[Wien] Problem with prepare_xsf_lapw

[Laurence Marks]

I cannot remember if Fabien posted a patch, but there are (many) problems
with this script if you run it on too many parallel nodes, I don't think
you can use more than a few. I think this has already come up on the list.

---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
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Co-Editor, Acta Cryst A


On Oct 10, 2017 21:53, "Gavin Abo" <gsabo at crimson.ua.edu> wrote:

> I suspect that the LAPW0 error comes first before the case.rho_74 error.
> However, I could be wrong as I'm not that familiar with the nlvdw
> calculations.
>
> It would help a little to know where those error appear.  The standard
> output/error file from the job?
>
> R2V files not present, which are required for mBJ or NLvdW => I think this
> indicates that it cannot find the file case.r2v_nlvdw.
>
> What does your case.innlvdw look like?  Do you have the "calculation of
> the potential (T or F)" line set to T.  If it set to T, I think it looks
> for case.r2v_nlvdw.  If you have it set, to F, it might look for case.r2v
> or case.r2v_grr instead.  If it cannot find this file, maybe it causes this
> error.
>
> 16  LAPW0-Error. Check file lapw0.error and case.output0*. => Did you
> check lapw0.error and case.output files as it says; any warning, error, or
> something odd (NaN, *, etc.) in them?
>
> What about the case.dayfile?  Is there any "input conversion error" for
> case.r2v_nlvdw like in the post at the following link:
>
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16383.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_msg16383.html&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=AuhrmqOB9bSJfcBYgk3ZKP6bahK8n7XHznoKWBFdCDw&s=EmHNpQenpXcjoqwuAu2yRLOldVC3PuX6HyaBcL9ZzSM&e=>
> On 10/10/2017 9:09 AM, Luigi Maduro - TNW wrote:
>
> Dear WIEN2k users,
>
>
>
> I am running WIEN2k 17.1 on Beowulf style clusters with a CentOS 7 Linux
> system. I am using WIEN2k to get optical properties of MoS2 using the
> non-local van der Waals functionals in WIEN2k 17.1.
>
> I am using a 2x2x1 supercell with Rkmax=6.5 and 1 kpoint under the
> influence of the optB88-vdW functional. I have no problems when running the
> code in sequential mode.
>
> Whenever I try to use parallel computation the code crashes. In order to
> manage jobs the clusters use the Torque (PBS implementation) queue manager.
> I have written a bash script (similar to the one in the FAQ page) to append
> the nodes in the .machines file. In the calculations I am using 1 node and
> 20 processors. Whenever I use the –nlvdw switch in the run_lapw command the
> script crashes. I get the following error:
>
>
>
> Traceback (most recent call last):
>
>   File "/home/WIEN2k_2/prepare_xsf_lapw", line 360, in <module>
>
>     write_xsf_grid(xcrzeilen, gridmatrix)
>
>   File "/home/WIEN2k_2/prepare_xsf_lapw", line 299, in write_xsf_grid
>
>     rho = open(os.path.basename(os.getcwd())+".rho_"+str(i+1),"r")
>
> IOError: [Errno 2] No such file or directory: 'case.rho_74'
>
> NLVDW END (case.inxsf created)
>
> [1]    Done                          mpirun -np 20 -machinefile
> .machinenlvdw /home/WIEN2k_2/nlvdw_mpi nlvdw.def >> .time00
>
> Child with myid of           19  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           19  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> application called MPI_Abort(MPI_COMM_WORLD, 1714408384) - process 19
>
> Child with myid of           16  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           16  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> Child with myid of           18  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           18  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> Child with myid of           12  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           12  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> Child with myid of           15  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           15  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> Child with myid of           17  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           17  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> Child with myid of           13  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           13  LAPW0-Error. Check file lapw0.error and case.output0*.
>
> application called MPI_Abort(MPI_COMM_WORLD, -1249474368) - process 16
>
> application called MPI_Abort(MPI_COMM_WORLD, -1730723776) - process 12
>
> application called MPI_Abort(MPI_COMM_WORLD, 58291520) - process 18
>
> Child with myid of           14  has an error
>
> 'LAPW0' - R2V files not present, which are required for mBJ or NLvdW
>
>           14  LAPW0-Error. Check file lapw0.error and case.output0*.
>
>
>
>
>
>
>
> I noticed that there is indeed no case.rho_74 file. Additionally the files
> case.tmp_74, case.output5_74, and case.rho_onedim_74 are missing.
>
> However, the files case.def_74, case.in5_74 are in the directory where I
> am doing my calculation. I think there might be something missing in the
> prepare_xsf_lapw file, but I cannot seem to correct the problem. I cannot
> find anything related to the problems I  am having with prepare_xsf_lapw in
> the mailing list.
>
>
>
> Any help is appreciated!
> Regards,
>
> Luigi Maduro
>
>
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