# Memory leak in dolfin from GhostValues update?

**URL:** <https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871>\
**Category:** General\
**Created:** [April 7, 2023, 10:29am UTC](https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871 "2023-04-07T10:29:31Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![grekas](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/grekas/32/1625_2.png) [@grekas](https://fenicsproject.discourse.group/u/grekas)\
**Post date:** [April 7, 2023, 10:29am UTC](https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871/1 "2023-04-07T10:29:31Z")

</div>

Recently I observed that my code was out of memory when I am using the command apply(‘insert’) for a function after updating its values. Is there any way to free this allocated memory? Here I present a brief code example where the memory usage has been increased from 4014740 to 9005872 (KiB Mem from top command) after 180000 iterations employing 16 processors in mpirun command.

```auto
from dolfin import*
import numpy as np
import sys

mesh = UnitCubeMesh(64, 64, 64)
print('coor shape = ', mesh.coordinates().shape)
V = VectorFunctionSpace(mesh, 'CG', 1)
u = Function(V)

u_array = u.vector().get_local()
# self._uv = self._mu.vector().vec()
mpiRank = MPI.rank(MPI.comm_world)
I =0
while(True):
    u_array =np.random.randn(u_array.shape[0])
    u.vector().set_local(u_array)
    u.vector().apply('insert')
    if i%1000 == 0 and mpiRank ==0:
        print(i, 'th iteration')
        sys.stdout.flush()
    i+=1

```

---

<div class="post-metadata">

**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\
**Post date:** [April 7, 2023, 11:38am UTC](https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871/2 "2023-04-07T11:38:11Z")

</div>

What version of PETSc are you using?

In their later releases (3.18 and onwards), they have changed how the garbage collection in Python works.

---

<div class="post-metadata">

**Author:** ![grekas](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/grekas/32/1625_2.png) [@grekas](https://fenicsproject.discourse.group/u/grekas)\
**Post date:** [April 7, 2023, 12:00pm UTC](https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871/3 "2023-04-07T12:00:30Z")

</div>

This happens in conda with petsc 3.15.5 version and in 2019.2.0.dev0 dolfin-version in ubuntu 18.04 where I do not know the petsc version exaclty, I found version 3.7.7 under /usr/lib.  
Is there any command that I can free this memory or can I combine dolfin with newer version of petsc? Many thanks

---

<div class="post-metadata">

**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\
**Post date:** [April 7, 2023, 3:31pm UTC](https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871/4 "2023-04-07T15:31:31Z")

</div>

I couldn’t reproduce this issue with 8 processes using

```bash
docker run -ti --network=host -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v $(pwd):/root/shared -w /root/shared --rm ghcr.io/scientificcomputing/fenics-gmsh:2023-03-01a

```

As you are using a quite outdated OS ([Ubuntu 18.04 EOL – keep your fleet of devices up and running | Ubuntu](https://ubuntu.com/blog/ubuntu-18-04-eol-for-devices)). The python version can also factor into this.

One thing I would recommend is to stor `u.vector()` outside the loop, and call `vec = u.vector()` and `v.set_local(...)` and `vec.apply(...)`

What happens if you remove the `apply` command on your system, does the memory not increase?

---

<div class="post-metadata">

**Author:** ![grekas](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/grekas/32/1625_2.png) [@grekas](https://fenicsproject.discourse.group/u/grekas)\
**Post date:** [April 7, 2023, 9:01pm UTC](https://fenicsproject.discourse.group/t/memory-leak-in-dolfin-from-ghostvalues-update/10871/5 "2023-04-07T21:01:14Z")

</div>

Yes indeed using the same docker image the memory leak is fixed.

I already did the recommendations to store u.vector() and set vet =u.vector() outside the loop in my script but for simplicity I added them under the while loop on the above example. The memory leak is consequence of the vec.apply(…), when I remove this part everything is fine with the memory, but other issues arise in my code. Thank you for the response I imagined that there is an issue with garbage collector so the simplest solutions is to upgrade the used release.