helpGna! Administration - Support: sr #3259, _pmiu_daemon(SIGCHLD)

 
 
Show feedback again

sr #3259: _pmiu_daemon(SIGCHLD)

Submitted by:  Ana Marija Sokovic <ana>
Submitted on:  Wed Jun 17 15:33:56 2015  
 
Category: OtherPriority: 5 - Normal
Severity: 4 - ImportantStatus: None
Privacy: PublicAssigned to: None
Open/Closed: OpenOperating System: GNU/Linux

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

Wed Jun 17 15:33:56 2015, original submission:

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)

Ana Marija Sokovic <ana>

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

Attached Files
file #24580:  SR1ABC_localtm.o3261400 added by ana (34kB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by ana (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Error: not logged in

     

     

    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Wed Jun 17 15:33:56 2015anaAttached File-=>Added SR1ABC_localtm.o3261400, #24580
    Show feedback again

    Back to the top


    Powered by Savane 3.1-cleanup