BBSaveState
ignore · restore_test · save_test · vector_play_init

BBSaveState

class BBSaveState

A more flexible, cell centered version of SaveState

The goal is to be able to save state to a file and restore state when the save and restore contexts have different numbers of processors, different distribution of gids, and different splitting. It needs to work efficiently in the context of many GByte file sizes and many thousands of processors.

The class was originally developed with the needs of the BlueBrain neocortical model in mind.

The following code fragment illustrates a basic test. When 'restore' is False, the simulation run stops half way and saves the state and then continues. When 'restore' is True, the simulation begins at the previous save time and continues to tstop.

 def prun(tstop, restore=False):
   pc.set_maxstep(10)
   h.stdinit()
   bbss = h.BBSaveState()
   if restore:
     bbss.restore_test()
     print 'after restore t=%g'%h.t
   else:
     pc.psolve(tstop/2)
     bbss.save_test()
   pc.psolve(tstop)

Note that files are saved in a subdirectory called "out" and restored from a subdirectory called "in". A script filter (see BBSaveState.save_test()) is needed to copy and sometimes concatenate files from the out to the in subfolders. These files have an ascii format.

BBSaveState has a c++ API that allows one to replace the file reader and writer. See nrn/src/nrniv/bbsavestate.cpp for a description of this API. The undocumented methods, save_test_bin and restore_test_bin demonstrate the use of this API.

The user can mark a point process IGNORE by calling the method bbss.ignore(point_process_object) on all the point processes to be ignored. The internal list of ignored point processes can be cleared by calling bbss.ignore()

Because a restore clears the event queue and because one cannot call finitialize from hoc without vitiating the restore, Vector.play will not work unless one calls BBSaveState.vector_play_init() after a restore (similarly frecord() must be called for Vector.record to work. Note that it is necessary that Vector.play use a tvec argument with a first element greater than or equal to the restore time.

Some model restrictions:

  1. "Real" cells must have gids.
  2. Artificial cells can have gids. If not they must be directly connected to just one synapse (e.g. NetStim -> NetCon -> synapse).
  3. There is only one spike output port per cell and that is associated with a base gid.
  4. NetCon.event in Hoc can be used only with NetCon's with a None source.

To allow extra state, such as Random sequence, to be saved for POINT_PROCESS or SUFFIX density nmodl mechanisms, declare FUNCTION bbsavestate() within the mechanism. That function is called when the mechanism instance is saved and restored. FUNCTION bbsavestate takes two pointers to double arrays xdir and xval. The first double array, xdir, has length 1 and xdir[0] is -1.0, 0.0, or 1.0 If xdir[0] == -1.0, then replace the xdir[0] with the proper number of elements of xval and return 0.0. If xdir[0] == 0.0, then save double values into the xval array (which will be sized correctly from a previous call with xdir[0] == -1.0). If xdir[0] == 1.0, then the saved double values are in xval and should be restored to their original values. The number of elements saved/restored has to be apriori known by the instance since the size of the xval that was saved is not sent to the instance on restore.

For example

   FUNCTION bbsavestate() {
     bbsavestate = 0
   VERBATIM
     double *xdir, *xval, *hoc_pgetarg();
     xdir = hoc_pgetarg(1);
     if (*xdir == -1.) { *xdir = 2; return 0.0; }
     xval = hoc_pgetarg(2);
     if (*xdir == 0.) { xval[0] = 20.; xval[1] = 21.;}
     if (*xdir == 1) { printf("%d %d\n", xval[0]==20.0, xval[1] == 21.0); }
   ENDVERBATIM
   }

BBSaveState.save_test()
Syntax:
.save_test()
Description:

State of the model is saved in files within the subdirectory, out. The file out/tmp contains the value of t. Other files have the filename format tmp.<gid>.<rank> . Only in the case of multisplit is it possible to have the same gid in more than one filename.

To prepare for a restore, the tmp.<gid>.<rank> files should be copied from the out subfolder to a subfolder called in, with the filename in/tmp.<gid> . Each file should begin with a first line that specifies the number of files in the out folder that had the same gid.

The following out2in.sh script shows how to do this (not particularly efficiently).

#!/bin/bash
rm -f in/*
cat out/tmp > in/tmp
for f in out/tmp.*.* ; do
  echo $f
  i=`echo "$f" | sed 's/.*tmp\.\([0-9]*\)\..*/\1/'`
  echo $i
  if test ! -f in/tmp.$i ; then
    cnt=`ls out/tmp.$i.* | wc -l`
    echo $cnt > in/tmp.$i
    cat out/tmp.$i.* >> in/tmp.$i
  fi
done

BBSaveState.restore_test()
Syntax:
.restore_test()
Description:
State of the model is restored from files within the subdirectory, "in". The file "in/tmp" supplies the value of t. Other files have the filename format tmp.<gid> and are read when that gid is restored. Note that in a multisplit context, the same "in/tmp.<gid>" file will be read by multiple ranks, but only the state assocated with sections that exist on a rank will be restored.

BBSaveState.ignore()
Syntax:
.ignore(ppobj)

Description:

Point processes can be marked IGNORE which will skip them on save/restore. The internal list of these ignored point processes must be the same on save and restore.

BBSaveState.vector_play_init()
Syntax:
.vector_play_init()
Description:
Allow Vector.play() to work. Call this method after a restore if there are any Vector.play in the model.

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