- Edit | Attach | Print version | PDF | History: r2 < r1 | Backlinks | View wiki text | Refresh | More topic actions
+ Edit | Attach | Print version | PDF | History: r2 < r1 | Backlinks | View wiki text | Refresh | More topic actions
Topic revision: r2 - 19 Jun 2012, AndreasSuter
@@ -190,7 +190,7 @@ Since quite some effort is going into the development and maintenance of the
- Edit | Attach | Print version | PDF | History: r16 < r15 < r14 < r13 | Backlinks | View wiki text | Refresh | More topic actions
+ Edit | Attach | Print version | PDF | History: r17 < r16 < r15 < r14 | Backlinks | View wiki text | Refresh | More topic actions
-Topic revision: r16 - 10 Jul 2011, wojek
+Topic revision: r17 - 03 Jul 2015, AndreasSuter
@@ -468,7 +468,7 @@ An example XML file looks as follows:
- Θ (°).
- msr2data <run> <extension> [optional parameters]
- A single run number.
- msr2data <firstRunNo> <lastRunNo> <extension> [optional parameters]
- An interval of run numbers is specified through the first and the last run number. The condition <firstRunNo> < <lastRunNo> is not necessary. -
- msr2data \[<run1> <run2> ... <runN> \] <extension> [optional parameters]
- A space separated list of run numbers can be enclosed in [ and ]. Every run that should be processed has to be specified explicitly by its run number. +
- msr2data \[ <runList> \] <extension> [optional parameters]
- Where <runList> is one or a combination of the following:(i) <run0>, <run1>, <run2>, ... <runN> : run numbers, e.g. 123 124, (ii) <run0>-<runN> : a range, e.g. 123-125 -> 123 124 125, (iii) <run0>:<runN>:<step> : a sequence, e.g. 123:127:2 -> 123 125 127. <step> has to be a positive integer. A <runList> can also combine (i)-(iii), e.g. 123 128-130 133, etc.
- msr2data <runListFileName> <extension> [optional parameters]
- An ASCII file containing a list of run numbers and optional external parameters is passed to
msr2data. For the structure of the ASCII file see below. - Bastian M. Wojek
- I am very much indebted to BMW for his rigorous testing of
musrfit, his many useful suggestions, contributions, and for the largest part of the user manual ofmusrfitwhich makes it accessible to a broader audience! Many thanks Bastian! - - 5.3 musrfit
- 5.4 musredit -
- 5.5 musrgui +
- 5.5 musrgui (obsolete)
- 5.6 Check of the installation @@ -167,10 +167,10 @@ pre {
- boost C++ libraries
- The powerful
Spiritparser framework used bymusrfitis included in that collection of libraries. Required version ≥ 1.33 - GNU Scientific Library
- A numerical
CandC++library which provides efficient implementations of various mathematical routines. Required version ≥ 1.9 - FFTW
- A
Cimplementation for the fast computation of discrete Fourier transforms. Required version ≥ 3.1 @@ -196,73 +196,102 @@ Each of the following sections focusing on the installation ofmusrfit
- Edit | Attach | Print version | PDF | History: r2 < r1 | Backlinks | View wiki text | Refresh | More topic actions
+ Edit | Attach | Print version | PDF | History: r3 < r2 < r1 | Backlinks | View wiki text | Refresh | More topic actions
-Topic revision: r2 - 10 Jul 2011, wojek
+Topic revision: r3 - 03 Jul 2015, AndreasSuter
@@ -273,7 +273,7 @@ The parameters are:
msr2data. These differ in how the list of runs which should be processed is supplied: msr2data contain the mandatory<
msr2data 8472 _tf_h13generates the DB file
out.db (can be changed by using the -o option) from 8472_tf_h13.msr.
msr2data 8472 8474 _tf_h13generates the DB file
out.db (can be changed by using the -o option) from 8472_tf_h13.msr, 8473_tf_h13.msr, and 8474_tf_h13.msr.
msr2data [8472 8470] _tf_h13generates the DB file
out.db (can be changed by using the -o option) from 8472_tf_h13.msr and 8470_tf_h13.msr.
+msr2data [8470:8474:2] _tf_h13generates the DB file
out.db (can be changed by using the -o option) from 8470_tf_h13.msr, 8472_tf_h13.msr, and 8474_tf_h13.msr.
msr2data run.list _tf_h13generates the DB file
out.db (can be changed by using the -o option) from all runs listed in the ASCII file run.list in the working directory. In this file it is also possible to include external parameters which should be put in the resulting DB file. The structure of the run.list is the following:
@@ -214,9 +215,9 @@ msr2data 8400 8460 _tf_h13 -oABC.db fit-8472Using
8472_tf_h13.msr as first template, msr2data generates subsequent msr input files 8400_tf_h13.msr through 8460_tf_h13.msr, calls musrfit to perform a fit of these files and collects the results of the fits together with the DB header in the new file ABC.db. Additionally, some information about external parameters like the temperature will be passed to ABC.db if it is present in the data files.
-msr2data [8500 8505] _zf fit-8472 noheader nosummary -o DEF.db +msr2data [8500 8502-8504 8507] _zf fit-8472 noheader nosummary -o DEF.db-Using
8472_zf.msr as first template, msr2data generates subsequent msr input files 8500_zf.msr and 8505_zf.msr, calls musrfit to perform a fit of these files and collects the results of the fits in the file DEF.db without writing the DB file header or attempting to read additional information from the data files.
+Using 8472_zf.msr as first template, msr2data generates subsequent msr input files 8500_zf.msr, 8502_zf.msr, 8503_zf.msr, 8504_zf.msr and 8507_zf.msr, calls musrfit to perform a fit of these files and collects the results of the fits in the file DEF.db without writing the DB file header or attempting to read additional information from the data files.
msr2data 8595 8585 "" noheader fit-8472! -oGHI.dat data nosummary -k@@ -337,7 +338,7 @@ msr2data 8471 8470 -OneRunFit_example -o OneRunFits.db
7 Bugtracking
-For reporting bugs or requesting new features and improvements please use the PSI Tracker or send an e-mail to A. Suter. +For reporting bugs or requesting new features and improvements please use the Bitbucket Issues, PSI Tracker or send an e-mail to A. Suter. -- BMW & AS @@ -351,7 +352,7 @@ For reporting bugs or requesting new features and improvements please use the -Topic revision: r39 - 16 Aug 2015, AndreasSuter
-
+
diff --git a/doc/html/user/MUSR/MusrFit.html b/doc/html/user/MUSR/MusrFit.html
index f3e74c9d..c44f32da 100644
--- a/doc/html/user/MUSR/MusrFit.html
+++ b/doc/html/user/MUSR/MusrFit.html
@@ -1,6 +1,6 @@
-
+
@@ -8,7 +8,7 @@
-
+
@@ -1610,7 +1610,7 @@ For reporting bugs or requesting new features and improvements please use the
- Edit | Attach | Print version | PDF | History: r126 < r125 < r124 < r123 | Backlinks | View wiki text | Refresh | More topic actions
+ Edit | Attach | Print version | PDF | History: r126 < r125 < r124 < r123 | Backlinks | View wiki text | Refresh | More topic actions
Topic revision: r126 - 29 May 2015, AndreasSuter
@@ -1656,7 +1656,7 @@ For reporting bugs or requesting new features and improvements please use the
-
+
diff --git a/doc/html/user/MUSR/MusrFitAcknowledgements.html b/doc/html/user/MUSR/MusrFitAcknowledgements.html
index 4ca69046..9109829f 100644
--- a/doc/html/user/MUSR/MusrFitAcknowledgements.html
+++ b/doc/html/user/MUSR/MusrFitAcknowledgements.html
@@ -1,6 +1,6 @@
-
+
@@ -8,7 +8,7 @@
-
+
@@ -120,9 +120,7 @@ pre {
Acknowledgements - musrfit
- Edit | Attach | Print version | PDF | History: r4 < r3 < r2 < r1 | Backlinks | View wiki text | Refresh | More topic actions
+ Edit | Attach | Print version | PDF | History: r5 < r4 < r3 < r2 | Backlinks | View wiki text | Refresh | More topic actions
-Topic revision: r4 - 10 Jul 2011, wojek
+Topic revision: r5 - 03 Jul 2015, AndreasSuter
@@ -190,7 +188,7 @@ pre {
1 Supported Operating Systems and Software Requirements
-This page is intended to demonstrate for the interested user which steps are necessary to set up the free software μSR data analysis frameworkmusrfit. While the preferred way is to run the software on GNU/Linux, with some restrictions it can also be set up under MS Windows and MacOS X. In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to read completely each section dealing with the present installation step before starting the installation process!
+This page is intended to demonstrate for the interested user which steps are necessary to set up the free software μSR data analysis framework musrfit. While the preferred way is to run the software on GNU/Linux or MacOS X, with some restrictions it can also be set up under MS Windows (cygwin, only for the very brave, probably it is easier for most MS Windows users to install a Virtual Machine running Linux). In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to read completely each section dealing with the present installation step before starting the installation process!
-Apart from GCC, the GNU Compiler Collection, the GNU build tools autoconf, automake and libtool as well as the helper tool pkg-config musrfit requires the installation of a few open-source libraries and programs: -
+Apart from GCC, the GNU Compiler Collection (gcc, g++), the GNU build tools autoconf, automake and libtool as well as the helper tool pkg-config
musrfit requires the installation of a few open-source libraries and programs including their header packages: musrfit (including the requirements) using Visual C++ has not been tested. If anybody likes to do this: Just go ahead and have fun! However, not very much assistance can be expected, although it would be an interesting experiment.
-10.6 Snow Leopard Qt3 for Mac is not supported any more since this was based on a 32-bit only API. Snow Leopard -users are advised to use the Qt4 based musredit or to rely on the standard Qt3 version for X11 in order to run musrgui.
+10.6 Snow Leopard Qt3 for Mac is not supported any more since this was based on a 32-bit only API. Snow Leopard -users are advised to use the Qt4 based musredit or to rely on the standard Qt3 version for X11 in order to run musrgui. On newer Mac OS X versions (>= 10.8) you should use the Qt4 base musredit only.
3 GNU/Linux
3.1 Requirements
3.1.1 Everything but ROOT and NeXus
Depending on the GNU/Linux distribution chosen, the above mentioned software—except the ROOT system and the NeXus library—should be available from the distributor and could be easily installed in the form of binary packages. If done in this way there should be taken care of installing both, the libraries and the header (dev, devel) files.-On a Scientific Linux (Red Hat) system the following command executed as superuser from the shell will do the trick: +On a Scientific Linux (Red Hat, other RPM-package base Linux distributions) system the following command executed as superuser from the shell will do the trick (never type the '$' it is the shell prompt of your system):
-yum install git boost-devel gsl-devel fftw-devel libxml2-devel qt-devel qtwebkit-devel +$ yum install git boost-devel gsl-devel fftw-devel libxml2-devel qt-devel qtwebkit-develWhen dealing with a distribution that uses the dpkg/apt package manager like Debian or Ubuntu the installation would look like:
-apt-get install git libboost-dev libgsl0-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-dev +$ apt-get install git libboost-dev libgsl0-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-devEveryone should know best himself which is the way to install distribution software on the chosen distribution
In case the distribution does not include the required software it has to be compiled from the source files which normally means to download the source code from the corresponding website, to unpack the source tree and call the following from the shell:
-./configure -make -make install +$ ./configure +$ make +$ make installIn order to obtain some information about the possible options for the installation, calling
./configure --help might give some useful hints. For any further information on the standard installation of software, please refer to the web search engine of choice and ask for "install software on linux"...
3.1.2 Installation of NeXus requirements (optional)
-Only if musrfit should support reading data files in the NeXus format the further required software has to be set up. The required libraries and header files could either be available through the user's GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. E.g. on Red Hat-like systems binary packages for MXML, HDF4, and HDF5 might be called mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel, on Debian-like systems libmxml1, libmxml-dev, libhdf4-dev, libhdf5-dev.
+Only if musrfit should support reading/writing data files in the NeXus format the further required software has to be set up. The required libraries and header files could either be available through the user's GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. E.g. on Red Hat-like systems binary packages for MXML, HDF4, and HDF5 might be called mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel, on Debian-like systems libmxml1, libmxml-dev, libhdf4-dev, libhdf5-dev.
Even though there might exist binary packages for the NeXus library, it is best to build and install it directly from the source code which can be found here.
3.1.3 ROOT
-Currently only ROOT 5.34/xx is support! Do NOT try to use ROOT 6.xx/yy!
+Currently only ROOT 5.34/xx is support! Do NOT try to use ROOT 6.xx/yy yet!
-The ROOT system may or may not be part of the GNU/Linux distribution. If it is, it should be checked that the provided binaries are of a recent version and then these in principle can be installed using a package manager as described above. -In case the distribution provides no or only outdated binary packages there are the following possibilities:
-
-
- Visit the
ROOTweb page and download the packed precompiled binary version matching best the GNU/Linux distribution. Then unpack the bundle to its final destination. - - If there is no precompiled binary version of
ROOTavailable for your system or e.g.ROOTshould be compiled with another version ofGCCvisit the web page and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system)(1), configure(2) it (here using the minimal set of options) and compile it as follows right below:-cd /opt/root-system -./configure linux --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml - (or in case of a 64 bit installation: ./configure linuxx8664gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml) -make - (or in case there are multiple processors available, e.g.: make -j4) +The
ROOTsystem may or may not be part of the GNU/Linux distribution. Some distributions are packingROOTin a manner incompatible with the way it is needed formusrfit. Therefore we advise to installROOTfrom source. Before installingROOTfrom source you will need to install some additional header packages. + +For RPM based systems (RedHat, Fedora, etc) this will likely to be libX11-devel, libXft-devel, libXpm-devel, and libXext-devel: ++$ yum install libX11-devel libXft-devel libXpm-devel libXext-devel +
+ +For a dpkg/apt based system (Debian, Ubuntu, etc) this will likely to be libX11-dev, libxft-dev, libxpm-dev, and libxext-dev: ++$ apt-get install libX11-dev libxft-dev libxpm-dev libxext-dev +
+ +Also make sure that you have installed all required packages listed under Requested Software (e.g. fftw, gsl, etc). + +For the following it is assumed thatROOTshall be installed under$HOME/Apps. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do not enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on. ++$ cd $HOME +$ # creat the Apps directory if not already present +$ mkdir Apps +$ cd Apps +$ git clone http://root.cern.ch/git/root.git +$ cd root +$ git tag -l +$ # git tag -l will list all available tags. In the next command choose the tag v5-34-xx +$ # where xx is the highest listed number, e.g. v5-34-32 +$ git checkout -b v5-34-32 v5-34-32 +$ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. +$ ./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml +$ # next will be the make. If running on a multicore CPU you can speed up tremendously by calling +$ # make with the option -j <number>, where <number> is the number of threads which you want to give, +$ # e.g. make -j8 +$ make +
+ +What is still missing is that the system should be told where to find theROOTinstallation, therefore the following is suggested:-
+
- As superuser create a file /etc/ld.so.conf.d/cern-root.conf where the path to the
libdirectory ofROOTis added and call /sbin/ldconfig afterwards. In the example mentioned above one way of doing this is:+$ echo "$HOME/Apps/root/lib" >> /etc/ld.so.conf.d/cern-root.conf +$ /sbin/ldconfig +
+ - Additionally, as normal user one should append the following lines to the ~/.bashrc and/or ~/.bash_profile (~./profile on Debian like systems, and then either restart the shell or call the same commands once more from the shell) in order to change some path-setting environment variables:
+$ export ROOTSYS=$HOME/Apps/root +$ export PATH=$ROOTSYS/bin:$PATH
ROOTinstallation, therefore the following is suggested:-
-
- As superuser create a file /etc/ld.so.conf.d/root-system.conf where the path to the
libdirectory ofROOTis added and call /sbin/ldconfig afterwards. In the example mentioned above one way of doing this is:-echo "/opt/root-system/lib" >> /etc/ld.so.conf.d/root-system.conf -/sbin/ldconfig + +If an update of
ROOTis needed, simple do the following:+$ cd $HOME/Apps/root +$ git pull +$ make
- - Additionally, as normal user one should append the following lines to the ~/.bashrc and/or ~/.bash_profile (and then either restart the shell or call the same commands once more from the shell) in order to change some path-setting environment variables:
-export ROOTSYS=/opt/root-system/ -export PATH=$ROOTSYS/bin:$PATH -
-
3.2
-When all required software has been set up it can be proceeded with themusrfitmusrfitinstallation. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal +When all required software has been set up it can be proceeded with themusrfitinstallation. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in $HOME/Apps this is achieved most easily calling from the terminal-cd -git clone https://bitbucket.org/muonspin/musrfit.git +$ cd $HOME/Apps +$ git clone https://bitbucket.org/muonspin/musrfit.git
or-cd -git clone git://gitorious.psi.ch/nemu/musrfit.git +$ cd $HOME/Apps +$ git clone git://gitorious.psi.ch/nemu/musrfit.git
Note: musrfit has moved from svn to git. In case you still have an old svn version of musrfit, it is advised to remove it first. For svn users: for a smooth transition from svn to git, please check the following link: @@ -270,8 +299,11 @@ git clone git://gitorious.psi.ch/nemu/musrfit.git If a local repository clone is already present, one can update it using:-cd musrfit -git pull +$ cd $HOME/Apps/musrfit +$ git pull +$ # the new version now needs to be compiled and installed +$ make +$ make install
As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket. @@ -294,14 +326,14 @@ After the source-code extraction the autogen.sh script is calle Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. The other paths should be detected automatically. If this does not work for some reason the configure script will terminate and ask for the information. -When the configure script has been called successfully everything is ready for building themusrfitlibraries and executables. A standard installation sequence (withoutNeXussupport) might then look like(3): +When the configure script has been called successfully everything is ready for building themusrfitlibraries and executables. A standard installation sequence (withoutNeXussupport) might then look like(3):-cd musrfit -sh autogen.sh -./configure --prefix=$ROOTSYS -make -make install -/sbin/ldconfig (as superuser) +$ cd $HOME/Apps/musrfit +$ sh autogen.sh +$ ./configure --prefix=$ROOTSYS +$ make +$ make install +$ /sbin/ldconfig # (as superuser)
In order to finish the installation ofmusrfittwo more things should be done:- Define the MUSRFITPATH environment variable containing the path to the
musrfitexecutables and XML files. E.g. if the location of the example above is used append the following line to the ~/.bashrc and ~/.bash_profile (and then either restart the shell or call the same commands once more from the shell):@@ -314,13 +346,14 @@ export MUSRFITPATH=/opt/root-system/bin
3.3
In the latest version ofmusreditmusrfitthe configure script tries to determine automatically ifQt4.6or higher is set up on the machine. In case this is found, the editormusreditis built already together withmusrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:-cd src/musredit -qmake musredit.pro +$ cd $HOME/Apps/musrfit/src/musredit +$ # for some distributions you will need qmake-qt4 for the next command +$ qmake musredit.pro
If everything went finemusreditcan be compiled and installed:-make -make install +$ make +$ make install
In case one does not like the executable musredit to be copied to the default installation directory $ROOTSYS/bin the last "make install" can be skipped and the executable can be copied somewhere else instead. However, the musredit_startup.xml should go to the installation directory MUSRFITPATH of themusrfitexecutables. Eventually, in the installed musredit_startup.xml the path specifications should be adjusted to match the localmusrfitinstallation. For detailed information on this XML file refer to the manual. @@ -333,19 +366,15 @@ If there are problems during theqmakestep, e.g. "uic: File genera In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in themusrfitsource tree at doc/examples/.
Ifmusrguihas been installed, just open one of the test-*.msr files in the editor and test themusrfitfunctionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:-cd doc/examples -musrview test-histo-ROOT-NPP.msr +$ cd $HOME/Apps/musrfit/doc/examples +$ musrview test-histo-ROOT-NPP.msr
Notes - 1 : In case only a single user is working at the machine it might be considerable to change the ownership of theROOTfolder so that the user has easy write access to this directory: - - 2 : When usingGCC≥ 4.2 please make sure that the environment variables USE_PARALLEL_MINUIT2 and USE_OPENMP are not set! OtherwiseMINUIT2will be compiled with parallelization support and cannot be used together withmusrfitafterwards since themusrfitcode is not fully thread-safe! When compiled withGCC≥ 4.2musrfititself will parallelize the χ2 calculation. - - 3 : In case the normal user has no write permissions to the $ROOTSYS and the installation path the "make install" commands have to be executed as superuser. + 3 : In case the normal user has no write permissions to the $ROOTSYS and the installation path the "make install" commands have to be executed as superuser. @@ -369,7 +398,7 @@ After these installations already most of the required software is present and t Since later on theboostheader files should be used and in the standard Cygwin installation these are found at a version specific location, the later handling will be easier if a symbolic link to these files is created now in the terminal (in case it had not been present before):-ln -sf /usr/include/boost-x_yy_z/boost /usr/include/boost +$ ln -sf /usr/include/boost-x_yy_z/boost /usr/include/boost
where x_yy_z has to be substituted by the correct version number, e.g. 1_33_1. @@ -378,46 +407,46 @@ where x_yy_z has to be substituted by the correct version numbe All other libraries have to be built from the sources. The following lines will track the installation ofJPEG6b,MXML2.9,HDF4.2.7-patch1, andNeXus4.3.2. The version numbers and source-code locations might of course change with time but should be easily adjustable.-cd -mkdir nexus -cd nexus -curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz -cd jpeg-6b -./configure --prefix=/usr/local --enable-static -make -make install -cd .. -curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz -cd mxml-2.9 -./configure --prefix=/usr/local --enable-static -make -make install -cd .. -curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.7-patch1.tar.gz -G | tar xz -cd hdf-4.2.7-patch1 -./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local -make -make install -cd .. -curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G | tar xz -cd nexus-4.3.2-20140413svn1919 -./configure --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local -make -make install +$ cd +$ mkdir nexus +$ cd nexus +$ curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G | tar xz +$ cd jpeg-6b +$ ./configure --prefix=/usr/local --enable-static +$ make +$ make install +$ cd .. +$ curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz +$ cd mxml-2.9 +$ ./configure --prefix=/usr/local --enable-static +$ make +$ make install +$ cd .. +$ curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.7-patch1.tar.gz -G | tar xz +$ cd hdf-4.2.7-patch1 +$ ./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local +$ make +$ make install +$ cd .. +$ curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G | tar xz +$ cd nexus-4.3.2-20140413svn1919 +$ ./configure --prefix=/usr/local --with-hdf4=/usr/local --with-hdf5=/usr --with-xml=/usr/local +$ make +$ make install
4.1.3
In order to install theROOTROOTsystem, there are two possibilities:- Download the precompiled Cygwin GCC 4.3 package of the most recent
ROOTversion from the web page and unpack it in a Cygwin shell (in order to get the line endings correctly) at the final location. Suppose the package has been downloaded to C:\ and theROOTtree should be in C:\root, this is achieved by:-cd /cygdrive/c -tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz +$ cd /cygdrive/c +$ tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz
- - If due to some reason there was no precompiled Cygwin GCC 4.3 package available or
ROOTshould be built from source, one has to visit the web page, download the 'complete source tree for all systems' and save it for instance in C:\.
Then go to the Cygwin shell and unpack this source tree, configure(2) it (here using the minimal set of options) and compile it as follows right below:-cd /cygdrive/c -tar xzf root_v5.xx.yy.source.tar.gz -cd root -./configure win32gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml -make +
- If due to some reason there was no precompiled Cygwin GCC 4.3 package available or
ROOTshould be built from source, one has to visit the web page, download the 'complete source tree for all systems' and save it for instance in C:\.
Then go to the Cygwin shell and unpack this source tree, configure(2) it (here using the minimal set of options) and compile it as follows right below:+$ cd /cygdrive/c +$ tar xzf root_v5.xx.yy.source.tar.gz +$ cd root +$ ./configure win32gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml +$ make
4.2 musrfitFirst, the most recent source code should be downloaded. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal-cd -git clone https://bitbucket.org/muonspin/musrfit.git +$ cd +$ git clone https://bitbucket.org/muonspin/musrfit.git
or-cd -git clone git://gitorious.psi.ch/nemu/musrfit.git +$ cd +$ git clone git://gitorious.psi.ch/nemu/musrfit.git
Note: musrfit has moved from svn to git. In case you still have an old svn version of musrfit, it is advised to remove it first. For svn users: for a smooth transition from svn to git, please check the following link: @@ -449,8 +478,8 @@ git clone git://gitorious.psi.ch/nemu/musrfit.git If the repository had been checked out already before, one can update the local copy using:-cd musrfit -git pull +$ cd musrfit +$ git pull
As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket. @@ -475,11 +504,11 @@ After the source-code extraction the autogen.sh script is calle Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. The other paths should be detected automatically. If this does not work for some reason the configure script will terminate and ask for the information. When the configure script has been called successfully everything is ready for building themusrfitlibraries and executables. A standard installation sequence (withoutNeXussupport) might then look like:-cd musrfit -sh autogen.sh -./configure --prefix=$ROOTSYS -make -make install +$ cd musrfit +$ sh autogen.sh +$ ./configure --prefix=$ROOTSYS +$ make +$ make install
In order to finish the installation ofmusrfitthe paths wheremusrfitsearches for data files should be adjusted in the installed musrfit_startup.xml (/cygdrive/c/root/bin/musrfit_startup.xml or C:\root\bin\musrfit_startup.xml). The paths have to obey thePOSIXnaming convention. For detailed information on this XML file refer to the manual. @@ -487,13 +516,13 @@ In order to finish the installation ofmusrfitthe paths where4.3 musreditIn the latest version ofmusrfitthe configure script tries to determine automatically ifQt4.5or higher is set up on the machine. In case this is found, the editormusreditis built already together withmusrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:-cd src/musredit -qmake-qt4 musredit.pro +$ cd src/musredit +$ qmake-qt4 musredit.pro
If everything went finemusreditcan be compiled and installed:-make -make install +$ make +$ make install
Eventually, in the installed musredit_startup.xml (/cygdrive/c/root/bin/musredit_startup.xml or C:\root\bin\musredit_startup.xml) the path specifications should be adjusted to match the localmusrfitinstallation. For detailed information on this XML file refer to the manual. @@ -518,20 +547,25 @@ IfQt4.5is not available butQt3is set upmusr In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in themusrfitsource tree at doc/examples/.
Ifmusrguihas been installed, just open one of the test-*.msr files in the editor and test themusrfitfunctionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:-cd doc/examples -musrview test-histo-ROOT-NPP.msr +$ cd doc/examples +$ musrview test-histo-ROOT-NPP.msr
4.6 Possible problems
It might be that especially when running on Windows 7musreditandmusrguiproduce errors like a "STATUS_ACCESS_VIOLATION". In this case, try to do the following: Close all Cygwin programs (including the terminals and X server) and run from a Windows command prompt (cmd)-C:\cygwin\bin\ash.exe /bin/rebaseall +$ C:\cygwin\bin\ash.exe /bin/rebaseall
If this does not resolve the problem, try to change the compatibility settings of C:\cygwin\bin\sh.exe and C:\cygwin\bin\bash.exe so that they are executed with administrator privileges.5 Mac OS X
-With Mac OS X the situation is up to some extent similar like on MS Windows but still different since Mac OS X is a UNIX system. The similarity is that also on OS X a helping framework—eitherMacPortsorFink—which provides open-source software is employed to fulfill the basic software requirements ofmusrfit. In the following, both possibilities (usingMacPortsorFink) are described but it is emphasized here that it should be followed only one of the possible routes. +With Mac OS X the situation is up to some extent similar like on MS Windows but still different since Mac OS X is a UNIX system. The similarity is that also on OS X a helping framework—eitherMacPortsorFink—which provides open-source software is employed to fulfill the basic software requirements ofmusrfit. In the following, both possibilities (usingMacPortsorFink) are described but it is emphasized here that it should be followed only one of the possible routes. + +WARNING: The instruction forFinkhaven't been updated/tested for quite a while and likely are slightly outdated. + + +5.1 Requirements (
MacPorts)5.1.1 Everything but
@@ -543,26 +577,26 @@ Before proceeding with the usage of theROOTandNeXusMacPorts install page, download the installer for your system and follow the installation instructions on the page. By default theMacPortssystem will be installed in /opt/local.
To be sure that the newest version of the software is used aMacPortsupgrade should be performed by typing in a terminal:-sudo port -v selfupdate +$ sudo port -v selfupdate
Remark:MacPortsuses rsync in order to synchronize the list of available packages. It frequently happens that this service is blocked by firewalls. In this case it should be possible to download a local version of the package repository and do the synchronization. If this step becomes necessary (and only then) it can be done in the following way:- Get a local version of the repository:
-svn co http://svn.macports.org/repository/macports/trunk/dports ~/dports +$ svn co http://svn.macports.org/repository/macports/trunk/dports ~/dports
- Edit the file /opt/local/etc/macports/sources.conf: At the end of the file, comment the line beginning with "rsync://" and add a new line pointing to your local copy, e.g.
file:///Users/username/dports
- Synchronize the packages:
-sudo port -v -d sync +$ sudo port -v -d sync
Then theMacPortssystem should be set up and can be used to install additional software.
The installation of the software mentioned above is then done in the terminal:-sudo port -v install pkgconfig autoconf automake libtool fftw-3 fftw-3-single gsl boost libxml2 qt4-mac +$ sudo port -v install pkgconfig autoconf automake libtool fftw-3 fftw-3-single gsl boost libxml2 qt4-mac
Withqt4-mac,musreditwill be installed. If it happens that you usedmusrguiin the past, please change over tomusreditsince there will be no further development formusrguianymore! @@ -570,40 +604,52 @@ Withqt4-mac,musreditwill be installed. If it Only ifmusrfitshould support reading data files in theNeXusformat the further required packages are set up:-sudo port -v install jpeg6b hdf4 hdf5 +$ sudo port -v install jpeg6b hdf4 hdf5
Unfortunately, theminixmlandNeXuslibraries have to be compiled and installed directly from the source code. Given the respective version numbers of 2.9 and 4.3.2 (which are subject to change with time) this can be achieved for example by:-cd -curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz -cd mxml-2.9 -./configure --prefix=/usr/local -make -sudo make install -cd .. -curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G | tar xz -cd nexus-4.3.2-20140413svn1919 -./configure --prefix=/usr/local -make -sudo make install +$ cd +$ curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz +$ cd mxml-2.9 +$ ./configure --prefix=/usr/local +$ make +$ sudo make install +$ cd .. +$ curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G | tar xz +$ cd nexus-4.3.2-20140413svn1919 +$ ./configure --prefix=/usr/local +$ make +$ sudo make install
5.1.3
-For installing theROOTROOTsystem there are two independent possibilities:-
-
- Visit the
ROOTweb page and download the packed precompiled binary version matching the OS X version. Then unpack the bundle to its final destination (e.g. /opt/root-system). - - If there is no precompiled binary version of
ROOTavailable for your system or e.g.ROOTshould be compiled with another version ofGCCvisit the web page and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system). In case only a single user is working at the machine it might be considerable to change the ownership of theROOTfolder so that the user ("username" in the example) has easy write access to this directory:sudo chown -R username:staff /opt/root-system/
Finally,ROOTcan be configured (here using the minimal set of options) and compiled as stated right below:-cd /opt/root-system -./configure --gminimal --enable-fink --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml -make -
and for Mac OS X 10.9 (Mavericks) for now (beginning 2014, subject to be changed hopefully soon):-cd /opt/root-system -./configure --gminimal --enable-builtin-freetype --enable-fink --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml -make +The best way to get
ROOTexactly the way needed formusrfitis to install it from source. Before describing it, please make sure that you have installed all required packages listed under Requested Software (e.g. fftw, gsl, etc). + +For the following it is assumed thatROOTshall be installed under$HOME/Apps. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do not enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on. ++$ cd $HOME +$ # creat the Apps directory if not already present +$ mkdir Apps +$ cd Apps +$ git clone http://root.cern.ch/git/root.git +$ cd root +$ git tag -l +$ # git tag -l will list all available tags. In the next command choose the tag v5-34-xx +$ # where xx is the highest listed number, e.g. v5-34-32 +$ git checkout -b v5-34-32 v5-34-32 +$ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. +$ ./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml +$ # next will be the make. If running on a multicore CPU you can speed up tremendously by calling +$ # make with the option -j <number>, where <number> is the number of threads which you want to give, +$ # e.g. make -j8 +$ make
- - In case you are just migrating to the latest Mac OS X version (e.g. from 10.7 to 10.8.1) often for a period of a few weeks it is necessary to work with the GIT trunk version of
ROOT, i.e. that you have to checkoutROOTviagit:-git clone http://root.cern.ch/git/root.git -
For details see Installing ROOT from Source. -
ROOTinstallation and to prepare already the installation ofmusrfitandmusrgui/musreditthis is a good time for setting necessary environment variables for the use in Mac OS X. Put the following lines (without the comments in parentheses and with the paths adjusted to your local installation) into the file ~/.MacOSX/environment.plist and re-login:
@@ -612,15 +658,62 @@ In order to finalize the
+For Mac OS X > 10.8: + +Here we will need two files placed under ~/Library/LaunchAgents, the first called setenv.ROOTSYS.plist with the content +ROOTinstallation and to prepare already t <plist version="1.0"> <dict> <key>MUSRFITPATH</key> - <string>/opt/root-system/bin</string> (where to find the musrfit executables) + <string>$HOME/Apps/root/bin</string> (where to find the musrfit executables) <key>QTDIR</key> <string>/opt/local/lib/qt3mac</string> (where to find Qt3 (for musrgui) or Qt4 (for musredit)) <key>ROOTSYS</key> - <string>/opt/root-system</string> (where to find the ROOT system) + <string>$HOME/Apps/root</string> (where to find the ROOT system) </dict> </plist>+<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> + <plist version="1.0"> + <dict> + <key>Label</key> + <string>setenv.ROOTSYS</string> + <key>ProgramArguments</key> + <array> + <string>/bin/launchctl</string> + <string>setenv</string> + <string>ROOTSYS</string> + <string>$HOME/Apps/root</string> + </array> + <key>RunAtLoad</key> + <true/> + <key>ServiceIPC</key> + <false/> +</dict> +</plist> +
+and the second called setenv.MUSRFITPATH.plist in the same directory with the content ++<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> + <plist version="1.0"> + <dict> + <key>Label</key> + <string>setenv.MUSRFITPATH</string> + <key>ProgramArguments</key> + <array> + <string>/bin/launchctl</string> + <string>setenv</string> + <string>MUSRFITPATH</string> + <string>$HOME/Apps/root/bin</string> + </array> + <key>RunAtLoad</key> + <true/> + <key>ServiceIPC</key> + <false/> +</dict> +</plist> +
+ Additionally, one might want to put a line in ~/.profile (or ~/.bash_profile) to look for executables also in theROOTandQtbinary directories:export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH @@ -640,7 +733,7 @@ Trees: local/main stable/main stable/crypto unstable/main
After applying the changes above to the configuration file, theFinkcore system should be upgraded to its newest version by typing in a terminal:-sudo fink selfupdate +$ sudo fink selfupdate
Then theFinksystem should be set up and can be used to install additional software.
TheFinkinstaller package also contains a graphical user interface calledFinkCommanderand it is suggested to use that for installing the following packages (or packages with revisions close to the following)—it is necessary to compile a few packages from source since no binary packages are available, however, this is done automatically by theFinkCommanderafter you have chosen the software packages for installation: @@ -651,16 +744,16 @@ Under OS X 10.6 Snow Leopard it will not be possible to installqt3mac< Also, due to some not fulfilled dependencies, it might not be possible to install FFTW3 through Fink. In this case (and ONLY in THIS case) simply download the FFTW3 source code from its download page and install it from a terminal using the following commands (for the FFTW version 3.x.y):-tar xz fftw-3.x.y -cd fftw-3.x.y -./configure --enable-single --enable-shared --enable-threads --prefix=/usr/local -make -sudo make install +$ tar xz fftw-3.x.y +$ cd fftw-3.x.y +$ ./configure --enable-single --enable-shared --enable-threads --prefix=/usr/local +$ make +$ sudo make install
Since later on theboostheader files should be used and in the standardFinkinstallation these are found at a version specific location, the later handling will be easier if a symbolic link to this files is created now in the terminal (if it did not exist earlier), e.g.:-ln -sf /sw/include/boost-x_yy_z/boost /sw/include/boost +$ ln -sf /sw/include/boost-x_yy_z/boost /sw/include/boost
where x_yy_z has to be substituted by the correct version number, e.g. 1_41_0. @@ -672,34 +765,48 @@ where x_yy_z has to be substituted by the correct version numbe Unfortunately, theminixmlandNeXuslibraries have to be compiled and installed directly from the source code. Given the respective version numbers of 2.9 and 4.3.2 (which are subject to change with time) this can be achieved for example by:-cd -curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz -cd mxml-2.9 -./configure --prefix=/usr/local -make -sudo make install -cd .. -curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G | tar xz -cd nexus-4.3.2-20140413svn1919 -./configure --prefix=/usr/local -make -sudo make install +$ cd +$ curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz +$ cd mxml-2.9 +$ ./configure --prefix=/usr/local +$ make +$ sudo make install +$ cd .. +$ curl http://download.nexusformat.org/kits/nexus-4.3.2-20140413svn1919.tar.gz -G | tar xz +$ cd nexus-4.3.2-20140413svn1919 +$ ./configure --prefix=/usr/local +$ make +$ sudo make install
5.2.3
-For installing theROOTROOTsystem there are some independent possibilities:-
-
- Visit the
ROOTweb page and download the packed precompiled binary version matching the OS X version. Then unpack the bundle to its final destination (e.g. /opt/root-system). - - If there is no precompiled binary version of
ROOTavailable for your system or e.g.ROOTshould be compiled with another version ofGCCvisit the web page and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system). In case only a single user is working at the machine it might be considerable to change the ownership of theROOTfolder so that the user ("username" in the example) has easy write access to this directory:sudo chown -R username:staff /opt/root-system/
Finally,ROOTcan be configured (here using the minimal set of options) and compiled as stated right below:-cd /opt/root-system -./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml -make -
and for Mac OS X 10.9 (Mavericks) for now (beginning 2014, subject to be changed hopefully soon):-cd /opt/root-system -./configure --gminimal --enable-builtin-freetype --enable-fink --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml -make +The best way to get
ROOTexactly the way needed formusrfitis to install it from source. Before describing it, please make sure that you have installed all required packages listed under Requested Software (e.g. fftw, gsl, etc). + +For the following it is assumed thatROOTshall be installed under$HOME/Apps. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do not enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on. ++$ cd $HOME +$ # creat the Apps directory if not already present +$ mkdir Apps +$ cd Apps +$ git clone http://root.cern.ch/git/root.git +$ cd root +$ git tag -l +$ # git tag -l will list all available tags. In the next command choose the tag v5-34-xx +$ # where xx is the highest listed number, e.g. v5-34-32 +$ git checkout -b v5-34-32 v5-34-32 +$ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. +$ ./configure --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml +$ # next will be the make. If running on a multicore CPU you can speed up tremendously by calling +$ # make with the option -j <number>, where <number> is the number of threads which you want to give, +$ # e.g. make -j8 +$ make
- -
ROOTis also available through theFinkCommander! Install root5 or root5-devel. However, this versions also have to be compiled locally since there are no binary packages. The manual installation mentioned right above should be preferred in this case. -
ROOTinstallation and to prepare already the installation ofmusrfitandmusrgui/musreditthis is a good time for setting necessary environment variables for the use in Mac OS X. Put the following lines (without the comments in parentheses and with the paths adjusted to your local installation) into the file ~/.MacOSX/environment.plist and re-login:
@@ -708,32 +815,77 @@ In order to finalize the
+For Mac OS X > 10.8: + +Here we will need two files placed under ~/Library/LaunchAgents, the first called setenv.ROOTSYS.plist with the content +ROOTinstallation and to prepare already t <plist version="1.0"> <dict> <key>MUSRFITPATH</key> - <string>/opt/root-system/bin</string> (where to find the musrfit executables) + <string>$HOME/Apps/root/bin</string> (where to find the musrfit executables) <key>QTDIR</key> - <string>/sw/lib/qt3mac</string> (where to find Qt3 (for musrgui) or Qt4 (for musredit)) + <string>/opt/local/lib/qt3mac</string> (where to find Qt3 (for musrgui) or Qt4 (for musredit)) <key>ROOTSYS</key> - <string>/opt/root-system</string> (where to find the ROOT system) + <string>$HOME/Apps/root</string> (where to find the ROOT system) </dict> </plist>+<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> + <plist version="1.0"> + <dict> + <key>Label</key> + <string>setenv.ROOTSYS</string> + <key>ProgramArguments</key> + <array> + <string>/bin/launchctl</string> + <string>setenv</string> + <string>ROOTSYS</string> + <string>$HOME/Apps/root</string> + </array> + <key>RunAtLoad</key> + <true/> + <key>ServiceIPC</key> + <false/> +</dict> +</plist> +
+and the second called setenv.MUSRFITPATH.plist in the same directory with the content ++<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> + <plist version="1.0"> + <dict> + <key>Label</key> + <string>setenv.MUSRFITPATH</string> + <key>ProgramArguments</key> + <array> + <string>/bin/launchctl</string> + <string>setenv</string> + <string>MUSRFITPATH</string> + <string>$HOME/Apps/root/bin</string> + </array> + <key>RunAtLoad</key> + <true/> + <key>ServiceIPC</key> + <false/> +</dict> +</plist> +
+ Additionally, one might want to put a line in ~/.profile (or ~/.bash_profile) to look for executables also in theROOTandQtbinary directories:export PATH=$ROOTSYS/bin:$QTDIR/bin:$PATH
- -5.3
-First, the most recent source code should be downloaded. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal +First, the most recent source code should be downloaded. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/Apps/musrfit this is achieved most easily calling from the terminalmusrfit-cd -git clone https://bitbucket.org/muonspin/musrfit.git +$ cd ~/Apps +$ git clone https://bitbucket.org/muonspin/musrfit.git
or-cd -git clone git://gitorious.psi.ch/nemu/musrfit.git +$ cd ~/Apps +$ git clone git://gitorious.psi.ch/nemu/musrfit.git
@@ -742,8 +894,8 @@ git clone git://gitorious.psi.ch/nemu/musrfit.git If a local repository clone is already present, one can update it using:-cd musrfit -git pull +$ cd ~/Apps/musrfit +$ git pull
As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket. @@ -768,11 +920,11 @@ After the source-code extraction the autogen.sh script is calle Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. The other paths should be detected automatically. If this does not work for some reason the configure script will terminate and ask for the information. When the configure script has been called successfully everything is ready for building themusrfitlibraries and executables. A standard installation sequence (withoutNeXussupport) might then look like:-cd musrfit -sh autogen.sh -./configure --prefix=$ROOTSYS -make -make install +$ cd ~/Apps/musrfit +$ sh autogen.sh +$ ./configure --prefix=$ROOTSYS +$ make +$ make install
In order to finish the installation ofmusrfitthe paths wheremusrfitsearches for data files should be adjusted in the installed musrfit_startup.xml ($ROOTSYS/bin/musrfit_startup.xml). For detailed information on this XML file refer to the manual. @@ -780,25 +932,25 @@ In order to finish the installation ofmusrfitthe paths where5.4 musreditIn the latest version ofmusrfitthe configure script tries to determine automatically ifQt4.5or higher is set up on the machine. In case this is found, the editormusreditis built already together withmusrfit. If not, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:-cd src/musredit -qmake musredit.pro +$ cd ~/Apps/musrfit/src/musredit +$ qmake musredit.pro
If everything went finemusreditcan be compiled and installed:-make -make install +$ make +$ make install
The last command copies musredit.app to the standard program directory /Applications and the musredit_startup.xml to $ROOTSYS/bin/musredit_startup.xml. Eventually, in the installed musredit_startup.xml the path specifications have to be adjusted to match the localmusrfitinstallation. For detailed information on this XML file refer to the manual. -5.5
+musrgui5.5
Ifmusrgui(obsolete)Qt3is set up the installation of themusrfiteditor can be done as follows from within the shell:-cd src/musrgui -qmake musrgui.pro -make -make install +$ cd ~/Apps/musrfit/src/musrgui +$ qmake musrgui.pro +$ make +$ make install
-The last command copies musrgui.app to the standard program directory /Applications (4) and the musrgui_startup.xml to $ROOTSYS/bin/musrgui_startup.xml. Eventually, in the installed musrgui_startup.xml the path-specifications have to be adjusted to match the localmusrfitinstallation. For detailed information on this XML file refer to the manual. +The last command copies musrgui.app to the standard program directory /Applications (4) and the musrgui_startup.xml to $ROOTSYS/bin/musrgui_startup.xml. Eventually, in the installed musrgui_startup.xml the path-specifications have to be adjusted to match the localmusrfitinstallation. For detailed information on this XML file refer to the manual. Under some circumstances it might happen, that ifmusrguiwas called fromFinderthe necessary libraries for executingmusrfitcould not be found. In that case, the only workaround for the moment is to export the environment variable DYLD_LIBRARY_PATH in the shell and callmusrguifrom a terminal! @@ -812,7 +964,9 @@ alias mgui='/Applications/musrgui.app/Contents/MacOS/musrgui' Notes - 4 : In the caseqt3-machas not been installed, there will be no musrgui.app but only the executable musrgui which will be placed in the directory $ROOTSYS/bin and has to be called from the terminal. + 2 : When usingGCC≥ 4.2 please make sure that the environment variables USE_PARALLEL_MINUIT2 and USE_OPENMP are not set! OtherwiseMINUIT2will be compiled with parallelization support and cannot be used together withmusrfitafterwards since themusrfitcode is not fully thread-safe! When compiled withGCC≥ 4.2musrfititself will parallelize the χ2 calculation. + + 4 : In the caseqt3-machas not been installed, there will be no musrgui.app but only the executable musrgui which will be placed in the directory $ROOTSYS/bin and has to be called from the terminal. @@ -822,11 +976,11 @@ Notes In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files together with the corresponding data files can be found in themusrfitsource tree at doc/examples/.
Ifmusrguihas been installed, just open one of the test-*.msr files in the editor and test themusrfitfunctionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:-cd doc/examples -musrview test-histo-ROOT-NPP.msr +$ cd ~/Apps/musrfit/doc/examples +$ musrview test-histo-ROOT-NPP.msr
--- BMW & AS +-- AS & BMW @@ -848,9 +1002,9 @@ musrview test-histo-ROOT-NPP.msr- Edit | Attach | Print version | PDF | History: r60 < r59 < r58 < r57 | Backlinks | View wiki text | Refresh | More topic actions + Edit | Attach | Print version | PDF | History: r61 < r60 < r59 < r58 | Backlinks | View wiki text | Refresh | More topic actions-Topic revision: r60 - 25 Oct 2014, AndreasSuter+Topic revision: r61 - 03 Jul 2015, AndreasSuter- + diff --git a/doc/html/user/MUSR/MusrGui.html b/doc/html/user/MUSR/MusrGui.html index 3e3fe0ab..fec3b3c6 100644 --- a/doc/html/user/MUSR/MusrGui.html +++ b/doc/html/user/MUSR/MusrGui.html @@ -1,6 +1,6 @@ - + @@ -8,7 +8,7 @@ - + @@ -329,7 +329,7 @@ For reporting bugs or requesting new features and improvements please use the - @@ -397,7 +397,7 @@ For reporting bugs or requesting new features and improvements please use the - + diff --git a/doc/html/user/MUSR/MusrRoot.html b/doc/html/user/MUSR/MusrRoot.html index fd8e52e1..8c58a595 100644 --- a/doc/html/user/MUSR/MusrRoot.html +++ b/doc/html/user/MUSR/MusrRoot.html @@ -1,6 +1,6 @@ - + @@ -8,7 +8,7 @@ - + @@ -1040,7 +1040,7 @@ Result in the@@ -894,7 +1048,7 @@ musrview test-histo-ROOT-NPP.msrRunHeader/SampleEnvironmentInfo: - - + diff --git a/doc/html/user/MUSR/QuickStart.html b/doc/html/user/MUSR/QuickStart.html index d424e328..c533e784 100644 --- a/doc/html/user/MUSR/QuickStart.html +++ b/doc/html/user/MUSR/QuickStart.html @@ -1,6 +1,6 @@ - + @@ -8,7 +8,7 @@ - + @@ -282,7 +282,7 @@ RUN 2008/lem08_his_8472 MUE4 PSI ROOT-NPP (name beamline institute dat- Edit | Attach | Print version | PDF | History: r7 < r6 < r5 < r4 | Backlinks | View wiki text | Refresh | More topic actions + Edit | Attach | Print version | PDF | History: r7 < r6 < r5 < r4 | Backlinks | View wiki text | Refresh | More topic actionsTopic revision: r7 - 10 Jul 2011, wojek@@ -328,7 +328,7 @@ RUN 2008/lem08_his_8472 MUE4 PSI ROOT-NPP (name beamline institute dat - + diff --git a/doc/html/user/MUSR/TutorialSingleHisto.html b/doc/html/user/MUSR/TutorialSingleHisto.html index fba0a695..6d3235c8 100644 --- a/doc/html/user/MUSR/TutorialSingleHisto.html +++ b/doc/html/user/MUSR/TutorialSingleHisto.html @@ -1,6 +1,6 @@ - + @@ -8,7 +8,7 @@ - + @@ -283,7 +283,7 @@ This page only summarizes the very basic features and options of the programs co - - + diff --git a/doc/html/user/MUSR/WebHome.html b/doc/html/user/MUSR/WebHome.html index 6f89856e..c2cf9dd6 100644 --- a/doc/html/user/MUSR/WebHome.html +++ b/doc/html/user/MUSR/WebHome.html @@ -1,6 +1,6 @@ - + @@ -8,7 +8,7 @@ - + @@ -136,7 +136,7 @@ pre { - Download the precompiled Cygwin GCC 4.3 package of the most recent
- Acknowledgements
- Edit | Attach | Print version | PDF | History: r50 < r49 < r48 < r47 | Backlinks | View wiki text | Refresh | More topic actions + Edit | Attach | Print version | PDF | History: r52 < r51 < r50 < r49 | Backlinks | View wiki text | Refresh | More topic actions-Topic revision: r50 - 29 May 2015, AndreasSuter+Topic revision: r52 - 16 Aug 2015, AndreasSuter- + diff --git a/src/classes/PMsrHandler.cpp b/src/classes/PMsrHandler.cpp index cafb2637..e851b315 100644 --- a/src/classes/PMsrHandler.cpp +++ b/src/classes/PMsrHandler.cpp @@ -3165,15 +3165,19 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines) if (tokens->GetEntries() < 2) { error = true; } else { - PIntVector group; + PUIntVector group; str = iter->fLine; - if (ParseDetectorGrouping(str, group)) { + PStringNumberList *rl = new PStringNumberList(str.Data()); + string errorMsg(""); + if (rl->Parse(errorMsg, true)) { + group = rl->GetList(); for (UInt_t i=0; i@@ -204,7 +204,7 @@ pre {GetEntries(); i++) { - ostr = dynamic_cast GetEntries(); i++) { - ostr = dynamic_cast - #include using namespace std; +#include +using namespace boost; + #include "PMusr.h" //+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ @@ -1741,3 +1743,167 @@ void PMsrRunBlock::SetMapGlobal(UInt_t idx, Int_t ival) // else do nothing at the moment return; } + +//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +// implementation PStringNumberList +//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +//-------------------------------------------------------------------------- +// Parse (public) +//-------------------------------------------------------------------------- +/** + * Helper class which parses list of numbers of the following 3 forms and its combination. + * (i) list of integers separted by spaces, e.g. 1 3 7 14 + * (ii) a range of integers of the form nS-nE, e.g. 13-27 which will generate 13, 14, 15, .., 26, 27 + * (iii) a sequence of integers of the form nS:nE:nStep, e.g. 10:20:2 which will generate 10, 12, 14, .., 18, 20 + * + * \param errorMsg error message + * \param ignoreFirstToken if true, the first parse token will be ignored + * + * @return true if parse has been successful, otherwise false + */ +bool PStringNumberList::Parse(string &errorMsg, bool ignoreFirstToken) +{ + bool result=true; + vector
splitVec; + int ival; + + // before checking tokens, remove 'forbidden' " - " and " : " + StripSpaces(); + + // split string into space separated tokens + split(splitVec, fString, is_any_of(" "), token_compress_on); + + unsigned int start=0; + if (ignoreFirstToken) + start=1; + + for (unsigned int i=start; i subSplitVec; + // split potential rStart:rEnd:rStep token + split(subSplitVec, splitVec[i], is_any_of(":"), token_compress_on); + + int start=-1, end=-1, step=-1; + unsigned int count=0; + for (unsigned int j=0; j This routine removes arbitray number of spaces between '-' and ':', + * e.g. 123 - 125 will be converted to 123-125, etc. + */ +void PStringNumberList::StripSpaces() +{ + string str=fString; + int pos=-1; + + // backward scan + for (int i=str.size(); i>=0; --i) { // check if first space is found + if ((str[i] == ' ') && (pos == -1)) { + pos = i; + } else if ((str[i] == '-') || (str[i] == ':')) { // check for '-' or ':' + if (pos != -1) { + str.erase(i+1, pos-i); + } + } else if (str[i] != ' ') { // anything but different than a space leads to a reset of the pos counter + pos = -1; + } + } + // forward scan + for (unsigned int i=0; i
@@ -87,12 +88,17 @@ void msr2data_syntax() cout << endl << " [fit [-k] [-t] | fit-[!] [-k] [-t] | msr-]"; cout << endl << "usage 2: msr2data [-o ] [new] [data] [[no]header] [nosummary] [global[+[!]]]"; cout << endl << " [fit [-k] [-t] | fit-[!] [-k] [-t] | msr-]"; - cout << endl << "usage 3: msr2data \\[ ... \\] [-o ] [new] [data] [[no]header] [nosummary] [global[+[!]]]"; + cout << endl << "usage 3: msr2data \\[ \\] [-o ] [new] [data] [[no]header] [nosummary] [global[+[!]]]"; cout << endl << " [fit [-k] [-t] | fit-[!] [-k] [-t] | msr-]"; cout << endl << "usage 4: msr2data [-o ] [new] [data] [[no]header] [nosummary] [global[+[!]]]"; cout << endl << " [fit [-k] [-t] | fit-[!] [-k] [-t] | msr-]"; cout << endl; - cout << endl << " , , , ... : run numbers"; + cout << endl << " can be:"; + cout << endl << " (i) , , , ... : run numbers, e.g. 123 124"; + cout << endl << " (ii) - : a range, e.g. 123-125 -> 123 124 125"; + cout << endl << " (iii) : : : a sequence, e.g. 123:127:2 -> 123 125 127"; + cout << endl << " will give the step width and has to be a positive number!"; + cout << endl << " a can also combine (i)-(iii), e.g. 123 128-130 133, etc."; cout << endl << " : msr-file extension, e.g. _tf_h13 for the file name 8472_tf_h13.msr"; cout << endl << " -o : specify the name of the DB or column-data output file; default: out.db/out.dat"; cout << endl << " if the option '-o none' is used, no output file will be written."; @@ -125,9 +131,27 @@ void msr2data_syntax() cout << endl << " from this pre-analysis for each run---they are not just copied from the template."; cout << endl << " The specification of '!' determines which fit mode (see above) is used for this pre-analysis."; cout << endl; + cout << endl << " Typical examples:"; + cout << endl; + cout << endl << " msr2data 2047 2050 _tf_histo fit-2046"; + cout << endl << " will use 2046_tf_histo.msr as templete, and subsequently generating 2047_tf_histo.msr until"; + cout << endl << " 2050_tf_histo.msr and fit them."; + cout << endl; + cout << endl << " msr2data 2047 2050 _tf_histo msr-2046"; + cout << endl << " will use 2046_tf_histo.msr as templete, and subsequently generating 2047_tf_histo.msr until"; + cout << endl << " 2050_tf_histo.msr, but NO fitting will be done."; + cout << endl; + cout << endl << " msr2data 2046 2050 _tf_histo -o fitParam.db"; + cout << endl << " will collect the fit parameters from runs 2046-2050 (msr-files 2046_tf_histo.msr etc.) and"; + cout << endl << " write them to the file fitParam.db (DB-format)."; + cout << endl; + cout << endl << " msr2data [2047:2053:2 2056] _tf_histo fit-2045"; + cout << endl << " will use 2045_tf_histo.msr as templete, and subsequently generating msr-files from the run-list:"; + cout << endl << " 2047 2049 2051 2053 2056 (2047_tf_histo.msr etc.) and fit them."; + cout << endl; cout << endl << " For further information please refer to"; - cout << endl << " https://intranet.psi.ch/MUSR/Msr2Data"; - cout << endl << " http://lmu.web.psi.ch/facilities/software/musrfit/user/intranet.psi.ch/MUSR/Msr2Data.html"; + cout << endl << " http://lmu.web.psi.ch/musrfit/user/MUSR/Msr2Data.html"; + cout << endl << " https://intranet.psi.ch/MUSR/Msr2Data"; cout << endl << endl; } @@ -449,8 +473,26 @@ int main(int argc, char *argv[]) return 0; } - for (unsigned int i(firstRunNumberInArg); i<=lastRunNumberInArg; ++i) - run_vec.push_back(boost::lexical_cast (arg[i])); + // generate run_list string + for (unsigned int i(firstRunNumberInArg); i<=lastRunNumberInArg; ++i) { + run_list += arg[i] + " "; + } + // parse run_list string + PStringNumberList *nl = new PStringNumberList(run_list); + if (nl == 0) { // couldn't invoke object + cerr << endl; + cerr << ">> msr2data: **ERROR** Couldn't invoke run_list parser object! Quitting now." << endl; + return 0; + } + string errorMsg(""); + if (!nl->Parse(errorMsg)) { + cerr << endl; + cerr << ">> msr2data: " << errorMsg << " - Quitting now." << endl; + return 0; + } + // get run list vector + run_vec = nl->GetList(); + delete nl; msrExtension = arg[rightbracket + 1]; diff --git a/src/musredit/PTextEdit.cpp b/src/musredit/PTextEdit.cpp index 8268fa78..71a55e8a 100644 --- a/src/musredit/PTextEdit.cpp +++ b/src/musredit/PTextEdit.cpp @@ -28,6 +28,7 @@ ***************************************************************************/ #include +#include using namespace std; #include @@ -679,42 +680,6 @@ void PTextEdit::doConnections( PSubTextEdit *e ) connect( e, SIGNAL( cursorPositionChanged() ), this, SLOT( currentCursorPosition() )); } -//---------------------------------------------------------------------------------------------------- -/** - * Validates a given runlist. - * - * \param runList run list string which should be a space separated list of run numbers. - */ -bool PTextEdit::validRunList(const QString runList) -{ - bool success = true; - - int i = 0; - QString subStr; - bool done = false; - int val = 0; - bool ok; - while (!done) { - subStr = runList.section(' ', i, i, QString::SectionSkipEmpty); - if (subStr.isEmpty()) { - done = true; - continue; - } - i++; - val = subStr.toInt(&ok); - if (!ok) { - done = true; - success = false; - } - } - - if (i == 0) { // no token found - success = false; - } - - return success; -} - //---------------------------------------------------------------------------------------------------- /** *
Start the dialog to enter a msr-file title. See also https://intranet.psi.ch/MUSR/MusrFit#4_1_The_Title @@ -1892,12 +1857,6 @@ void PTextEdit::musrMsr2Data() break; case 1: // run list runList = fMsr2DataParam->runList; - if (!validRunList(runList)) { - QMessageBox::critical(this, "**ERROR**", - "Invalid Run List!\nThe run list needs to be a space separated list of run numbers.", - QMessageBox::Ok, QMessageBox::NoButton); - return; - } break; case 2: // run list file name runListFileName = fMsr2DataParam->runListFileName; diff --git a/src/musredit/PTextEdit.h b/src/musredit/PTextEdit.h index 149ab0bf..46a6e282 100644 --- a/src/musredit/PTextEdit.h +++ b/src/musredit/PTextEdit.h @@ -77,7 +77,6 @@ private: void load( const QString &f, const int index=-1 ); PSubTextEdit *currentEditor() const; void doConnections( PSubTextEdit *e ); - bool validRunList(const QString runList); void fileSystemWatcherActivation(); private slots: diff --git a/src/musrgui/PTextEdit.cpp b/src/musrgui/PTextEdit.cpp index 85a3641b..357d3791 100644 --- a/src/musrgui/PTextEdit.cpp +++ b/src/musrgui/PTextEdit.cpp @@ -493,40 +493,6 @@ void PTextEdit::doConnections( PSubTextEdit *e ) connect( e, SIGNAL( cursorPositionChanged(int, int) ), this, SLOT( currentCursorPosition(int, int) )); } -//---------------------------------------------------------------------------------------------------- -/** - *
- */ -bool PTextEdit::validRunList(const QString runList) -{ - bool success = true; - - int i = 0; - QString subStr; - bool done = false; - int val; - bool ok; - while (!done) { - subStr = runList.section(' ', i, i, QString::SectionSkipEmpty); - if (subStr.isEmpty()) { - done = true; - continue; - } - i++; - val = subStr.toInt(&ok); - if (!ok) { - done = true; - success = false; - } - } - - if (i == 0) { // no token found - success = false; - } - - return success; -} - //---------------------------------------------------------------------------------------------------- /** *
@@ -1500,12 +1466,6 @@ void PTextEdit::musrMsr2Data() break; case 1: // run list runList = fMsr2DataParam->runList; - if (!validRunList(runList)) { - QMessageBox::critical(this, "**ERROR**", - "Invalid Run List!\nThe run list needs to be a space separated list of run numbers.", - QMessageBox::Ok, QMessageBox::NoButton); - return; - } break; case 2: // run list file name runListFileName = fMsr2DataParam->runListFileName; diff --git a/src/musrgui/PTextEdit.h b/src/musrgui/PTextEdit.h index 77f50261..455194d7 100644 --- a/src/musrgui/PTextEdit.h +++ b/src/musrgui/PTextEdit.h @@ -64,7 +64,6 @@ private: void load( const QString &f, const int index=-1 ); PSubTextEdit *currentEditor() const; void doConnections( PSubTextEdit *e ); - bool validRunList(const QString runList); private slots: void fileNew();
- As superuser create a file /etc/ld.so.conf.d/cern-root.conf where the path to the