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<p>Dear Matthias, <br>
</p>
<p>Do you know if there is a easy way to use plumed modules beyond
the default ones with these docker images ? Some modules I need
are deactivated by default. I have no experience in editing docker
images, and this may rather be a question for the plumed forum...</p>
<p>Thank you again,</p>
<p>Q.<br>
</p>
<div class="moz-cite-prefix">On 09/11/2023 15:57, Krack Matthias
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:ZRAP278MB0827795C76D23FF284B7D273F4AFA@ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM">
<meta name="Generator"
content="Microsoft Word 15 (filtered medium)">
<div class="WordSection1">
<p class="MsoNormal"><span lang="DE-CH">Dear Quentin</span></p>
<p class="MsoNormal"><span lang="DE-CH"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I am glad to read that
you could solve the problems by using the provided container
images.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">For future reference, I
would like the mention that the README and the docker files
for CP2K production containers have been moved to a separate
repository on GitHub called <a
href="https://github.com/cp2k/cp2k-containers"
moz-do-not-send="true">cp2k-containers</a>, recently.
Therefore, the links in my previous mail are no longer
valid. The CP2K production containers can be download from
DockerHub
<a href="https://hub.docker.com/r/cp2k/cp2k/tags/"
moz-do-not-send="true">here</a>.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Best</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Matthias</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<div id="mail-editor-reference-message-container">
<div>
<div>
<p class="MsoNormal">
<b><span>From: </span></b><span><a class="moz-txt-link-abbreviated" href="mailto:cp2k@googlegroups.com">cp2k@googlegroups.com</a>
<a class="moz-txt-link-rfc2396E" href="mailto:cp2k@googlegroups.com"><cp2k@googlegroups.com></a> on behalf of Quentin
Pessemesse <a class="moz-txt-link-rfc2396E" href="mailto:q.pessemesse@gmail.com"><q.pessemesse@gmail.com></a><br>
<b>Date: </b>Thursday, 9 November 2023 at 15:33<br>
<b>To: </b>cp2k <a class="moz-txt-link-rfc2396E" href="mailto:cp2k@googlegroups.com"><cp2k@googlegroups.com></a><br>
<b>Subject: </b>Re: [CP2K:19485] Memory Leak on CP2k
9.1</span></p>
</div>
<p class="MsoNormal"><span>Dear Matthias,
</span></p>
<div>
<p class="MsoNormal"><span>Thank you very much for your
help, we were able to solve the memory leak issue by
using the mpi that is compiled with the image, with
some modifications to the command you provided to
account for specificities of the cluster.</span></p>
</div>
<div>
<p class="MsoNormal"><span>Best,</span></p>
</div>
<div>
<p class="MsoNormal"><span>Quentin</span></p>
</div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<p class="MsoNormal"><span>Le vendredi 6 octobre 2023 à
15:16:09 UTC+2, Krack Matthias a écrit :</span></p>
</div>
<blockquote>
<div>
<div>
<p class="MsoNormal">
<span lang="EN-US">Dear Quentin</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">These containers are built
differently following the usual cp2k toolchain
installation process. There is no
</span><span>/opt/cp2k-toolchain/</span><span
lang="EN-US"> folder but the folder
/opt/cp2k/tools/toolchain/install/. There is no
need, however, to source that setup file,
because the <a
href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/Dockerfile.2023.2_mpich_generic_psmp#L83"
target="_blank" moz-do-not-send="true">
entrypoint.sh</a> script takes already care of
that. You should be able to run the container as
described in the</span><span lang="EN-US">
<a
href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md"
target="_blank" moz-do-not-send="true">
READ.me</a>.</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">Best</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">Matthias</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">
<b><span>From: </span></b><span><span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>
<<span class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>>
on behalf of Quentin Pessemesse <<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:q.pess...@gmail.com">q.pess...@gmail.com</a></span>><br>
<b>Date: </b>Friday, 6 October 2023 at
14:59<br>
<b>To: </b>cp2k <<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>><br>
<b>Subject: </b>Re: [CP2K:19312] Memory
Leak on CP2k 9.1</span><span></span></p>
</div>
<div>
<p class="MsoNormal">
<span>Dear Matthias, </span></p>
</div>
<div>
<p class="MsoNormal">
<span>Thank you kindly for your advice, I
will try these different versions as soon
as possible.</span></p>
</div>
<div>
<p class="MsoNormal">
<span>I've built the docker image for an
openmpi version of CP2k on the cluster.
With version 2023.1, I used to source the
environment variables using " source
/opt/cp2k-toolchain/install/setup". This
does not work anymore. Is it a problem on
the image's end or on the cluster end ?</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Best,</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Quentin</span></p>
</div>
<div>
<p class="MsoNormal">
<span> </span></p>
</div>
<p class="MsoNormal">
<span> </span></p>
<div>
<div>
<p class="MsoNormal">
<span>Le vendredi 6 octobre 2023 à
11:27:26 UTC+2, Krack Matthias a écrit :</span></p>
</div>
<blockquote>
<div>
<div>
<p class="MsoNormal">
<span lang="DE-CH">Hi Quentin</span><span></span></p>
<p class="MsoNormal">
<span lang="DE-CH"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">There are some more
cp2k 2023.2 docker containers for
<a
href="https://github.com/mkrack/cp2k/tree/master/tools/docker/production"
target="_blank"
moz-do-not-send="true">
production</a> available (build
with MPICH or OpenMPI) which can
also be pulled with apptainer (see
<a
href="https://github.com/mkrack/cp2k/blob/master/tools/docker/production/README.md"
target="_blank"
moz-do-not-send="true">
READ.me</a> for details). Maybe,
you have more luck with one of
these.</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">Best</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">Matthias</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">
<b><span>From: </span></b><span><span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>
<<span class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>>
on behalf of Quentin
Pessemesse <<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:q.pess...@gmail.com">q.pess...@gmail.com</a></span>><br>
<b>Date: </b>Friday, 6
October 2023 at 10:47<br>
<b>To: </b>cp2k <<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>><br>
<b>Subject: </b>Re:
[CP2K:19310] Memory Leak on
CP2k 9.1</span><span></span></p>
</div>
<div>
<p class="MsoNormal">
<span>Dear all, </span></p>
</div>
<div>
<p class="MsoNormal">
<span>The cluster staff has
moved to using a docker with a
CP2k image, with CP2k 2023.1 (<a
href="https://hub.docker.com/r/cp2k/cp2k/tags" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">https://hub.docker.com/r/cp2k/cp2k/tags</a>).
The program experiences
serious memory leaks
(out-of-memory crash after
less than 24 hours on AIMD
with a system less than 100
atoms with 256 GB). The
cluster cannot use intelmpi
versions older than intelmpi
20. Is there a more recent
version of CP2k which is
stable and does not experience
this type of large memory
leaks?</span></p>
</div>
<div>
<p class="MsoNormal">
<span>We've tried to compile our
own versions of CP2k with
multiple versions of openMPI
to no avail. The only stable
CP2k version we have is CP2k
6.1, which is used with
intelMPI 18 but it is on a
legacy container where no new
software can be installed.</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Has anyone managed to use
this docker image succesfully,
and if so, which MPI
package/version have you used
? If necessary, we can
downgrade down to CP2k 9.1.</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Best,</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Quentin</span></p>
</div>
<div>
<p class="MsoNormal">
<span> </span></p>
</div>
<div>
<div>
<p class="MsoNormal">
<span>Le mercredi 5 octobre
2022 à 13:19:26 UTC+2, Krack
Matthias (PSI) a écrit :</span></p>
</div>
<blockquote>
<div>
<div>
<p class="MsoNormal">
<span lang="DE-CH">Hi
Quentin</span><span></span></p>
<p class="MsoNormal">
<span lang="DE-CH"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">It
seems that you are using
OpenMPI which is known
to have leaks in some
versions. Check
<a
href="https://github.com/cp2k/cp2k/issues/1830#issuecomment-1012561166"
target="_blank"
moz-do-not-send="true">
this issue</a> and <a
href="https://groups.google.com/g/cp2k/c/BJ9c21ey0Ls/m/2UDxnhBRAQAJ"
target="_blank"
moz-do-not-send="true">
this discussion</a>
here on this forum for
further information.</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">HTH</span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<p class="MsoNormal">
<span lang="EN-US">Matthias
</span><span></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">
<span lang="EN-US"> </span><span></span></p>
<div>
<p class="MsoNormal">
<b><span>From: </span></b><span>"<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>"
<<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>>
on behalf of Quentin
Pessemesse <<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:q.pess...@gmail.com">q.pess...@gmail.com</a></span>><br>
<b>Reply to: </b>"<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>"
<<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>><br>
<b>Date: </b>Wednesday,
5 October 2022 at
12:39<br>
<b>To: </b>"<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>"
<<span
class="MsoHyperlink"><a class="moz-txt-link-abbreviated" href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a></span>><br>
<b>Subject: </b>[CP2K:17807]
Memory Leak on CP2k
9.1</span><span></span></p>
</div>
<div>
<p class="MsoNormal">
<span> </span></p>
</div>
<div>
<p class="MsoNormal">
<span>Dear all, </span></p>
</div>
<div>
<p class="MsoNormal">
<span>Our group is
encountering a memory
leak issue that makes
running DFT-MD
impossible with large
systems (~100 atoms)
on one of the clusters
we have access to,
even though the same
calculations run
correctly on other
machines.</span></p>
</div>
<div>
<p class="MsoNormal">
<span>The cluster
support sent me the
following valgrind
output and asked me to
find suggestions on
how to proceed. Does
anyone have input on
how to deal with such
memory leaks ?</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Best,</span></p>
</div>
<div>
<p class="MsoNormal">
<span>Quentin P.</span></p>
</div>
<div>
<p class="MsoNormal">
<span> </span></p>
</div>
<div>
<p class="MsoNormal">
<span>==62== Invalid
write of size 4 ==62==
at 0x1EA9887:
grid_ref_create_task_list
(in
/ccc/products2/cp2k-9.1/Rhel_8__x86_64/gcc--8.3.0__openmpi--4.0.1/plumed/bin/cp2k.psmp)
==62== by 0x1E7A772:
grid_create_task_list
(in
/ccc/products2/cp2k-9.1/Rhel_8__x86_64/gcc--8.3.0__openmpi--4.0.1/plumed/bin/cp2k.psmp)
==62== by 0x1E790B3:
__grid_api_MOD_grid_create_task_list
(grid_api.F:938)
==62== by 0x104AA67:
__task_list_methods_MOD_generate_qs_task_list
(task_list_methods.F:623) ==62== by 0xF58353:
__qs_update_s_mstruct_MOD_qs_env_update_s_mstruct
(qs_update_s_mstruct.F:187) ==62== by 0xCC03AB:
__qs_energy_init_MOD_qs_energies_init
(qs_energy_init.F:311)
==62== by 0xCBF0A1:
__qs_energy_MOD_qs_energies
(qs_energy.F:84)
==62== by 0xCE087E:
__qs_force_MOD_qs_forces
(qs_force.F:212)
==62== by 0xCE4349:
__qs_force_MOD_qs_calc_energy_force
(qs_force.F:117)
==62== by 0x9AE2C0:
__force_env_methods_MOD_force_env_calc_energy_force
(force_env_methods.F:271) ==62== by 0x50CD0C:
__md_run_MOD_qs_mol_dyn_low
(md_run.F:372) ==62==
by 0x50DCF2:
__md_run_MOD_qs_mol_dyn
(md_run.F:153) ==62==
Address 0x26d18670 is
16 bytes before a
block of size 10
free'd ==62== at
0x4C35FAC: free
(vg_replace_malloc.c:538)
==62== by 0x2B73E68:
__offload_api_MOD_offload_timeset
(offload_api.F:137)
==62== by 0x2B60EDA:
__timings_MOD_timeset_handler
(timings.F:278) ==62==
by 0x2BE2C6D:
__message_passing_MOD_mp_waitany
(message_passing.F:4597) ==62== by 0x2963EA5:
__realspace_grid_types_MOD_rs_pw_transfer_distributed
(realspace_grid_types.F:1439) ==62== by 0x2966559:
__realspace_grid_types_MOD_rs_pw_transfer
(realspace_grid_types.F:711) ==62== by 0xC9310B:
__qs_collocate_density_MOD_calculate_rho_core
(qs_collocate_density.F:966) ==62== by 0xF57698:
__qs_update_s_mstruct_MOD_qs_env_update_s_mstruct
(qs_update_s_mstruct.F:109) ==62== by 0xCC03AB:
__qs_energy_init_MOD_qs_energies_init
(qs_energy_init.F:311)
==62== by 0xCBF0A1:
__qs_energy_MOD_qs_energies
(qs_energy.F:84)
==62== by 0xCE087E:
__qs_force_MOD_qs_forces
(qs_force.F:212)
==62== by 0xCE4349:
__qs_force_MOD_qs_calc_energy_force
(qs_force.F:117)
==62== Block was
alloc'd at ==62== at
0x4C34DFF: malloc
(vg_replace_malloc.c:307)
==62== by 0x2F21116:
_gfortrani_xmallocarray
(memory.c:66) ==62==
by 0x2F1C271:
_gfortran_string_trim
(string_intrinsics_inc.c:167) ==62== by 0x2B73E1C:
__offload_api_MOD_offload_timeset
(offload_api.F:137)
==62== by 0x2B60EDA:
__timings_MOD_timeset_handler
(timings.F:278) ==62==
by 0x2BE2C6D:
__message_passing_MOD_mp_waitany
(message_passing.F:4597) ==62== by 0x2963EA5:
__realspace_grid_types_MOD_rs_pw_transfer_distributed
(realspace_grid_types.F:1439) ==62== by 0x2966559:
__realspace_grid_types_MOD_rs_pw_transfer
(realspace_grid_types.F:711) ==62== by 0xC9310B:
__qs_collocate_density_MOD_calculate_rho_core
(qs_collocate_density.F:966) ==62== by 0xF57698:
__qs_update_s_mstruct_MOD_qs_env_update_s_mstruct
(qs_update_s_mstruct.F:109) ==62== by 0xCC03AB:
__qs_energy_init_MOD_qs_energies_init
(qs_energy_init.F:311)
==62== by 0xCBF0A1:
__qs_energy_MOD_qs_energies
(qs_energy.F:84)
</span></p>
</div>
</div>
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