FAQs¶
How to convert CIF (any other format) to pmdini?¶
First you can try to convert any file to pmdini by using napsys.py as,
$ napsys.py convert hoge pmdini
If napsys.py can read the hoge file, it will be converted to pmdini.
If not, one should convert the file to either POSCAR or dump using any converter program, and then convert it to pmdini using napsys.py.
There are not enough slots available...¶
If you get the following error message when you run pmd with some
number of parallel processes,
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
pmd
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
you may have to increase the number of slots available by the
--oversubscribe option as, :
$ mpirun --oversubscribe -np 4 pmd
Reference:
A system call failed during shared memory initialization...¶
The following error message could appear at the end of pmd output,
when the number of MPI processes and the number of automatically
determined spatial decomposition divisions are different.
--------------------------------------------------------------------------
A system call failed during shared memory initialization that should
not have. It is likely that your MPI job will now either abort or
experience performance degradation.
Local host: mbp-rk-eth.ogt.nitech.ac.jp
System call: unlink(2) /var/folders/fh/cd90qtsj3d1fr3wmjw954xt40000gn/T//ompi.mbp-rk-eth.501/pid.52045/1/vader_segment.mbp-rk-eth.95f30001.2
Error: No such file or directory (errno 2)
--------------------------------------------------------------------------
But the pmd results are correct. You can remove it by setting an
environment variable as, :
export OMPI_MCA_btl=self,tcp
Reference: