loading other modules before
+----
+<code>
+module avail
+</code>
+  * shows available modules.
+  * searches paths given by ''%%MODULEPATH%%''
+  * own modules can be added by extending ''%%MODULEPATH%%''
+  * If multiple modules with the same name/version are present in different directories, the first found by ''%%MODULEPATH%%'' will be used.
+  * two parts:
+    * software name (directory)
+    * version (file with definitions)
+<code>
+ls /opt/sw/Modules/Libraries/hdf5
+.6.10  1.8.14      1.8.14-SERIAL  1.8.18      1.8.18-SERIAL
+.8.12  1.8.14-MPI  1.8.16         1.8.18-MPI
+</code>
+----
+<code>
+module load <modulename>
+</code>
+<code>
+[markus@l33 ~]$ module load hdf5/1.8.18-MPI
+You are not meeting the prereq of this module. Currently loaded modules:
+None
+The following modules combinations can be loaded:
+(1): module load intel/15 intel-mpi/5 hdf5/1.8.18-MPI
+(2): module load intel/16 intel-mpi/5 hdf5/1.8.18-MPI
+(3): module load gcc/5.3 intel-mpi/5 hdf5/1.8.18-MPI
+(4): module load intel/17 intel-mpi/2017 hdf5/1.8.18-MPI
+</code>
+Do copy and paste:
+<code>
+module load intel/16 intel-mpi/5 hdf5/1.8.18-MPI
+</code>
+----
+<code>
+module list
+</code>
+  * list currently loaded modules
+----
+<code>
+module purge
+</code>
+  * remove all loaded modules;
+  * recommended in job scripts before loading any modules (reproducibility)
+<code>
+module remove <modulename> <modulename> ...
+</code>
+  * removes a list of modules
+----
+<code>
+module show  <modulename>
+</code>
+  * shows the variables added to your environment by a module
+<code>
+module show hdf5/1.8.18-MPI
+/opt/sw/Modules/Libraries/hdf5/1.8.18-MPI:
+conflict         hdf5
+setenv           VSC_HDF5_ROOT      /opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5/1.8.18-MPI/intel/16/intel-mpi/5
+prepend-path     CPATH                  $VSC_HDF5_ROOT/include
+prepend-path     INCLUDE                $VSC_HDF5_ROOT/include
+setenv           VSC_HDF5_INCLUDE       $VSC_HDF5_ROOT/include
+prepend-path     LD_LIBRARY_PATH        $VSC_HDF5_ROOT/lib
+prepend-path     LIBRARY_PATH           $VSC_HDF5_ROOT/lib
+setenv           VSC_HDF5_LIB           $VSC_HDF5_ROOT/lib
+prepend-path     PATH                   $VSC_HDF5_ROOT/bin
+setenv           VSC_HDF5_BIN           $VSC_HDF5_ROOT/bin
+setenv           VSC_HDF5_VERSION_MAJOR 1
+setenv           VSC_HDF5_VERSION_MINOR 8
+setenv           VSC_HDF5_VERSION_MICRO 18-MPI
+setenv           VSC_HDF5_VERSION 1.8
+-------------------------------------------------------------------
+</code>
+===== Exercises =====
+  * look at your user environment:
+<code>
+env
+env |grep PATH
+echo $PATH |tr ':' '\n'
+echo $LD_LIBRARY_PATH |tr ':' '\n'
+echo $MODULEPATH |tr ':' '\n'
+</code>
+  * inspect the contents of the directories in MODULEPATH
+  * look at directory structure of installed software, e.g.:
+<code>
+tree -d /opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5
+</code>
+  * try the module commands
+<code>
+module avail
+module load hdf5/1.8.18-MPI #follow instructions in shell!
+module list
+module show hdf5/1.8.18-MPI
+module purge
+</code>
+  * compare ''%%PATH%%'' and ''%%LD_LIBRARY_PATH%%'' before and after loading a module
+===== Adding own gnuplot module =====
+  * setup your own modules directory and a directory for gnuplot
+<code>
+mkdir ${HOME}/mymodules
+mkdir ${HOME}/mymodules/gnuplot
+</code>
+  * prepend own module directory to ''%%MODULEPATH%%'':
+<code>
+export MODULEPATH=${HOME}/mymodules:$MODULEPATH
+</code>
+  * create module file: ''%%${HOME}/mymodules/gnuplot/5.0.5%%'':
+<code>
+#%Module
+set inst_base $env(HOME)/mysoftware/gnuplot/5.0.5
+prepend-path PATH $inst_base/bin
+prepend-path LD_LIBRARY_PATH $inst_base/lib
+append-path CPATH $inst_base/include
+setenv MYVAR test1234
+</code>
+===== Exercises =====
+  * check how module is loaded by default VSC-3 modules
+<code>
+module avail 2>&1  | less #search for gnuplot; use '/' within less for searching
+module load gnuplot/5.0.5
+module show gnuplot/5.0.5
+</code>
+  * create own module environment as described on previous slide, create a directory within your training sub-folder
+  * check again, how the module is loaded.
+===== Simple example =====
+eg. from HDF5:
+<code>
+EXAMPLE=$VSC_HDF5_ROOT/share/hdf5_examples/c/ph5example.c
+</code>
+Compile using Intel C Compiler ([[examples/compile-intel.sh|file]]):
+<code>
+module purge
+module load intel/16 \
+    intel-mpi/5 hdf5/1.8.18-MPI
+cp $EXAMPLE .
+mpiicc -lhdf5 ph5example.c -o ph5example
+</code>
+Compile using Gnu C Compiler ([[examples/compile-gnu.sh|file]]):
+<code>
+module purge
+module load gcc/5.3 \
+    intel-mpi/5 hdf5/1.8.18-MPI
+cp $EXAMPLE .
+mpicc -lhdf5 ph5example.c -o ph5example
+</code>
+If needed add e.g. include directory explicitly:
+<code>
+mpiicc -I$VSC_HDF5_INCLUDE -lhdf5 ph5example.c -o ph5example
+</code>
+----
+===== Compiler names =====
+Hint:
+  * mpiifort
+  * mpifort
+  * mpicc
+  * mpiicc