diff --git a/BioEM_labbook.org b/BioEM_labbook.org
index 6c85d4dc2d1cdaf16ab729e6b03ca4c664215bce..d9eae88c1a4abfa526e0b1c2c8c22276cbb3fa0e 100644
--- a/BioEM_labbook.org
+++ b/BioEM_labbook.org
@@ -19,6 +19,374 @@
 ** ?Xeon Phi
 * Ideas
 * Important codes
+** Recipes for compilations and runs
+*** [error] dvl machine - problems at CUDA runtime
+**** Machine description
+     - Local machines at MPCDF for development
+     - dvl01:
+       + 20 CPU cores Intel machine (Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz)
+       + 2 K40 GPUs
+     - dvl02:
+       + 20 CPU cores Intel machine (Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz)
+       + 2 Nvidia K20Xm GPUs
+**** Installation with gnu compilers
+
+#+BEGIN_SRC 
+# Loading necessary modules
+module purge 
+module load git/2.7.4
+module load gcc/4.9
+module load impi/5.1.3
+module load cmake/3.6
+module load boost/gcc/1.57
+module load fftw/gcc/3.3.4
+module load cuda/7.5
+
+# Paths
+SRC_DIR="$afsdir/BioEM_fork"
+BUILD_DIR="$HOME/BioEM_project/build"
+mkdir -p $BUILD_DIR
+cd $BUILD_DIR
+
+# Deleting files from previous installations previous 
+rm -rf $BUILD_DIR/*
+rm -rf $SRC_DIR/CMakeFiles $SRC_DIR/CMakeCache.txt $SRC_DIR/Makefile $SRC_DIR/cmake_install.cmake
+
+# Configuration and compilation
+cmake -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_CUDA=ON -DPRINT_CMAKE_VARIABLES=ON -DCUDA_FORCE_GCC=ON $SRC_DIR/
+make -j5 VERBOSE=1
+#+END_SRC
+
+**** Installation with Intel compilers
+
+#+BEGIN_SRC 
+# Loading necessary modules
+module purge 
+module load git/2.7.4
+module load intel/15.0
+module load impi/5.1.3
+module load cmake/3.6
+module load boost/intel/1.57
+module load fftw/3.3.4
+module load cuda/7.5
+
+# Paths
+SRC_DIR="$afsdir/BioEM_fork"
+BUILD_DIR="$HOME/BioEM_project/build"
+mkdir -p $BUILD_DIR
+cd $BUILD_DIR
+
+# Deleting files from previous installations previous 
+rm -rf $BUILD_DIR/*
+rm -rf $SRC_DIR/CMakeFiles $SRC_DIR/CMakeCache.txt $SRC_DIR/Makefile $SRC_DIR/cmake_install.cmake
+
+# Configuration and compilation
+cmake -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_CUDA=ON -DPRINT_CMAKE_VARIABLES=ON -DCUDA_FORCE_GCC=ON $SRC_DIR/
+make -j5 VERBOSE=1
+#+END_SRC
+
+**** Running Tutorial example
+
+#+BEGIN_SRC 
+# Loading necessary modules if needed (check installation gcc/Intel)
+
+# Environment variables
+export OMP_NUM_THREADS=5
+export OMP_PLACES=cores
+export FFTALGO=1
+export GPU=1
+export GPUDEVICE=-1
+export GPUWORKLOAD=100
+
+# Paths
+TUTORIAL_DIR="$afsdir/BioEM_fork/Tutorial_BioEM"
+BUILD_DIR="$HOME/BioEM_project/build"
+
+# Running tutorial test
+mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $TUTORIAL_DIR/Param_Input --Modelfile $TUTORIAL_DIR/Model_Text --Particlesfile $TUTORIAL_DIR/Text_Image_Form
+#+END_SRC
+
+**** Running larger example from the paper
+
+#+BEGIN_SRC 
+# Loading necessary modules if needed (check installation gcc/Intel)
+
+# Environment variables
+export OMP_NUM_THREADS=5
+export OMP_PLACES=cores
+export FFTALGO=1
+export GPU=1
+export GPUDEVICE=-1
+export GPUWORKLOAD=100
+
+# Paths
+INPUT_DIR="$HOME/BioEM_project/inputs"
+BUILD_DIR="$HOME/BioEM_project/build"
+
+# Running only few iterations, reading already generated maps (only if they are avaialble in the same folder
+BIOEM_DEBUG_BREAK=4 BIOEM_DEBUG_OUTPUT=2 mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $INPUT_DIR/INPUT_FRH_Sep2016 --Modelfile $INPUT_DIR/Mod_X-ray_PDB --Particlesfile $INPUT_DIR/2000FRH_Part --LoadMapDump
+
+# Running full example
+BIOEM_DEBUG_OUTPUT=0 mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $INPUT_DIR/INPUT_FRH_Sep2016 --Modelfile $INPUT_DIR/Mod_X-ray_PDB --Particlesfile $INPUT_DIR/2000FRH_Part
+#+END_SRC
+
+*** [error] miy (Minsky) machine - problems at CUDA runtime
+**** Machine description
+     - 3 identical machine with IBM Power 8+ architecture
+     - Local machines at MPCDF for development and testing Power8 capabilities
+     - miy01-miy03:
+       + 2 Power8+ CPUs (160 cores?)
+       + 4 Nvidia P100 GPUs
+**** Installation with gnu compilers
+
+   - On Minsky machine problems with gcc options that are not supported by Power8 (IBM) machine:
+     + c++: error: unrecognized command line option ‘-march=native’
+     + c++: error: unrecognized command line option ‘-mfpmath=sse’
+     + c++: error: unrecognized command line option ‘-minline-all-stringops’
+   - Without it, it is possible to compile the project
+   - Neither Git nor AFS are available
+
+#+BEGIN_SRC 
+# Loading necessary modules
+module purge 
+module load gcc/5.4
+module load smpi/10.1
+module load fftw/gcc-5.4
+module load cuda/8.0
+
+# Paths
+SRC_DIR="$HOME/BioEM_project/BioEM"
+BUILD_DIR="$HOME/BioEM_project/build"
+mkdir -p $BUILD_DIR
+cd $BUILD_DIR
+
+# Deleting files from previous installations previous 
+rm -rf $BUILD_DIR/*
+rm -rf $SRC_DIR/CMakeFiles $SRC_DIR/CMakeCache.txt $SRC_DIR/Makefile $SRC_DIR/cmake_install.cmake
+
+# Configuration and compilation
+cmake -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_CUDA=ON -DPRINT_CMAKE_VARIABLES=ON -DCUDA_FORCE_GCC=ON $SRC_DIR/
+make -j5 VERBOSE=1
+#+END_SRC
+
+**** Running Tutorial example
+
+#+BEGIN_SRC 
+# Loading necessary modules if needed (check installation gcc/Intel)
+
+# Environment variables
+export OMP_NUM_THREADS=5
+export OMP_PLACES=cores
+export FFTALGO=1
+export GPU=1
+export GPUDEVICE=-1
+export GPUWORKLOAD=100
+
+# Paths
+TUTORIAL_DIR="$HOME/BioEM_project/BioEM/Tutorial_BioEM"
+BUILD_DIR="$HOME/BioEM_project/build"
+
+# Running tutorial test
+mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $TUTORIAL_DIR/Param_Input --Modelfile $TUTORIAL_DIR/Model_Text --Particlesfile $TUTORIAL_DIR/Text_Image_Form
+#+END_SRC
+
+**** Running larger example from the paper
+
+#+BEGIN_SRC 
+# Loading necessary modules if needed (check installation gcc/Intel)
+
+# Environment variables
+export OMP_NUM_THREADS=5
+export OMP_PLACES=cores
+export FFTALGO=1
+export GPU=1
+export GPUDEVICE=-1
+export GPUWORKLOAD=100
+
+# Paths
+INPUT_DIR="$HOME/BioEM_project/inputs"
+BUILD_DIR="$HOME/BioEM_project/build"
+
+# Running only few iterations, reading already generated maps (only if they are avaialble in the same folder
+BIOEM_DEBUG_BREAK=4 BIOEM_DEBUG_OUTPUT=2 mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $INPUT_DIR/INPUT_FRH_Sep2016 --Modelfile $INPUT_DIR/Mod_X-ray_PDB --Particlesfile $INPUT_DIR/2000FRH_Part --LoadMapDump
+
+# Running full example
+BIOEM_DEBUG_OUTPUT=0 mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $INPUT_DIR/INPUT_FRH_Sep2016 --Modelfile $INPUT_DIR/Mod_X-ray_PDB --Particlesfile $INPUT_DIR/2000FRH_Part
+#+END_SRC
+
+*** [partially working] hydra machine
+**** Machine description (from http://www.mpcdf.mpg.de/services/computing/hydra/about-the-system)
+
+     In October 2013, the main part of the iDataPlex HPC system HYDRA
+     was installed at the MPCDF with Intel Ivy Bridge processors (~
+     3500 nodes with 20 cores @ 2.8 GHz each), in addition to the
+     Intel Sandy Bridge-EP processors (610 nodes with 16 cores @ 2.6
+     GHz each) that are available since Sept 2012. 350 of the Ivy
+     Bridge nodes are equipped with accelerator cards (338 nodes with
+     2 NVIDIA K20X GPGPUs each, 12 nodes with 2 Intel Xeon Phi cards
+     each).
+
+     Most of the compute nodes have a main memory of 64 GB, 2 x 100 of
+     the Ivy Bridge nodes and 20 of the Sandy Bridge nodes have a main
+     memory of 128 GB.
+
+     In total there are ~ 83.000 cores with a main memory of 280 TB
+     and a peak performance of about 1.7 PetaFlop/s. The accelerator
+     part of the HPC cluster has a peak performance of about 1
+     PetaFlop/s.
+
+     In addition to the compute nodes there are 8 login nodes and 26
+     I/O nodes that serve the 5 PetaByte of disk storage.
+
+     The common interconnect is a fast InfiniBand FDR14 network.
+
+     The compute nodes are bundled into 5 domains, three domains
+     (including the old Sandy Bridge processor domain) with 628 nodes
+     each, one big domain with more than 1800 nodes, and one domain
+     consisting of the 350 nodes with accelerator cards.  Within one
+     domain, the InfiniBand network topology is a 'fat tree' topology
+     for high efficient communication. The InfiniBand connection
+     between the domains is much weaker, so batch jobs are restricted
+     to a single domain.
+
+**** [problems with compilation] Installation with gnu compilers
+
+#+BEGIN_SRC 
+# Loading necessary modules
+module purge 
+module load cmake/3.5
+module load gcc/4.9
+module load mpi.ibm/1.4.0
+module load fftw/gcc/3.3.4
+module load boost/gcc/1.61
+module load cuda/7.5
+
+# Paths
+SRC_DIR="$afsdir/BioEM_fork"
+BUILD_DIR="$HOME/BioEM_project/build"
+mkdir -p $BUILD_DIR
+cd $BUILD_DIR
+
+# Deleting files from previous installations previous 
+rm -rf $BUILD_DIR/*
+rm -rf $SRC_DIR/CMakeFiles $SRC_DIR/CMakeCache.txt $SRC_DIR/Makefile $SRC_DIR/cmake_install.cmake
+
+# There are some strange problems with CUDA, however this small hack with links seems to solve the issue
+ln -s /u/system/SLES11/soft/cuda/libcuda/libcuda.so.352.79 libcuda.so.1
+ln -s libcuda.so.1 libcuda.so
+
+# Configuration and compilation (need to manually add CUDA_rt_LIBRARY)
+cmake -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_CUDA=ON -DPRINT_CMAKE_VARIABLES=ON -DCUDA_FORCE_GCC=ON -DCUDA_rt_LIBRARY=/u/system/SLES11/soft/cuda/7.5/lib64/libcudart.so -DCUDA_SDK_ROOT_DIR=/u/system/SLES11/soft/cuda/7.5/samples/common -DCUDA_CUDA_LIBRARY=$PWD/libcuda.so $SRC_DIR/
+make -j5 VERBOSE=1
+#+END_SRC
+
+**** [working] Installation with Intel compilers
+
+#+BEGIN_SRC 
+# Loading necessary modules
+module purge 
+module load cmake/3.5
+module load gcc/4.9
+module load mpi.ibm/1.4.0
+module load fftw/gcc/3.3.4
+module load boost/gcc/1.61
+module load cuda/7.5
+
+# Paths
+SRC_DIR="$afsdir/BioEM_fork"
+BUILD_DIR="$HOME/BioEM_project/build"
+mkdir -p $BUILD_DIR
+cd $BUILD_DIR
+
+# Deleting files from previous installations previous 
+rm -rf $BUILD_DIR/*
+rm -rf $SRC_DIR/CMakeFiles $SRC_DIR/CMakeCache.txt $SRC_DIR/Makefile $SRC_DIR/cmake_install.cmake
+
+# There are some strange problems with CUDA, however this small hack with links seems to solve the issue. Probably CMake needs to be improved
+ln -s /u/system/SLES11/soft/cuda/libcuda/libcuda.so.352.79 libcuda.so.1
+ln -s libcuda.so.1 libcuda.so
+
+# Configuration and compilation (need to manually add CUDA_rt_LIBRARY and CUDA_SDK_ROOT_DIR)
+cmake -DUSE_MPI=ON -DUSE_OPENMP=ON -DUSE_CUDA=ON -DPRINT_CMAKE_VARIABLES=ON -DCUDA_FORCE_GCC=ON -DCUDA_rt_LIBRARY=/u/system/SLES11/soft/cuda/7.5/lib64/libcudart.so -DCUDA_SDK_ROOT_DIR=/u/system/SLES11/soft/cuda/7.5/samples/common -DCUDA_CUDA_LIBRARY=$PWD/libcuda.so $SRC_DIR/
+make -j5 VERBOSE=1
+#+END_SRC
+
+**** [untested] Running interactive Tutorial example (no GPUs)
+
+#+BEGIN_SRC 
+# Loading necessary modules if needed (check installation gcc/Intel)
+
+# Environment variables
+export OMP_NUM_THREADS=5
+export OMP_PLACES=cores
+export FFTALGO=1
+export GPU=0
+
+# Specific for interactive tests on hydra
+export MP_TASK_AFFINITY=core:$OMP_NUM_THREADS
+echo localhost > host.list
+echo localhost >> host.list
+echo localhost >> host.list
+echo localhost >> host.list
+
+# Paths
+TUTORIAL_DIR="$afsdir/BioEM_fork/Tutorial_BioEM"
+BUILD_DIR="$HOME/BioEM_project/build"
+
+# Running tutorial test
+mpiexec -n 4 $BUILD_DIR/bioEM --Inputfile $TUTORIAL_DIR/Param_Input --Modelfile $TUTORIAL_DIR/Model_Text --Particlesfile $TUTORIAL_DIR/Text_Image_Form
+#+END_SRC
+
+**** [untested] Running larger example from the paper
+
+#+BEGIN_SRC 
+# @ shell=/bin/bash
+#
+# Sample script for LoadLeveler
+#
+# @ error   = job.err.$(jobid)
+# @ output  = job.out.$(jobid)
+# @ job_type = parallel
+# @ requirements = (Feature=="gpu")
+# @ node_usage= not_shared
+# @ node = 1
+# @ tasks_per_node = 1
+# @ resources = ConsumableCpus(20)
+# @ network.MPI = sn_all,not_shared,us
+# @ wall_clock_limit = 01:00:00
+# @ notification = complete
+# @ notify_user = $(user)@rzg.mpg.de
+# @ queue
+
+# Loading necessary modules for Intel compilers
+module purge 
+module load cmake/3.5
+module load gcc/4.9
+module load mpi.ibm/1.4.0
+module load fftw/gcc/3.3.4
+module load boost/gcc/1.61
+module load cuda/7.5
+
+# Environment variables
+export OMP_NUM_THREADS=5
+export OMP_PLACES=cores
+export FFTALGO=1
+export GPU=1
+export GPUDEVICE=-1
+export GPUWORKLOAD=80
+
+# Paths
+INPUT_DIR="$HOME/BioEM_project/inputs"
+BUILD_DIR="$HOME/BioEM_project/build"
+
+
+mpiexec -n 2 $BUILD_DIR/bioEM --Inputfile $INPUT_DIR/INPUT_FRH_Sep2016 --Modelfile $INPUT_DIR/Mod_X-ray_PDB --Particlesfile $INPUT_DIR/2000FRH_Part --LoadMapDump
+
+# Running full example
+cd /ptmp/$USER/
+poe $BUILD_DIR/bioEM --Inputfile $INPUT_DIR/INPUT_FRH_Sep2016 --Modelfile $INPUT_DIR/Mod_X-ray_PDB --Particlesfile $INPUT_DIR/2000FRH_Part
+#+END_SRC
+
 * Summaries, papers, reports 
 =put here links to potential external repositories=