parallelize sequential flag with drmaa or multiple cores

cubids/cli.py

@@ -8,12 +8,14 @@
 import tempfile
 import tqdm
 import shutil
+import drmaa
 import pandas as pd
 from cubids import CuBIDS
+from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
 from .validator import (build_validator_call,
                         run_validator, parse_validator_output,
-                        build_subject_paths)
+                        build_subject_paths, build_drmaa_batch)
 from .metadata_merge import merge_json_into_json
 
 logging.basicConfig(level=logging.INFO)
@@ -68,6 +70,17 @@ def cubids_validate():
                         'sub-01 sub-02 sub-03',
                         nargs='+',
                         required=False)
+    parser.add_argument('--drmaa',
+                        action='store_true',
+                        default=False,
+                        help='When running the validator sequentially, submit jobs to scheduler instead of running subprocess',
+                        required=False)
+    parser.add_argument('--n_cpus',
+                        action='store',
+                        type=int,
+                        default=1,
+                        help='Number of cores to utilize',
+                        required=False)
     opts = parser.parse_args()
 
     # Run directly from python using subprocess
@@ -111,6 +124,8 @@ def cubids_validate():
             # iterate over the dictionary
 
             parsed = []
+            # it's easier to parallelize a queue
+            queue = [] if opts.drmaa is True or opts.n_cpus > 1 else False
 
             if opts.sequential_subjects:
                 subjects_dict = {k: v for k, v in subjects_dict.items()
@@ -121,44 +136,115 @@ def cubids_validate():
 
                 logger.info(" ".join(["Processing subject:", subject]))
                 # create a temporary directory and symlink the data
-                with tempfile.TemporaryDirectory() as tmpdirname:
-                    for fi in files_list:
-
-                        # cut the path down to the subject label
-                        bids_start = fi.find(subject)
-
-                        # maybe it's a single file
-                        if bids_start < 1:
-                            bids_folder = tmpdirname
-                            fi_tmpdir = tmpdirname
-
-                        else:
-                            bids_folder = Path(fi[bids_start:]).parent
-                            fi_tmpdir = tmpdirname + '/' + str(bids_folder)
-
-                        if not os.path.exists(fi_tmpdir):
-                            os.makedirs(fi_tmpdir)
-                        output = fi_tmpdir + '/' + str(Path(fi).name)
-                        shutil.copy2(fi, output)
-
-                    # run the validator
-                    nifti_head = opts.ignore_nifti_headers
-                    subj_consist = opts.ignore_subject_consistency
-                    call = build_validator_call(tmpdirname,
-                                                nifti_head,
-                                                subj_consist)
+                # TMPDIR isn't networked (available on login + exec nodes), so use bids_dir
+                tmpdir = tempfile.TemporaryDirectory(dir=opts.bids_dir, prefix=".")
+                for fi in files_list:
+
+                    # cut the path down to the subject label
+                    bids_start = fi.find(subject)
+
+                    # maybe it's a single file
+                    if bids_start < 1:
+                        bids_folder = tmpdir.name
+                        fi_tmpdir = tmpdir.name
+
+                    else:
+                        bids_folder = Path(fi[bids_start:]).parent
+                        fi_tmpdir = tmpdir.name + '/' + str(bids_folder)
+
+                    if not os.path.exists(fi_tmpdir):
+                        os.makedirs(fi_tmpdir)
+                    output = fi_tmpdir + '/' + str(Path(fi).name)
+                    shutil.copy2(fi, output)
+
+                # run the validator
+                nifti_head = opts.ignore_nifti_headers
+                subj_consist = opts.ignore_subject_consistency
+                call = build_validator_call(tmpdir.name,
+                                            nifti_head,
+                                            subj_consist)
+
+                if queue is False:
                     ret = run_validator(call)
-                    # parse output
+                    # execute and parse output immediately
                     if ret.returncode != 0:
                         logger.error("Errors returned "
-                                     "from validator run, parsing now")
+                                        "from validator run, parsing now")
 
                     # parse the output and add to list if it returns a df
                     decoded = ret.stdout.decode('UTF-8')
                     tmp_parse = parse_validator_output(decoded)
                     if tmp_parse.shape[1] > 1:
                         tmp_parse['subject'] = subject
                         parsed.append(tmp_parse)
+                else:
+                    queue.append({
+                        'call': call,
+                        'tmpdir': tmpdir
+                    })
+
+
+            if opts.drmaa:
+                try:
+                    drmaa_ses = drmaa.Session()
+                    drmaa_ses.initialize()
+                    tmpfiles = []
+                    jids = []
+
+                    for batch in build_drmaa_batch(queue):
+                        tmp = tempfile.NamedTemporaryFile(delete=False, dir=opts.bids_dir, prefix=".", suffix=".sh")
+                        tmp.write(batch['script'].encode())
+                        tmp.close() # this is very important
+                        os.chmod(tmp.name, 0o755) # make executable
+                        tmpfiles.append(tmp.name)
+                        jt = drmaa_ses.createJobTemplate()
+                        jt.remoteCommand = tmp.name
+                        # jt.args = call[1:]
+                        jt.blockEmail = False
+                        trash = ':' + os.devnull
+                        jt.outputPath = trash
+                        jt.errorPath = trash
+                        jids.append(drmaa_ses.runJob(jt))
+
+                    # wait for all jobs to finish to parse results
+                    logger.info("Waiting for jobs to complete")
+                    drmaa_ses.synchronize(jids, drmaa.Session.TIMEOUT_WAIT_FOREVER, True)
+                    for q in queue:
+                        # parse output
+                        tmpdir = q['tmpdir']
+                        with open(os.path.join(tmpdir.name, ".cubids"), 'r') as file:
+                            decoded = file.read()
+                            tmp_parse = parse_validator_output(decoded)
+                            if tmp_parse.shape[1] > 1:
+                                tmp_parse['subject'] = subject
+                                parsed.append(tmp_parse)
+
+                        tmpdir.cleanup()
+                    drmaa_ses.exit()
+                except Exception as e:
+                    exc_type, exc_obj, exc_tb = sys.exc_info()
+                    fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
+                    print(repr(e), fname, exc_tb.tb_lineno)
+                finally:
+                    for tmp in tmpfiles:
+                        os.remove(tmp)
+            elif opts.n_cpus > 1:
+                # run in parallel on multiple cores
+                logger.info("Running validator in parallel")
+                with ThreadPoolExecutor(max_workers = opts.n_cpus) as p:
+                    ret = p.map(run_validator, [q['call'] for q in queue])
+
+                for q in queue:
+                    q['tmpdir'].cleanup()
+
+                # parse output
+                for r in ret:
+                    decoded = r.stdout.decode('UTF-8')
+                    tmp_parse = parse_validator_output(decoded)
+                    if tmp_parse.shape[1] > 1:
+                        tmp_parse['subject'] = subject
+                        parsed.append(tmp_parse)
+
 
             # concatenate the parsed data and exit, we're goin home fellas
             if len(parsed) < 1:

cubids/validator.py

@@ -68,6 +68,22 @@ def run_validator(call, verbose=True):
                          stderr=subprocess.PIPE)
     return(ret)
 
+def build_drmaa_batch(queue):
+    batch_size = 10 if len(queue) < 1000 else len(queue) // 10
+    batch = []
+    for batch_start in range(0, len(queue), batch_size):
+        script = []
+        tmpdirs = []
+        for idx in range(batch_start, min(batch_start + batch_size, len(queue))):
+            # bids validator ignore files starting with . https://github.com/bids-standard/bids-validator/issues/348
+            line = " ".join(queue[idx]['call']) + ' > ' + os.path.join(queue[idx]['tmpdir'].name, ".cubids")
+            script.append(line)
+            tmpdirs.append(queue[idx]['tmpdir'])
+        batch.append({
+            'script': "\n".join(script),
+            'tmpdirs': tmpdirs
+        })
+    return batch
 
 def parse_validator_output(output):
     """Parse the JSON output of the BIDS validator into a pandas dataframe

requirements.txt

@@ -0,0 +1 @@
+drmaa