import z2pack error

Sat Feb 11 20:40:40 CET 2017

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> 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 <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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