URL:
<http://gna.org/support/?3260>
Summary: _pmiu_daemon(SIGCHLD)
Project: relax
Submitted by: ana
Submitted on: Wed 17 Jun 2015 03:39:54 PM UTC
Category: None
Priority: 5 - Normal
Severity: 4 - Important
Status: None
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: GNU/Linux
_______________________________________________________
Details:
HI,
I am running this on CrayXE6 machine with 32 cores per node, I can request up
to 500 nodes...
when I run it via:
aprun -n 256 python
/lustre/beagle2/lkpicton/virtualenv-12.1.1/relax-3.3.8/relax --multi='mpi4py'
--tee log.localtm /lustre/beagle2/lkpicton/SR1ABC_relax/SR1ABC_localtm.py
I got this error (and the whole output file is in attach)
send_launch_mesg: PENID_STR 544*8
get_apinit_info: nodeName nid00544
acceptControlConn: accept 10.128.2.37, socket 9
control_loop: setting FdCompressList fd -8 poll fd 8 to -1
doExportReady: sending ALPSMSG_EXPORTREADY message
aprun: Apid 5831930: Caught signal Terminated, sending to application
doStderr: received 108 bytes ALPSSTDIO_MSGTEXT
_pmiu_daemon(SIGCHLD): [NID 00544] [c5-0c0s0n2] [Tue Jun 16 11:54:20 2015] PE
RANK 4 exit signal Terminated
aprun: Apid 5831930: Caught signal Terminated, sending to application
Application 5831930 exit codes: 143
My Python script is this:
# Python module imports.
from time import asctime, localtime
# relax module imports.
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
# Analysis variables.
#####################
# The diffusion model.
DIFF_MODEL = 'local_tm'
# The model-free models. Do not change these unless absolutely necessary,
the
protocol is likely to fail if these are changed.
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9']
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 500
# Automatic looping over all rounds until convergence (must be a boolean
value
of True or False).
CONV_LOOP = True
# Set up the data pipe.
#######################
# The following sequence of user function calls can be changed as needed.
# Create the data pipe.
pipe_bundle = "mf (%s)" % asctime(localtime())
name = "origin - " + pipe_bundle
pipe.create(name, 'mf', bundle=pipe_bundle)
# Load the PDB file.
structure.read_pdb('Monomer_with_serine_with_loop_with_C_term2.6_MF.pdb',
set_mol_name='SR1ABC')
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
structure.load_spins('@N', ave_pos=True)
structure.load_spins('@H', ave_pos=True)
spin.isotope('15N', spin_id='@N*')
spin.isotope('1H', spin_id='@H*')
# Set up the 15N spins (alternative to the structure-based approach).
#sequence.read(file='noe.500.out', dir=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
#spin.element(element='N', spin_id='@N*')
#spin.isotope('15N', spin_id='@N*')
# Generate the 1H spins for the magnetic dipole-dipole relaxation interaction
(alternative to the structure-based approach).
#sequence.attach_protons()
# Load the relaxation data.
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.132818*1e6,
file='SR1ABC_R1_600_new.csv', res_num_col=1, res_name_col=2, spin_num_col=3,
spin_name_col=4, data_col=5, error_col=6)
relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.132818*1e6,
file='SR1ABC_R2_600.csv', res_num_col=1, res_name_col=2, spin_num_col=3,
spin_name_col=4, data_col=5, error_col=6)
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.132818*1e6,
file='SR1ABC_NOE_600.csv', res_num_col=1, res_name_col=2, spin_num_col=3,
spin_name_col=4, data_col=5, error_col=6)
relax_data.read(ri_id='R1_500', ri_type='R1', frq=499.802344*1e6,
file='SR1ABC_R1_500_new.csv', res_num_col=1, res_name_col=2, spin_num_col=3,
spin_name_col=4, data_col=5, error_col=6)
relax_data.read(ri_id='R2_500', ri_type='R2', frq=499.802344*1e6,
file='SR1ABC_R2_500.csv', res_num_col=1, res_name_col=2, spin_num_col=3,
spin_name_col=4, data_col=5, error_col=6)
relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=499.802344*1e6,
file='SR1ABC_NOE_500.csv', res_num_col=1, res_name_col=2, spin_num_col=3,
spin_name_col=4, data_col=5, error_col=6)
# Deselect spins to be excluded (including unresolved and specifically
excluded spins).
#deselect.read(file='unresolved', dir=None, spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None, boolean='AND', change_all=False)
#deselect.read(file='exclude', spin_id_col=1)
# Define the magnetic dipole-dipole relaxation interaction.
interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)
interatom.unit_vectors()
# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa', spin_id='@N*')
# Execution.
############
# Do not change!
dAuvergne_protocol(pipe_name=name, pipe_bundle=pipe_bundle,
diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM,
conv_loop=CONV_LOOP)
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wed 17 Jun 2015 03:39:54 PM UTC Name: SR1ABC_localtm.o3261400 Size:
34kB By: ana
<http://gna.org/support/download.php?file_id=24581>
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[sr #3260] _pmiu_daemon(SIGCHLD)