95 lines
2.2 KiB
Python
95 lines
2.2 KiB
Python
#+
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# ARES/HADES/BORG Package -- ./scripts/merge_mpi_restart.py
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# Copyright (C) 2014-2020 Guilhem Lavaux <guilhem.lavaux@iap.fr>
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# Copyright (C) 2009-2020 Jens Jasche <jens.jasche@fysik.su.se>
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#
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# Additional contributions from:
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# Guilhem Lavaux <guilhem.lavaux@iap.fr> (2023)
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#
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#+
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import os
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import h5py as h5
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import errno
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from ares_tools import rebuild_spliced_h5
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def detect_ncpus(path):
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ncpu = 0
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try:
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while True:
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with open("%s_%d" % (path,ncpu), mode= "rb") as f:
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ncpu += 1
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except IOError as e:
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if e.errno != errno.ENOENT:
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raise e
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return ncpu
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def detect_job_to_merge(path):
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array_list=[]
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other_list=[]
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group_list=[]
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def _handle_item(name, obj):
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if isinstance(obj, h5.Group):
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group_list.append(name)
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if not isinstance(obj, h5.Dataset):
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return
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if len(obj.shape) >= 3:
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array_list.append(name)
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else:
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other_list.append(name)
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with h5.File("%s_0" % path, mode="r") as f:
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f.visititems(_handle_item)
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return array_list,other_list,group_list
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def load_nonarray(path, objlist):
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arr = {}
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with h5.File("%s_0" % path, mode="r") as f:
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for oname in objlist:
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print("Loading %s..." % oname)
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if oname == '/scalars/BORG_version':
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arr[oname] = np.array([f[oname][0]], dtype='S')
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else:
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arr[oname] = f[oname][:]
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return arr
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def load_merged(path):
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ncpu = detect_ncpus(path)
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array_list,nonarray_list,group_list = detect_job_to_merge(path)
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array_elts = ['.'.join(e.split('/')) for e in array_list]
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print("Loading spliced arrays")
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arr = load_nonarray(path, nonarray_list)
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arr2 = rebuild_spliced_h5(path, array_elts, ncpu, verbose=True)
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for k in arr2.keys():
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arr['/'.join(k.split('.'))] = arr2[k]
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return arr,group_list
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def save_merged(outpath, omap):
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omap,group_list = omap
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with h5.File(outpath, mode="w") as f:
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for g in group_list:
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if not g in f:
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f.create_group(g)
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for o in omap.keys():
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print("Saving object '%s'" % o)
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f.create_dataset(o, data=omap[o])
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if __name__=="__main__":
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merged_obj = load_merged("./restart.h5")
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save_merged("./merged_restart.h5", merged_obj)
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