[Wien] k-point parallel problem
liyh
lyhua at fudan.edu.cn
Fri Jan 7 02:16:44 CET 2005
Dear Blaha,
Could you tell me which parameter we should change in our queuing sysytem. We are using a pbs system.
Then I will talk about it with our system manager.
Best wish to you!
Yonghua
>You have a problem with your queuing system. Aparently there is a time
>limit of 60 seconds, so small jobs (Si) run, longer don't.
>You need to check with your system manager.
>
>> Dear Peter Blaha,
>>
>> This time we calculate the bulk of Si. which is much smaller.there is no problem in k-point parral. Only in the end the state flag is "E" when we use "qstat -a". We use 12 nodes and 24 CPUs, 74 k-points.
>> Then we test a larger system (16 atoms).
>> 1,we run the program directly in the masternode. " run_lapw -i 1 -ec 0.0001", there is no problem.
>> 2,Then we submit the program using pbs and run it in serial model.
>> qsub ./wienifc.pbs -l nodes=1:ppn=1 -q high -N sisiy4
>> the command line in wienifc.pbs is: "run_lapw -i 1 -ec 0.0001 >run.output"
>> I use the "top" comand look at the process. It gave an error message after the lapw1c run 1min.
>> "You should submit the program use pbs."
>>
>> the dayfile is:
>>
>> Calculating sisiy4 in /people/gong/lyhua/ADP/sisiy4
>> on comp10 with PID 19621
>>
>> start (Thu Jan 6 11:13:48 CST 2005) with lapw0 (1/20 to go)
>> > lapw0 (11:13:48) 31.840u 0.310s 0:32.58 98.6% 0+0k 0+0io 172pf+0w
>> > lapw1 -c (11:14:20) Killed
>> 38.870u 0.680s 0:39.85 99.2% 0+0k 0+0io 238pf+0w
>>
>> > stop error
>> ~
>> the lapw1.error is
>>
>> Error in LAPW1
>>
>> 3, then we test the parallel model.
>> qsub ./wienifc.pbs -l nodes=2:ppn=1 -q high -N sisiy4
>> the comand line in wienifc.pbs is:
>> "run_lapw -i 1 -ec 0.0001 -p > run.output"
>> as above it give an error message:
>> "You should submit the program use pbs"
>>
>> ______________________________
>> the case.dayfile is:
>>
>>
>> Calculating sisiy4 in /people/gong/lyhua/ADP/sisiy4
>> on comp10 with PID 16465
>>
>> start (Thu Jan 6 10:38:00 CST 2005) with lapw0 (1/20 to go)
>> > lapw0 -p (10:38:00) starting parallel lapw0 at Thu Jan 6 10:38:00 CST 2005
>> --------
>> running lapw0 in single mode
>> 32.020u 0.350s 0:33.17 97.5% 0+0k 0+0io 1823pf+0w
>> > lapw1 -c -p (10:38:33) starting parallel lapw1 at Thu Jan 6 10:38:33 CST 2005
>> -> starting parallel LAPW1 jobs at Thu Jan 6 10:38:33 CST 2005
>> running LAPW1 in parallel mode (using .machines)
>> 2 number_of_parallel_jobs
>> ** LAPW1 crashed!
>> 0.150u 0.220s 1:28.34 0.4% 0+0k 0+0io 21900pf+0w
>>
>> > stop error
>> _______________________________________
>>
>> the lapw1.error is:
>>
>>
>> ** Error in Parallel LAPW1
>> ** LAPW1 STOPPED at Thu Jan 6 10:40:01 CST 2005
>> ** check ERROR FILES!
>> Error in LAPW1
>> Error in LAPW1
>> _______________________________________
>>
>> the end of case.output1 is:
>>
>> 1.3497807 1.3891706 1.3891808 1.3933397 1.3935096
>> 1.4114150 1.4118608 1.4128885 1.4133827
>> 0 EIGENVALUES BELOW THE ENERGY -7.00000
>> ********************************************************
>>
>> NUMBER OF K-POINTS: 1
>> ===> TOTAL CPU TIME: 204.3 (INIT = 0.8 + K-POINTS = 203.6)
>> > SUM OF WALL CLOCK TIMES: 206.6 (INIT = 1.0 + K-POINTS = 205.5)
>> Maximum WALL clock time: 207.062600851059
>> Maximum CPU time: 204.480000000000
>> ________________________________________
>>
>> the case.scf1 is empty.
>>
>>
>>
>>
>> >First: please use a number of processors which is compatible with the
>> >number of k-points you have (check case.klist). What I mean is: I suppose
>> >you have 18 k-points, so reasonable machine-numbers are 18 (each processor
>> >does 1 k-point), 9 (each does 2), 6, 3 or 2.
>> >Of course you can use 16, but the program will be not faster (in fact even
>> >slower since summation takes longer) than with 9 processors.
>> >
>> >Second: Your message is not quite clear: it failed when run the lapw1para...
>> > There is no problem when run lapw1 in parral. ???
>> >
>> >Third: In your script please change (sorry, it was incorrect on the faq page
>> > but it should not be responsible for the problems)
>> >echo 'extrafine' >>.machines to
>> >echo 'extrafine:1' >>.machines
>> >
>> >Fourth: Could be a timelimit the cause for these problems ? Increase the
>> >cpu-time-limit of the pbs job.
>> >In addition your pbs job should produce output and error files and they may
>> >contain further information.
>> >
>> >
>> >
>> > P.Blaha
>> >--------------------------------------------------------------------------
>> >Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> >Phone: +43-1-58801-15671 FAX: +43-1-58801-15698
>> >Email: blaha at theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/
>> >--------------------------------------------------------------------------
>> >
>> >_______________________________________________
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>> >Wien at zeus.theochem.tuwien.ac.at
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>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>>
>> ?
>> ?!
>>
>>
>> liyh
>> lyhua at fudan.edu.cn
>> 2005-01-06
>>
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
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>>
>
>
> P.Blaha
>--------------------------------------------------------------------------
>Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>Phone: +43-1-58801-15671 FAX: +43-1-58801-15698
>Email: blaha at theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/
>--------------------------------------------------------------------------
>
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致
礼！
liyh
lyhua at fudan.edu.cn
2005-01-07
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