find . -name \*.txt -type f -exec /Users/ruess/Downloads/pandoc-2.7.2/bin/pandoc -f mediawiki -t markdown -o {}.md {} \;
then replace all .txt.md files by .txt
and finally run git mv on all .txt files to convert to .md files

kkrimp/prepare.md

+###### Prepare for running the KKRimp program {#prepare_for_running_the_kkrimp_program}
+
+##### Source code for KKRimp program {#source_code_for_kkrimp_program}
+
+#### Common code version {#common_code_version}
+
+\<WRAP center round download 60%\> Download recent impurity code package
+from: <https://iffgit.fz-juelich.de/kkr/kkrimp> </WRAP>
+
+#### Compile
+
+Go to the folder containing the source code (called *SOURCE*) and type:
+
+`[USER@iff123 IMP_CODE_DIRECTORY/SOURCE]$ make`
+
+If you want to have an MPI parallelized version type:
+
+`[USER@iff123 IMP_CODE_DIRECTORY/SOURCE]$ make mpi`
+
+If using a small to moderately sized cluster, the \"make mpi\" option
+should be sufficient. However, for larger clusters (\#imp atoms \> 150),
+you should compile with the make hybrid option. Then the code will be
+hybrid parallel.
+
+Consider a code which takes 40 energy points on its complex contour.
+Then the maximum scalability of the impurity program would be 1 node per
+energy point (MPI), with all processors on each node working together
+(OpenMP / MKL). Using JUROPA as an example: <code>
+
+1.  !/bin/bash -x
+2.  MSUB -l nodes=40:ppn=8 //specify 40 nodes; 1 node per energy; 8
+    processors per node
+3.  MSUB -l walltime=05:59:59
+4.  MSUB -v tpt=8 //8 threads per MPI task
+5.  MSUB -N IrFe211
+
+export MKL\_NUM\_THREADS=8 export OMP\_NUM\_THREADS=8
+
+cd \$PBS\_O\_WORKDIR echo \"Work Directory is: \$PBS\_O\_WORKDIR\"
+NSLOTS=40 echo \"Running \$NSLOTS MPI tasks with \$MKL\_NUM\_THREADS
+processors per task\"
+
+mpiexec -np 40 \--exports=MKL\_NUM\_THREADS,OMP\_NUM\_THREADS
+./kkrflex.exe \> out
+
+</code> A comprehensive list of all available options for the make
+command is given here:
+
+` * make hybrid    -    MPI + OMP (using MKL) for hybrid parallel`\
+` * make           -    standart compilation using ifort on a single core`\
+` * make mpi       -    for using MPI parallelization with ifort`\
+` * make gfort     -    uses gfort as the compiler`\
+` * make pg        -    uses portland group compiler`\
+` * make mac       -    uses compiler options for MacOSX`\
+` * make clean     -    removes all *.o files`\
+` * make openmp    -    uses openmp`\
+` * make rwth      -    for compilation on RWTH cluster`\
+` * make rwthmpi   -    compilation on RWTH cluster with mpi`\
+` * make rwthhybrid-    compilation on RWTH cluster in hybrid OpenMP/MPI mode`\
+` * make jureca    -    compilation on Jureca cluster with MPI`
+
+FIXME Do all these options work?
+
+:   ?: make mac works only if libraries are saved locally on the mac
+
+<!-- -->
+
+:   ?: does openmp implementation work?
+
+##### Main files {#main_files}
+
+` * `[`config.cfg`](kkrimp:config_file "wikilink")\
+` * `[`kkrflex_*`` ``files`](kkrimp:kkrflex_files "wikilink")
+
+##### Special files {#special_files}
+
+` * `[`kkrflex_angle`](kkrimp:kkrflex_angle "wikilink")` (contains the non-collinear angles for all atoms in the impurity cluster)`