Hi Nick,
Many thanks for your prompt response! I will follow your suggestions and
have more tests. Cheers!
Jin
On 27/08/2015 10:20 PM, Nick Papior wrote:
Phonons does NOT work in parallel, you cannot use mpirun on it.
Phonon calculations simply do require huge amounts of memory, this is
a current concern in the development of Inelastica, some initiatives
have been taken to minimize memory usage.
Please update to the latest Inelastica version if you already haven't.
If this does not help you, then try and run the calculation in single
precision (check the flags for phonons).
2015-08-27 14:41 GMT+02:00 Jingxian Yu <[email protected]
<mailto:[email protected]>>:
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
--
Kind regards Nick
