How to use mems_path method in autotest

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...80 # current version assumes shared cgroup hierarchy81 return os.path.join(super_root_path, container_name, 'io.'+attr)82def tasks_path(container_name):83 return os.path.join(full_path(container_name), 'tasks')84def mems_path(container_name):85 return cpuset_attr(container_name, 'mems')86def memory_path(container_name):87 return os.path.join(super_root_path, container_name, 'memory')88def cpus_path(container_name):89 return cpuset_attr(container_name, 'cpus')90def container_exists(name):91 return name is not None and os.path.exists(tasks_path(name))92def move_tasks_into_container(name, tasks):93 task_file = tasks_path(name)94 for task in tasks:95 try:96 logging.debug('moving task %s into container "%s"', task, name)97 utils.write_one_line(task_file, task)98 except Exception:99 if utils.pid_is_alive(task):100 raise # task exists but couldn't move it101 # task is gone or zombie so ignore this exception102def move_self_into_container(name):103 me = str(os.getpid())104 move_tasks_into_container(name, [me])105 logging.debug('running self (pid %s) in container "%s"', me, name)106def _avail_mbytes_via_nodes(parent):107 # total mbytes of mem nodes available for new containers in parent108 free_nodes = available_exclusive_mem_nodes(parent)109 mbytes = nodes_avail_mbytes(free_nodes)110 # don't have exact model for how container mgr measures mem space111 # better here to underestimate than overestimate112 mbytes = max(mbytes - node_mbytes//2, 0)113 return mbytes114def _avail_bytes_via_pages(parent):115 # Get memory bytes available to parent container which could116 # be allocated exclusively to new child containers.117 # This excludes mem previously allocated to existing children.118 available = container_bytes(parent)119 mem_files_pattern = os.path.join(full_path(parent),120 '*', 'memory.limit_in_bytes')121 for mem_file in glob.glob(mem_files_pattern):122 child_container = unpath(os.path.dirname(mem_file))123 available -= container_bytes(child_container)124 return available125def avail_mbytes(parent=SUPER_ROOT):126 # total mbytes available in parent, for exclusive use in new containers127 if fake_numa_containers:128 return _avail_mbytes_via_nodes(parent)129 else:130 return _avail_bytes_via_pages(parent) >> 20131def delete_leftover_test_containers():132 # recover mems and cores tied up by containers of prior failed tests:133 for child in inner_containers_of(SUPER_ROOT):134 _release_container_nest(child)135def my_lock(lockname):136 # lockname is 'inner'137 lockdir = os.environ['AUTODIR']138 lockname = os.path.join(lockdir, '.cpuset.lock.'+lockname)139 lockfile = open(lockname, 'w')140 fcntl.flock(lockfile, fcntl.LOCK_EX)141 return lockfile142def my_unlock(lockfile):143 fcntl.flock(lockfile, fcntl.LOCK_UN)144 lockfile.close()145# Convert '1-3,7,9-12' to set(1,2,3,7,9,10,11,12)146def rangelist_to_set(rangelist):147 result = set()148 if not rangelist:149 return result150 for x in rangelist.split(','):151 if re.match(r'^(\d+)$', x):152 result.add(int(x))153 continue154 m = re.match(r'^(\d+)-(\d+)$', x)155 if m:156 start = int( end = int( result.update(set(range(start, end+1)))159 continue160 msg = 'Cannot understand data input: %s %s' % (x, rangelist)161 raise ValueError(msg)162 return result163def my_container_name():164 # Get current process's inherited or self-built container name165 # within /dev/cpuset or /dev/cgroup. Is '' for root container.166 name = utils.read_one_line('/proc/%i/cpuset' % os.getpid())167 return name[1:] # strip leading /168def get_mem_nodes(container_name):169 # all mem nodes now available to a container, both exclusive & shared170 file_name = mems_path(container_name)171 if os.path.exists(file_name):172 return rangelist_to_set(utils.read_one_line(file_name))173 else:174 return set()175def _busy_mem_nodes(parent_container):176 # Get set of numa memory nodes now used (exclusively or shared)177 # by existing children of parent container178 busy = set()179 mem_files_pattern = os.path.join(full_path(parent_container),180 '*', cpuset_prefix+'mems')181 for mem_file in glob.glob(mem_files_pattern):182 child_container = os.path.dirname(mem_file)183 busy |= get_mem_nodes(child_container)184 return busy185def available_exclusive_mem_nodes(parent_container):186 # Get subset of numa memory nodes of parent container which could187 # be allocated exclusively to new child containers.188 # This excludes nodes now allocated to existing children.189 need_fake_numa()190 available = get_mem_nodes(parent_container)191 available -= _busy_mem_nodes(parent_container)192 return available193def my_mem_nodes():194 # Get set of numa memory nodes owned by current process's container.195 discover_container_style()196 if not mem_isolation_on:197 return set() # as expected by vmstress198 return get_mem_nodes(my_container_name())199def my_available_exclusive_mem_nodes():200 # Get subset of numa memory nodes owned by current process's201 # container, which could be allocated exclusively to new child202 # containers. This excludes any nodes now allocated203 # to existing children.204 return available_exclusive_mem_nodes(my_container_name())205def node_avail_kbytes(node):206 return node_mbytes << 10 # crude; fixed numa node size207def nodes_avail_mbytes(nodes):208 # nodes' combined user+avail size, in Mbytes209 return sum(node_avail_kbytes(n) for n in nodes) // 1024210def container_bytes(name):211 if fake_numa_containers:212 return nodes_avail_mbytes(get_mem_nodes(name)) << 20213 else:214 while True:215 file = memory_path(name) + '.limit_in_bytes'216 limit = int(utils.read_one_line(file))217 if limit < NO_LIMIT:218 return limit219 if name == SUPER_ROOT:220 return root_container_bytes221 name = os.path.dirname(name)222def container_mbytes(name):223 return container_bytes(name) >> 20224def mbytes_per_mem_node():225 # Get mbyte size of standard numa mem node, as float226 # (some nodes are bigger than this)227 # Replaces utils.node_size().228 numa = get_boot_numa()229 if numa.endswith('M'):230 return float(numa[:-1]) # mbyte size of fake nodes231 elif numa:232 nodecnt = int(numa) # fake numa mem nodes for container isolation233 else:234 nodecnt = len(utils.numa_nodes()) # phys mem-controller nodes235 # Use guessed total physical mem size, not kernel's236 # lesser 'available memory' after various system tables.237 return utils.rounded_memtotal() / (nodecnt * 1024.0)238def get_cpus(container_name):239 file_name = cpus_path(container_name)240 if os.path.exists(file_name):241 return rangelist_to_set(utils.read_one_line(file_name))242 else:243 return set()244def get_tasks(container_name):245 file_name = tasks_path(container_name)246 try:247 tasks = [x.rstrip() for x in open(file_name).readlines()]248 except IOError:249 if os.path.exists(file_name):250 raise251 tasks = [] # container doesn't exist anymore252 return tasks253def inner_containers_of(parent):254 pattern = os.path.join(full_path(parent), '*/tasks')255 return [unpath(os.path.dirname(task_file))256 for task_file in glob.glob(pattern)]257def _release_container_nest(nest):258 # Destroy a container, and any nested sub-containers259 nest_path = full_path(nest)260 if os.path.exists(nest_path):261 # bottom-up walk of tree, releasing all nested sub-containers262 for child in inner_containers_of(nest):263 _release_container_nest(child)264 logging.debug("releasing container %s", nest)265 # Transfer any survivor tasks (e.g. self) to parent container266 parent = os.path.dirname(nest)267 move_tasks_into_container(parent, get_tasks(nest))268 # remove the now-empty outermost container of this nest269 if os.path.exists(nest_path):270 os.rmdir(nest_path) # nested, or dead manager271def release_container(container_name=None):272 # Destroy a container273 my_container = my_container_name()274 if container_name is None:275 container_name = my_container276 _release_container_nest(container_name)277 displaced = my_container_name()278 if displaced != my_container:279 logging.debug('now running self (pid %d) in container "%s"',280 os.getpid(), displaced)281def remove_empty_prio_classes(prios):282 # remove prio classes whose set of allowed priorities is empty283 # e.g 'no:3;rt:;be:3;id:' --> 'no:3;be:3'284 return ';'.join(p for p in prios.split(';') if p.split(':')[1])285def all_drive_names():286 # list of all disk drives sda,sdb,...287 paths = glob.glob('/sys/block/sd*')288 if not paths:289 paths = glob.glob('/sys/block/hd*')290 return [os.path.basename(path) for path in paths]291def set_io_controls(container_name, disks=[], ioprio_classes=[PROPIO_NORMAL],292 io_shares=[95], io_limits=[0]):293 # set the propio controls for one container, for selected disks294 # writing directly to /dev/cgroup/container_name/io.io_service_level295 # without using containerd or container.py296 # See wiki ProportionalIOScheduler for definitions297 # ioprio_classes: list of service classes, one per disk298 # using numeric propio service classes as used by kernel API, namely299 # 1: RT, Real Time, aka PROPIO_PRIO300 # 2: BE, Best Effort, aka PROPIO_NORMAL301 # 3: PROPIO_IDLE302 # io_shares: list of disk-time-fractions, one per disk,303 # as percentage integer 0..100304 # io_limits: list of limit on/off, one per disk305 # 0: no limit, shares use of other containers' unused disk time306 # 1: limited, container's use of disk time is capped to given DTF307 # ioprio_classes defaults to best-effort308 # io_limit defaults to no limit, use slack time309 if not disks: # defaults to all drives310 disks = all_drive_names()311 io_shares = [io_shares [0]] * len(disks)312 ioprio_classes = [ioprio_classes[0]] * len(disks)313 io_limits = [io_limits [0]] * len(disks)314 if not (len(disks) == len(ioprio_classes) and len(disks) == len(io_shares)315 and len(disks) == len(io_limits)):316 raise error.AutotestError('Unequal number of values for io controls')317 service_level = io_attr(container_name, 'io_service_level')318 if not os.path.exists(service_level):319 return # kernel predates propio features320 # or io cgroup is mounted separately from cpusets321 disk_infos = []322 for disk,ioclass,limit,share in zip(disks, ioprio_classes,323 io_limits, io_shares):324 parts = (disk, str(ioclass), str(limit), str(share))325 disk_info = ' '.join(parts)326 utils.write_one_line(service_level, disk_info)327 disk_infos.append(disk_info)328 logging.debug('set_io_controls of %s to %s',329 container_name, ', '.join(disk_infos))330def abbrev_list(vals):331 """Condense unsigned (0,4,5,6,7,10) to '0,4-7,10'."""332 ranges = []333 lower = 0334 upper = -2335 for val in sorted(vals)+[-1]:336 if val != upper+1:337 if lower == upper:338 ranges.append(str(lower))339 elif lower <= upper:340 ranges.append('%d-%d' % (lower, upper))341 lower = val342 upper = val343 return ','.join(ranges)344def create_container_with_specific_mems_cpus(name, mems, cpus):345 need_fake_numa()346 os.mkdir(full_path(name))347 utils.write_one_line(cpuset_attr(name, 'mem_hardwall'), '1')348 utils.write_one_line(mems_path(name), ','.join(map(str, mems)))349 utils.write_one_line(cpus_path(name), ','.join(map(str, cpus)))350 logging.debug('container %s has %d cpus and %d nodes totalling %s bytes',351 name, len(cpus), len(get_mem_nodes(name)),352 utils.human_format(container_bytes(name)) )353def create_container_via_memcg(name, parent, bytes, cpus):354 # create container via direct memcg cgroup writes355 os.mkdir(full_path(name))356 nodes = utils.read_one_line(mems_path(parent))357 utils.write_one_line(mems_path(name), nodes) # inherit parent's nodes358 utils.write_one_line(memory_path(name)+'.limit_in_bytes', str(bytes))359 utils.write_one_line(cpus_path(name), ','.join(map(str, cpus)))360 logging.debug('Created container %s directly via memcg,'361 ' has %d cpus and %s bytes',362 name, len(cpus), utils.human_format(container_bytes(name)))363def _create_fake_numa_container_directly(name, parent, mbytes, cpus):364 need_fake_numa()365 lockfile = my_lock('inner') # serialize race between parallel tests366 try:367 # Pick specific mem nodes for new cpuset's exclusive use368 # For now, arbitrarily pick highest available node numbers369 needed_kbytes = mbytes * 1024370 nodes = sorted(list(available_exclusive_mem_nodes(parent)))371 kbytes = 0...

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1import os2import subprocess3from sys import stdout, exit4from collections import defaultdict5from collections import namedtuple6mem = namedtuple('Mem', ['x', 'y', 'c', 'd', 'val', 'j', "exon_part_id"])7globals()[mem.__name__] = mem # Global needed for multiprocessing8def find_mems_mummer(mummer_path, outfolder, read_path, refs_path, mummer_out_path, min_mem):9 with open(mummer_out_path, "w") as output_file:10 # print('Running spoa...', end=' ')11 stdout.flush()12 null = open(os.path.join(outfolder, "mummer_errors.1") , "w")13 subprocess.check_call([ mummer_path, '-maxmatch', '-l' , str(min_mem), refs_path, read_path], stdout=output_file, stderr=null)14 # print('Done.')15 stdout.flush()16 output_file.close()17def find_mems_slamem(slamem_path, mummer_path, outfolder, read_path, refs_path, out_path, min_mem):18 # time slaMEM -l 14 /Users/kxs624/tmp/ULTRA/human_test/refs_sequences.fa /Users/kxs624/tmp/ULTRA/human_test_new_flanking_strat/reads_tmp.fq -o /Users/kxs624/tmp/ULTRA/human_test/slamem_test.tx19 # with open(out_path, "w") as output_file:20 tmp = out_path.split("seeds_batch_")[1]21 batch_id = tmp.split('.')[0]22 stdout.flush()23 stderr_file = open(os.path.join(outfolder, "slamem_stderr_{0}.1".format(batch_id)) , "w")24 stdout_file = open(os.path.join(outfolder, "slamem_stdout_{0}.1".format(batch_id)) , "w")25 try: # slaMEM throws error if no MEMs are found in any of the sequences26 subprocess.check_call([ slamem_path, '-l' , str(min_mem), refs_path, read_path, '-o', out_path ], stdout=stdout_file, stderr=stderr_file, env = os.environ)27 print("Using SLAMEM")28 except:29 find_mems_mummer(mummer_path, outfolder, read_path, refs_path, out_path, min_mem)30 print("Using MUMMER")31 print('Done.')32 stdout.flush()33 # output_file.close()34def find_nams_strobemap(slamem_path, outfolder, read_path, refs_path, out_path, nr_cores, min_mem):35 # /usr/bin/time -l ./StrobeMap -n 2 -k 9 -w 30 -t 3 -s -o /Users/kxs624/tmp/ULTRA/human_test/refs_sequences.fa /Users/kxs624/tmp/ULTRA/human_test_new_flanking_strat/reads_tmp.fq36 # StrobeMap -n 2 -k 9 -w 30 -t 3 -s  -o ~/tmp/STROBEMERS/multithreading/ /Users/kxs624/tmp/ULTRA/dros_tmp/refs_sequences.fa /Users/kxs624/tmp/ULTRA/dros_test/reads_16xrep.fa37 # with open(out_path, "w") as output_file:38 stdout.flush()39 stderr_file = open(os.path.join(outfolder, "strobemap_stderr.1") , "w")40 stdout_file = open(os.path.join(outfolder, "strobemap_stdout.1") , "w")41 try: # slaMEM throws error if no MEMs are found in any of the sequences42 subprocess.check_call([ 'StrobeMap', '-n' , "2", '-k' , '10', '-v' , "11", '-w' , "35", '-C' , '500', '-L' , '1000', '-S', '-t', str(nr_cores), '-s', '-o', outfolder, refs_path, read_path ], stdout=stdout_file, stderr=stderr_file)43 print("Using StrobeMap")44 print([ 'StrobeMap', '-n' , "2", '-k' , '10', '-v' , "11", '-w' , "35", '-C' , '500', '-L' , '1000', '-S', '-t', str(nr_cores), '-s', '-o', outfolder, refs_path, read_path ])45 except:46 find_mems_slamem(slamem_path, outfolder, read_path, refs_path, out_path, min_mem)47 print("An unexpected error happend in StrobeMap, check error log at:", stderr_file)48 print("If you beileive this is a bug in StrobeMap, report an issue at:")49 print("You can always sidestep this issue by providing another seed finder to uLTRA, i.e., remove option --use_NAM_seeds.")50 sys.exit()51 stdout.flush()52# def parse_results(mems_path):53# # file = open(os.path.join(mems_folder, "mummer_mems.txt"), 'r')54# mems_db = {}55# # read_mems_tmp = {}56# for i, line in enumerate(open(mems_path, 'r')):57# if line[0] == '>':58# if i == 0:59# read_acc = line.split()[1].strip() # mems_db[line.split()[1].strip)()] = [] 60# else:61# mems_db[read_acc] = read_mems_tmp 62# read_acc = line.split()[1].strip() 63 64# read_mems_tmp = defaultdict(list)65# else:66# vals = line.split() #11404_11606 1 11405 20267# exon_part_id = vals[0]68# chr_id, ref_coord_start, ref_coord_end = exon_part_id.split('^')69# mem_len = int(vals[3])70# mem_ref_exon_part_start = int(vals[1])71# mem_read_start = int(vals[2])72# # convert to 0-indexed as python, however last coordinate is inclusive of the hit, not as in python end-indexing73# mem_tuple = mem(int(ref_coord_start) + mem_ref_exon_part_start - 1, int(ref_coord_start) + mem_ref_exon_part_start -1 + mem_len - 1,74# mem_read_start-1, mem_read_start-1 + mem_len - 1, 75# mem_len, None, exon_part_id)76 77# read_mems_tmp[chr_id].append( mem_tuple )78# # print(line)79# # add last read80# mems_db[read_acc] = read_mems_tmp 81# return mems_db82def get_mem_records(mems_path, reads):83 '''84 Reads contains all the relevant reads in the batch to read mems from 85 '''86 relevant = False87 relevant_read_cnt = 088 for i, line in enumerate(open(mems_path, 'r')):89 if line[0] == '>':90 acc = line[1:].strip()91 if acc not in reads:92 relevant = False93 continue94 else:95 relevant = True96 relevant_read_cnt +=197 if relevant_read_cnt == 1:98 read_acc = acc 99 else:100 for chr_id in list(read_mems_tmp.keys()):101 coordinate_sorted_tuples = sorted(read_mems_tmp[chr_id], key = lambda x: x[1])102 sorted_mems = [ mem(x,y,c,d,val,j,e_id) for j, (x, y, c, d, val, e_id) in enumerate(coordinate_sorted_tuples) ]103 read_mems_tmp[chr_id] = sorted_mems104 yield read_acc, read_mems_tmp105 read_acc = acc 106 107 read_mems_tmp = defaultdict(list)108 elif relevant:109 vals = line.split() #11404_11606 1 11405 202110 exon_part_id = vals[0]111 chr_id, ref_coord_start, ref_coord_end = exon_part_id.split('^')112 chr_id = int(chr_id)113 mem_len = int(vals[3])114 # convert to 0-indexed reference as in python115 # however, for MEM length last coordinate is inclusive of the hit in MEM solvers, not as in python end-indexing116 mem_ref_exon_part_start = int(vals[1]) - 1117 mem_read_start = int(vals[2]) - 1118 ref_coord_start = int(ref_coord_start) # has already been 0-indexed when constructing parts119 mem_genome_start = ref_coord_start + mem_ref_exon_part_start120 121 122 # mem_tuple = mem(int(ref_coord_start) - 1 + mem_ref_exon_part_start - 1, int(ref_coord_start) - 1 + mem_ref_exon_part_start -1 + mem_len - 1,123 # mem_read_start-1, mem_read_start-1 + mem_len - 1, 124 # mem_len, None, exon_part_id)125 # read_mems_tmp[chr_id].append( mem_tuple )126 info_tuple = ( mem_genome_start, mem_genome_start + mem_len - 1,127 mem_read_start, mem_read_start + mem_len - 1, 128 mem_len, exon_part_id)129 read_mems_tmp[chr_id].append( info_tuple )130 for chr_id in list(read_mems_tmp.keys()):131 coordinate_sorted_tuples = sorted(read_mems_tmp[chr_id], key = lambda x: x[1])132 sorted_mems = [ mem(x,y,c,d,val,j,e_id) for j, (x, y, c, d, val, e_id) in enumerate(coordinate_sorted_tuples) ]133 read_mems_tmp[chr_id] = sorted_mems134 print("READ {0} RECORDS.".format(relevant_read_cnt))135 yield read_acc, read_mems_tmp136# def find_file_positions(read_pos_list, mummer_out_path, mummer_out_path_rc):...

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