import z2pack error
Dominik Gresch
greschd at phys.ethz.ch
Mon Feb 13 23:44:34 CET 2017
Dear Wei Li,
The Bi example should run with the supplied input files. However, you
need to install a modified version of Wannier90, as explained in the
installation instructions:
http://z2pack.ethz.ch/doc/2.0/tutorial_installation.html#setting-up-first-principles-codes
For Wannier90 2.1 or newer this is no longer necessary because we added
a specific interface to run with Z2Pack, but unfortunately VASP only
supports Wannier90 version 1.x.
Best regards,
Dominik Gresch
On 13.02.2017 23:40, Wei Li wrote:
> Hi Dominik,
>
> Thanks, it runs well now.
>
> For the given example (Bi) calculation, I need to set up the
> search_shells number. What’s the value you recommend?
> I have increased to 30 from default value 12, it still can not satisfy
> the B1 condition:
>
> Unable to satisfy B1 with any of the first 30 shells
> Your cell might be very long, or you may have an irregular MP grid
> Try increasing the parameter search_shells in the win file (default=12)
>
> Or do I need to check other parameters?
>
> Here is my input:
>
> num_wann = 10
> num_bands = 10
> spinors : true
> search_shells=30
> num_iter 0
> exclude_bands 11-15
>
> Regards
> Wei Li
>
>
>> On Feb 11, 2017, at 4:00 PM, Dominik Gresch <greschd at phys.ethz.ch
>> <mailto:greschd at phys.ethz.ch>> wrote:
>>
>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.phys.ethz.ch/private/z2pack/attachments/20170213/60e44ee7/attachment.html>
More information about the Z2Pack
mailing list