bin scripts

Brief description of the scripts included in pencil-code/bin.

Script	Purpose
auto-test
build-testcase-cvs	Create a directory called auto-test/ containing the output generated by the LATEST CVS VERSION (without any user mods) using run.in and start.in, also copied to the auto-test dir.
combine_videofiles	Runs a helper executable; builds it first, if necessary
copy-snapshots	Copy snapshots VAR# and TAVG# from /scratch to $PBS_O_WORKDIR (from where the code started). Relies on PBS (and on tcsh) and is needed on Horseshoe (the Odense cluster). Should better be a Perl script.
copy-snapshots_exp	Copy snapshots VAR# and TAVG# from /scratch to the current data directory. Should better be a Perl script.
cvs-add-rundir	Add the current run directory to the CVS repository. Assumes that the directory above (`..’) is already under CVS.
cvsci_run	This script adds a new run to the repository and checks in all *.in files as well as material from the data and src directories.
cvsci_run_bash	This script adds a new run to the repository and checks in all *.in files as well as material from the data and src directories.
cvsci_run_old	This script adds a new run to the repository and checks in all *.in files as well as material from the data and src directories.
dx_get_datadir	Read in a datadir.in if it exists and output the contents For reading into DX
dx_list_varfiles	Get list of VAR? files available or return 0 for var.dat only For reading into DX
dx_table2csv	Read in a time_series.dat file and output a CSV version For reading into DX
dx_var.general	Take 2 parameters $1 - Snapshot number (0 = current) $2 - Processor number
getconf.csh	Initiate some variables related to MPI and the calling sequence, and do other setup needed by both start.csh and run.csh.
git-pc
gitci_run	Simple script for checking in a Pencil Code run directory to a Git repository.
gpgrowth	Extract growth information for velocity or B-field from run.log or other file and display via gnuplot.
mass-changer.pl	Authors:
mkdotin	Given a set of files (normally Makefile and Makefile.local), scan through all lines of the type MAGNETIC=magnetic and construct the files ./start.in, ./run.in (if they don’t exist as yet) corresponding to the moduels which are used and those which are not used.
mkinpars	Under OSF1, a newly started csh does not inherit PATH:
mkproc-tree	Makes a processor directory tree
mkwww	Makes a skeleton for a html file were result of run can be recorded. README, start.in, and run.in are included in file. File is put in the a public directory which is linked to the run directory. Still messy!
move-slice	Example: move-slice data2
nl2idl	Convert F90 namelists into an idl function that returns an anomymous structure containing all the namelist variables.
nl2python	Convert F90 namelists into a Python class that provides all namelist slots as fields.
pc_about
pc_auto-test	Test compilation and results on a set of sample directories to validate the pencil code. Uses Perl because I started to do this with the Test/Test::Harness module and because we need to do pattern matching to extract the relevant output lines.
pc_autocorrect_config
pc_build	Compile the Pencil Code, using settings from the ‘Makefile’ section in the appropriate configuration files.
pc_check_dir
pc_check_revision	12-nov-2010/dintrans: coded Allow to check old revisions of the code with a given sample –> useful to find the revision that broke a sample that is not daily checked in the auto-test list Results of each successive test are written in: /tmp/(revision number).out_OK –> the revision is OK /tmp/(revision number).out_not_OK –> the revision is not OK then exit
pc_check_varfile	Checks if varfile sizes are consistent
pc_cleansrc	Removes all symbolic links created by ‘pc_setupsrc’. Removes all compiled executables and other build objects. Localized source files (see pc_localize) are maintained. Data and other files in the run directory are maintained.
pc_codecov	Known issues: - Information on which tests access a particular line is not displayed.
pc_codingstyle	Fortran95 coding style tester for the Pencil Code style. Currently, only basic checks are performed, e.g. indentation. Feel free to add more tests carefully.
pc_collect	Runs a helper executable; builds it first, if necessary
pc_collect_all	Script to automatically collect distributed VARN files into one single file that will be stored in data/allprocs.
pc_collect_exp	Runs a helper executable; builds it first, if necessary
pc_config.sh	Initiate some variables related to MPI and the calling sequence, and do other setup needed by both pc_start and pc_run execution scripts
pc_configtest	Script to automatically check correctness of the *.in files.
pc_copyvar	Author: Anders Johansen
pc_copyvar_old	Author: Anders Johansen
pc_cvsup	Script to update the Pencil-Code tree from CVS
pc_debug	Compile and run the code with the maximum of available diagnostic options
pc_deprecated_slice_links
pc_diffruns	Compare *.in and *.local files of two Pencil Code run directories.
pc_distribute	Runs a helper executable; builds it first, if necessary
pc_distribute_z	Runs a helper executable; builds it first, if necessary
pc_dump_config	Dump the configuration settings.
pc_edit	This script is a wrapper for an arbitrary editor $1 working on a file identified by path $2. It checks whether $2 exists in $PENCIL_HOME or any subdirectory down to the 3rd level, and if so, opens the editor with file $PENCIL_HOME/…/$2. For convenience, one would individually define a shell alias like alias <short name>=’pc_edit <preferred editor>’ and then use <short name> <path>.
pc_extract	Runs a helper executable; builds it first, if necessary
pc_findconfig	This file tries to set the PENCIL_HOME environment variable if it doesn’t exist yet, and then adds stuff to your PATH and IDL_PATH.
pc_fix_svn_properties	For all files containing a SVN keywords line, set the corresponding svn:keywords property So far, we handle only <dollar>Id<dollar>, which is probably enough.
pc_functions.sh
pc_get_param_state	Evaluate ‘params.log’ and generate a proper ‘run.in’ for a given time.
pc_git
pc_grep	Allow to search recursively a given string using grep Usage: pc_grep string suffix By default, suffix=’*.f90’such that pc_grep ‘eos.h’ will search the ‘eos.h’ string in all of f90 files
pc_helper	Runs a helper executable; builds it first, if necessary
pc_inspectrun	The script prints the header (legend) and the last few lines of the time_series.dat file.
pc_isolated-test	DANGER: things can break horribly if you edit this script while it is running.
pc_jobtransfer	checks that a valid NEWDIR file exists, and that in the new directory there is another valid NEWDIR file. Only if everything is ok, this script will touch STOP to initialize the job transfer. This script should help wasting precious queue time by having wrong NEWDIR files.
pc_llsub	Wrapper script to pass start.csh and run.csh (or both) to IBM Loadleveler God knows why it does not take any useful command line options on its own. (Or does it?)
pc_localize	Materialize a link to one or several files or directories (the latter will not work under some unices (but under Linux).
pc_mkdatadir	This script generates a link to a data directory with the same name as the current working directory but that is located on a data disk. The name of the desired data disk will be different and different machine, so you may need to add your particular machine name below
pc_mkproctree	Makes a processor directory tree
pc_mkproctree_par	Makes a processor directory tree
pc_mkspecial.sh	Undoes the changes that are automatically made to the source files when multiple special modules are used. See target special_preps in Makefile.src.
pc_move_var	Usage: ./pc_move_var SRC DST
pc_newrun	This script uses pc_mkdatadir which links the subdirectory data to some data disk (which is machine dependent and therefore you may want to adapt pc_mkdatadir for your particular machine).
pc_news
pc_nowarn_to_kcq	A small program to replace all instances of ALWAYS_FALSE with keep_compiler_quiet. Use with extreme care, not all cases are handled automatically.
pc_pencil_swap	Check for existence of src/cparam_pencils.inc
pc_phonelist
pc_piechart	usage: ‘pc_piechart [rotationangle]’ where rotation angle is a number between 0 and 360 that sets the rotation of the pie chart, which can be set in order to optimize the positioning of the text. For the current version of doc/citations/notes.tex (as of August 2016), 290 works nicely for this parameter. Current copy of plot also available at http://alexrichert.com/graphics
pc_qsub	Handle queue submission transparently across different machines
pc_radmc3d	Link files into a local radmc3d directory
pc_reduce	Runs a helper executable; builds it first, if necessary
pc_reduce_all	Script to automatically reduce distributed VARN files into one single file that will be stored in data/reduced.
pc_rename	renames a run directory including the link to the data directory
pc_restore_from_backup	Wrapper to overwrite var.dat with var.dat.bck
pc_restrict	Creates a new run directory for continuation of an existing run, but with restricted z extent, according to the range of z processors [from-z-proc,to-z-proc] provided. If to-z-proc < from-z-proc and the z boundary condition is periodic, the z-extent is interpreted to stretch across the upper z boundary. Invokes pc_newrun. cparam.local, run.in and param.nml are modified to render the new run compile-and-run ready. start.x must not be executed.
pc_run	Run the Pencil Code, using settings from the ‘runtime’ section in the appropriate configuration files.
pc_script_test	Run tests in tests/ directories. These are normally tests of Python or IDL scripts, or similar. For each directory given, we recursively scan for subdirectories named ‘tests’. If no directories are given, the directories tests/, samples/, runs/ of ${PENCIL_HOME} are used as starting points.
pc_sed	Provides workaround for missing –follow-symlinks option of sed. Requires that the file to be edited (typically in-place) is the last argument.
pc_setupsrc	Link files into a local src directory Also link script files from the bin directory ==> should be renamed
pc_start	Neat wrapper for running start.x through pc_run.
pc_svn_add_rundir	Add the current run directory to a SVN repository. Assumes that the directory above (`..’) is already under SVN.
pc_svn_transfer_changes
pc_svnstatus_ignlinks	Quick script to ignore symbolic links when getting ‘svn status’.
pc_svnup	Script to update the Pencil Code tree from svn.
pc_tar_run	This script creates a tar file from the current run. It takes all in and light data files.
pc_tecplot	Runs a helper executable; builds it first, if necessary
pc_tecplot_solid	Runs a helper executable; builds it first, if necessary
pc_tsnap	Extract time information from a snapshot file. Assumes the following to be written to the file: write a write t [,x,y,z]
pc_update_autotest.sh	If $PC_SET_VALIDATED is set, then update validated.dat Otherwise, don’t do anything. This script is used by auto-test and pc_auto-test.
pc_update_validated.sh	If $PC_SET_VALIDATED is set, then update validated.dat Otherwise, don’t do anything. This script is used by auto-test and pc_auto-test.
pc_upgraderun	Transform and validate run.in/start.in/Makefile.local files from older pencil-code incarnations to the current version.
pc_useutil
pc_videofiles	Script to automatically generate the slices, if not already done.
pc_worldmap	Creates a map of Pencil contributor locations based on $PENCIL_HOME/license/developers.txt Be sure to check out the Python modules used before trying to run it (the most obscure being ‘geopy’: https://pypi.python.org/pypi/geopy). This script requires that license/developers.txt stay perfectly formatted! Also, locations in column 7 of license/developers.txt need to be resolvable *either* with Bing or Google Maps. Current copy of plot also available at http://alexrichert.com/graphics
pc_xmlexport	Name: pc_xmlexport Author: Antony Mee (A.J.Mee@ncl.ac.uk) Started: 04-Aug-2005 Usage: Hello
pencil-test	Run the pencil code’s auto test on some remote host(s) and wrap results in HTML if required. Can be used from crontab.
read_all_videofiles	Runs a helper executable; builds it first, if necessary
read_vectorfiles	Runs a helper executable; builds it first, if necessary
read_videofiles	Runs a helper executable; builds it first, if necessary
read_videofiles.csh	Run read_videofiles.x – to read_videofiles
read_xyaver_alpha	Runs a helper executable; builds it first, if necessary
reaper	Run a shell script like run.csh and kill it and its child processes after a given time, including subprocesses started via mpirun/mpiexec. CAVEAT: As there is apparently no portable way to processes we initiated via mpirun/mpiexec, we simply kill _any_ process of the given name that didn’t exist when this script started.
reload	interface to input information for log file
remote-top	does top -bn1 on all procs of nodelist, write to datadir
restart-new-dir	Example: restart-new-dir ../hydro256e
restart-new-dir-VAR	Example: restart-new-dir ../hydro256e
restart-new-dir-axel	Example: restart-new-dir ../hydro256e
run.csh	run.csh ——— Run src/run.x (timestepping for src/run.x). Run parameters are set in run.in.
scp-proc-to-proc	Purpose: copies directory trees to another machine
scpdatadir	make tarball of data directory and secure copy to $1 tarek Nov 26 2002
setup-src
start.csh	start.csh ———– Run src/start.x (initialising f for src/run.x). Start parameters are set in start.in.
start_run.csh	start_run.csh ————— Run first src/start.x (unless data/proc0/var.dat already exists) and then src/run.x. On machines with local scratch disks this saves the overhead associated with copying to and from that disk.
summarize-history	Evaluate `params.log’ and print a history of changes.
tar_run	This script adds a new run to the repository and checks in all *.in files as well as material from the data and src directories.
tar_run_bash	This script adds a new run to the repository and checks in all *.in files as well as material from the data and src directories.