Author: varioustoxins
Date: Fri Mar 30 09:00:39 2007
New Revision: 3249
URL: http://svn.gna.org/viewcvs/relax?rev=3249&view=rev
Log:
more work to remove specious calls to module mpi4py when starting
uniprocessor version feedback prints correctly
Modified:
branches/multi_processor/multi/commands.py
branches/multi_processor/multi/mpi4py_processor.py
branches/multi_processor/multi/uni_processor.py
branches/multi_processor/specific_fns/model_free.py
Modified: branches/multi_processor/multi/commands.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor/multi/commands.py?rev=3249&r1=3248&r2=3249&view=diff
==============================================================================
--- branches/multi_processor/multi/commands.py (original)
+++ branches/multi_processor/multi/commands.py Fri Mar 30 09:00:39 2007
@@ -1,6 +1,7 @@
from multi.processor import Memo,Slave_command
from multi.processor import Result_command,Result_string,NULL_RESULT
+from re import match
from maths_fns.mf import Mf
from minimise.generic import generic_minimise
@@ -24,7 +25,7 @@
result = Result_string(msg,True)
processor.return_object(result)
-#not quit a momento so a memo
+#not quite a momento so a memo
class MF_completion_memo(Memo):
def __init__(self,model_free,index,sim_index,run,param_set,scaling):
self.index = index
@@ -78,19 +79,27 @@
'csa':None, 'num_frq':0, 'frq':None, 'num_ri':None,
'remap_table':None, 'noe_r1_table':None,
'ri_labels':None, 'gx':0, 'gh':0, 'g_ratio':0,
'h_bar':0, 'mu0':0, 'num_params':None, 'vectors':None}
-
+ self.info_map={'res_id':None,'grid_size':1}
#FIXME: bad names
def set_mf(self, **kwargs):
self.mf_map.update(**kwargs)
def set_minimise(self,**kwargs):
+ print kwargs
+ if 'res_id' in kwargs:
+ self.info_map['res_id']= kwargs['res_id']
+ del kwargs['res_id']
+ if 'grid_size' in kwargs:
+ self.info_map['grid_size']= kwargs['grid_size']
+ del kwargs['grid_size']
self.minimise_map.update(**kwargs)
def build_mf(self):
return Mf(**self.mf_map)
def do_minimise(self,memo):
+
self.mf = self.build_mf()
results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc,
d2func=self.mf.d2func, **self.minimise_map)
@@ -100,8 +109,29 @@
gc=gc,hc=hc, warning=warning,
run=memo.run,
index=memo.index,sim_index=memo.sim_index,
param_set=memo.param_set,scaling=memo.scaling)
+
+ def do_feedback(self):
+ # Print out.
+
#print_flag,param_set,residue_num,residue_name,min_algor,grid_size=None
+ m_m=self.minimise_map
+ m_f=self.mf_map
+ i_m=self.info_map
+ if m_m['print_flag'] >= 1:
+ # Individual residue stuff.
+ if m_f['param_set'] == 'mf' or m_f['param_set'] == 'local_tm':
+ if m_m['print_flag'] >= 2:
+ print "\n\n"
+ string = "Fitting to residue: " + i_m['res_id']
+ print "\n\n" + string
+ print len(string) * '~'
+ if match('^[Gg]rid', m_m['min_algor']):
+ print "Unconstrained grid search size: " +
`i_m['grid_size']` + " (constraints may decrease this size).\n"
+
def run(self,processor):
self.mf = self.build_mf()
+
+
+ self.do_feedback()
results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc,
d2func=self.mf.d2func, **self.minimise_map)
param_vector, func, iter, fc, gc, hc, warning = results
Modified: branches/multi_processor/multi/mpi4py_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor/multi/mpi4py_processor.py?rev=3249&r1=3248&r2=3249&view=diff
==============================================================================
--- branches/multi_processor/multi/mpi4py_processor.py (original)
+++ branches/multi_processor/multi/mpi4py_processor.py Fri Mar 30 09:00:39
2007
@@ -5,20 +5,31 @@
import os
import math
import time,datetime
+import textwrap
from multi.processor import Memo,Slave_command
from multi.processor import Result,Result_command,Result_string
from multi.commands import Exit_command
-#FIXME: me move top generic command module
+
# load mpi
try:
from mpi4py import MPI
except ImportError:
- raise Exception('test')
- sys.stderr.write("The dependency 'mpi4py' has not been installed.\n")
+ msg = '''The dependency 'mpi4py' has not been installed. You should
either
+
+ 1. run without multiprocessor support i.e. remove the
+ --multi mpi4py flag from the command line
+
+ 2. install mpi4py
+
+ 3. choose another multi processor method to give to the
+ --multi command line flag\n'''
+ msg=textwrap.dedent(msg)
+ sys.stderr.write(msg)
+ sys.stderr.write('exiting...\n\n')
sys.exit()
# save original sys.exit to call after wrapper
@@ -106,11 +117,6 @@
MPI.COMM_WORLD.Send(buf=result, dest=0)
-# def process_commands(self,commands):
-# self.assert_on_master()
-#
-# for i in range(1,MPI.size):
-# MPI.COMM_WORLD.Send(buf=command,dest=i)
def run_command_globally(self,command):
queue = [command for i in range(1,MPI.size)]
@@ -119,16 +125,6 @@
def run_command_queue(self,queue):
self.assert_on_master()
-# for i in range(1,MPI.size):
-# MPI.COMM_WORLD.Send(buf=command,dest=i)
-# for i in range(1,MPI.size):
-# elem = MPI.COMM_WORLD.Recv(source=i)
-# if type(elem) == 'object':
-# elem.run(relax_instance, relax_instance.processor)
-# else:
-# #FIXME can't cope with multiple lines
-# print i,elem
- #queue = [command for i in range(1,MPI.size*2)]
running_set=set()
idle_set=set([i for i in range(1,MPI.size)])
@@ -172,27 +168,9 @@
raise Exception(message)
-# 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):
-# if MPI.rank == 0:
-# self.relax_instance.multi_mode='multi_master'
-# else:
-# self.relax_instance.multi_mode='multi_slave'
-# self.relax_instance.mode='slave'
-# self.relax_instance.script_file=None
-# self.relax_instance.dummy_mode=True
-# #self.relax_instance.run()
if MPI.rank ==0:
@@ -201,12 +179,12 @@
end_time = time.time()
time_diff= end_time - start_time
time_delta = datetime.timedelta(seconds=time_diff)
- sys.stderr.write('overall runtime: ' + time_delta.__str__() +
'\n')
- sys.stderr.flush()
- # note this a mdofied exit that kills all MPI processors
+ print 'overall runtime: ' + time_delta.__str__() + '\n'
+
+ # note this a modified exit that kills all MPI processors
sys.exit()
else:
- #self.relax_instance.run(deamon=True)
+
while not self.do_quit:
command = MPI.COMM_WORLD.Recv(source=0)
try:
@@ -216,9 +194,7 @@
- #if data=='close':
- # exit_mpi()
- # return
+
Modified: branches/multi_processor/multi/uni_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor/multi/uni_processor.py?rev=3249&r1=3248&r2=3249&view=diff
==============================================================================
--- branches/multi_processor/multi/uni_processor.py (original)
+++ branches/multi_processor/multi/uni_processor.py Fri Mar 30 09:00:39 2007
@@ -44,8 +44,8 @@
end_time = time.clock()
time_diff= end_time - start_time
time_delta = datetime.timedelta(seconds=time_diff)
- sys.stderr.write('overall runtime: ' + time_delta.__str__() + '\n')
- sys.stderr.flush()
+ print 'overall runtime: ' + time_delta.__str__() + '\n'
+
Modified: branches/multi_processor/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor/specific_fns/model_free.py?rev=3249&r1=3248&r2=3249&view=diff
==============================================================================
--- branches/multi_processor/specific_fns/model_free.py (original)
+++ branches/multi_processor/specific_fns/model_free.py Fri Mar 30 09:00:39
2007
@@ -2168,17 +2168,17 @@
if constraints:
A, b = self.linear_constraints(index=index)
- # Print out.
- if self.print_flag >= 1:
- # Individual residue stuff.
- if self.param_set == 'mf' or self.param_set == 'local_tm':
- if self.print_flag >= 2:
- print "\n\n"
- string = "Fitting to residue: " +
`self.relax.data.res[self.run][index].num` + " " +
self.relax.data.res[self.run][index].name
- print "\n\n" + string
- print len(string) * '~'
- if match('^[Gg]rid', min_algor):
- print "Unconstrained grid search size: " +
`self.grid_size` + " (constraints may decrease this size).\n"
+# # Print out.
+# if self.print_flag >= 1:
+# # Individual residue stuff.
+# if self.param_set == 'mf' or self.param_set == 'local_tm':
+# if self.print_flag >= 2:
+# print "\n\n"
+# string = "Fitting to residue: " +
`self.relax.data.res[self.run][index].num` + " " +
self.relax.data.res[self.run][index].name
+# print "\n\n" + string
+# print len(string) * '~'
+# if match('^[Gg]rid', min_algor):
+# print "Unconstrained grid search size: " +
`self.grid_size` + " (constraints may decrease this size).\n"
# Initialise the iteration counter and function, gradient, and
Hessian call counters.
#FIXME: move to processor command
@@ -2329,73 +2329,6 @@
-# # Initialise the function to minimise.
-# ######################################
-# print 'initialise Mf'
-# print 'init_params',self.param_vector
-# print 'param_se',self.param_set
-# print 'diff_type',diff_type
-# print 'diff_params',diff_params
-# print 'scaling_matrix',self.scaling_matrix
-# print 'num_res',num_res
-# print 'equations',equations
-# print 'param_types',param_types
-# print 'param_values',param_values
-# print 'relax_data',relax_data
-# print 'errors',relax_error
-# print 'bond_length',r
-# print 'csa=',csa
-# print 'num_frq',num_frq
-# print 'frq',frq
-# print 'num_ri',num_ri
-# print 'remap_table',remap_table
-# print 'noe_r1_table',noe_r1_table
-# print 'ri_labels',ri_labels
-# print 'gx',self.relax.data.gx
-# print 'gh',self.relax.data.gh
-# print 'g_ratio',self.relax.data.g_ratio
-# print 'h_bar',self.relax.data.h_bar
-# print 'mu0',self.relax.data.mu0
-# print 'num_params',num_params
-# print 'vectors',xh_unit_vectors
-#
-# data_list = [ 'initialise Mf',
-# 'init_params',self.param_vector,
-# 'param_set',self.param_set,
-# 'diff_type',diff_type,
-# 'diff_params',diff_params,
-# 'scaling_matrix',self.scaling_matrix,
-# 'num_res',num_res,
-# 'equations',equations,
-# 'param_types',param_types,
-# 'param_values',param_values,
-# 'relax_data',relax_data,
-# 'errors',relax_error,
-# 'bond_length',r,
-# 'csa=',csa,
-# 'num_frq',num_frq,
-# 'frq',frq,
-# 'num_ri',num_ri,
-# 'remap_table',remap_table,
-# 'noe_r1_table',noe_r1_table,
-# 'ri_labels',ri_labels,
-# 'gx',self.relax.data.gx,
-# 'gh',self.relax.data.gh,\
-# 'g_ratio',self.relax.data.g_ratio,
-# 'h_bar',self.relax.data.h_bar,
-# 'mu0',self.relax.data.mu0,
-# 'num_params',num_params,
-# 'vectors',xh_unit_vectors]
-# for elem in data_list:
-# marshal.loads(marshal.dumps(elem))
-# self.mf = Mf(init_params=self.param_vector,
param_set=self.param_set, diff_type=diff_type,
-# diff_params=diff_params,
scaling_matrix=self.scaling_matrix, num_res=num_res,
-# equations=equations, param_types=param_types,
param_values=param_values,
-# relax_data=relax_data, errors=relax_error,
bond_length=r, csa=csa, num_frq=num_frq,
-# frq=frq, num_ri=num_ri, remap_table=remap_table,
noe_r1_table=noe_r1_table,
-# ri_labels=ri_labels, gx=self.relax.data.gx,
gh=self.relax.data.gh,
-# g_ratio=self.relax.data.g_ratio,
h_bar=self.relax.data.h_bar,
-# mu0=self.relax.data.mu0, num_params=num_params,
vectors=xh_unit_vectors)
command=MF_minimise_command()
command.set_mf(init_params=self.param_vector,
param_set=self.param_set, diff_type=diff_type,
@@ -2446,34 +2379,25 @@
# Minimisation.
###############
- #FIXME remove old version
-# if constraints:
-# results = generic_minimise(func=self.mf.func,
dfunc=self.mf.dfunc, d2func=self.mf.d2func, args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options, func_tol=func_tol,
grad_tol=grad_tol, maxiter=max_iterations, A=A, b=b, full_output=1,
print_flag=print_flag)
-# else:
-# results = generic_minimise(func=self.mf.func,
dfunc=self.mf.dfunc, d2func=self.mf.d2func, args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options, func_tol=func_tol,
grad_tol=grad_tol, maxiter=max_iterations, full_output=1,
print_flag=print_flag)
-# if results == None:
-# return
#FIXME??? strange contraints
+ #residue_num,residue_name,min_algor,grid_size=None
+ res_num = self.relax.data.res[self.run][index].num
+ res_name = self.relax.data.res[self.run][index].name
+ res_id = `res_num` + ' ' + res_name
+
if constraints:
command.set_minimise(args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options,
func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, A=A, b=b, full_output=1,
- print_flag=print_flag)
+
print_flag=print_flag,res_id=res_id,grid_size=self.grid_size)
else:
command.set_minimise(args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options,
func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, full_output=1,
- print_flag=print_flag)
+
print_flag=print_flag,res_id=res_id,grid_size=self.grid_size)
memo =
MF_completion_memo(model_free=self,index=index,sim_index=sim_index,run=self.run,param_set=self.param_set,scaling=scaling)
self.relax.processor.add_to_queue(command,memo)
- #self.relax.processor.add_to_queue()
-
- #command.do_minimise(memo)
- #command.memo_id
-
- #param_vector, func, iter, fc, gc, hc, warning = command.results
-
#self.disassemble_result(param_vector=param_vector,func=func,iter=iter,fc=fc,gc=gc,hc=hc,warning=warning,
- #
run=memo.run,index=memo.index,sim_index=memo.sim_index,
param_set=memo.param_set,scaling=memo.scaling)
+
self.relax.processor.run_queue()
@@ -2483,12 +2407,7 @@
self.warning=warning
self.param_vector=param_vector
- #FIXME something is resetting the count between each calculation!
-# self.iter_count = iter
-# self.f_count = fc
-# self.g_count = gc
-# self.h_count = hc
-
+ #FIXME this is a fix for old code
self.iter_count = self.iter_count + iter
self.f_count = self.f_count + fc
self.g_count = self.g_count + gc
r3249 - in /branches/multi_processor: multi/ specific_fns/