import z2pack error

Dominik Gresch greschd at phys.ethz.ch
Sat Feb 11 22:00:11 CET 2017


Dear Wei Li,

If everything work correctly, Z2Pack should automatically call VASP (via 
the command given) and read the .mmn file after VASP has generated it. 
This is because Z2Pack needs to iteratively change the k-point path with 
which VASP is called and the overlap file is calculated.

In your case, it seems that you are submitting the VASP run to some 
scheduler -- this means the command returns immediately, before the .mmn 
file has been generated. As a result, Z2Pack tries to read the file, but 
it does not exist yet. You can solve this problem by submitting instead 
the Python process running Z2Pack, and then running VASP within that 
same job.

Best regards,

Dominik


On 11.02.2017 20:40, Wei Li wrote:
> Dear Dominik,
>
> From what I understand, after calling the first principle code (in my 
> case, it is VASP), the next step is to
> read the .mmn file in the top level of the build file. So I give the 
> mmn path like below:
>
> system = z2pack.fp.System(
> input_files=["input/CHGCAR", "input/INCAR", "input/POSCAR", 
> "input/POTCAR", "input/wannier90.win"],
>     kpt_fct=z2pack.fp.kpoint.vasp,
>     kpt_path="KPOINTS",
>     command="qsub /home/work/mtg/users/verali/Bi_Z2/Z2/paral.qs"
> mmn_path="wannier90.mmn"
> )
>
> But it does not work.
>
> Could you advise how to read the mmn file?
>
> Regards
> Wei Li
>
>
>> On Feb 10, 2017, at 2:59 PM, Wei Li <verali at udel.edu 
>> <mailto:verali at udel.edu>> wrote:
>>
>> Dear Dominik,
>>
>> Thanks for your reply. I solved this problem.
>>
>> I generated the build file as following:
>>
>> CHG     CONTCAR EIGENVAL  INCAR    OSZICAR  paral.qs.o889660 POSCAR  
>> REPORT       wannier90.eig  wannier90.win WAVECAR
>> CHGCAR  DOSCAR IBZKPT    KPOINTS  OUTCAR   PCDAT POTCAR  vasprun.xml  
>> wannier90.mmn  wannier90.wout XDATCAR
>>
>> There is no error.
>>
>> which script do I need to read the .mmn file to plot the result? So 
>> far, the result file is empty.
>>
>> Regards
>> Vera
>>
>>
>>> On Feb 8, 2017, at 11:16 AM, Dominik Gresch <greschd at phys.ethz.ch 
>>> <mailto:greschd at phys.ethz.ch>> wrote:
>>>
>>> Dear Wei Li,
>>>
>>> It seems you are running multiple instances of the Python 
>>> interpreter, due to the 'mpirun' command. There seems to be a bit of 
>>> a race condition when they all try to create the 'results' folder.
>>>
>>> In general, you shouldn't run Python itself with mpirun, only the 
>>> first-principles command (command="mpirun YOUR_VASP_COMMAND" in the 
>>> z2pack.fp.System options).
>>>
>>> Best regards,
>>>
>>> Dominik Gresch
>>>
>>>
>>> On 08.02.2017 17:08, Wei Li wrote:
>>>> Dear Dominik Gresch,
>>>>
>>>> Thanks a lot.
>>>>
>>>> I activated py35 and it works.
>>>>
>>>> Do I need to change any parameters if I want to run the example 
>>>> given here:
>>>> https://github.com/Z2PackDev/Z2Pack/tree/master/2.0.x/examples/fp/Bi_vasp
>>>>
>>>> I run it directly and I got the attached output, I did not find any 
>>>> error in output file or log file, but the process is terminated.
>>>>
>>>>
>>>> Regards
>>>> Wei Li
>>>>
>>>>
>>>>> On Feb 8, 2017, at 4:53 AM, Dominik Gresch <greschd at phys.ethz.ch 
>>>>> <mailto:greschd at phys.ethz.ch>> wrote:
>>>>>
>>>>> Dear Wei Li,
>>>>>
>>>>> The python version on which you installed Z2Pack (3.5.2) is 
>>>>> probably not the same as you are using to run the script. Since it 
>>>>> seems you are using a virtualenv (py35) when running Python from 
>>>>> the command line, you should make sure the same virtualenv is also 
>>>>> active in your job (i.e., "source py35/bin/activate" in your script).
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Dominik Gresch
>>>>>
>>>>> On 08.02.2017 10:31, Wei Li wrote:
>>>>>> Dear Z2pack team,
>>>>>>
>>>>>> I have complied Wannier90 1.2 on top of VASP, and then I 
>>>>>> downloaded and installed z2pack like below:
>>>>>>
>>>>>> (py35) [verali at farber input]$ python
>>>>>> Python 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 
>>>>>> 17:53:06)
>>>>>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
>>>>>> Type "help", "copyright", "credits" or "license" for more 
>>>>>> information.
>>>>>> >>> import z2pack
>>>>>> >>> z2pack.__version__
>>>>>> '2.0.3'
>>>>>> >>>
>>>>>>
>>>>>> I think this means I have successfully installed z2pack, right?
>>>>>>
>>>>>> But when I run run.py script, it had the error:
>>>>>>
>>>>>>   File "run.py", line 14, in <module>
>>>>>> Traceback (most recent call last):
>>>>>> File "run.py", line 14, in <module>
>>>>>>   import z2pack
>>>>>> ImportError: No module named z2pack
>>>>>> Traceback (most recent call last):
>>>>>> File "run.py", line 14, in <module>
>>>>>>
>>>>>>
>>>>>> *Below is my job file:*
>>>>>>
>>>>>>
>>>>>>
>>>>>> vpkg_require intel/2015.3.187
>>>>>> vpkg_require openmpi/1.8.5
>>>>>>
>>>>>> #$ -pe mpi 40
>>>>>> #$ -l m_mem_free=3G
>>>>>> #$ -l h_cpu=09:00:00
>>>>>> ##$ -l exclusive=1
>>>>>>
>>>>>> MY_EXE="/home/work/mtg/users/bin/vasp_ncl"
>>>>>>
>>>>>> MY_EXE_ARGS=()
>>>>>>
>>>>>> #
>>>>>> # Uncomment to enable lots of additional information as OpenMPI 
>>>>>> executes
>>>>>> # your job:
>>>>>> #
>>>>>> #SHOW_MPI_DEBUGGING=YES
>>>>>>
>>>>>> ##
>>>>>> ## You should NOT need to change anything after this comment.
>>>>>> ##
>>>>>> OPENMPI_FLAGS="--display-map --mca btl ^openib --mca 
>>>>>> oob_tcp_if_exclude lo,ib0 --mca btl_tcp_if_exclude lo,ib0"
>>>>>> if [ "${WANT_CPU_AFFINITY:-NO}"= "YES"]; then
>>>>>> OPENMPI_FLAGS="${OPENMPI_FLAGS} --bind-to core"
>>>>>> fi
>>>>>> if [ "${WANT_NPROC:-0}"-gt 0 ]; then
>>>>>> OPENMPI_FLAGS="${OPENMPI_FLAGS} --np ${WANT_NPROC} --map-by node"
>>>>>> fi
>>>>>> if [ "${SHOW_MPI_DEBUGGING:-NO}"= "YES"]; then
>>>>>> OPENMPI_FLAGS="${OPENMPI_FLAGS} --debug-devel --debug-daemons 
>>>>>> --display-devel-map --display-devel-allocation --mca mca_verbose 
>>>>>> 1 --mca coll_base_verbose 1 --mca ras_base_verbose 1 --mca 
>>>>>> ras_gridengine_debug 1 --mca ras_gridengine_verbose 1 --mca 
>>>>>> btl_base_verbose 1 --mca mtl_base_verbose 1 --mca 
>>>>>> plm_base_verbose 1 --mca pls_rsh_debug 1"
>>>>>> if [ "${WANT_CPU_AFFINITY:-NO}"= "YES"]; then
>>>>>>   OPENMPI_FLAGS="${OPENMPI_FLAGS} --report-bindings"
>>>>>> fi
>>>>>> fi
>>>>>>
>>>>>> echo "GridEngine parameters:"
>>>>>> echo " mpirun        = "`which mpirun`
>>>>>> echo " nhosts        = $NHOSTS”
>>>>>> echo "  nproc       = $NSLOTS"
>>>>>> echo " executable    = $MY_EXE"
>>>>>> echo "  MPI flags     = $OPENMPI_FLAGS"
>>>>>> echo "-- begin OPENMPI run -- on "
>>>>>> mpirun ${OPENMPI_FLAGS} python run.py
>>>>>> echo "-- end OPENMPI run -- on “
>>>>>>
>>>>>> Pls help to advise how can I solve this problem.
>>>>>>
>>>>>> Thanks in advance.
>>>>>>
>>>>>> Wei Li
>>>>>> Ph.D student
>>>>>> University of Delaware
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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