import z2pack error

[Dominik Gresch]

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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