testing Pelegant on elegantExamples
Posted: 15 Jul 2013, 11:22
by marlibgin
I am testing Pelegant
[This is elegant 25.0.3, Mar 2 2012, by M. Borland, W. Guo, V. Sajaev, Y. Wang, Y. Wu, and A. Xiao.
Parallelized by Y. Wang, H. Shang, and M. Borland.]
on our local cluster. I have started with some examples taken from elegantExamples/parallel/DA,FMA,LMA. All worked fine. I then (maybe naively) tried to run another, randomly chosen case with Pelegant. I have picked up elegantExamples/acceptance/energyscan1 and submitted a job with Pelegant.
qsub -V -q ap-high.q -pe openmpi 4 /dls_sw/apps/openmpi/1.6.5/64/bin/mpirun Pelegant run.ele
The job crashed leaving a log file with this message:
Fatal error in PMPI_Bcast: Invalid root, error stack:
PMPI_Bcast(1478): MPI_Bcast(buf=0x993788, count=1, MPI_LONG, root=1, MPI_COMM_WORLD) failed
PMPI_Bcast(1440): Invalid root (value given was 1)
--------------------------------------------------------------------------
orterun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
My question is. Can any of the elegantExamples be run with Pelegant, or are there some limitations on its use?
Concerning the error above, is there any advice/clue about it?
Thanks very much for the kind attention , Marco
Re: testing Pelegant on elegantExamples
Posted: 15 Oct 2015, 20:47
by tiansk
I meet an other problem.
I test the Pelegant with the example
/home/tiansk/elegantExamples/acceptance/energyScan1
as follow,tThere is no error in the process of simulation
mpiexec -np 2 Pelegant run.ele
Running elegant at Fri Oct 16 09:27:24 2015
This is elegant 28.1.0, Jul 24 2015, by M. Borland, M. Carla', N. Carmignani, M. Ehrlichman, L. Emery, W. Guo, V. Sajaev, R. Soliday, C.-X. Wang, Y. Wang, Y. Wu, and A. Xiao.
Parallelized by Y. Wang, H. Shang, and M. Borland.
Link date: Jul 24 2015 11:14:16
statistics: ET: 00:00:00 CP: 0.00 BIO:0 DIO:0 PF:0 MEM:20048
&run_setup
lattice = lattice.lte,
use_beamline = bl,
rootname = {NULL},
output = {NULL},
centroid = %s.cen,
sigma = %s.sig,
final = %s.fin,
acceptance = %s.acc,
losses = %s.los,
magnets = {NULL},
semaphore_file = {NULL},
parameters = {NULL},
combine_bunch_statistics = 0,
wrap_around = 1,
final_pass = 0,
default_order = 2,
concat_order = 0,
print_statistics = 0,
show_element_timing = 0,
monitor_memory_usage = 0,
random_number_seed = 987654321,
correction_iterations = 1,
echo_lattice = 0,
p_central = 0.000000000000000e+00,
p_central_mev = 1.000000000000000e+03,
always_change_p0 = 0,
load_balancing_on = 0,
random_sequence_No = 1,
expand_for = {NULL},
tracking_updates = 1,
search_path = {NULL},
element_divisions = 0,
&end
Seeding random number generators (mode=3)
length of beamline BL per pass: 5.109999999999996e+01 m
statistics: ET: 00:00:00 CP: 0.00 BIO:0 DIO:0 PF:0 MEM:20155
&run_control
n_steps = 1,
bunch_frequency = 0.000000000000000e+00,
n_indices = 1,
n_passes = 1,
reset_rf_for_each_step = 1,
first_is_fiducial = 0,
restrict_fiducialization = 0,
reset_scattering_seed = 0,
&end
statistics: ET: 00:00:00 CP: 0.00 BIO:0 DIO:0 PF:0 MEM:20155
&vary_element
index_number = 0,
index_limit = 21,
name = MALIN,
item = DP,
initial = -5.000000000000000e-01,
final = 5.000000000000000e-01,
differential = 0,
geometric = 0,
multiplicative = 0,
enumeration_file = {NULL},
enumeration_column = {NULL},
&end
statistics: ET: 00:00:00 CP: 0.00 BIO:0 DIO:0 PF:0 MEM:20155
&bunched_beam
bunch = %s.bun,
n_particles_per_bunch = 1000,
time_start = 0.000000000000000e+00,
matched_to_cell = {NULL},
emit_x = 1.000000000000000e-06,
emit_nx = 0.000000000000000e+00,
beta_x = 1.000000000000000e+02,
alpha_x = 0.000000000000000e+00,
eta_x = 0.000000000000000e+00,
etap_x = 0.000000000000000e+00,
emit_y = 1.000000000000000e-06,
emit_ny = 0.000000000000000e+00,
beta_y = 1.000000000000000e+02,
alpha_y = 0.000000000000000e+00,
eta_y = 0.000000000000000e+00,
etap_y = 0.000000000000000e+00,
use_twiss_command_values = 0,
Po = 1.956950762296902e+03,
sigma_dp = 0.000000000000000e+00,
sigma_s = 0.000000000000000e+00,
dp_s_coupling = 0.000000000000000e+00,
emit_z = 0.000000000000000e+00,
beta_z = 0.000000000000000e+00,
alpha_z = 0.000000000000000e+00,
momentum_chirp = 0.000000000000000e+00,
one_random_bunch = 1,
save_initial_coordinates = 1,
limit_invariants = 0,
symmetrize = 0,
halton_sequence[0] = 0, 0, 0,
halton_radix[0] = 0, 0, 0, 0, 0, 0,
optimized_halton = 0,
randomize_order[0] = 0, 0, 0,
limit_in_4d = 0,
enforce_rms_values[0] = 0, 0, 0,
distribution_cutoff[0] = 1.000000000000000e+00, 1.000000000000000e+00, 2.000000000000000e+00,
distribution_type[0] = uniform-ellipse, uniform-ellipse, gaussian,
centroid[0] = 0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00, 0.000000000000000e+00,
0.000000000000000e+00, 0.000000000000000e+00,
first_is_fiducial = 0,
&end
statistics: ET: 00:00:00 CP: 0.00 BIO:0 DIO:0 PF:0 MEM:20158
&track
center_on_orbit = 0,
center_momentum_also = 1,
offset_by_orbit = 0,
offset_momentum_also = 1,
soft_failure = 1,
use_linear_chromatic_matrix = 0,
longitudinal_ring_only = 0,
ibs_only = 0,
stop_tracking_particle_limit = -1,
&end
vary counter reset
121 matrices (re)computed
tracking step 1.1
generating bunch 1.1
dumping bunch
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:24: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:24: Rf phases/references reset.
188 particles transmitted, total effort of 188 particle-turns
125440 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 188, n_total = 1000, n_lost = 812
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:00 CP: 0.07 BIO:0 DIO:0 PF:0 MEM:22770
counter advanced: 1
values advanced: -4.500000e-01
1 matrices (re)computed
tracking step 2.2
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:24: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:24: Rf phases/references reset.
206 particles transmitted, total effort of 206 particle-turns
257808 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 206, n_total = 1000, n_lost = 794
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:00 CP: 0.12 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 2
values advanced: -4.000000e-01
1 matrices (re)computed
tracking step 3.3
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:24: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:24: Rf phases/references reset.
227 particles transmitted, total effort of 227 particle-turns
398168 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 227, n_total = 1000, n_lost = 773
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:00 CP: 0.17 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 3
values advanced: -3.500000e-01
1 matrices (re)computed
tracking step 4.4
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:24: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:24: Rf phases/references reset.
241 particles transmitted, total effort of 241 particle-turns
545536 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 241, n_total = 1000, n_lost = 759
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:00 CP: 0.22 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 4
values advanced: -3.000000e-01
1 matrices (re)computed
tracking step 5.5
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:24: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:24: Rf phases/references reset.
246 particles transmitted, total effort of 246 particle-turns
698176 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 246, n_total = 1000, n_lost = 754
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.27 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 5
values advanced: -2.500000e-01
1 matrices (re)computed
tracking step 6.6
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
257 particles transmitted, total effort of 257 particle-turns
855784 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 257, n_total = 1000, n_lost = 743
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.34 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 6
values advanced: -2.000000e-01
1 matrices (re)computed
tracking step 7.7
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
265 particles transmitted, total effort of 265 particle-turns
1018212 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 265, n_total = 1000, n_lost = 735
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.39 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 7
values advanced: -1.500000e-01
1 matrices (re)computed
tracking step 8.8
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
264 particles transmitted, total effort of 264 particle-turns
1182532 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 264, n_total = 1000, n_lost = 736
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.45 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 8
values advanced: -1.000000e-01
1 matrices (re)computed
tracking step 9.9
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
264 particles transmitted, total effort of 264 particle-turns
1348228 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 264, n_total = 1000, n_lost = 736
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.51 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 9
values advanced: -5.000000e-02
1 matrices (re)computed
tracking step 10.10
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
267 particles transmitted, total effort of 267 particle-turns
1517400 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 267, n_total = 1000, n_lost = 733
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.56 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 10
values advanced: 0.000000e+00
1 matrices (re)computed
tracking step 11.11
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
275 particles transmitted, total effort of 275 particle-turns
1689476 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 275, n_total = 1000, n_lost = 725
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:01 CP: 0.62 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 11
values advanced: 5.000000e-02
1 matrices (re)computed
tracking step 12.12
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:25: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:25: Rf phases/references reset.
281 particles transmitted, total effort of 281 particle-turns
1865240 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 281, n_total = 1000, n_lost = 719
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 0.68 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 12
values advanced: 1.000000e-01
1 matrices (re)computed
tracking step 13.13
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
281 particles transmitted, total effort of 281 particle-turns
2043620 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 281, n_total = 1000, n_lost = 719
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 0.75 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 13
values advanced: 1.500000e-01
1 matrices (re)computed
tracking step 14.14
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
280 particles transmitted, total effort of 280 particle-turns
2224624 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 280, n_total = 1000, n_lost = 720
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 0.82 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 14
values advanced: 2.000000e-01
1 matrices (re)computed
tracking step 15.15
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
288 particles transmitted, total effort of 288 particle-turns
2409104 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 288, n_total = 1000, n_lost = 712
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 0.88 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 15
values advanced: 2.500000e-01
1 matrices (re)computed
tracking step 16.16
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
292 particles transmitted, total effort of 292 particle-turns
2595304 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 292, n_total = 1000, n_lost = 708
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 0.94 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 16
values advanced: 3.000000e-01
1 matrices (re)computed
tracking step 17.17
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
296 particles transmitted, total effort of 296 particle-turns
2782676 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 296, n_total = 1000, n_lost = 704
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 1.01 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 17
values advanced: 3.500000e-01
1 matrices (re)computed
tracking step 18.18
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
306 particles transmitted, total effort of 306 particle-turns
2972816 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 306, n_total = 1000, n_lost = 694
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:02 CP: 1.08 BIO:0 DIO:0 PF:0 MEM:22816
counter advanced: 18
values advanced: 4.000000e-01
1 matrices (re)computed
tracking step 19.19
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:26: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:26: Rf phases/references reset.
312 particles transmitted, total effort of 312 particle-turns
3164708 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 312, n_total = 1000, n_lost = 688
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:03 CP: 1.15 BIO:0 DIO:0 PF:0 MEM:22849
counter advanced: 19
values advanced: 4.500000e-01
1 matrices (re)computed
tracking step 20.20
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:27: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:27: Rf phases/references reset.
320 particles transmitted, total effort of 320 particle-turns
3358608 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 320, n_total = 1000, n_lost = 680
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:03 CP: 1.22 BIO:0 DIO:0 PF:0 MEM:22849
counter advanced: 20
values advanced: 5.000000e-01
1 matrices (re)computed
tracking step 21.21
0 matrices (re)computed after correction
tracking 1000 particles
16 Oct 15 09:27:27: This step establishes energy profile vs s (fiducial beam).
16 Oct 15 09:27:27: Rf phases/references reset.
326 particles transmitted, total effort of 326 particle-turns
3552768 multipole kicks done
Dumping acceptance output...done.
Dumping lost-particle data...
n_left = 326, n_total = 1000, n_lost = 674
done.
Dumping centroid data...done.
Dumping sigma data...done.
Dumping final properties data...done.
Post-tracking output completed.
Tracking step completed ET: 00:00:03 CP: 1.28 BIO:0 DIO:0 PF:0 MEM:22849
Finished tracking.
End of input data encountered.
statistics: ET: 00:00:03 CP: 1.28 BIO:0 DIO:0 PF:0 MEM:22846
=====================================================================================
Thanks for using Pelegant. Please cite the following references in your publications:
M. Borland, "elegant: A Flexible SDDS-Compliant Code for Accelerator Simulation,"
Advanced Photon Source LS-287, September 2000.
Y. Wang and M. Borland, "Pelegant: A Parallel Accelerator Simulation Code for
Electron Generation and Tracking", Proceedings of the 12th Advanced Accelerator
Concepts Workshop, AIP Conf. Proc. 877, 241 (2006).
If you use a modified version, please indicate this in all publications.
=====================================================================================
but,when I try to plot some pictures,I meet an error report.
sddsplot -column=x,y run.los -split=page -sep=page -graph=dot -samescales
warning: problem reading data from file run.los
Error:
Unable to read page--unrecognized data mode (SDDS_ReadPageSparse)
error: no datasets to plot
I think in the output file run.los,there is no data.
I run the command
mpiexec -np 2 Pelegant run.ele
in the cygwin on a windows computer,the program is running very well andthere are no error report!