Errors with Pelegant on Debian

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tiansk
Posts: 39
Joined: 16 Mar 2012, 22:01

Errors with Pelegant on Debian

Post by tiansk » 13 Oct 2015, 21:05

I am testing Pelegant

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.

I run it on a Debian system with 40 CPUs with the file in the ‘elegantExamples/parallel/’,but it turn out some error

mpiexec -np 2 Pelegant fma1p.ele

Running elegant at Wed Oct 14 09:42:39 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 14:11:56
statistics: ET: 00:00:00 CP: 0.05 BIO:0 DIO:0 PF:0 MEM:324751
&run_setup
lattice = parTrack.lte,
use_beamline = par0,
rootname = {NULL},
output = {NULL},
centroid = {NULL},
sigma = {NULL},
final = {NULL},
acceptance = {NULL},
losses = {NULL},
magnets = {NULL},
semaphore_file = %s.done,
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 = 4.500000000000000e+02,
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)
computed value for AP.X_MAX is 6.100000000000000e-02
computed value for AP.Y_MAX is 1.950000000000000e-02
computed value for RF.FREQ is 9.775824092965543e+06
length of beamline PAR0 per pass: 3.066670000000001e+01 m
statistics: ET: 00:00:00 CP: 0.07 BIO:0 DIO:0 PF:0 MEM:324817
&run_control
n_steps = 1,
bunch_frequency = 0.000000000000000e+00,
n_indices = 0,
n_passes = 256,
reset_rf_for_each_step = 1,
first_is_fiducial = 0,
restrict_fiducialization = 0,
reset_scattering_seed = 0,
&end
statistics: ET: 00:00:00 CP: 0.08 BIO:0 DIO:0 PF:0 MEM:333009
&twiss_output
filename = %s.twi,
matched = 1,
output_at_each_step = 0,
output_before_tune_correction = 0,
final_values_only = 0,
statistics = 0,
radiation_integrals = 0,
beta_x = 1.000000000000000e+00,
alpha_x = 0.000000000000000e+00,
eta_x = 0.000000000000000e+00,
etap_x = 0.000000000000000e+00,
beta_y = 1.000000000000000e+00,
alpha_y = 0.000000000000000e+00,
eta_y = 0.000000000000000e+00,
etap_y = 0.000000000000000e+00,
reference_file = {NULL},
reference_element = {NULL},
reference_element_occurrence = 0,
reflect_reference_values = 0,
concat_order = 3,
higher_order_chromaticity = 0,
higher_order_chromaticity_points = 5,
higher_order_chromaticity_range = 4.000000000000000e-04,
quick_higher_order_chromaticity = 0,
chromatic_tune_spread_half_range = 0.000000000000000e+00,
cavities_are_drifts_if_matched = 1,
compute_driving_terms = 0,
leading_order_driving_terms_only = 0,
s_dependent_driving_terms_file = {NULL},
local_dispersion = 1,
n_periods = 1,
&end
96 matrices recomputed for periodic Twiss parameter computation
Error:
unable to open file fma1p.twi for writing--file is locked (SDDS_InitializeOutput)
Running elegant at Wed Oct 14 09:42:39 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 14:11:56
statistics: ET: 00:00:00 CP: 0.15 BIO:0 DIO:0 PF:0 MEM:332943
&run_setup
lattice = parTrack.lte,
use_beamline = par0,
rootname = {NULL},
output = {NULL},
centroid = {NULL},
sigma = {NULL},
final = {NULL},
acceptance = {NULL},
losses = {NULL},
magnets = {NULL},
semaphore_file = %s.done,
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 = 4.500000000000000e+02,
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)
computed value for AP.X_MAX is 6.100000000000000e-02
computed value for AP.Y_MAX is 1.950000000000000e-02
computed value for RF.FREQ is 9.775824092965543e+06
length of beamline PAR0 per pass: 3.066670000000001e+01 m
statistics: ET: 00:00:00 CP: 0.17 BIO:0 DIO:0 PF:0 MEM:333009
&run_control
n_steps = 1,
bunch_frequency = 0.000000000000000e+00,
n_indices = 0,
n_passes = 256,
reset_rf_for_each_step = 1,
first_is_fiducial = 0,
restrict_fiducialization = 0,
reset_scattering_seed = 0,
&end
statistics: ET: 00:00:00 CP: 0.17 BIO:0 DIO:0 PF:0 MEM:333009
&twiss_output
filename = %s.twi,
matched = 1,
output_at_each_step = 0,
output_before_tune_correction = 0,
final_values_only = 0,
statistics = 0,
radiation_integrals = 0,
beta_x = 1.000000000000000e+00,
alpha_x = 0.000000000000000e+00,
eta_x = 0.000000000000000e+00,
etap_x = 0.000000000000000e+00,
beta_y = 1.000000000000000e+00,
alpha_y = 0.000000000000000e+00,
eta_y = 0.000000000000000e+00,
etap_y = 0.000000000000000e+00,
reference_file = {NULL},
reference_element = {NULL},
reference_element_occurrence = 0,
reflect_reference_values = 0,
concat_order = 3,
higher_order_chromaticity = 0,
higher_order_chromaticity_points = 5,
higher_order_chromaticity_range = 4.000000000000000e-04,
quick_higher_order_chromaticity = 0,
chromatic_tune_spread_half_range = 0.000000000000000e+00,
cavities_are_drifts_if_matched = 1,
compute_driving_terms = 0,
leading_order_driving_terms_only = 0,
s_dependent_driving_terms_file = {NULL},
local_dispersion = 1,
n_periods = 1,
&end
periodic Twiss parameters (chromaticity valid for fully second-order calculation only!):
beta alpha nu eta eta' dnu/d(dp/p) dbeta/(dp/p) accept.
m 1/2pi m 1/2pi m mm-mrad
--------------------------------------------------------------------------------------------------------------------
x: 2.001130e+00 -1.013079e-15 2.169700e+00 5.415971e-03 9.272097e-16 -6.290009e-01 -1.506821e+01 7.767044e+02
y: 9.802921e+00 1.186551e-15 1.216952e+00 0.000000e+00 0.000000e+00 3.772852e+00 -1.765334e+02 2.773467e+01
x acceptance limited by L5 ending at 2.342503e+01 m
y acceptance limited by B1 ending at 1.285168e+01 m
statistics: ET: 00:00:00 CP: 1.95 BIO:0 DIO:0 PF:0 MEM:423280
&frequency_map
output = %s.fma,
xmin = -2.000000000000000e-02,
xmax = 2.000000000000000e-02,
ymin = 1.000000000000000e-06,
ymax = 2.000000000000000e-02,
delta_min = 0.000000000000000e+00,
delta_max = 0.000000000000000e+00,
nx = 41,
ny = 41,
ndelta = 1,
verbosity = 1,
include_changes = 1,
quadratic_spacing = 0,
&end
tracking step 1
Tracking fiducial particle
14 Oct 15 09:42:39: This step establishes energy profile vs s (fiducial beam).
14 Oct 15 09:42:39: Rf phases/references reset.
Finished all tracking steps.
Finished frequency map analysis.
End of input data encountered.
statistics: ET: 00:01:32 CP: 94.61 BIO:0 DIO:0 PF:0 MEM:424653
=====================================================================================
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.
=====================================================================================
Creating semaphore file fma1p.done
--------------------------------------------------------------------------
mpiexec noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------



I also test the example on Scientific Linux release 7.1 (Nitrogen)
mpiexec -np 2 Pelegant fma1p.ele





Running elegant at Wed Oct 14 09:30:46 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 = parTrack.lte,
use_beamline = par0,
rootname = {NULL},
output = {NULL},
centroid = {NULL},
sigma = {NULL},
final = {NULL},
acceptance = {NULL},
losses = {NULL},
magnets = {NULL},
semaphore_file = %s.done,
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 = 4.500000000000000e+02,
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)
computed value for AP.X_MAX is 6.100000000000000e-02
computed value for AP.Y_MAX is 1.950000000000000e-02
computed value for RF.FREQ is 9.775824092965543e+06
length of beamline PAR0 per pass: 3.066670000000001e+01 m
statistics: ET: 00:00:00 CP: 0.00 BIO:0 DIO:0 PF:0 MEM:20114
&run_control
n_steps = 1,
bunch_frequency = 0.000000000000000e+00,
n_indices = 0,
n_passes = 256,
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:20114
&twiss_output
filename = %s.twi,
matched = 1,
output_at_each_step = 0,
output_before_tune_correction = 0,
final_values_only = 0,
statistics = 0,
radiation_integrals = 0,
beta_x = 1.000000000000000e+00,
alpha_x = 0.000000000000000e+00,
eta_x = 0.000000000000000e+00,
etap_x = 0.000000000000000e+00,
beta_y = 1.000000000000000e+00,
alpha_y = 0.000000000000000e+00,
eta_y = 0.000000000000000e+00,
etap_y = 0.000000000000000e+00,
reference_file = {NULL},
reference_element = {NULL},
reference_element_occurrence = 0,
reflect_reference_values = 0,
concat_order = 3,
higher_order_chromaticity = 0,
higher_order_chromaticity_points = 5,
higher_order_chromaticity_range = 4.000000000000000e-04,
quick_higher_order_chromaticity = 0,
chromatic_tune_spread_half_range = 0.000000000000000e+00,
cavities_are_drifts_if_matched = 1,
compute_driving_terms = 0,
leading_order_driving_terms_only = 0,
s_dependent_driving_terms_file = {NULL},
local_dispersion = 1,
n_periods = 1,
&end
96 matrices recomputed for periodic Twiss parameter computation
periodic Twiss parameters (chromaticity valid for fully second-order calculation only!):
beta alpha nu eta eta' dnu/d(dp/p) dbeta/(dp/p) accept.
m 1/2pi m 1/2pi m mm-mrad
--------------------------------------------------------------------------------------------------------------------
x: 2.001130e+00 -1.013079e-15 2.169700e+00 5.415971e-03 9.272097e-16 -6.290009e-01 -1.506821e+01 7.767044e+02
y: 9.802921e+00 1.186551e-15 1.216952e+00 0.000000e+00 0.000000e+00 3.772852e+00 -1.765334e+02 2.773467e+01
x acceptance limited by L5 ending at 2.342503e+01 m
y acceptance limited by B1 ending at 1.285168e+01 m
statistics: ET: 00:00:00 CP: 0.01 BIO:0 DIO:0 PF:0 MEM:20273
&frequency_map
output = %s.fma,
xmin = -2.000000000000000e-02,
xmax = 2.000000000000000e-02,
ymin = 1.000000000000000e-06,
ymax = 2.000000000000000e-02,
delta_min = 0.000000000000000e+00,
delta_max = 0.000000000000000e+00,
nx = 41,
ny = 41,
ndelta = 1,
verbosity = 1,
include_changes = 1,
quadratic_spacing = 0,
&end
tracking step 1
Tracking fiducial particle
14 Oct 15 09:30:46: This step establishes energy profile vs s (fiducial beam).
14 Oct 15 09:30:46: Rf phases/references reset.
About 1.1% done after 1 s wall time, completion expected in about 92.3889 s
About 2.5% done after 1 s wall time, completion expected in about 39.0238 s
About 3.6% done after 2 s wall time, completion expected in about 54.0333 s
About 5.0% done after 3 s wall time, completion expected in about 57.0357 s
About 6.1% done after 4 s wall time, completion expected in about 61.9216 s
About 7.4% done after 4 s wall time, completion expected in about 50.2258 s
About 8.4% done after 5 s wall time, completion expected in about 54.1901 s
About 9.9% done after 6 s wall time, completion expected in about 54.759 s
About 10.9% done after 6 s wall time, completion expected in about 48.8152 s
About 12.3% done after 7 s wall time, completion expected in about 50.1214 s
About 13.3% done after 8 s wall time, completion expected in about 52.0357 s
About 14.8% done after 9 s wall time, completion expected in about 52.004 s
About 15.8% done after 10 s wall time, completion expected in about 53.1955 s
About 17.1% done after 10 s wall time, completion expected in about 48.3681 s
About 18.2% done after 11 s wall time, completion expected in about 49.4281 s
About 19.6% done after 12 s wall time, completion expected in about 49.1273 s
About 20.7% done after 13 s wall time, completion expected in about 49.796 s
About 22.0% done after 13 s wall time, completion expected in about 46.0622 s
About 23.1% done after 14 s wall time, completion expected in about 46.6546 s
About 24.5% done after 15 s wall time, completion expected in about 46.2015 s
About 25.6% done after 16 s wall time, completion expected in about 46.5488 s
About 26.9% done after 16 s wall time, completion expected in about 43.5044 s
About 28.0% done after 17 s wall time, completion expected in about 43.8021 s
About 29.4% done after 18 s wall time, completion expected in about 43.251 s
About 30.5% done after 19 s wall time, completion expected in about 43.3809 s
About 31.8% done after 19 s wall time, completion expected in about 40.8109 s
About 32.8% done after 20 s wall time, completion expected in about 40.9058 s
About 34.3% done after 21 s wall time, completion expected in about 40.2865 s
About 35.3% done after 22 s wall time, completion expected in about 40.2593 s
About 36.6% done after 22 s wall time, completion expected in about 38.0357 s
About 37.7% done after 23 s wall time, completion expected in about 37.9826 s
About 39.1% done after 24 s wall time, completion expected in about 37.3131 s
About 40.2% done after 25 s wall time, completion expected in about 37.1672 s
About 41.5% done after 25 s wall time, completion expected in about 35.2077 s
About 42.6% done after 26 s wall time, completion expected in about 35.0419 s
About 44.0% done after 27 s wall time, completion expected in about 34.3338 s
About 45.1% done after 28 s wall time, completion expected in about 34.095 s
About 46.4% done after 28 s wall time, completion expected in about 32.3436 s
About 47.5% done after 29 s wall time, completion expected in about 32.089 s
About 48.9% done after 30 s wall time, completion expected in about 31.3504 s
About 50.0% done after 31 s wall time, completion expected in about 31.0369 s
About 51.3% done after 31 s wall time, completion expected in about 29.4536 s
About 52.3% done after 32 s wall time, completion expected in about 29.1273 s
About 53.8% done after 33 s wall time, completion expected in about 28.3639 s
About 54.8% done after 34 s wall time, completion expected in about 27.9892 s
About 56.2% done after 34 s wall time, completion expected in about 26.5445 s
About 57.2% done after 35 s wall time, completion expected in about 26.159 s
About 58.7% done after 36 s wall time, completion expected in about 25.3753 s
About 59.7% done after 37 s wall time, completion expected in about 24.9492 s
About 61.0% done after 37 s wall time, completion expected in about 23.6209 s
About 62.1% done after 38 s wall time, completion expected in about 23.1858 s
About 63.5% done after 39 s wall time, completion expected in about 22.3848 s
About 64.6% done after 40 s wall time, completion expected in about 21.9153 s
About 65.9% done after 40 s wall time, completion expected in about 20.6859 s
About 67.0% done after 41 s wall time, completion expected in about 20.2087 s
About 68.4% done after 42 s wall time, completion expected in about 19.393 s
About 69.5% done after 43 s wall time, completion expected in about 18.8861 s
About 70.8% done after 43 s wall time, completion expected in about 17.742 s
About 71.9% done after 44 s wall time, completion expected in about 17.2285 s
About 73.3% done after 45 s wall time, completion expected in about 16.4002 s
About 74.4% done after 46 s wall time, completion expected in about 15.8608 s
About 75.7% done after 46 s wall time, completion expected in about 14.7909 s
About 76.7% done after 47 s wall time, completion expected in about 14.2457 s
About 78.2% done after 48 s wall time, completion expected in about 13.4064 s
About 79.2% done after 49 s wall time, completion expected in about 12.8386 s
About 80.5% done after 49 s wall time, completion expected in about 11.8338 s
About 81.6% done after 50 s wall time, completion expected in about 11.2609 s
About 83.0% done after 51 s wall time, completion expected in about 10.4119 s
About 84.1% done after 52 s wall time, completion expected in about 9.81895 s
About 85.4% done after 52 s wall time, completion expected in about 8.87187 s
About 86.5% done after 53 s wall time, completion expected in about 8.27442 s
About 87.9% done after 54 s wall time, completion expected in about 7.41678 s
About 89.0% done after 54 s wall time, completion expected in about 6.67781 s
About 90.3% done after 55 s wall time, completion expected in about 5.9058 s
About 91.4% done after 55 s wall time, completion expected in about 5.19206 s
About 92.8% done after 56 s wall time, completion expected in about 4.34359 s
About 93.9% done after 57 s wall time, completion expected in about 3.72053 s
About 95.2% done after 57 s wall time, completion expected in about 2.88562 s
About 96.3% done after 58 s wall time, completion expected in about 2.25834 s
About 97.7% done after 58 s wall time, completion expected in about 1.37759 s
About 98.8% done after 59 s wall time, completion expected in about 0.746386 s
Finished all tracking steps.
Finished frequency map analysis.
End of input data encountered.
statistics: ET: 00:00:59 CP: 59.33 BIO:0 DIO:0 PF:0 MEM:21415
=====================================================================================
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.
=====================================================================================
Creating semaphore file fma1p.done


I think the result is good,and simulation time is shortened.But on the Debian system, it turns out the error message and the simulation time isn't shortened,I use the "top" command
to see the cpu information,it turns out only 1 cpu used.

What can I do to solve this problem and what causes this problem??


NOTE:ON THE SCIENTIFIC LINUX RELEASE 7.1 (NITROGEN) ,I HAVE THE ROOT PERMISSIONS,BUT ON THE DEBIAN SYSTEM,I DON'T HAVE THE ROOT PERMISSIONS

michael_borland
Posts: 1796
Joined: 19 May 2008, 09:33
Location: Argonne National Laboratory
Contact:

Re: Errors with Pelegant on Debian

Post by michael_borland » 23 Oct 2015, 08:55

I've referred this problem to Bob Soliday, since he may have a Debian system for testing. He'll return in a few days.

--Michael

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