[gmx-developers] freeing nbnxn_atomdata_t array

Tue Jun 16 21:31:01 CEST 2015

Thanks, I understand now.

Thanks,
Sikandar

On Thu, Jun 11, 2015 at 4:00 AM, <
gromacs.org_gmx-developers-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
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>    1. Re: freeing nbnxn_atomdata_t array
>       (Mirabzadeh, Christopher (mira2978 at vandals.uidaho.edu))
>    2. Re: freeing nbnxn_atomdata_t array (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Jun 2015 17:23:16 +0000
> From: "Mirabzadeh, Christopher (mira2978 at vandals.uidaho.edu)"
>         <mira2978 at vandals.uidaho.edu>
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] freeing nbnxn_atomdata_t array
> Message-ID: <FD00D4BF-6654-496F-9A18-97FA5AAD6DEC at vandals.uidaho.edu>
> Content-Type: text/plain; charset="utf-8"
>
> I?m not sure what file you are editing but I?ll attempt an answer at this.
> What I?ve noticed is that there is a Gromacs wrapper for free() called
> ?sfree()?. I can?t recall where I?ve found it defined but I?ve used it in
> my own code to free memory allocated for arrays. What you may find is that
> the array is either freed in the .c file that you are editing, or you may
> find that it is freed where it is initialized, if a pointer. In my own
> project, the arrays that I am taking advantage of are defined and freed in
> src/gromacs/gmxlib/typedefs.c.
>
> If the file you are editing is a .cpp, the garbage collection may be
> automatic, but that depends on the structure type.
>
> I hope that helps!
>
> Cheers,
>
> -ChrisM
>
> Mirabzadeh, Christopher
> Research Assistant/Physics Instructor
> Department of Physics
> University of Idaho
> Moscow, Id
> (509)339-5647
>
>
>
> On Jun 9, 2015, at 3:26 PM, Sikandar Mashayak <mashayak at votca.org<mailto:
> mashayak at votca.org>> wrote:
>
> Hi,
>
> I am trying to find out the location in the source code where the arrays,
> e..g, real *x, of the structure nbnxn_atomdata_t are freed? Are they freed
> explicitly or they are automatically deallocated when the program ends.
>
> Thanks,
> Sikandar
> --
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> ------------------------------
>
> Message: 2
> Date: Wed, 10 Jun 2015 18:15:46 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] freeing nbnxn_atomdata_t array
> Message-ID:
>         <
> CAMNuMAQEFaKs8BbLnSvBhqiKB+BqCDUbtycqNkNPT+EMPG1zmw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> On Wed, Jun 10, 2015 at 7:23 PM Mirabzadeh, Christopher (
> mira2978 at vandals.uidaho.edu) <mira2978 at vandals.uidaho.edu> wrote:
>
> >  I?m not sure what file you are editing but I?ll attempt an answer at
> > this. What I?ve noticed is that there is a Gromacs wrapper for free()
> > called ?sfree()?. I can?t recall where I?ve found it defined but I?ve
> used
> > it in my own code to free memory allocated for arrays. What you may find
> is
> > that the array is either freed in the .c file that you are editing, or
> you
> > may find that it is freed where it is initialized, if a pointer. In my
> own
> > project, the arrays that I am taking advantage of are defined and freed
> in
> > src/gromacs/gmxlib/typedefs.c.
> >
> >  If the file you are editing is a .cpp, the garbage collection may be
> > automatic, but that depends on the structure type.
> >
>
> No, mdrun likely will never do garbage collection, for multiple reasons.
> Various smart pointers are on the way in, but if you're allocating heap
> memory each MD step then you need to go and re-think the pace of your life
> ;-)
>
> I hope that helps!
> >
> >  Cheers,
> >
> >  -ChrisM
> >
> >   Mirabzadeh, Christopher
> > Research Assistant/Physics Instructor
> > Department of Physics
> > University of Idaho
> > Moscow, Id
> > (509)339-5647
> >
> >
> >
> >  On Jun 9, 2015, at 3:26 PM, Sikandar Mashayak <mashayak at votca.org>
> wrote:
> >
> >   Hi,
> >
> >  I am trying to find out the location in the source code where the
> arrays,
> > e..g, real *x, of the structure nbnxn_atomdata_t are freed?
> >
> >
> Probably they are not freed (because mdrun is currently built to be good
> enough to run a single simulation and then terminate), but the intent is to
> allocate and free such arrays using the function pointer members of
> nbnxn_atomdata_t. Search for alloc and free in nbnxn_atomdata.c
>
>
> > Are they freed explicitly or they are automatically deallocated when the
> > program ends.
> >
> > Unix processes have their memory reclaimed by the OS when they terminate;
> currently there is no "destructor" ever called for such arrays. That's
> dirty, but sufficient what is currently normal GROMACS usage.
>
> Mark
>
>
> >  Thanks,
> >  Sikandar
> >  --
> > Gromacs Developers mailing list
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> >
> >
> >  --
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