fix cluster settings

bfps/code.py

@@ -104,13 +104,9 @@ class code(base):
             raise IOError('header not there:\n' +
                           '{0}\n'.format(os.path.join(bfps.header_dir, 'base.hpp')) +
                           '{0}\n'.format(bfps.dist_loc))
-        libraries = ['fftw3_mpi',
-                     'fftw3',
-                     'fftw3f_mpi',
-                     'fftw3f',
-                     'bfps']
+        libraries = ['bfps'] + bfps.install_info['extra_libraries']
 
-        command_strings = ['mpicxx']
+        command_strings = ['g++']
         command_strings += [self.name + '.cpp', '-o', self.name]
         command_strings += ['-O2'] + bfps.install_info['extra_compile_args']
         command_strings += ['-I' + idir for idir in bfps.install_info['include_dirs']]
@@ -186,8 +182,6 @@ class code(base):
         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')
@@ -201,7 +195,12 @@ class code(base):
                     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('mpiexec -machinefile $TMPDIR/machines ' +
+                          '-genv LD_LIBRARY_PATH ' +
+                          '"' +
+                          ':'.join([bfps.lib_dir] + bfps.install_info['library_dirs']) +
+                          '" ' +
+                          '-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()

machine_settings.py

@@ -7,6 +7,7 @@ import os
 hostname = os.getenv('HOSTNAME')
 
 extra_compile_args = ['-mtune=native', '-ffast-math', '-std=c++11']
+extra_libraries = []
 
 if hostname == 'chichi-G':
     include_dirs = ['/usr/local/include',
@@ -15,14 +16,16 @@ if hostname == 'chichi-G':
                     '/usr/lib/mpich']
 
 if hostname in ['frontend01', 'frontend02']:
-    include_dirs = ['/usr/lib64/mpi/gcc/openmpi/include',
-                    '/usr/include/mpich',
-                    '/usr/nld/mvapich2-1.9a2-gcc/include',
+    include_dirs = ['/usr/nld/mvapich2-1.9a2-gcc/include',
+                    '/usr/nld/gcc-4.7.2/include',
                     '/usr/nld/fftw-3.3.3-mvapich2-1.9a2-gcc/include',
                     '/usr/nld/fftw-3.3.3-float-mvapich2-1.9a2-gcc/include']
 
-    library_dirs = ['/usr/nld/fftw-3.3.3-mvapich2-1.9a2-gcc/lib',
+    library_dirs = ['/usr/nld/mvapich2-1.9a2-gcc/lib',
+                    '/usr/nld/gcc-4.7.2/lib64',
+                    '/usr/nld/fftw-3.3.3-mvapich2-1.9a2-gcc/lib',
                     '/usr/nld/fftw-3.3.3-float-mvapich2-1.9a2-gcc/lib']
+    extra_libraries = ['mpich']
 
 if hostname == 'tolima':
     local_install_dir = '/scratch.local/chichi/installs'

setup.py

@@ -20,7 +20,7 @@
 
 
 
-from machine_settings import include_dirs, library_dirs, extra_compile_args
+from machine_settings import include_dirs, library_dirs, extra_compile_args, extra_libraries
 import pickle
 
 
@@ -38,14 +38,6 @@ try:
     git_revision = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip()
 except:
     git_revision = ''
-pickle.dump(
-        {'include_dirs' : include_dirs,
-         'library_dirs' : library_dirs,
-         'extra_compile_args' : extra_compile_args,
-         'install_date' : now,
-         'git_revision' : git_revision},
-        open('bfps/install_info.pickle', 'wb'),
-        protocol = 2)
 
 VERSION = date_name
 
@@ -72,6 +64,18 @@ libraries = ['fftw3_mpi',
              'fftw3f_mpi',
              'fftw3f']
 
+libraries += extra_libraries
+
+pickle.dump(
+        {'include_dirs' : include_dirs,
+         'library_dirs' : library_dirs,
+         'extra_compile_args' : extra_compile_args,
+         'extra_libraries' : extra_libraries,
+         'install_date' : now,
+         'git_revision' : git_revision},
+        open('bfps/install_info.pickle', 'wb'),
+        protocol = 2)
+
 from setuptools import setup, Extension
 
 libbfps = Extension(