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Hi Stefano, Thanks for looking into this. Since createWithArray calls VecCreateMPIWithArray which, as Matt noted and is documented (https: //petsc. org/main/manualpages/Vec/VecCreateMPIWithArray/) doesn’t free the memory, then there’s a memory
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Hi Stefano,
<div><br>
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<div>Thanks for looking into this. Since createWithArray calls VecCreateMPIWithArray which, as Matt noted and is documented (<a href="https://urldefense.us/v3/__https://petsc.org/main/manualpages/Vec/VecCreateMPIWithArray/__;!!G_uCfscf7eWS!YpH_OGif6W8Ql9KZDYBiRMKyALSRhMZOHRnkCkBHqBcVB4ef_UBHFbT_EuTgx8ivGmDNQU8bRVaOc-B_tqQ2heGjdvoE9tp8ZbPi3QQ$">https://petsc.org/main/manualpages/Vec/VecCreateMPIWithArray/</a>)
doesn’t free the memory, then there’s a memory leak (and, furthermore, calling del on the original array will have no effect).</div>
<div><br>
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<div>Lisandro: would be great if you can provide some guidance.</div>
<div><br>
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<div>Thanks,</div>
<div><br>
</div>
<div>Samar</div>
<div>
<div><br>
<blockquote type="cite">
<div>On May 3, 2024, at 12:45 PM, Stefano Zampini <stefano.zampini@gmail.com> wrote:</div>
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<div dir="ltr">While waiting for our Python wizard to shed light on this, I note that, from the documentation of PyArray_FROM_OTF <a href="https://urldefense.us/v3/__https://numpy.org/devdocs/user/c-info.how-to-extend.html*converting-an-arbitrary-sequence-object__;Iw!!G_uCfscf7eWS!YpH_OGif6W8Ql9KZDYBiRMKyALSRhMZOHRnkCkBHqBcVB4ef_UBHFbT_EuTgx8ivGmDNQU8bRVaOc-B_tqQ2heGjdvoE9tp8_QyxtQk$" target="_blank">https://numpy.org/devdocs/user/c-info.how-to-extend.html#converting-an-arbitrary-sequence-object</a>,
we have
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<div>The object can be any Python object convertible to an ndarray. If the object is already (a subclass of) the ndarray that satisfies the requirements then a new reference is returned.</div>
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<div>I guess we should call "del" on the ndarray returned by iarray_s after having called self.set_attr('__array__', array) in this case, but let's wait for Lisandro to confirm</div>
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<div dir="ltr" class="gmail_attr">Il giorno ven 3 mag 2024 alle ore 11:42 Samar Khatiwala <<a href="mailto:samar.khatiwala@earth.ox.ac.uk" target="_blank">samar.khatiwala@earth.ox.ac.uk</a>> ha scritto:<br>
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Hi Matt, Thanks so much for the quick reply! Regarding #2, I put some debug statement in my code and what I find is that when I use createWithArray on my Cython-allocated numpy array, the destructor I set for it is no longer called when I delete
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<div>Hi Matt,
<div><br>
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<div>Thanks so much for the quick reply!</div>
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<div>Regarding #2, I put some debug statement in my code and what I find is that when I use <font face="sans-serif"><span style="white-space:pre-wrap">createWithArray on my Cython-allocated numpy array, the destructor I set for it is no longer called when I
delete the array. (If I don’t use </span></font><span style="font-family:sans-serif;white-space:pre-wrap">createWithArray then the destructor is triggered.)
</span><font face="sans-serif"><span style="white-space:pre-wrap">I interpret that to suggest that the petsc4py Vec is somehow ’taking over’ management of the numpy array. But I don’t understand where that could be happening. (I don’t think it has to do with
the actual freeing of memory by PETSc's VecDestroy.) </span></font></div>
<div><span style="font-family:sans-serif;white-space:pre-wrap"><br>
</span></div>
<div><span style="font-family:sans-serif;white-space:pre-wrap">createWithArray calls
</span>iarray_s which in turn calls PyArray_FROM_OTF. Could it be there’s something going on there? The numpy documentation is unclear. </div>
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<div>Lisandro: do you have any thoughts on this?</div>
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<div>Thanks,</div>
<div><font face="sans-serif"><span style="white-space:pre-wrap"><br>
</span></font>
<div>Samar</div>
<div><br>
<blockquote type="cite">
<div>On May 2, 2024, at 11:56 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div>
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<div dir="ltr">On Thu, May 2, 2024 at 12:53 PM Samar Khatiwala <<a href="mailto:samar.khatiwala@earth.ox.ac.uk" target="_blank">samar.khatiwala@earth.ox.ac.uk</a>> wrote:<br>
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<pre style="font-family:sans-serif;font-size:12px;white-space:pre-wrap">Hello,
I have a couple of questions about createWithArray in petsc4py:
1) What is the correct usage for creating a standard MPI Vec with it? Something like this seems to work but is it right?:
On each rank do:
a = np.zeros(localSize)
v = PETSc.Vec().createWithArray(a, comm=PETSc.COMM_WORLD)
Is that all it takes?</pre>
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<div>That looks right to me.</div>
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<pre style="font-family:sans-serif;font-size:12px;white-space:pre-wrap">2) Who ‘owns’ the underlying memory for a Vec created with the createWithArray method, i.e., who is responsible for managing it and doing garbage collection? In my problem, the numpy array is created in a Cython module where memory is allocated, and a pointer to it is associated with a numpy ndarray via PyArray_SimpleNewFromData and PyArray_SetBaseObject. I have a deallocator method of my own that is called when the numpy array is deleted/goes out of scope/whenever python does garbage collection. All of that works fine. But if I use this array to create a Vec with createWithArray what happens when the Vec is, e.g., destroyed? Will my deallocator be called? </pre>
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<div>No. The PETSc struct will be deallocated, but the storage will not be touched. </div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<pre style="font-family:sans-serif;font-size:12px;white-space:pre-wrap">Or does petsc4py know that it doesn’t own the memory and won’t attempt to free it? I can’t quite figure out from the petsc4py code what is going on. And help would be appreciated.
Thanks very much.
Samar
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<div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dXZuKR18IO2hZ4uPEqHaG0Jb0ALPgw1T0dm4HAWfyBfsCvkYTmq7aG7yw3yc-5CVhcFMaUL3WzGM8YHlBTTA_JMs_dYUCTX81-bKyrM$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a></div>
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<span class="gmail_signature_prefix">-- </span><br>
<div dir="ltr" class="gmail_signature">Stefano</div>
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