From 61997d670aee58310dda9414d65e22208a3f1a34 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 7 Jan 2014 17:01:40 +0100
Subject: [PATCH 1/4] Added auto codelet generation

---
 bin/irpf90               |  2 +-
 src/codelet.py           | 45 ++++++++++++++++++++++++++++++++++++++++
 src/command_line.py      | 23 ++++++++++++++++++++
 src/irpf90.py            | 13 +++++++++---
 src/irpf90_t.py          |  2 ++
 src/makefile.py          |  6 +++---
 src/preprocessed_text.py |  1 +
 src/profile.py           |  2 +-
 8 files changed, 86 insertions(+), 8 deletions(-)
 create mode 100644 src/codelet.py

diff --git a/bin/irpf90 b/bin/irpf90
index e537e26..d9d2360 120000
--- a/bin/irpf90
+++ b/bin/irpf90
@@ -1 +1 @@
-../src/irpf90.exe
\ No newline at end of file
+../src/irpf90_python.exe
\ No newline at end of file
diff --git a/src/codelet.py b/src/codelet.py
new file mode 100644
index 0000000..c11d95e
--- /dev/null
+++ b/src/codelet.py
@@ -0,0 +1,45 @@
+#!/usr/bin/python
+from command_line import command_line
+import irpf90_t
+
+def run():
+  template = """
+program codelet_%(name)s
+  implicit none
+  integer :: i
+  double precision :: ticks_0, ticks_1, cpu_0, cpu_1
+  integer, parameter :: irp_imax = %(NMAX)d
+
+  %(precondition)s
+
+  call provide_%(name)s
+
+  double precision :: irp_rdtsc
+
+  call cpu_time(cpu_0)
+  ticks_0 = irp_rdtsc()
+  do i=1,irp_imax
+    call bld_%(name)s
+  enddo
+  ticks_1 = irp_rdtsc()
+  call cpu_time(cpu_1)
+  print *, '%(name)s'
+  print *, '-----------'
+  print *, 'Cycles:'
+  print *,  (ticks_1-ticks_0)/dble(irp_imax)
+  print *, 'Seconds:'
+  print *,  (cpu_1-cpu_0)/dble(irp_imax)
+end
+
+  """
+
+  name, NMAX, precondition, filename = command_line.codelet
+  if precondition is None:
+    precondition = ""
+  else:
+    precondition = "PROVIDE "+precondition
+  file = open(filename,'w')
+  file.write(template%locals())
+  file.close()
+
+
diff --git a/src/command_line.py b/src/command_line.py
index 4524ecf..35569d0 100644
--- a/src/command_line.py
+++ b/src/command_line.py
@@ -49,6 +49,7 @@ options['r'] = [ 'no_directives', 'Ignore all compiler directives !DEC$ and !DIR
 options['n'] = [ 'inline'       , 'all|providers|builders : Force inlining of providers or builders', 1 ]
 options['u'] = [ 'unused'       , 'Print unused providers', 0 ]
 options['I'] = [ 'include'      , 'Include directory', 1 ]
+options['c'] = [ 'codelet'      , 'entity:NMAX or entity:precondition:NMAX  : Generate a codelet to profile a provider running NMAX times', 1 ]
 
 class CommandLine(object):
 
@@ -100,6 +101,28 @@ class CommandLine(object):
     return self._substituted
   substituted = property(fget=substituted)
 
+  def codelet(self):
+    if '_codelet' not in self.__dict__:
+      self._codelet = []
+      for o,a in self.opts:
+        if o in [ "-c", '--'+options['c'][0] ]:
+          buffer = a.split(':')
+          filename = 'codelet_'+buffer[0]+'.irp.f'
+          if len(buffer) == 2:
+            self._codelet = [buffer[0], int(buffer[1]), None, filename]
+          elif len(buffer) == 3:
+            self._codelet = [buffer[0], int(buffer[2]), buffer[1], filename]
+          else:
+            print """
+Error in codelet definition. Use:
+--codelet=provider:NMAX
+or
+--codelet=provider:precondition:NMAX
+"""
+            sys.exit(1)
+    return self._codelet
+  codelet = property(fget=codelet)
+
   def preprocessed(self):
     if '_preprocessed' not in self.__dict__:
       self._preprocessed = []
diff --git a/src/irpf90.py b/src/irpf90.py
index 4cc43c1..eaed0e9 100644
--- a/src/irpf90.py
+++ b/src/irpf90.py
@@ -35,8 +35,9 @@ except:
   pass
 sys.setcheckinterval(1000)
 
+from command_line import command_line
+
 def main():
-  from command_line import command_line
 
   vim.install()
 
@@ -72,9 +73,14 @@ def main():
         for x in parents:
           print "- %s"%(x,)
 
-  if not command_line.do_run:
-    return
+  if command_line.do_codelet:
+     import profile
+     profile.build_rdtsc()
+     import codelet
+     codelet.run()
 
+  if not command_line.do_run:
+     return
 
   init()
 
@@ -102,3 +108,4 @@ def main():
 
 if __name__ == '__main__':
   main()
+
diff --git a/src/irpf90_t.py b/src/irpf90_t.py
index 1068ada..57658c4 100644
--- a/src/irpf90_t.py
+++ b/src/irpf90_t.py
@@ -351,6 +351,8 @@ def create_irpf90_files():
   result = filter ( is_irpf90_file, os.listdir(os.getcwd()) )
   for dir in command_line.include_dir:
     result += map(lambda x: dir+x, filter ( is_irpf90_file, os.listdir(dir) ) )
+  if command_line.do_codelet:
+    result += [command_line.codelet[3]]
   return result
 irpf90_files = create_irpf90_files()
 
diff --git a/src/makefile.py b/src/makefile.py
index 03ea7fd..311b887 100644
--- a/src/makefile.py
+++ b/src/makefile.py
@@ -61,8 +61,7 @@ irpf90.make: $(wildcard *.irp.f)
 
 ######################################################################
 def run():
-  from modules import modules
-  if os.fork() == 0:
+    from modules import modules
     mod = []
     for m in modules.values():
       mod.append(m)
@@ -94,6 +93,8 @@ def run():
     print >>file, "OBJ1 = $(OBJ) %sirp_touches.irp.o"%(irpdir),
     if command_line.do_profile:
       print >>file, " %sirp_profile.irp.o"%(irpdir), " irp_rdtsc.o",
+    if command_line.do_codelet:
+      print >>file, " irp_rdtsc.o",
     if command_line.do_openmp:
       print >>file, " %sirp_locks.irp.o"%(irpdir),
     else:
@@ -191,4 +192,3 @@ def run():
     print >>file, "\t- rm -rf "+irpdir+" "+mandir+" irpf90.make irpf90_variables dist\n"
 
     file.close()
-    sys.exit(0)
diff --git a/src/preprocessed_text.py b/src/preprocessed_text.py
index 4941ea2..9eb2db3 100644
--- a/src/preprocessed_text.py
+++ b/src/preprocessed_text.py
@@ -788,6 +788,7 @@ def check_begin_end(text):
     error.fail(text[begin],"Missing 'end%s'"%(x,))
 
   def find_matching_end_subfunpro(begin,x):
+    line = text[begin]
     for i in range(begin+1,len(text)):
       line = text[i]
       if type(line) == x:
diff --git a/src/profile.py b/src/profile.py
index f1321d6..abf0b92 100644
--- a/src/profile.py
+++ b/src/profile.py
@@ -20,7 +20,6 @@ import subprocess
 import tempfile
 import os
 import threading
-from variables import variables
 
 def build_rdtsc():
   file,filename = tempfile.mkstemp()
@@ -36,6 +35,7 @@ def build_rdtsc():
   threading.Thread(target=t).start()
 
 def build_module():
+  from variables import variables
   data = """
 module irp_timer
  double precision :: irp_profile(3,%(n)d) 

From 89ab32443ccb5badade8d311aa34ccfe3f292e04 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 27 Feb 2014 14:06:31 +0100
Subject: [PATCH 2/4] Corrected bug with unexisting directories

---
 README               |   5 +++--
 man/man1/irpf90.1.gz | Bin 1329 -> 1471 bytes
 src/command_line.py  |   2 ++
 src/init.py          |   9 ++++++++-
 src/irpf90_t.py      |   6 +++++-
 src/module.py        |   2 +-
 src/version.py       |   2 +-
 7 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/README b/README
index da145fc..a0d98c3 100644
--- a/README
+++ b/README
@@ -7,7 +7,7 @@ Dependencies
 
 - GNU make (>= 3.81 recommended)
 - Python > 2.3
-- Any Fortran 90 compiler (Intel recommended, for example)
+- Any Fortran 90 compiler (Intel recommended)
 
 Installing IRPF90
 -----------------
@@ -21,6 +21,7 @@ ${IRPF90_HOME} is the location of your irpf90 directory::
   export PATH=${IRPF90_HOME}/bin:${PATH}
   export MANPATH=${IRPF90_HOME}/man:${MANPATH}
   EOF
+  . ${HOME}/.bash_profile
 
 
 Using IRPF90
@@ -43,6 +44,6 @@ Author
 ------
 
 | Anthony Scemama, LCPQ-IRSAMC, CNRS-Universite Paul Sabatier
-| scemama@irsamc.ups-tlse.fr
+| <scemama@irsamc.ups-tlse.fr>
 | http://scemama.mooo.com
 
diff --git a/man/man1/irpf90.1.gz b/man/man1/irpf90.1.gz
index 19b980fd63735b02d03d8b8f66004f7460eb41ab..2e0b640df0b1ebd4d280207fad1caa290f8aa9f5 100644
GIT binary patch
literal 1471
zcmV;w1wi^AiwFq7J^E4r18H(_W;rk}F#wfUZExE)5dO|zaWyia#bU*FR}AwoU|!<3
z1{%k(9Be}s6tqO!L?lupDLXFu<M)t~Y&T7?^^3)q<Gnoh+>wrw4qbCaC0`3#3ndJ9
zBBPbj1sM@LQ>CslB3p<D7qN)FJBVmCq(QI$Q_}4Xl5W3G{Wrt@fNmF;5o6KfJx%7b
zx4-nLPn`~R`q7|=PlrYEdzy}}$E?{-y7X2XXS@$auMIB>sn%3k|2rwlT&B{|T&#o<
zDi!23%{Zil6UM@!NEtHL4GONhQe{H9ZZ5VWr=H);MBneuMF|_%+^nTyNpjYwBvBu6
zq6kZOtUlrwpVHOt*V4l$<eoiw$GYs>&EDM;i~Xk-2X`!L;+RaY#?u9hkg@1dOn^=d
zSw!=gd~_IngUYiWK8E6nvkjs@_Mb7Xts6FO((SbMljh?fU+ehB40d#$eJ7aDX1iPa
zro`@hH6noTIZ%Z_LE`xD>CG&j#4M@<re4%Lj9*7@m^9@I1plZ@C$+LLb;Ra4f~Ko+
zd^w-Y7L%JPi)`5*^!2cnnXp9stJ)B1D~(o#M|HQ6>4vQIg|d>6ZHkGV95|<~<m5Ku
zKkJEJqAFhzCL5ha47!L4Z3Iy!9GAI0Cv*j#1!b;s+DM*LCY_PX$~T3bbephQ^7I}p
zg+aqsT3Ae0ljMhubLH^jq7E>sN}F_DZbh^*$!Zp`xCt;k0(F7CKhP<zU_R+4-At^c
z66`8`EYR6<II_$INuMeYL`KWKcf_}uPm{M~9h#O$%tl9jlSZFZX<lWJt-lD!h!nx?
zkD|O0<<<)0*eG>!3yqdWaXg+cPW97dMSN*7K4(T0dMlm~I%-ZE&8f~rF5DsVpO2CI
znB0Ciy&nBV0JNE+=2NWzKG+rZ*pS-x3``n*KEdF^N&+2zO1#O8I`Q7ZA-WdUB3VQF
zb2P{PyNdz6Y*_1yeRxhefTn)`Ri_3$*u<iBa3-@M?YeTXy3Dz{58}U4rNl!CAd!qp
z)m0P)f;YrQDOXB)Mu*6pEQCGck{y!0tkx%hhj~N`kW7KLq*o!&X=RKr2wN=;T!8}@
zt4gKb(Tmm|+sQnqCD>`Cs_(EsR^&xx++be0vT|&<5z3=1jCal>{(y)v<kaXsCvMqJ
zKpVF~#pUca1OVcLAsL#Ug~i}mbL1rD>n5}&FDJp(E5T|AD`fHH<fb{f5qZgGJ_<-l
zOJRPHk_TQ(2U5d#p3Bcr)?jqtcSM&cXK$D@6cw*>hu6TpsM(^LIu`|+Jx4X{w7K`b
zwdc`qPJGMT63OLSv625JZVcbs<~C1tQ9`k4&dV**?TuLBY7ozSv5r1W-c1h`9r=dF
z!~;j?0_q3-zr7w%7{GO(g<yvvpPaC>+@l1Ry7F1wpSV~wE*2<D#8U%UPrMqP@<95F
zOq|S4&Z`5kp5Y8aUs`V2FUv~ien3O-Gg@nqLf{O!JcxNZwUS50x@`g*k=~>9SiI3Y
z)YS%EntUl1@^kP8Z;-ubuo3@MKruV2C=a9(FqWdE>-cQAJ=!(@w)4qFS7=$!YSu?|
zYsIR{Y2~|qsIs-snisbWody>`C|0}iytk>5<yVc&G!7{J=_J9EwelB;Ptp_lrx#b_
z%d^0O7gv+{*-@Kqw4t6Y+8u5e79WP7M_%DH?(R%eu61d>+pKxO1~1Wha1o>}dI<bc
zExE>m(^a}*SJIX_u&poD&|>{{%8kbg0{(JCTVP@04S2#H?wvJ)QN9=8=EVc2D(YU>
znyMO8m8y_|hIjSk$c&@-wh`ZA6*+J7*i3zEsBh3m?}&IjrqPG^=Fy8}M#;-%MFan?
zz<cI&<^NpDUzr%)F5chF*+`+^t3Ac3D0sm^hVcDe8q15+>u6PkSK0AT11{xEr|5^d
Z1(Q|y*ReAao!0-k_!ob5-!+X40055{;I{w(

literal 1329
zcmV-11<v{(iwFoqY^YKI18H(_W;rk}F#wfTTW{J(6n>vyaT;Z%RvR23-G@b5Y1u$q
zq?RB|9#(Z!4fYt1V$XQz0-@@U-*d(W+>~gy58%0+`{g?mB^U6CE2#NKz(y!xxDy%V
zMps}&?2J#HHzHe!Cl|4Zy+4v@HG*M(aFg@~L;MY3a5H-Q7VcNK5o6Kn1I(6-cfa>x
z02dc<F^GnJ{9Ldo{s8mwrzvZ%lODX&#u>7~=#Al3CDjJJrT<w~mok+OmLeBMs8oQ{
zu;54~oG=y*ij)Ck-LT@SCsiht>y=_FO6b#NCI)o76gBGj#LY%3mL!)0ND}oKIjV5<
zz#0}hJSXdL-%yXv(7nj{z<TV*%l^Ze!@;@3;RB0WKW6jEbiQH{W-NN<6NXNVSOm)$
z$U9v95S14#d>)E3ylq5(9lW4iTQ_RWg!}oyPFPL@eIw%sHF%@T>?ecyVzzsYZA$EZ
zRw6p^GYmdBibWj%J-=JTvzSGV!_bfV$MsG08<VEavA{p;+DWY}syfByv_eUfX?(k!
zEmpI;Ig4z4V5EN7%1l@Q{#|bfwUtJzilVwJWLkig)F`<`+P0Zkhv5pgl7lP6fA$l+
z#;$w=xG8iNF_Z;RX(IqK;kYdA6(B0`EC_SnX(M?FnRG_3J%Pebx*}ZGJbgq+VJKlM
zEow~iS@KKaTs^wJZXAq!ZIhlWt%!1y<ckoCyAXzFL0#e9Ux*YFRG;*cUM6y>1e=79
z#prA~8nP}0NJ<q2B7^mw3?Z2LGJ6NsA!t#=Y;=-0YvoCmmOew;=8Fy)k)m_^6De;=
zxwXPLHcp+~qC^YhIG!$7UHLG}fv+vDub2^)-ik9sC&}5-skPs91c!YDD-5Q>^nlKT
zKdCo{5^w$5Xzwrp*SS|ImDqJ#Fox}9S;88#V5DlWIwS@4tBf1mdslnMc7;$_O_+Hq
zD@>Jml8%-fTG>~?E!zo{#%&OBySN7@D@rg%BE#mks4-a9vUFVAw639DxhzG;x#lEj
z4Q@fIvo2@Rau%Yj*@C=4Drq6?k5uxQKj|=eXge?ER}|L9=$OX{Zn11hF=tpj+?Nig
z-lHI^0AteBv#1c%IA(pP%_G@%;K#n|*j64&p_CiN#`F)|7{0gd)Jk<#qhQnW%dN1C
zlvv@KAYM{Yjz7-c&ySTGQR6c4#IZv$>PPv1+zcTs&~(Z|(8DmF9PnnncLLVhQ&#sK
z6RXz53d;}uX#&`6NQ_Q-fTZh8baownbqs7tjfO<u4z*>!t-UO10VA>*AtX?t;|z0o
zB%^XVP@V+qR&ZK~^bvuP#f9EkL@`7oAfT+|*I*6K+C5dU5&w9MVs;WyAB#$$vQ${x
z_-6x39?s|uL&-&WJ5)Vusy>2yD{@~#PUsf8Y(rTia?4V!5a`Goum#n<O^vL-Ygp47
zp!Ancf@d2=KuJkDlYe+MnciN8DtI-SEiX^fY%2}>**b}sDp-76VtJGvxp78i8cMBe
zOJ=k7p%$#HMT&rz9-@biKkFseYH-@81)E4)ml)e-a1dHL8XMeDtdM{}9ASZl4Jn|4
zJ>u&Iol%4ZIAL&*djhkLD&MN|%3}uFx@$J4$~cj4Tk<WQV$KhFY_|jr&7^oXFXQPH
z#vkLmXOnjU$?LU;A<a*m+uf7@Gkm^NF}`1YxLdNZ!a=C^5T~Nz6~|%--#?|Xyh=&N
nK}2|coF2zGd@`LP9+nm>S%ug2&PYUBdPM&VKhBllbqfFhh%R-t

diff --git a/src/command_line.py b/src/command_line.py
index 35569d0..593f807 100644
--- a/src/command_line.py
+++ b/src/command_line.py
@@ -74,6 +74,8 @@ class CommandLine(object):
       self._include_dir = []
       for o,a in self.opts:
         if o in [ "-I", '--'+options['I'][0] ]:
+          if len(a) < 1: 
+            print "Error: -I option needs a directory"
           if a[-1] != '/':
             a = a+'/'
           self._include_dir.append(a)
diff --git a/src/init.py b/src/init.py
index 4fd25d1..7bddb42 100644
--- a/src/init.py
+++ b/src/init.py
@@ -63,10 +63,17 @@ def init():
   makefile.create()
   
   # Copy current files in the irpdir
+  ls = os.listdir(os.getcwd())
+  print ls
   for dir in ['./']+command_line.include_dir:
+    try:
+      os.stat(dir)
+    except:
+      print dir,'not in dir'
+      continue
     for filename in os.listdir(dir):
       filename = dir+filename
-      if not filename[0].startswith(".") and not os.path.isdir(filename):
+      if not filename.startswith(".") and not os.path.isdir(filename):
         try:
           file  = open(filename,"r")
         except IOError:
diff --git a/src/irpf90_t.py b/src/irpf90_t.py
index 57658c4..ae1b73a 100644
--- a/src/irpf90_t.py
+++ b/src/irpf90_t.py
@@ -350,7 +350,11 @@ def create_irpf90_files():
     return filename.endswith(".irp.f") and not filename.startswith('.')
   result = filter ( is_irpf90_file, os.listdir(os.getcwd()) )
   for dir in command_line.include_dir:
-    result += map(lambda x: dir+x, filter ( is_irpf90_file, os.listdir(dir) ) )
+    try:
+      os.stat(dir)
+      result += map(lambda x: dir+x, filter ( is_irpf90_file, os.listdir(dir) ) )
+    except:
+      continue
   if command_line.do_codelet:
     result += [command_line.codelet[3]]
   return result
diff --git a/src/module.py b/src/module.py
index 4bb9f49..a817f40 100644
--- a/src/module.py
+++ b/src/module.py
@@ -47,7 +47,7 @@ class Fmodule(object):
   def __init__(self,text,filename):
     self.text = put_info(text,filename)
     self.filename = filename[:-6]
-    self.name = "%s_mod"%(self.filename).replace('/','__')
+    self.name = "%s_mod"%(self.filename).replace('/','__').replace('.','Dot')
 
   def is_main(self):
     if '_is_main' not in self.__dict__:
diff --git a/src/version.py b/src/version.py
index 35ec9a3..cfa2db6 100644
--- a/src/version.py
+++ b/src/version.py
@@ -1 +1 @@
-version = "1.3.1"
+version = "1.3.3"

From d71c2c42297ce49f5bec0addbe880257ebc7ce3e Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 27 Feb 2014 14:07:20 +0100
Subject: [PATCH 3/4] Fixed man error in make

---
 Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 31a6ddf..97732c1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,10 @@
 .PHONY: all src man
 
-all: src man
-
 src:
 	$(MAKE) -C $@
 
 man:
 	- $(MAKE) -C $@
 
+all: src man
+

From b508923bab68d1db0ecc4644de732a3abd1f6377 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Fri, 28 Feb 2014 11:12:20 +0100
Subject: [PATCH 4/4] Forgot to remove debug print

---
 src/init.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/init.py b/src/init.py
index 7bddb42..94b82c1 100644
--- a/src/init.py
+++ b/src/init.py
@@ -63,8 +63,6 @@ def init():
   makefile.create()
   
   # Copy current files in the irpdir
-  ls = os.listdir(os.getcwd())
-  print ls
   for dir in ['./']+command_line.include_dir:
     try:
       os.stat(dir)