diff --git a/fairmq/FairMQDevice.cxx b/fairmq/FairMQDevice.cxx
index 148578bb..d8fb3803 100644
--- a/fairmq/FairMQDevice.cxx
+++ b/fairmq/FairMQDevice.cxx
@@ -30,13 +30,13 @@
 #include "FairMQSocket.h"
 #include "FairMQDevice.h"
 #include "FairMQLogger.h"
-#include "FairMQTools.h"
+#include "tools/FairMQTools.h"
 
-#include "FairMQProgOptions.h"
-#include "FairMQTransportFactoryZMQ.h"
-#include "FairMQTransportFactorySHM.h"
+#include "options/FairMQProgOptions.h"
+#include "zeromq/FairMQTransportFactoryZMQ.h"
+#include "shmem/FairMQTransportFactorySHM.h"
 #ifdef NANOMSG_FOUND
-#include "FairMQTransportFactoryNN.h"
+#include "nanomsg/FairMQTransportFactoryNN.h"
 #endif
 
 using namespace std;
diff --git a/fairmq/devices/FairMQBenchmarkSampler.cxx b/fairmq/devices/FairMQBenchmarkSampler.cxx
index e077014b..a60c028a 100644
--- a/fairmq/devices/FairMQBenchmarkSampler.cxx
+++ b/fairmq/devices/FairMQBenchmarkSampler.cxx
@@ -12,13 +12,14 @@
  * @author D. Klein, A. Rybalchenko
  */
 
+#include "FairMQBenchmarkSampler.h"
+
 #include <vector>
 #include <chrono>
 #include <thread>
 
-#include "FairMQBenchmarkSampler.h"
-#include "FairMQLogger.h"
-#include "FairMQProgOptions.h"
+#include "../FairMQLogger.h"
+#include "../options/FairMQProgOptions.h"
 
 using namespace std;
 
diff --git a/fairmq/devices/FairMQMerger.cxx b/fairmq/devices/FairMQMerger.cxx
index 5f866223..1b047b0d 100644
--- a/fairmq/devices/FairMQMerger.cxx
+++ b/fairmq/devices/FairMQMerger.cxx
@@ -12,10 +12,10 @@
  * @author D. Klein, A. Rybalchenko
  */
 
-#include "FairMQLogger.h"
 #include "FairMQMerger.h"
-#include "FairMQPoller.h"
-#include "FairMQProgOptions.h"
+#include "../FairMQLogger.h"
+#include "../FairMQPoller.h"
+#include "../options/FairMQProgOptions.h"
 
 using namespace std;
 
diff --git a/fairmq/devices/FairMQMultiplier.cxx b/fairmq/devices/FairMQMultiplier.cxx
index 58613ab4..f4169cf0 100644
--- a/fairmq/devices/FairMQMultiplier.cxx
+++ b/fairmq/devices/FairMQMultiplier.cxx
@@ -6,9 +6,10 @@
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "FairMQLogger.h"
 #include "FairMQMultiplier.h"
-#include "FairMQProgOptions.h"
+
+#include "../FairMQLogger.h"
+#include "../options/FairMQProgOptions.h"
 
 using namespace std;
 
diff --git a/fairmq/devices/FairMQProxy.cxx b/fairmq/devices/FairMQProxy.cxx
index 66d83f4e..2252ab1e 100644
--- a/fairmq/devices/FairMQProxy.cxx
+++ b/fairmq/devices/FairMQProxy.cxx
@@ -12,9 +12,10 @@
  * @author A. Rybalchenko
  */
 
-#include "FairMQLogger.h"
 #include "FairMQProxy.h"
-#include "FairMQProgOptions.h"
+
+#include "../FairMQLogger.h"
+#include "../options/FairMQProgOptions.h"
 
 using namespace std;
 
diff --git a/fairmq/devices/FairMQSink.cxx b/fairmq/devices/FairMQSink.cxx
index 6bb39c33..9ec5a2bc 100644
--- a/fairmq/devices/FairMQSink.cxx
+++ b/fairmq/devices/FairMQSink.cxx
@@ -12,11 +12,12 @@
  * @author D. Klein, A. Rybalchenko
  */
 
+#include "FairMQSink.h"
+
 #include <chrono>
 
-#include "FairMQSink.h"
-#include "FairMQLogger.h"
-#include "FairMQProgOptions.h"
+#include "../FairMQLogger.h"
+#include "../options/FairMQProgOptions.h"
 
 using namespace std;
 
diff --git a/fairmq/devices/FairMQSplitter.cxx b/fairmq/devices/FairMQSplitter.cxx
index ecd3d191..aecb26af 100644
--- a/fairmq/devices/FairMQSplitter.cxx
+++ b/fairmq/devices/FairMQSplitter.cxx
@@ -12,9 +12,10 @@
  * @author D. Klein, A. Rybalchenko
  */
 
-#include "FairMQLogger.h"
 #include "FairMQSplitter.h"
-#include "FairMQProgOptions.h"
+
+#include "../FairMQLogger.h"
+#include "../options/FairMQProgOptions.h"
 
 using namespace std;
 
diff --git a/fairmq/logger/CMakeLists.txt b/fairmq/logger/CMakeLists.txt
deleted file mode 100644
index dde4b2ff..00000000
--- a/fairmq/logger/CMakeLists.txt
+++ /dev/null
@@ -1,53 +0,0 @@
- ################################################################################
- #    Copyright (C) 2014 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH    #
- #                                                                              #
- #              This software is distributed under the terms of the             # 
- #         GNU Lesser General Public Licence version 3 (LGPL) version 3,        #  
- #                  copied verbatim in the file "LICENSE"                       #
- ################################################################################
-# Create a library  
-
-set(INCLUDE_DIRECTORIES
-    ${CMAKE_SOURCE_DIR}/fairmq/logger
-    ${CMAKE_SOURCE_DIR}/fairmq/logger/run
-    )
-
-include_directories(${INCLUDE_DIRECTORIES})
-
-set(SYSTEM_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
-include_Directories(SYSTEM ${SYSTEM_INCLUDE_DIRECTORIES})
-
-set(LINK_DIRECTORIES ${Boost_LIBRARY_DIRS}) 
-
-link_directories(${LINK_DIRECTORIES})
-
-set(SRCS logger.cxx)
-
-set(LIBRARY_NAME fairmq_logger)
-
-set(DEPENDENCIES
-    ${Boost_LOG_LIBRARY}
-    ${Boost_LOG_SETUP_LIBRARY}
-    ${Boost_THREAD_LIBRARY}
-    ${Boost_THREAD_LIBRARY}
-    ${Boost_DATE_TIME_LIBRARY}
-    ${Boost_FILESYSTEM_LIBRARY}
-    ${Boost_SYSTEM_LIBRARY}
-    pthread
-  )
-
-install(FILES logger.h logger_def.h DESTINATION include/logger)
-if("${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}" VERSION_LESS "1.56")
-    install(FILES fairroot_null_deleter.h DESTINATION include/logger)
-endif()
-
-
-
-GENERATE_LIBRARY()
-
-# generate test executable
-set(EXE_NAME runtestLogger)
-set(SRCS run/testLogger.cxx)
-set(DEPENDENCIES fairmq_logger)
-GENERATE_EXECUTABLE()
-
diff --git a/fairmq/run/runBenchmarkSampler.cxx b/fairmq/run/runBenchmarkSampler.cxx
index 2bb727b6..efae1c36 100644
--- a/fairmq/run/runBenchmarkSampler.cxx
+++ b/fairmq/run/runBenchmarkSampler.cxx
@@ -1,13 +1,13 @@
 /********************************************************************************
- *    Copyright (C) 2014 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH    *
+ *  Copyright (C) 2014-2017 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH *
  *                                                                              *
  *              This software is distributed under the terms of the             *
- *         GNU Lesser General Public Licence version 3 (LGPL) version 3,        *
+ *              GNU Lesser General Public Licence (LGPL) version 3,             *
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "runFairMQDevice.h"
-#include "FairMQBenchmarkSampler.h"
+#include <runFairMQDevice.h>
+#include <devices/FairMQBenchmarkSampler.h>
 
 namespace bpo = boost::program_options;
 
diff --git a/fairmq/run/runMerger.cxx b/fairmq/run/runMerger.cxx
index efd8b3db..2c73be8d 100644
--- a/fairmq/run/runMerger.cxx
+++ b/fairmq/run/runMerger.cxx
@@ -6,8 +6,8 @@
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "runFairMQDevice.h"
-#include "FairMQMerger.h"
+#include <runFairMQDevice.h>
+#include <devices/FairMQMerger.h>
 
 namespace bpo = boost::program_options;
 
diff --git a/fairmq/run/runMultiplier.cxx b/fairmq/run/runMultiplier.cxx
index f21f0828..1b9cbeba 100644
--- a/fairmq/run/runMultiplier.cxx
+++ b/fairmq/run/runMultiplier.cxx
@@ -6,8 +6,8 @@
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "runFairMQDevice.h"
-#include "FairMQMultiplier.h"
+#include <runFairMQDevice.h>
+#include <devices/FairMQMultiplier.h>
 
 namespace bpo = boost::program_options;
 
diff --git a/fairmq/run/runProxy.cxx b/fairmq/run/runProxy.cxx
index 4e583da1..fbe16c79 100644
--- a/fairmq/run/runProxy.cxx
+++ b/fairmq/run/runProxy.cxx
@@ -6,8 +6,8 @@
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "runFairMQDevice.h"
-#include "FairMQProxy.h"
+#include <runFairMQDevice.h>
+#include <devices/FairMQProxy.h>
 
 namespace bpo = boost::program_options;
 
diff --git a/fairmq/run/runSink.cxx b/fairmq/run/runSink.cxx
index f6acb27c..abbd60b9 100644
--- a/fairmq/run/runSink.cxx
+++ b/fairmq/run/runSink.cxx
@@ -6,8 +6,8 @@
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "runFairMQDevice.h"
-#include "FairMQSink.h"
+#include <runFairMQDevice.h>
+#include <devices/FairMQSink.h>
 
 namespace bpo = boost::program_options;
 
diff --git a/fairmq/run/runSplitter.cxx b/fairmq/run/runSplitter.cxx
index c0df0b69..2464337b 100644
--- a/fairmq/run/runSplitter.cxx
+++ b/fairmq/run/runSplitter.cxx
@@ -6,8 +6,8 @@
  *                  copied verbatim in the file "LICENSE"                       *
  ********************************************************************************/
 
-#include "runFairMQDevice.h"
-#include "FairMQSplitter.h"
+#include <runFairMQDevice.h>
+#include <devices/FairMQSplitter.h>
 
 namespace bpo = boost::program_options;
 
diff --git a/fairmq/runFairMQDevice.h b/fairmq/runFairMQDevice.h
index 5bfa811a..09438203 100644
--- a/fairmq/runFairMQDevice.h
+++ b/fairmq/runFairMQDevice.h
@@ -9,9 +9,9 @@
 #include <boost/program_options.hpp>
 
 #include "FairMQLogger.h"
-#include "FairMQProgOptions.h"
+#include "options/FairMQProgOptions.h"
 #include "FairMQDevice.h"
-#include "runSimpleMQStateMachine.h"
+#include "tools/runSimpleMQStateMachine.h"
 
 template <typename R>
 class GenericFairMQDevice : public FairMQDevice
diff --git a/fairmq/shmem/FairMQContextSHM.cxx b/fairmq/shmem/FairMQContextSHM.cxx
index 28e21dcb..002f7bf2 100644
--- a/fairmq/shmem/FairMQContextSHM.cxx
+++ b/fairmq/shmem/FairMQContextSHM.cxx
@@ -48,11 +48,11 @@ FairMQContextSHM::~FairMQContextSHM()
 
     if (boost::interprocess::shared_memory_object::remove("FairMQSharedMemory"))
     {
-        printf("Successfully removed shared memory after the device has stopped.\n");
+        fprintf(stderr, "Successfully removed shared memory after the device has stopped.\n");
     }
     else
     {
-        printf("Did not remove shared memory after the device stopped. Already removed?\n");
+        fprintf(stderr, "Did not remove shared memory after the device stopped. Already removed?\n");
     }
 }
 
diff --git a/fairmq/tools/runSimpleMQStateMachine.h b/fairmq/tools/runSimpleMQStateMachine.h
index cb6f3b4d..47ebe8c4 100644
--- a/fairmq/tools/runSimpleMQStateMachine.h
+++ b/fairmq/tools/runSimpleMQStateMachine.h
@@ -11,8 +11,8 @@
 #include "FairMQLogger.h"
 #include "FairMQConfigPlugin.h"
 #include "FairMQControlPlugin.h"
-#include "FairMQParser.h"
-#include "FairMQProgOptions.h"
+#include "options/FairMQParser.h"
+#include "options/FairMQProgOptions.h"
 
 #include <iostream>
 #include <string>