issue CmPA#49: created ipic.py to replace ipic scripts

scripts/ipic.py

@@ -0,0 +1,232 @@
+#!/usr/bin/env python
+
+import sys
+import getopt
+# http://docs.python.org/2/library/collections.html#collections.deque
+from collections import deque # double-ended queue
+import os
+#from optparse import OptionParser
+
+# useful documentation:
+#
+# http://effbot.org/zone/python-list.htm
+# http://pymotw.com/2/subprocess/
+# http://stackoverflow.com/questions/3777301/how-to-call-a-shell-script-from-python-code
+
+def ipic_ctags(args):
+    # create tags file using ctags
+    create_tags_command = \
+        '''find . -name '*.cpp' -or -name '*.h' | xargs ctags --extra=+qf'''
+    print create_tags_command
+    os.system(create_tags_command)
+    # sort tags file
+    sort_tags_command = '''LC_ALL=C sort -u tags -o tags'''
+    print sort_tags_command
+    os.system(sort_tags_command)
+
+def ipic_help():
+    print '''
+  To build, in the iPic3D directory you can use:
+  
+    rm -rf build # if necessary
+    mkdir build
+    cd build
+    cmake ..
+    make # or "make -j" to compile in parallel
+  
+  To run the code you can use
+  
+    mkdir data
+    mpiexec -n 4 exec/iPic3D ../inputfiles/GEM.inp
+  
+  where 4 = XLEN times YLEN times ZLEN (defined in GEM.inp).
+  
+  Available subcommands:
+
+    ''', progname, '''help ctags
+    ''', progname, '''help mic
+  '''
+
+def ipic_help_mic(args):
+    print '''
+  See "ipic help".  Modifications are as follows.
+
+  To run on the Xeon host processor, use something like:
+  
+    mpiexec.hydra -n 8 -env OMP_NUM_THREADS=4 exec/iPic3D ../inputfiles/GEM.inp
+  
+  where 8 = XLEN times YLEN times ZLEN.
+  
+  If you want to cross-compile for the MIC, then the instructions are
+  different:
+  
+      mkdir build.phi
+      cd build.phi
+      cmake .. -DCMAKE_TOOLCHAIN_FILE=../cmake/cmake_template.cmake.XeonPhi
+      make -j
+  
+  And to run you use, e.g.:
+  
+    mkdir data
+    mpiexec.hydra -host knc2-mic0 -n 50 -env OMP_NUM_THREADS=4 exec/iPic3D ../inputfiles/GEM.inp
+  
+  where 50 = XLEN times YLEN times ZLEN.
+    '''
+
+def ipic_help_ctags(args):
+    print '''
+  Make sure that you are in the source code directory
+  and then run
+
+    ''', progname, '''ctags
+    '''
+
+def ipic_help_git(args):
+    print '''
+    ### This stub gives examples of git commands ###
+
+    # show branch information
+    git branch -avv
+    # examining the .git directory reveals a wealth of information, e.g.:
+    cat .git/config
+    # with --stat all files checked in are displayed.
+    git log --stat
+    # for the following I just do "git tree" (see .gitconfig below):
+    git log --oneline --decorate --graph --branches --source
+    git status # shows file statuses
+    git remote -v # show remote repositories
+    # show commits in chronological order.
+    git reflog
+    # git reflog is useful to get the sha-1 hash of a commit
+    # that you recently made and whose branch you accidentally
+    # deleted, making it no longer reachable.  Note that
+    # each snapshot that you commit should stay in its local
+    # repository for 90 days before being garbage collected
+    # unless you do something like "git gc".  See also
+    # http://gitready.com/advanced/2009/01/17/restoring-lost-commits.html
+    #
+    # show file
+    git show mybranch:myfile
+    eg cat myfile # slightly nicer than git show
+    # show who checked in what line when under what commit.
+    git blame myfile # on current branch
+    git blame amaya-library iPic3D.cpp
+
+  for modification:
+
+    # initialize a repository
+    mkdir localrepository; cd localrepository; git init
+    # creating/removing remote:
+    git remote add myremote  https://github.com/alecjohnson/iPic3D.git
+    git remote rm myremote  
+    # get all branches and their filesystem snapshots
+    # from myremote that are not already in localrepository
+    git fetch myremote 
+    # check in mods
+    git stage myfile
+    git rm oldfile
+    git commit
+    # modify a commit message
+    git commit --amend
+    # create a branch and check it out
+    git checkout -b newbranch
+    # push branch to server
+    eg push --branch newbranch myremote
+    # pull changes from server into current branch
+    git pull
+    # delete a branch on server (!):
+    git push myremote --delete mybranch
+
+  # example of global configuration file:
+
+    $ cat ~/.gitconfig
+    [user]
+    name = eajohnson
+    email = [email protected]
+    [alias]
+    tree = log --oneline --decorate --graph --branches --source
+    undo-commit = reset --soft HEAD~1
+    '''
+
+def help(args):
+    if len(args) == 0:
+      ipic_help()
+      sys.exit()
+
+    command = deque.popleft(args)
+    if command == "mic":
+      ipic_help_mic(args)
+    elif command == "ctags":
+      ipic_help_ctags(args)
+    elif command == "git":
+      ipic_help_git(args)
+    else:
+        print "ipic help", command, "is not supported"
+        sys.exit(-1)
+
+def usage():
+    print '''
+  usage: ''', progname, ''' [options] <command>
+
+  Available commands:
+    ''', progname, '''ctags
+    ''', progname, '''help
+      '''
+
+def main():
+
+    global progname
+    progname = os.path.basename(sys.argv[0])
+    global dirname
+    dirname = os.path.dirname(sys.argv[0])
+
+    # it might be better to use the argparse module rather than getopt,
+    # but unfortunately argparse is only available beginning with python 2.7
+    # and most HPC platforms seem to have python 2.6 installed.
+    # optparse has been deprecated and does not seem to be in python 3;
+    # note, however, that argparse was initially an extension of optparse
+    # before giving up on backward compatibility.
+    #
+    try:
+      opts, args = getopt.getopt(sys.argv[1:], 'ho:', ['help', 'output='])
+    except getopt.GetoptError, e:
+      if e.opt == 'o' and 'requires argument' in e.msg:
+        print 'ERROR: -o requires filename'
+      else:
+        usage()
+        sys.exit(-1)
+
+    for o, a in opts:
+        if o in ("-h", "--help"):
+          usage()
+          sys.exit()
+        elif o in ("-o", "--output"):
+          output = a
+        #else:
+        #  assert False, "unhandled option"
+
+    numargs = len(args)
+    if numargs==0:
+      usage()
+      sys.exit()
+
+    #print args
+    args = deque(args)
+    command = deque.popleft(args)
+    #print list(args)
+
+    if command == "help":
+        help(args)
+    elif command == "ctags":
+        ipic_ctags(args)
+        #print "ctags not yet implemented"
+    else:
+        print progname, command, "not supported"
+        sys.exit(-1)
+
+    #print os.path.basename(__file__)
+    #print os.path.dirname(__file__)
+
+if __name__ == '__main__':
+    main()
+