Re: [Wien] Problem with prepare_xsf_lapw

2017-10-10 Thread 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
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On Oct 10, 2017 21:53, "Gavin Abo"  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
> 
> 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 
>
> 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

Re: [Wien] Problem with prepare_xsf_lapw

2017-10-10 Thread Gavin Abo 
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

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 

    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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[Wien] Problem with prepare_xsf_lapw

2017-10-10 Thread Luigi Maduro - TNW 
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 
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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