import z2pack error

[Wei Li]

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> 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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