diff --git a/bfps/__init__.py b/bfps/__init__.py
index 435355db570b53259cb83c5ff31c41a4472dbcd3..550f00e6820ebd1672436108777409f7eff24616 100644
--- a/bfps/__init__.py
+++ b/bfps/__init__.py
@@ -40,14 +40,9 @@ try:
except DistributionNotFound:
__version__ = ''
-machine_settings = pickle.load(
+install_info = pickle.load(
open(os.path.join(os.path.dirname(here),
- 'machine_settings.pickle'),
- 'r'))
-
-version_info = pickle.load(
- open(os.path.join(os.path.dirname(here),
- 'version_info.pickle'),
+ 'install_info.pickle'),
'r'))
from .code import code
diff --git a/bfps/code.py b/bfps/code.py
index e38cdd37f159d786c2fc9ca5080df149d2cd3cb0..8cef4ab0e1464376a9a33b52395124669365f3e9 100644
--- a/bfps/code.py
+++ b/bfps/code.py
@@ -26,89 +26,6 @@ import os
import shutil
import pickle
-class cluster_launcher:
- def __init__(
- self,
- file_name = None,
- queue = None,
- environment = None,
- envprocs = None,
- nprocesses = None,
- name_of_run = None,
- command_atoms = None,
- hours = None,
- minutes = None,
- seconds = None,
- err_file = None,
- out_file = None,
- mail_address = None,
- mail_events = None):
- self.file_name = file_name
- self.queue = queue
- self.environment = environment
- self.nprocesses = nprocesses
- self.name_of_run = name_of_run
- self.command_atoms = command_atoms
- self.hours = hours
- self.minutes = minutes
- self.seconds = seconds
- self.err_file = err_file
- self.out_file = out_file
- self.mail_address = mail_address
- self.mail_events = mail_events
- if type(envprocs) == type(None):
- self.envprocs = self.nprocesses
- return None
- def write_pbs_file(self):
- script_file = open(file_name, 'w')
- script_file.write('#!/bin/tcsh\n'
- + '#PBS -q ' + queue + '\n'
- + '#PBS -l walltime={0}:{1}:{2}\n'.format(hours, minutes, seconds))
- if nprocesses%8 == 0:
- script_file.write('#PBS -l nodes={0}:ppn=8\n'.format(nprocesses/8))
- else:
- script_file.write('#PBS -l nodes={0}\n'.format(nprocesses))
- script_file.write('#PBS -j n\n'
- + '#PBS -e ' + err_file + '\n'
- + '#PBS -o ' + out_file + '\n'
- + '#PBS -N ' + name_of_run + '\n\n')
- if mail_address != None:
- script_file.write('#PBS -M {0}\n'.format(mail_address))
- if mail_events != None:
- script_file.write('#PBS -m {0}\n\n'.format(mail_events))
- script_file.write('cd $PBS_O_WORKDIR\n'
- + 'setenv MPI_NPROCS `wc -l $PBS_NODEFILE`\n'
- + 'echo "Workdir is $PBS_O_WORKDIR"\n'
- + 'echo Start time is `date`\n'
- + 'mpirun -machinefile $PBS_NODEFILE ' + name_of_executable + '\n'
- + 'echo End time is `date`\n')
- script_file.close()
- return None
- def write_sge_file(self):
- script_file = open(self.file_name, 'w')
- script_file.write('#!/bin/bash\n')
- # export all environment variables
- script_file.write('#$ -V\n')
- # job name
- script_file.write('#$ -N {0}\n'.format(self.name_of_run))
- # use current working directory
- script_file.write('#$ -cwd\n')
- # error file
- if not type(self.err_file) == type(None):
- script_file.write('#$ -e ' + self.err_file + '\n')
- # output file
- if not type(self.out_file) == type(None):
- script_file.write('#$ -o ' + self.out_file + '\n')
- if not type(self.environment) == type(None):
- script_file.write('#$ -pe {0} {1}\n'.format(self.environment, self.envprocs))
- script_file.write('echo "got $NSLOTS slots."\n')
- script_file.write('echo Start time is `date`\n')
- script_file.write('mpiexec -machinefile $TMPDIR/machines -n {0} {1}\n'.format(self.nprocesses, ' '.join(self.command_atoms)))
- script_file.write('echo End time is `date`\n')
- script_file.write('exit 0\n')
- script_file.close()
- return None
-
class code(base):
def __init__(self):
super(code, self).__init__()
@@ -164,6 +81,12 @@ class code(base):
}
//endcpp
"""
+ self.host_info = {'type' : 'cluster',
+ 'environment' : None,
+ 'deltanprocs' : 1,
+ 'queue' : '',
+ 'mail_address': '',
+ 'mail_events' : None}
return None
def write_src(self):
with open(self.name + '.cpp', 'w') as outfile:
@@ -189,21 +112,28 @@ class code(base):
command_strings = ['mpicxx']
command_strings += [self.name + '.cpp', '-o', self.name]
- command_strings += ['-O2'] + bfps.machine_settings['extra_compile_args']
- command_strings += ['-I' + idir for idir in bfps.machine_settings['include_dirs']]
+ command_strings += ['-O2'] + bfps.install_info['extra_compile_args']
+ command_strings += ['-I' + idir for idir in bfps.install_info['include_dirs']]
command_strings.append('-I' + bfps.header_dir)
- command_strings += ['-L' + ldir for ldir in bfps.machine_settings['library_dirs']]
+ command_strings += ['-L' + ldir for ldir in bfps.install_info['library_dirs']]
command_strings.append('-L' + bfps.lib_dir)
for libname in libraries:
command_strings += ['-l' + libname]
+ print('compiling code with command\n' + ' '.join(command_strings))
return subprocess.call(command_strings)
+ def set_host_info(
+ self,
+ host_info = {}):
+ self.host_info.update(host_info)
+ return None
def run(self,
ncpu = 2,
simname = 'test',
iter0 = 0,
out_file = 'out_file',
err_file = 'err_file',
- hostinfo = {'type' : ''}):
+ hours = 1,
+ minutes = 0):
if self.compile_code() == 0:
current_dir = os.getcwd()
if not os.path.isdir(self.work_dir):
@@ -214,25 +144,22 @@ class code(base):
with open(self.name + '_version_info.txt', 'w') as outfile:
outfile.write(self.version_message)
os.chdir(current_dir)
- command = ['mpirun',
- '-np',
- '{0}'.format(ncpu),
- './' + self.name,
- simname,
- '{0}'.format(iter0)]
- if hostinfo['type'] == 'cluster':
- cl = cluster_launcher(
+ command_atoms = ['mpirun',
+ '-np',
+ '{0}'.format(ncpu),
+ './' + self.name,
+ simname,
+ '{0}'.format(iter0)]
+ if self.host_info['type'] == 'cluster':
+ self.write_sge_file(
file_name = os.path.join(self.work_dir, 'run_' + simname + '.sh'),
- environment = hostinfo['environment'],
nprocesses = ncpu,
name_of_run = self.name + '_' + simname,
- command_atoms = command[3:],
- hours = 1,
- minutes = 0,
- seconds = 0,
+ command_atoms = command_atoms[3:],
+ hours = hours,
+ minutes = minutes,
out_file = out_file,
err_file = err_file)
- cl.write_sge_file()
elif hostinfo['type'] == 'pc':
os.chdir(self.work_dir)
os.environ['LD_LIBRARY_PATH'] += ':{0}'.format(bfps.lib_dir)
@@ -240,5 +167,43 @@ class code(base):
stdout = open(out_file + '_' + simname, 'w'),
stderr = open(err_file + '_' + simname, 'w'))
os.chdir(current_dir)
- return command
+ return None
+ def write_sge_file(
+ self,
+ file_name = None,
+ nprocesses = None,
+ name_of_run = None,
+ command_atoms = [],
+ hours = None,
+ minutes = None,
+ out_file = None,
+ err_file = None):
+ script_file = open(file_name, 'w')
+ script_file.write('#!/bin/bash\n')
+ # export all environment variables
+ script_file.write('#$ -V\n')
+ # job name
+ script_file.write('#$ -N {0}\n'.format(name_of_run))
+ # use current working directory
+ script_file.write('#$ -cwd\n')
+ script_file.write('#$ -v LD_LIBRARY_PATH="' +
+ ':'.join([bfps.lib_dir] + bfps.install_info['library_dirs']) + '"\n')
+ # error file
+ if not type(err_file) == type(None):
+ script_file.write('#$ -e ' + err_file + '\n')
+ # output file
+ if not type(out_file) == type(None):
+ script_file.write('#$ -o ' + out_file + '\n')
+ if not type(self.host_info['environment']) == type(None):
+ envprocs = (nprocesses / self.host_info['deltanprocs'] + 1) * self.host_info['deltanprocs']
+ script_file.write('#$ -pe {0} {1}\n'.format(
+ self.host_info['environment'],
+ envprocs))
+ script_file.write('echo "got $NSLOTS slots."\n')
+ script_file.write('echo Start time is `date`\n')
+ script_file.write('mpiexec -machinefile $TMPDIR/machines -n {0} {1}\n'.format(nprocesses, ' '.join(command_atoms)))
+ script_file.write('echo End time is `date`\n')
+ script_file.write('exit 0\n')
+ script_file.close()
+ return None
diff --git a/setup.py b/setup.py
index b4d6f94c70056667457d6c79cd2c92c0c3178e07..12c072116b14d06beb6767fa013eab0d25b425ba 100644
--- a/setup.py
+++ b/setup.py
@@ -22,12 +22,6 @@
from machine_settings import include_dirs, library_dirs, extra_compile_args
import pickle
-pickle.dump(
- {'include_dirs' : include_dirs,
- 'library_dirs' : library_dirs,
- 'extra_compile_args' : extra_compile_args},
- open('bfps/machine_settings.pickle', 'wb'),
- protocol = 2)
AUTHOR = 'Cristian C Lalescu'
@@ -45,9 +39,12 @@ try:
except:
git_revision = ''
pickle.dump(
- {'install_date' : now,
+ {'include_dirs' : include_dirs,
+ 'library_dirs' : library_dirs,
+ 'extra_compile_args' : extra_compile_args,
+ 'install_date' : now,
'git_revision' : git_revision},
- open('bfps/version_info.pickle', 'wb'),
+ open('bfps/install_info.pickle', 'wb'),
protocol = 2)
VERSION = date_name
@@ -91,8 +88,7 @@ setup(
install_requires = ['numpy>=1.8', 'matplotlib>=1.3'],
ext_modules = [libbfps],
package_data = {'bfps': header_list + ['../machine_settings.py',
- 'machine_settings.pickle',
- 'version_info.pickle']},
+ 'install_info.pickle']},
########################################################################
# useless stuff folows
########################################################################