def __init__(self):
Project.__init__(self,
'8616',
'PRJEB4019',
'1000GENOMES_phase_1',
populations=self.SUPER_POPULATIONS_G1k_PHASE1,
populations_to_exclude=['ALL'])
def __init__(self,
uri,
worktree=None,
gitdir=None,
revision='master',
remote=None,
pattern=None,
bare=False,
*args,
**kws):
self.bare = bare
if not worktree:
if bare and gitdir:
worktree = gitdir
elif uri:
worktree = os.path.basename(uri)
if bare and not gitdir and worktree:
gitdir = worktree
# gitdir will be secured before executing the command per time
GitCommand.__init__(self, gitdir, worktree, *args, **kws)
if uri is None:
ret, url = self.ls_remote('--get-url')
if ret == 0:
ulp = urlparse(url)
uri = ulp.path.lstrip('/')
Project.__init__(self, uri, worktree, revision, _ensure_remote(remote),
pattern, *args, **kws)
def __init__(self,
uri,
worktree=None,
gitdir=None,
revision='master',
remote=None,
pattern=None,
bare=False,
*args,
**kws):
self.bare = bare
if not worktree:
if bare and gitdir:
worktree = gitdir
elif uri:
worktree = os.path.basename(uri)
if bare and not gitdir and worktree:
gitdir = worktree
# gitdir will be secured before executing the command per time
GitCommand.__init__(self, gitdir, worktree, *args, **kws)
Project.__init__(self, uri, worktree, revision, _ensure_remote(remote),
pattern, *args, **kws)
def __init__(self,
uri,
path=None,
revision=None,
remote=None,
options=None,
*args,
**kws):
Project.__init__(self, uri, path, revision, remote, *args, **kws)
RepoCommand.__init__(self, *args, **kws)
self.options = options
def __init__(self):
Project.__init__(self)
# TODO: Pour bien faire il faudrait ajouter la libgz à la machine.
self._optionsComp[u"COMMON_FILE_COMPRESS_GZ"][u"default"][u"replace"]["__LIBGZ__"] = u"-lz"
self._optionsComp[u"COMMON_FILE_COMPRESS_GZ"][False][u"replace"]["__LIBGZ__"] = u""
self._optionsComp[u"RESTRICT"] = {
u"database_id": u"RESTRICT",
u"default": {u"replace": {u"__RESTRICT__": u"__restrict"}, u"database_val": u"__restrict"},
False: {
u"replace": {u"__RESTRICT__": u""},
u"database_val": u"",
u"searchInName": re.compile(u"_NO_RESTRICT"),
},
}
def __init__(self):
Project.__init__(self)
# TODO: Pour bien faire il faudrait ajouter la libgz à la machine.
self._optionsComp[u"COMMON_FILE_COMPRESS_GZ"][u'default'][u'replace'][
'__LIBGZ__'] = u'-lz'
self._optionsComp[u"COMMON_FILE_COMPRESS_GZ"][False][u'replace'][
'__LIBGZ__'] = u''
self._optionsComp[u'RESTRICT'] = {
u'database_id': u'RESTRICT',
u'default': {
u'replace': {
u'__RESTRICT__': u'__restrict'
},
u'database_val': u'__restrict'
},
False: {
u'replace': {
u'__RESTRICT__': u''
},
u'database_val': u'',
u'searchInName': re.compile(u'_NO_RESTRICT')
}
}
def __init__(self, project_internal_id, prj_id, name):
Project.__init__(self, project_internal_id, prj_id, name, populations=UK10K_POPULATIONS)
def __init__(self):
Project.__init__(self, '2', 'PRJEB5439', 'ESP_6500')
def __init__(self):
Project.__init__(self, '301', 'PRJEB6930', '1000GENOMES_phase_3',
SUPER_POPULATIONS_G1k_PHASE3,
SUPER_POPULATIONS_G1k_PHASE3.keys())
def __init__(self):
Project.__init__(self, '156', 'PRJEB5829', 'GONL')
def __init__(self, file_name):
Project.__init__(self, file_name)
self.build_options = {
"CFLAGS" : "-O2",
"LIBS" : ""
}
def __init__(self):
""" Initialise Hips"""
## Binaries
BINARIES = {}
BINARIES[u'DBMATRIX'] = [
{
u'names' : [u'testSAVE.ex',
u'testDirect.ex',
u'testDirect2.ex'],
u'parameters' : []},
{
u'names' : [u'testCut.ex',
u'testDBMatrix.ex',
u'testDBMatrixGEMM1',
u'testDBMatrixGEMM2',
u'testDBMatrixLOAD.ex',
u'testDirectPhidal.ex',
u'testFillIn.ex',
u'testFind.ex',
u'testGEMM.ex'],
u'parameters' : [u'domsize']}]
BINARIES[u'DEBUG_PARALLEL'] = [
{
u'names' : [u'testHIPS_DEBUG.ex'],
u'parameters': [u'domsize']}]
BINARIES[u'GRID'] = [
{
u'names' : [u'testGRID.ex',
u'testILUT_GRID.ex'],
u'parameters': [u'domsize']}]
BINARIES[u'MISC_DEVEL'] = [
{
u'names' : [u'testGEMM.ex'],
u'parameters' : [u'ndom', u'ndom2']},
{
u'names' : [u'testICCT_GRID.ex'],
u'parameters' : [u'domsize', u'levelfor']},
{
u'names' : [u'testICCT_ML.ex',
u'testILUT_ML.ex'],
u'parameters' : [u'ndom', u'levelfor']},
{
u'names' : [u'testILUK.ex'],
u'parameters' : [u'levelk']},
{
u'names' : [u'testILUT_GRID.ex',
u'testPHIDAL.ex'],
u'parameters' : [u'domsize']},
{
u'names' : [u'testPHIDAL_DD.ex'],
u'parameters' : [u'ndom']},
{
u'names' : [u'testIOHB.ex'],
u'parameters' : [u'matrix', u'matrix2', u'type']},
{
u'names' : [u'testDrivers.ex'],
u'parameters' : []}]
BINARIES[u'MISC_PARALLEL'] = [
{
u'names' : [u'testDBDistrMatrix.ex',
u'testALLREAD_DBDistrMatrix.ex',
u'testALLREAD_BROADCAST_HIPS.ex',
u'testBROADCAST_HIPS.ex',
u'testUSERPART_HIPS.ex'],
u'parameters' : [u'domsize']},
{
u'names' : [u'GenereProcessorsLocalData.ex'],
u'parameters' : [u'domsize', u'nproc']},
{
u'names' : [u'testDBDistrMatrix_debug.ex',
u'testALLREAD_HIPS.ex'],
u'parameters' : []}]
BINARIES[u'ORDERING'] = [
{
u'names' : [u'testSizedDomains.ex'],
u'parameters' : [u'maxdomsize']},
{
u'names' : [u'testXPartition.ex'],
u'parameters' : [u'']},
{
u'names' : [u'testORDERING.ex'],
u'parameters' : [u'ndom']}]
BINARIES[u'PARALLEL'] = [
{
u'names' : [u'testHIPS1-Fortran.ex',
u'testHIPS2-Fortran.ex',
u'testHIPS3-Fortran.ex',
u'testHIPS.ex',
u'testHIPS1.ex',
u'testHIPS2.ex',
u'testHIPS3.ex',
u'testHIPS4.ex',
u'testHIPS-RUN.ex',
u'testHIPS-RUN2.ex',
u'testHIPS-NR.ex',
u'testHIPS-DEBUG.ex',
u'testHIPS-Assembly.ex',
u'testHIPS-CheckSol.ex',
u'testHIPS-Mem.ex',
u'testHIPS2-Mem.ex'],
u'parameters' : [u'domsize']},
{
u'names' : [u'testHIPS-Save.ex'],
u'parameters' : [u'nbpproc', u'domsize']},
{
u'names' : [u'testHIPS-Grid.ex'],
u'parameters' : [u'domsize', u'nc', u'cube']},
{
u'names' : [u'testHIPS-Laplace1-Fortran.ex',
u'testHIPS-Laplace2-Fortran.ex',
u'testHIPS4-Fortran.ex',
u'testHIPS-Load.ex'],
u'parameters' : []}]
BINARIES[u'PETSc'] = [
{
u'names' : [u'testPETSc-LOAD.ex',
u'testPETSc-Mtx.ex',
u'testPETSc-GRID.ex',
u'testPETSc-Mtx-SAVE.ex',
u'testPETSc-GRID-SAVE.ex'],
u'parameters' : []}]
BINARIES[u'SEQUENTIAL'] = [
{
u'names' : [u'testPHIDAL.ex'],
u'parameters' : [u'domsize']}]
BINARIES[u'SOLVERMATRIX'] = [
{
u'names' : [u'testDirect.ex'],
u'parameters' : []}]
for dirname in BINARIES:
for nameparam in BINARIES[dirname]:
for name in nameparam[u'names']:
self._binaries[u'%s_%s' % (dirname, name)] = {
u'filename' : name,
u'build_dir' : u'TESTS/%s' % dirname,
u'make_cmd' : name,
u'binary' : u'TESTS/%s/%s' % (dirname,name),
u'parameters': nameparam[u'parameters']}
Project.__init__(self)
return
def __init__(self, filename, offset):
Project.__init__(self, filename, offset)
self.flaFuncs = []
self.symbolicExec = LLVMIOSThumb2SymbolicExec()
self.flaRecover = None
def __init__(self):
Project.__init__(self, '130', 'PRJEB8661', 'EXAC')
def __init__(self, file_name):
Project.__init__(self, file_name)
self.build_options = {"CFLAGS": "-O2", "LIBS": ""}
def __init__(self):
""" Initialise Hips"""
## Binaries
BINARIES = {}
BINARIES[u'DBMATRIX'] = [{
u'names': [u'testSAVE.ex', u'testDirect.ex', u'testDirect2.ex'],
u'parameters': []
}, {
u'names': [
u'testCut.ex', u'testDBMatrix.ex', u'testDBMatrixGEMM1',
u'testDBMatrixGEMM2', u'testDBMatrixLOAD.ex',
u'testDirectPhidal.ex', u'testFillIn.ex', u'testFind.ex',
u'testGEMM.ex'
],
u'parameters': [u'domsize']
}]
BINARIES[u'DEBUG_PARALLEL'] = [{
u'names': [u'testHIPS_DEBUG.ex'],
u'parameters': [u'domsize']
}]
BINARIES[u'GRID'] = [{
u'names': [u'testGRID.ex', u'testILUT_GRID.ex'],
u'parameters': [u'domsize']
}]
BINARIES[u'MISC_DEVEL'] = [{
u'names': [u'testGEMM.ex'],
u'parameters': [u'ndom', u'ndom2']
}, {
u'names': [u'testICCT_GRID.ex'],
u'parameters': [u'domsize', u'levelfor']
}, {
u'names': [u'testICCT_ML.ex', u'testILUT_ML.ex'],
u'parameters': [u'ndom', u'levelfor']
}, {
u'names': [u'testILUK.ex'],
u'parameters': [u'levelk']
}, {
u'names': [u'testILUT_GRID.ex', u'testPHIDAL.ex'],
u'parameters': [u'domsize']
}, {
u'names': [u'testPHIDAL_DD.ex'],
u'parameters': [u'ndom']
}, {
u'names': [u'testIOHB.ex'],
u'parameters': [u'matrix', u'matrix2', u'type']
}, {
u'names': [u'testDrivers.ex'],
u'parameters': []
}]
BINARIES[u'MISC_PARALLEL'] = [{
u'names': [
u'testDBDistrMatrix.ex', u'testALLREAD_DBDistrMatrix.ex',
u'testALLREAD_BROADCAST_HIPS.ex', u'testBROADCAST_HIPS.ex',
u'testUSERPART_HIPS.ex'
],
u'parameters': [u'domsize']
}, {
u'names': [u'GenereProcessorsLocalData.ex'],
u'parameters': [u'domsize', u'nproc']
}, {
u'names': [u'testDBDistrMatrix_debug.ex', u'testALLREAD_HIPS.ex'],
u'parameters': []
}]
BINARIES[u'ORDERING'] = [{
u'names': [u'testSizedDomains.ex'],
u'parameters': [u'maxdomsize']
}, {
u'names': [u'testXPartition.ex'],
u'parameters': [u'']
}, {
u'names': [u'testORDERING.ex'],
u'parameters': [u'ndom']
}]
BINARIES[u'PARALLEL'] = [{
u'names': [
u'testHIPS1-Fortran.ex', u'testHIPS2-Fortran.ex',
u'testHIPS3-Fortran.ex', u'testHIPS.ex', u'testHIPS1.ex',
u'testHIPS2.ex', u'testHIPS3.ex', u'testHIPS4.ex',
u'testHIPS-RUN.ex', u'testHIPS-RUN2.ex', u'testHIPS-NR.ex',
u'testHIPS-DEBUG.ex', u'testHIPS-Assembly.ex',
u'testHIPS-CheckSol.ex', u'testHIPS-Mem.ex',
u'testHIPS2-Mem.ex'
],
u'parameters': [u'domsize']
}, {
u'names': [u'testHIPS-Save.ex'],
u'parameters': [u'nbpproc', u'domsize']
}, {
u'names': [u'testHIPS-Grid.ex'],
u'parameters': [u'domsize', u'nc', u'cube']
}, {
u'names': [
u'testHIPS-Laplace1-Fortran.ex',
u'testHIPS-Laplace2-Fortran.ex', u'testHIPS4-Fortran.ex',
u'testHIPS-Load.ex'
],
u'parameters': []
}]
BINARIES[u'PETSc'] = [{
u'names': [
u'testPETSc-LOAD.ex', u'testPETSc-Mtx.ex',
u'testPETSc-GRID.ex', u'testPETSc-Mtx-SAVE.ex',
u'testPETSc-GRID-SAVE.ex'
],
u'parameters': []
}]
BINARIES[u'SEQUENTIAL'] = [{
u'names': [u'testPHIDAL.ex'],
u'parameters': [u'domsize']
}]
BINARIES[u'SOLVERMATRIX'] = [{
u'names': [u'testDirect.ex'],
u'parameters': []
}]
for dirname in BINARIES:
for nameparam in BINARIES[dirname]:
for name in nameparam[u'names']:
self._binaries[u'%s_%s' % (dirname, name)] = {
u'filename': name,
u'build_dir': u'TESTS/%s' % dirname,
u'make_cmd': name,
u'binary': u'TESTS/%s/%s' % (dirname, name),
u'parameters': nameparam[u'parameters']
}
Project.__init__(self)
return
