* yes you can create the exit file just with a touch command
* no don't create it in the submission script, there is no sensible
reason to create it with the submission script, maybe I have not
been clear, the program stops as soon as it finds the exit file, if
you created it with the submission file, the program would stop just
after starting without doing nothing. what for ?
* if you have doubts about the reliability of your saved data it is
probably better to copy the last positions obtained by you previous
run in the input and restart from scratch from those coordinates.
* if you really want to change prefix (this is another thing which is
not very frequently needed actually) just copy the whole prefix.save
directory into new_prefix.save directory
On 08/07/19 21:22, Yeon, Jejoon wrote:
1) no it's not correct. prefix.EXIT is a file that the user creates to
make the program stop before completion. When the program finds this
file in the outdir or in the working directory the program stops
writes the restart files and deletes prefix.EXIT, so the file is
practically never present after the program has stopped unless
something has gone wrong. To restart a relaxation you just need the
files contained in the prefix.save directory and possibly the restart
files.
>> Thanks to let me know. May I ask how to createprefix.EXIT file? Is this an empty file
just with that name, that I can make from shell command in submission
script?
Also, I think my previous jobswerenot "cleanly stopped", because I
didn't used "max_seconds" neither I created any prefix.EXIT file at
any moment. So that is why I think my stopped jobs cannot be continued.
But let me try to continue this one. Inside the prefix.save folder of
corresponding job, I can only find 3
files: charge-density.dat, data-file-schema.xml, and paw.txt. So, I
need to copy those files to outdir location, and submit restart job
with different name of .in and .out file in the same folder, and set
restart_mode to restart. Right?
2) max_seconds uses the same time as printed in the WALL_TIME which is
the time elapsed since the job has started CPU_TIME is the time
actually used by the CPU they differ because a CPU usage is not always
100%, may be less but if you use multithreading may also be much
larger than 100%. Consider only WALL time to keep things simple.
Just look at the seconds the program takes to make an scf loop and set
smax_seconds to one week minus that time. This already very
conservative, no need to use a longer time.
3) do not change the prefix name ...
To restart the program will look for a directory called prefix.save
if you change the prefix the program will not be able to read anything...
>> Thank you so much for the answers. Are there any links which explained of how to restart QE
jobs in detail? I searched in user manual and input file description
webpage but I couldn't find any useful info...
Thank you again!!
------------------------------------------------------------------------
*From:* users <[email protected]> on behalf of
SISSA <[email protected]>
*Sent:* Monday, July 8, 2019 2:38:00 PM
*To:* Quantum ESPRESSO users Forum
*Subject:* Re: [QE-users] Question about restarting relaxation jobs
1) no it's not correct. prefix.EXIT is a file that the user creates to
make the program stop before completion. When the program finds this
file in the outdir or in the working directory the program stops
writes the restart files and deletes prefix.EXIT, so the file is
practically never present after the program has stopped unless
something has gone wrong. To restart a relaxation you just need the
files contained in the prefix.save directory and possibly the restart
files.
2) max_seconds uses the same time as printed in the WALL_TIME which is
the time elapsed since the job has started CPU_TIME is the time
actually used by the CPU they differ because a CPU usage is not always
100%, may be less but if you use multithreading may also be much
larger than 100%. Consider only WALL time to keep things simple.
Just look at the seconds the program takes to make an scf loop and set
smax_seconds to one week minus that time. This already very
conservative, no need to use a longer time.
3) do not change the prefix name ...
To restart the program will look for a directory called prefix.save
if you change the prefix the program will not be able to read anything...
Il 8 lug 2019 6:43 PM, "Yeon, Jejoon" <[email protected]> ha scritto:
Thank you so much Pietro
May I ask one more question?
1) This is just double checking question. I checked the folder
where the relaxation was stopped by cluster due to wall time limit
(I didn't set max seconds). In the output folder, I can see
prefix.save/ folder and pwscf.save/ folder, and prefix.update and
prefix.bfgs file. But because I have no prefix.EXIT folder neither
prefix.EXIT file, I cannot restart this simulation. Is this correct?
2) Now I'm setting "max_seconds" to all my QE DFT works. But I
found that CPU time and wall time is slightly different. From my
recent finished calculation, it is written at the end of the
output file:
PWSCF : 4d21h44m CPU 4d22h12m WALL
This run was terminated on: 21:27:26 1Jul2019
I used 30 cores, and set 7 days of wall time. Simulation finished
before wall time, but I'm not sure why this slight difference of
CPU time and wall time occur.
In this case, what would be the good time of max seconds CPU time
when compared to wall time? If I request 7 days of wall time to
cluster, then would it be more "safe" to set 6 days or 6.5 days of
CPU time for max seconds?
3) This is also double checking question. If I wish to start the
restart in same folder, I would better to change prefix from
"SimulatinoA" to "SimulationA_restart1", would it be OK? Also, if
I wish to use different folder, I need to copy entire files inside
prefix.EXIT folder to the new restart folder, is this correct?
Thank you so much for friendly answers to beginner question!!
------------------------------------------------------------------------
*From:* users <[email protected]> on behalf
of Pietro Davide Delugas <[email protected]>
*Sent:* Monday, July 8, 2019 4:14:06 AM
*To:* [email protected]
*Subject:* Re: [QE-users] Question about restarting relaxation jobs
Hello
1) and 2) PW writes the restart files only when it terminates
before convergence is reached either because the max number of
steps (and the max number may be either the number of electronic
steps during scf of number of ionic steps during structural
relaxation) or the the execution time exceed max_seconds
specified in input or because the user has stopped the calculation
creating a file in the outdir called prefix.EXIT.
If restart_mode in &control is set to "restart" pw will try to
restart the relaxation from the last POSITIONS which have been
saved in the prefix.save directory using the last saved charge
density and wave functions. If it finds the restart files it will
use them also. This mechanism works fine if positions, charge
density and wave functions data have been saved regularly, but
if the calculation is going to be stopped abruptly, for example by
the job manager, there is no way to prevent that the stop arrives
when the program is writing these data. The safer way to go when
you are using a job manager is to set the max_seconds variable to
a number consistently lower than the time allocated by the job
manager, the difference between these two times should be enough
to allow to the program to pass through one of the check_points at
which, during execution, it checks if the execution time has
exceeded the max_seconds s or if the user has created a
prefix.EXIT file. To estimate how long should be the difference
between max_seconds and the scheduled execution time check how
long it takes to the program to make an scf loop, this one will a
very safe estimate, you could reduce this time significantly and
things should be working.
3) I don't understans what you want to do. You create the
prefix.EXIT file when you want to stop your calculation and you
want the calculation to finish smoothly saving all restart
information so that it can resatart from more or less the same
point when it was interrupted. It is completely senseless to
rename the output file as prefix.EXIT because it will make the
program to stop as soon as a check_point detects the file and the
file will be deleted. The only thing that you have to do when
restarting a calculation is
* Specify restart_mode = 'restart' in the input.in file
* take care that the information saved in output.out is not
rewritten by the new execution just use something as mpirun
pw.x < input.in >> output.out which appends the new output to
the old one or redirect the output to files with different names
4) outdir must be the same or if you want to use a different one
you have to create the new outdir befor restarting and copy there
all the data of the previous calculation i.e. the prefix.save
directory.
5) don't complicate things too much
Pietro
On 7/6/19 3:59 PM, Yeon, Jejoon wrote:
Hello
I have very small amount of experience using QE, so please
excuse my beginner question. I'm about to start relaxation of
big crystal structure, and I wish to make my QE relaxation
jobs ready for restart. Here are my questions:
1) According to "restarting" section from manual,
(https://www.quantum-espresso.org/Doc/pw_user_guide/node20.html)
it seems that QE does not creates the dedicated restart file,
is this correct?
2) If I set up "max_seconds" option as 604800 seconds (1
week), and request wall time to server 1 week, do my
calculation jobs are ready to restart after 1 week? (1 week is
just example but our server cluster have maximum some
walltime limitation, and I don't think any of my relaxation
works will be finished within that time. ) Also, does this
"max_seconds" option must be required to restart?
3) When I execute QE in the submit script, I use something
similar as:
mpirun pw.x < input.in > output.out
In this case, if the relaxation job is killed due to wall time
limit (without setting max_seconds), can I just change the
name of the output.out to prefix.EXIT, (of course I set up
prefix in the input file) and then include restart_mode =
"restart" in the input file, then submit a job for restart?
I have old files which are finished after reaching wall time
limit without "max_seconds" option, and I'm curious if I can
use those files to restart.
4) I also use outdir option in the input file, does the outdir
option should be the same when restart?
5) Are there any other things or useful hints that I need to
consider when restart?
Thank you
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
<http://www.max-centre.eu/quantum-espresso>)
users mailing [email protected]
<mailto:[email protected]>
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
