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@phys.ethz.ch mailto:greschd@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@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