[CP2K-user] [CP2K:14265] Re: Hybrid functional calculation problem
mattwa... at gmail.com
Sun Nov 22 16:55:18 UTC 2020
Your input has
This means that each MPI task (which can be multiple cores) should be able
to allocate 4GBi of memory _exclusively_ for the 2 electron integrals. If
there is less than that available it will crash as the memory allocation
can't occur. I guess your main cluster has less memory than the smaller
one. You need to leave space for the operating system and the rest of the
cp2k run besides the 2 electron integrals.
There is another thread where Juerg answers HFX memory in more detail form
earlier this year.
On Sunday, November 22, 2020 at 4:42:47 PM UTC fa... at gmail.com wrote:
> Can cp2k access all the memory on the cluster? On linux you can use
> ulimit -s unlimited
> to remove any limit on the amount of memory a process can use.
> I usually use SCREEN_ON_INITIAL_P. I found that for large systems it is
> faster to run two energy minimizations with the key word enabled (such that
> the second restarts from a converged PBE0 wfn) than running a single
> minimization without SCREEN_ON_INITIAL_P. But that probably depends on the
> system you simulate.
> You should converge the cutoff with respect to the properties that you are
> interested in. Run a test system with increasing cutoff and look at, e.g.
> the energy, pdos, etc.
> Number of sph. ERI's calculated on the fly: 4763533420139
> This number should always be 0. If it is larger, increase the memory cp2k
> has available.
> On Sunday, 22 November 2020 at 17:24:13 UTC+1 Lucas Lodeiro wrote:
>> Dear Fabian,
>> Thanks for your advise. I forgot to clarify the time ejecution... my
>> The calculation runs for 5 or 7 minutes, and stops... the walltime for
>> the calculation was set as 72hrs, then I do not believe this is the
>> problem. Now I am running the same input in a littler cluster (different
>> form the problematic crash) with 64 proc and 250GB RAM, and the calculation
>> works fine (so so slow, 9 hr per scf step, but runs... the total RAM
>> assigned for the ERI's is not sufficient but the problem is not appear)...
>> It is no practical to use this little cluster, then I need to fix the
>> problem in the big one, to use more RAM and more processors (more than 220
>> it is possible), but as the program does not show what is happening, I
>> cannot tell anything to the cluster admin to recompile or fix the problem.
>> This is the output in the little cluster:
>> Step Update method Time Convergence Total energy
>> HFX_MEM_INFO| Est. max. program size before HFX [MiB]:
>> *** WARNING in hfx_energy_potential.F:605 :: The Kohn Sham matrix is not
>> *** 100% occupied. This may result in incorrect Hartree-Fock results.
>> Try ***
>> *** to decrease EPS_PGF_ORB and EPS_FILTER_MATRIX in the QS section. For
>> *** more information see FAQ: https://www.cp2k.org/faq:hfx_eps_warning
>> HFX_MEM_INFO| Number of cart. primitive ERI's calculated:
>> HFX_MEM_INFO| Number of sph. ERI's calculated:
>> HFX_MEM_INFO| Number of sph. ERI's stored in-core:
>> HFX_MEM_INFO| Number of sph. ERI's stored on disk:
>> HFX_MEM_INFO| Number of sph. ERI's calculated on the fly:
>> HFX_MEM_INFO| Total memory consumption ERI's RAM [MiB]:
>> HFX_MEM_INFO| Whereof max-vals [MiB]:
>> HFX_MEM_INFO| Total compression factor ERI's RAM:
>> HFX_MEM_INFO| Total memory consumption ERI's disk [MiB]:
>> HFX_MEM_INFO| Total compression factor ERI's disk:
>> HFX_MEM_INFO| Size of density/Fock matrix [MiB]:
>> HFX_MEM_INFO| Size of buffers [MiB]:
>> HFX_MEM_INFO| Number of periodic image cells considered:
>> HFX_MEM_INFO| Est. max. program size after HFX [MiB]:
>> 1 NoMix/Diag. 0.40E+00 ****** 5.46488333 -20625.2826573514
>> About the SCREEN_ON_INITIAL_P, I read that to use it, you need a very
>> good guess (more than de GGA converged one) as for example the last step or
>> frame from a GEO_OPT or MD... Is it really useful when the guess is the GGA
>> About the CUTOFF_RADIUS, I read that 6 or 7 it is a good compromise, and
>> as my cell is approximately twice, I use the minimal image convention to
>> decide the 8.62 number which is near the recomended (6 or 7). If I reduce
>> it, does the computational cost diminish considerably?
>> Regards - Lucas
>> El dom, 22 nov 2020 a las 12:53, fa... at gmail.com (<fa... at gmail.com>)
>>> Dear Lucas,
>>> cp2k was computes the four-center integrals during (or prior) to the
>>> first SCF cycle. I assume the job ran out of time during this task For a
>>> system with more than 1000 atoms this takes a lot of time. With only 220
>>> CPUs this could take several hours in fact.
>>> To speed up the calculation you should use SCREEN_ON_INITIAL_P T and
>>> restart using a well converged PBE wfn. Other than that, there is little
>>> you can do other than assign the job more time and/or CPUs. (Of course,
>>> reducing CUTOFF_RADIUS 8.62 would help too but could negatively
>>> affect the result).
>>> On Sunday, 22 November 2020 at 01:21:05 UTC+1 Lucas Lodeiro wrote:
>>>> Hi all,
>>>> I need to perform a hybrid calculation with CP2K7.1, over a big system
>>>> (+1000 atoms). I study the manual, the tutorials and some videos of CP2K
>>>> developers to improve my input. But the program exits the calculation when
>>>> the HF part is running... I see the memory usage on the fly, and there is
>>>> no peak which explains the fail (I used 4000Mb with 220 processors).
>>>> The output does not show some explanation... Thinking in the memory, I
>>>> try with a largemem node at our cluster, using 15000Mb with 220 processors,
>>>> but the program exists at the same point without message, just killing the
>>>> The output shows a warning:
>>>> *** WARNING in hfx_energy_potential.F:591 :: The Kohn Sham matrix is
>>>> not ***
>>>> *** 100% occupied. This may result in incorrect Hartree-Fock results.
>>>> Try ***
>>>> *** to decrease EPS_PGF_ORB and EPS_FILTER_MATRIX in the QS section.
>>>> For ***
>>>> *** more information see FAQ: https://www.cp2k.org/faq:hfx_eps_warning
>>>> but I read this is not a very complicated issue, and the calculation
>>>> has to continue and not crash
>>>> Also I decrease the EPS__PGF_ORB, but the warning and the problem
>>>> I do not know if the problem could be located in other parts of my
>>>> input... for example I use the PBE0-T_C-LR (I use PBC for XY), and ADMM. In
>>>> the ADMM options, I use ADMM_PURIFICATION_METHOD = NONE, due to I read that
>>>> ADMM1 is the only one useful for smearing calculations.
>>>> I run this system with PBE (for the first guess of PBE0), and there is
>>>> no problem in that case.
>>>> Moreover, I try with other CP2K versions (7.0, 6.1 and 5.1) compiled
>>>> into the cluster with (libint_max_am=6), and the calculation crash, but
>>>> show this problem:
>>>> * ___
>>>> * / \
>>>> * [ABORT]
>>>> * \___/ CP2K and libint were compiled with different
>>>> LIBINT_MAX_AM. *
>>>> * |
>>>> * O/|
>>>> * /| |
>>>> * / \
>>>> hfx_libint_wrapper.F:134 *
>>>> ===== Routine Calling Stack =====
>>>> 2 hfx_create
>>>> 1 CP2K
>>>> It seems like this problem is not present in the 7.1 version, as the
>>>> program does not show it, and the compilation information does not
>>>> show LIBINT_MAX_AM value...
>>>> If somebody could give me some advice, I will appreciate it. :)
>>>> I attach the input file, and the output file for 7.1 version.
>>>> Regards - Lucas Lodeiro
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