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allow for AVX2 #197

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merged 1 commit into from
Sep 4, 2017
Merged

allow for AVX2 #197

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4 changes: 4 additions & 0 deletions CHANGELOG
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
v2.2.2 - 4 Sept 2017
-----
Allow the use of

v2.2.1 - 20 Feb 2017
-----
Remove use of Biopythons sub_features function which has been deprecated.
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2 changes: 1 addition & 1 deletion VERSION
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
2.2.1
2.2.2
10 changes: 6 additions & 4 deletions python/gubbins/RAxMLExecutable.py
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Expand Up @@ -26,8 +26,8 @@ class RAxMLExecutable(object):
def __init__(self, threads, model = 'GTRCAT', verbose = False ):
self.verbose = verbose
self.threads = threads
self.single_threaded_executables = ['raxmlHPC-AVX','raxmlHPC-SSE3','raxmlHPC']
self.multi_threaded_executables = ['raxmlHPC-PTHREADS-AVX','raxmlHPC-PTHREADS-SSE3','raxmlHPC-PTHREADS']
self.single_threaded_executables = ['raxmlHPC-AVX2','raxmlHPC-AVX','raxmlHPC-SSE3','raxmlHPC']
self.multi_threaded_executables = ['raxmlHPC-PTHREADS-AVX2','raxmlHPC-PTHREADS-AVX','raxmlHPC-PTHREADS-SSE3','raxmlHPC-PTHREADS']
self.model = model

self.raxml_executable = self.select_executable_based_on_threads()
Expand Down Expand Up @@ -59,7 +59,9 @@ def choose_executable_from_list(self,list_of_executables):

for executable in list_of_executables:
if os.path.exists('/proc/cpuinfo'):
if re.search('AVX', executable) and 'avx' not in flags:
if re.search('AVX2', executable) and 'avx2' not in flags:
continue
elif re.search('AVX', executable) and 'avx' not in flags:
continue
elif re.search('SSE3', executable) and 'ssse3' not in flags:
continue
Expand Down Expand Up @@ -107,5 +109,5 @@ def select_executable_based_on_threads(self):
if multi_threaded_exec != None:
return multi_threaded_exec
else:
sys.exit("No usable version of RAxML could be found, please ensure one of these executables is in your PATH:\nraxmlHPC-PTHREADS-AVX\nraxmlHPC-PTHREADS-SSE3\nraxmlHPC-PTHREADS\n raxmlHPC-AVX\nraxmlHPC-SSE3\nraxmlHPC")
sys.exit("No usable version of RAxML could be found, please ensure one of these executables is in your PATH:\nraxmlHPC-PTHREADS-AVX2\nraxmlHPC-PTHREADS-AVX\nraxmlHPC-PTHREADS-SSE3\nraxmlHPC-PTHREADS\nraxmlHPC-AVX2\nraxmlHPC-AVX\nraxmlHPC-SSE3\nraxmlHPC")