Hello Erik, I haven't found any recover.par. May be I have an older version of the simfactory. So, I tried just to run with my par file. First i used this command ./simfactory/sim create-submit recover_test2 --parfile=par/myparfile.par --procs=8 --walltime=0:10:0 then ./simfactory/sim submit recover_test2 --parfile=par/myparfile.par --procs=8 --walltime=0:10:0 and I got the following error message: Simulation Factory: [log] Submitting: [log] Restart id "0000" is active Aborting.
Thank you. Petr.
Here is a LOG file: LOG FILE for simulation "recover_test2" ================================================================================
-------------------------------------------------------------------------------- 2011-11-21 10:08:19 ettest04@qb4.loni.org: Skeleton created Job directory: "/scratch/ettest04/simulations/recover_test2" Machine: "queenbee" Simulation id: "simulation-recover_test2-queenbee-qb4.loni.org-ettest04-2011.11.21-10.08.19-8396" Source dir: "/home/ettest04/Cactus" Configuration: "sim" Config id: "config-sim-qb4.loni.org-home-ettest04-Cactus" Build id: "build-sim-qb4.loni.org-ettest04-2011.11.08-19.43.33-31159" Executable: "/home/ettest04/Cactus/exe/cactus_sim" Option list: "configs/sim/OptionList" Script file: "/home/ettest04/Cactus/configs/sim/ScriptFile" Parameter file: "par/rns_64_25km_1lev_tvd_vanleerMC2_hlle_MADM_1.432_HarmF_2_HarmN_1_g12.par" --------------------------------------------------------------------------------
-------------------------------------------------------------------------------- 2011-11-21 10:08:19 ettest04@qb4.loni.org: Submitting: Using restart id "0000" Not recovering since there are no restart ids Created restart directory Activated restart directory Created job script Created parameter file About to submit job Executing: cd /scratch/ettest04/simulations/recover_test2/output-0000 && { qsub SIMFACTORY/ScriptFile ; } Submitted job Job id is "583945" --------------------------------------------------------------------------------
-------------------------------------------------------------------------------- 2011-11-21 10:47:32 ettest04@qb4.loni.org: Submitting: Restart id "0000" is active --------------------------------------------------------------------------------
Tha
On Sun, Nov 13, 2011 at 8:48 AM, Erik Schnetter schnetter@cct.lsu.eduwrote:
Petr
In most cases, a simple "submit" (with the same simulation name) should suffice. --from-restart-id allows restarting from a particular restart, in case you don't want to restart from the previous restart.
Simfactory has a parameter file simfactory/etc/parfiles/recover.par. Could you try this? You would submit it on a single process, let it run for a few minutes, and then submit it again:
./bin/sim submit recover --parfile=simfactory/etc/parfiles/recover.par --walltime=0:10:0
and later
./bin/sim submit recover --parfile=simfactory/etc/parfiles/recover.par --walltime=0:10:0 This should work.
-erik
On Sat, Nov 12, 2011 at 8:57 PM, Petr Tsatsin ptsatsin@fau.edu wrote:
Hello,
I'm trying to restart my simulation on queenbee using simfactory. I tried "./sim submit --from-restart-id ..." and I got "Simulation Factory: [log] Submitting: [log] Using restart id "0002" [log] Requested recovering from restart id "0" [log] Could not find checkpoint files in restart id "0000" Aborting.'' Inside my parameter file for this simulation I set up HDF5 check
pointing in
following way: "IO::out_dir = $parfile IOHDF5::checkpoint = "yes" IO::checkpoint_every = 100000 IO::checkpoint_file = $parfile IO::checkpoint_dir = $parfile IO::recover="auto" IO::recover_file = $parfile IO::recover_dir = $parfile" I checked that h5 check point files are actually inside the output-0000 directory. Any suggestions how can I restart the my simulation from HDF5 checkpoint with a simfactory? Thank you. -- Petr Tsatsin Graduate Student- Department of Physics Charles E. Schmidt College of Science Florida Atlantic University (561)-297-3386 ptsatin@fau.edu, ptsatsin@gmail.com
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-- Erik Schnetter schnetter@cct.lsu.edu http://www.cct.lsu.edu/~eschnett/