removed unuseful file for this branch

_modules/common_OCL_Kernels.py.old

-import pyopencl as cl
-import os
-
-## Need that for being able to test on my imac on GPU and macbookpro CPU
-class parmsForTesting:
-    def __init__(self):
-        self.mac_max_dim1 =-1
-        self.testing_on_cpu=False
-        if os.getenv("OSX_TESTING_ON_GPU") != None or os.getenv("OSX_TESTING_ON_CPU") != None:
-            self.mac_max_dim1 = 256
-        if os.getenv("OSX_TESTING_ON_CPU") != None:
-            self.testing_on_cpu=True
-
-
-
-## Gets the number of threads that we can run on the chosen device.
-# @param input: the number of elements to process (reads or sequences in our case)
-# @param input: (device characteristics): maximum number of threads that we can out un dim 1.
-def getNbThreads(nb_elem_to_process,device_max_thread_dim1):
-    remainder = nb_elem_to_process % device_max_thread_dim1
-    if (remainder != 0):
-        nb_threads_dim1 = nb_elem_to_process - remainder + device_max_thread_dim1
-    else:
-        nb_threads_dim1 = nb_elem_to_process
-    return nb_threads_dim1
-
-## gets platform and device.
-#
-# instanciates context and command queue and also get memory flags.
-def getOpenCLElements():
-    parms=parmsForTesting()
-    l_platforms = cl.get_platforms()
-    idx_platform = 0
-    idx_device = -1
-    gpu_found=False
-    type_flags = cl.device_type
-    for p in l_platforms:
-        l_devices = p.get_devices(device_type=type_flags.GPU)
-        if len(l_devices) > 0:
-            gpu_found=True
-            idx_device = 0  # for the moment, choose the 1rst GPU device we find
-            break
-        idx_platform += 1
-
-    platform = cl.get_platforms()[idx_platform]
-    if (gpu_found and not parms.testing_on_cpu):
-        device = platform.get_devices(device_type=type_flags.GPU)[idx_device]
-        #device = platform.get_devices()[0]
-    else:
-        print "Warning : No GPU found or CPU testing mode, trying to run openCL on CPU"
-        device = platform.get_devices(device_type=type_flags.CPU)[0]
-
-    print "will run on: "
-    print "    Device name:", device.name
-    print "    Device type:", cl.device_type.to_string(device.type)
-    print "    Device memory: ", device.global_mem_size // 1024 // 1024, 'MB'
-    print "    Device max clock speed:", device.max_clock_frequency, 'MHz'
-    print "    Device compute units:", device.max_compute_units
-    print "    Device max work items:", device.get_info(cl.device_info.MAX_WORK_ITEM_SIZES)
-    print "    Device local memory:", device.get_info(cl.device_info.LOCAL_MEM_SIZE) // 1024, 'KB'
-    print type(device.get_info(cl.device_info.MAX_WORK_ITEM_SIZES))
-    #m=device.get_info(cl.device_info.MAX_WORK_ITEM_SIZES)[0]
-    if parms.mac_max_dim1!=-1: # need that as workaround for the buggy openCL implementation on osx. Need to run my tests.
-        max_dim1=parms.mac_max_dim1
-    else:
-        max_dim1=device.get_info(cl.device_info.MAX_WORK_ITEM_SIZES)[0]
-    ctx = cl.Context([device])
-    queue = cl.CommandQueue(ctx)
-    mf = cl.mem_flags
-    return ctx,queue,mf,max_dim1
-
-
-## Utility method to process the result of upd_reads_nb_occ_in_sequences_str kernel
-def getMaxNbOccPerSeq(o_nb_occ_foreach_extract_in_seqs,nb_reads,nb_seq):
-    m=0
-    for idx_s in range(0,nb_seq):
-        line_start=idx_s*2*nb_reads
-        tmp=o_nb_occ_foreach_extract_in_seqs[line_start+2*nb_reads-1]+o_nb_occ_foreach_extract_in_seqs[line_start+2*nb_reads-2]
-        if tmp>m: m=tmp
-    return m