Dear All,
I have successfully generated all required *.TSHS files by dividing the
large system into small fragments, plus required only-S files. When I
attempt to calculate phonon-electron coupling using the following
command line
____________________________________________________________
Phonons -c --DeviceFirst=65 --DeviceLast=226 --FCfirst=81 --FClast=210
--FCwildcard="./FCrun*" PHrun
____________________________________________________________
our computer starts the calculation without any problem, but always
terminates the job after 4-7 minutes no matter whether I run the
calculation in a parallel or sequential mode. But the computer echoes
different error messages. It shows "=>> PBS: job killed: mem 34582064kb
exceeded limit 31457280kb" in the sequential mode, while it is "mpirun
noticed that process rank 17 with PID 25741 on node r2949 exited on
signal 9 (Killed)" in the parallel mode.
It is clear that a sequential calculation requires a greater memory
size. I am not sure whether the same memory size issue results in the
termination of a parallel job because the message echoed from a parallel
is not informative to me.
Could I have your comments and suggestions on this calculation? Your
help will be sincerely appreciated. Cheers!
Jin
On 14/08/2015 6:11 PM, Nick Papior wrote:
You shouldn't need to rename the files, nor delete files, try first
and do the straightforward thing. Do them separately in their own
directories:
FCrun_11-11
FCrun_12-12
Then do
Phonons --FCwildcard="./FCrun_*" ...
This should work fine.
2015-08-14 8:26 GMT+00:00 Jingxian Yu <[email protected]
<mailto:[email protected]>>:
Dear All,
I need to calculate force constants for a large system (containing
more than 300 atoms). It would take more than 1000 hours on a
16-core node. So I attempt to divide the large job into small
pieces. My plan is to divide device atoms into 10 consecutive
sections, and calculate the Hamiltonian (TSHS files) for each
section. Then I will rename them, so they can link together.
I had a test with the AuH2 example. Unfortunately, my idea was not
successful.
In brief, I set the following lines to calculate the Hamiltonian
for the atom 11,
MD.FCfirst 11
MD.FClast 11
then I set the following lines to calculate the Hamiltonian for
the atom 12,
MD.FCfirst 12
MD.FClast 12
After two jobs completed, I renamed "Chain 12 1.TSHS" to
"Chain 11 7.TSHS", and so on. Also, I deleted the file "Chain
12 0.TSHS".
Regarding overlap calculations, I followed the setting suggested
on the tutorial.
However I got the following message when I ran "Phonons -c
--DeviceFirst=10 --DeviceLast=13 --FCfirst=11 --FClast=12 PHrun",
...
Phonons.GetFileLists: WARNING - Inconsistent number of *.TSHS
files in directory ./FCrun
...
ValueError: could not broadcast input array from shape (0,3) into
shape (22,3)
...
Is my idea too naive? Your comments will be appreciated! Cheers!
Jin
--
Kind regards Nick
