garyt@xxxxxxxxxxxxxxx wrote:
Dear Ed
d this is a good enough point to tell you how to run things and what to
install for the mpi version i am testing with
I have installed mpipy and lam
lam should be available in your linux distribution ??? ;-)
mpi4py came from http://www.python.org/pypi/mpi4py (there is an mpi4py
website but it is out of date, however, mpi4py is under recent development)
follow the instructions to install mpi4py
create the file 'test_multi1.py'
-------------------8<-----------------------
import multi
cmd = multi.mpi4py_processor.Get_name_command()
self.relax.processor.run_command(cmd)
-------------------8<-----------------------
then type lamboot
and to run the test type:
mpirun -np 6 python relax --multi mpi4py test_mult1.py
to get:
relax repository checkout
Protein dynamics by NMR relaxation data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
This is free software which you are welcome to modify and redistribute
under the conditions of the
GNU General Public License (GPL). This program, including all modules,
is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'.
Assistance in using this program
can be accessed by typing 'help'.
script = 'test_mult1.py'
----------------------------------------------------------------------------------------------------
import sys
import multi
cmd = multi.mpi4py_processor.Get_name_command()
self.relax.processor.run_command(cmd)
----------------------------------------------------------------------------------------------------
1 fbsdpcu156-9377
2 fbsdpcu156-9378
3 fbsdpcu156-9379
4 fbsdpcu156-9380
5 fbsdpcu156-9381
hope this is useful!
Now a question what is the best way to get an etrenally running relax
interpreter I can just fire commands at (for the slaves)?
basically I just need to
1. do some setup
2. send a command object
but without quitting at the end of the script
do i modify interpreter.run to take a quit varaiable set to False so
that run_script can be
run with quit = false?
regards
gary
Author: varioustoxins
Date: Mon Mar 19 16:13:15 2007
New Revision: 3237
URL: http://svn.gna.org/viewcvs/relax?rev=3237&view=rev
Log:
implimentation of basic command structure and simplistic processor name command
Modified:
branches/multi_processor/multi/mpi4py_processor.py
branches/multi_processor/relax
Modified: branches/multi_processor/multi/mpi4py_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor/multi/mpi4py_processor.py?rev=3237&r1=3236&r2=3237&view=diff
==============================================================================
--- branches/multi_processor/multi/mpi4py_processor.py (original)
+++ branches/multi_processor/multi/mpi4py_processor.py Mon Mar 19 16:13:15
2007
@@ -1,7 +1,7 @@
#!/usr/bin/env python
import sys
-
+import os
# load mpi
@@ -23,14 +23,22 @@
def exit_mpi():
if MPI.Is_initialized() and not MPI.Is_finalized() and MPI.rank == 0:
- sendbuf = ['close']
+ sendbuf = Exit_command()
for i in range(MPI.size):
if i != 0:
MPI.COMM_WORLD.Send(buf=sendbuf,dest=i)
+#FIXME do some inheritance
+class Exit_command(object):
+ def run(self,processor):
+ processor.do_quit=True
+class Get_name_command(object):
+ def run(self,processor):
+ result = '%s-%s' % (MPI.Get_processor_name(),os.getpid())
+ MPI.COMM_WORLD.Send(buf=result, dest=0)
-
+#FIXME do some inheritance
class Mpi4py_processor:
@@ -41,6 +49,35 @@
# wrap sys.exit to close down mpi before exiting
sys.exit= exit
self.do_quit=False
+
+ def exit(self):
+ exit_mpi()
+
+ def run_command(self,command):
+ for i in range(1,MPI.size):
+ if i != 0:
+ MPI.COMM_WORLD.Send(buf=command,dest=i)
+ for i in range(1,MPI.size):
+ buf=[]
+ if i !=0:
+ elem = MPI.COMM_WORLD.Recv(source=i)
+ if type(elem) == 'object':
+ elem.run(relax_instance)
+ else:
+ #FIXME can't cope with multiple lines
+ print i,elem
+
+
+# for i in range(MPI.size):
+# buf=[]
+# if i !=0:
+# print 'try',i
+# MPI.COMM_WORLD.Recv(buf=buf, source=i)
+# for i,elem in enumerate(buf):
+# if elem.type!='object':
+# print i,elem
+# else:
+# elem.run()
def run(self):
@@ -53,10 +90,13 @@
self.relax_instance.run()
sys.exit()
else:
- data = MPI.COMM_WORLD.Recv(source=0)
- if data=='close':
- exit_mpi()
- return
+ while not self.do_quit:
+ data = MPI.COMM_WORLD.Recv(source=0)
+ data.run(self)
+
+ #if data=='close':
+ # exit_mpi()
+ # return
Modified: branches/multi_processor/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor/relax?rev=3237&r1=3236&r2=3237&view=diff
==============================================================================
--- branches/multi_processor/relax (original)
+++ branches/multi_processor/relax Mon Mar 19 16:13:15 2007
@@ -561,7 +561,9 @@
clazz = getattr(modules[-1], class_name)
else:
raise RelaxError("can't load class %s from module %s" %
(class_name,module_path))
+
object = clazz(relax_instance)
+ relax_instance.processor = object
return object
if __name__ == "__main__":
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--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: garyt@xxxxxxxxxxxxxxx Fax +44-113-2331407
-------------------------------------------------------------------
Re: r3237 - in /branches/multi_processor: multi/mpi4py_processor.py relax