Hi Sacha,
in this case the logfile didn't really help, but I have a guess what
could be wrong. There are some sanity checks missing in check_temp.
Please make sure that the option cg.inverse.kBT in your xml setting file
and the line with ref_t of the mdp file contain normal float formated
numbers, like XXX.XXX). Can you check that?
Cheers,
Christoph
Am 05/27/2011 11:08 AM, schrieb Sacha Mould:
Hi Christoph,
Sure, here it is:
update_ibi_pot.pl: OK
update_ibi_single.sh: OK
update_ibm.sh: OK
update_imc.sh: OK
csg_table: OK
imcdata_from_blocks.octave: OK
linsolve.m: OK
linsolve.octave: OK
CsgFunctions.pm: OK
------------------------
Prepare (dir step_000)
------------------------
Running critical command '/usr/local/share/votca/scripts/inverse/
prepare_generic.sh --help'
Running subscript 'prepare_generic.sh '(from tags prepare ibi)
For all non-bonded
for_all: run 'do_external prepare_single ibi'
Running critical command '/usr/local/share/votca/scripts/inverse/
prepare_generic_single.sh --help'
Running subscript 'prepare_generic_single.sh '(from tags
prepare_single ibi)
Using initial guess from dist A-A.dist.tgt for A-A
Running critical command 'csg_resample --in /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/A-A.dist.tgt --out A-A.dist.tgt --grid
0:0.01:1.36 --comment Created on Fri May 27 01:20:35 WEST 2011 by
sacha@ubuntu
called from prepare_generic_single.sh, version 1.1.2
settings file: /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
settings.xml
working directory: /home/sacha/Documents/votca-tutorials-1.1/propane/
ibm/step_000'
Running critical command '/usr/local/share/votca/scripts/inverse/
RDF_to_POT.pl --help'
Running subscript 'RDF_to_POT.pl A-A.dist.tgt A-A.pot.new'(from tags
rdf pot)
for_all: run 'do_external prepare_single ibi'
Running critical command '/usr/local/share/votca/scripts/inverse/
prepare_generic_single.sh --help'
Running subscript 'prepare_generic_single.sh '(from tags
prepare_single ibi)
Using initial guess from dist B-B.dist.tgt for B-B
Running critical command 'csg_resample --in /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/B-B.dist.tgt --out B-B.dist.tgt --grid
0:0.01:1.38 --comment Created on Fri May 27 01:20:35 WEST 2011 by
sacha@ubuntu
called from prepare_generic_single.sh, version 1.1.2
settings file: /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
settings.xml
working directory: /home/sacha/Documents/votca-tutorials-1.1/propane/
ibm/step_000'
Running critical command '/usr/local/share/votca/scripts/inverse/
RDF_to_POT.pl --help'
Running subscript 'RDF_to_POT.pl B-B.dist.tgt B-B.pot.new'(from tags
rdf pot)
for_all: run 'do_external prepare_single ibi'
Running critical command '/usr/local/share/votca/scripts/inverse/
prepare_generic_single.sh --help'
Running subscript 'prepare_generic_single.sh '(from tags
prepare_single ibi)
Using initial guess from dist A-B.dist.tgt for A-B
Running critical command 'csg_resample --in /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/A-B.dist.tgt --out A-B.dist.tgt --grid
0:0.01:1.36 --comment Created on Fri May 27 01:20:35 WEST 2011 by
sacha@ubuntu
called from prepare_generic_single.sh, version 1.1.2
settings file: /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
settings.xml
working directory: /home/sacha/Documents/votca-tutorials-1.1/propane/
ibm/step_000'
Running critical command '/usr/local/share/votca/scripts/inverse/
RDF_to_POT.pl --help'
Running subscript 'RDF_to_POT.pl A-B.dist.tgt A-B.pot.new'(from tags
rdf pot)
Running critical command '/usr/local/share/votca/scripts/inverse/
prepare_generic_gromacs.sh --help'
Running subscript 'prepare_generic_gromacs.sh '(from tags
prepare_generic gromacs)
cp_from_main_dir: 'conf.gro'
Running critical command 'cp_from_to --from /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm conf.gro'
Running critical command 'mv conf.gro confout.gro'
step 0 done
-------------------------------
Doing iteration 1 (dir step_001)
-------------------------------
Step 1 started at Fri May 27 01:20:35 WEST 2011
cp_from_main_dir: 'grompp.mdp topol.top table.xvg table_a1.xvg
table_b1.xvg index.ndx'
Running critical command 'cp_from_to --from /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm grompp.mdp topol.top table.xvg
table_a1.xvg table_b1.xvg index.ndx'
Running critical command '/usr/local/share/votca/scripts/inverse/
initialize_step_generic.sh --help'
Running subscript 'initialize_step_generic.sh '(from tags initstep
ibi)
For all non-bonded
for_all: run 'cp_from_last_step $(csg_get_interaction_property
name).pot.new'
cp_from_last_step: 'A-A.pot.new'
Running critical command 'cp_from_to --from /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/step_000 A-A.pot.new'
for_all: run 'cp_from_last_step $(csg_get_interaction_property
name).pot.new'
cp_from_last_step: 'B-B.pot.new'
Running critical command 'cp_from_to --from /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/step_000 B-B.pot.new'
for_all: run 'cp_from_last_step $(csg_get_interaction_property
name).pot.new'
cp_from_last_step: 'A-B.pot.new'
Running critical command 'cp_from_to --from /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/step_000 A-B.pot.new'
For all non-bonded
for_all: run 'mv $(csg_get_interaction_property name).pot.new $
(csg_get_interaction_property name).pot.cur'
for_all: run 'mv $(csg_get_interaction_property name).pot.new $
(csg_get_interaction_property name).pot.cur'
for_all: run 'mv $(csg_get_interaction_property name).pot.new $
(csg_get_interaction_property name).pot.cur'
Running critical command '/usr/local/share/votca/scripts/inverse/
initialize_step_generic_gromacs.sh --help'
Running subscript 'initialize_step_generic_gromacs.sh '(from tags
initstep_generic gromacs)
cp_from_last_step: 'confout.gro'
Running critical command 'cp_from_to --from /home/sacha/Documents/
votca-tutorials-1.1/propane/ibm/step_000 confout.gro'
Running critical command 'mv confout.gro conf.gro'
For all non-bonded
for_all: run 'do_external convert_potential gromacs'
Running critical command '/usr/local/share/votca/scripts/inverse/
potential_to_gromacs.sh --help'
Running subscript 'potential_to_gromacs.sh '(from tags
convert_potential gromacs)
Convert A-A.pot.cur to table_A_A.xvg
Running critical command 'csg_resample --in A-A.pot.cur --out smooth_A-
A.pot.cur --grid 0:0.002:1.36 --comment Created on Fri May 27 01:20:35
WEST 2011 by sacha@ubuntu
called from potential_to_gromacs.sh, version 1.1.2
settings file: /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
settings.xml
working directory: /home/sacha/Documents/votca-tutorials-1.1/propane/
ibm/step_001'
Running critical command '/usr/local/share/votca/scripts/inverse/
table_to_xvg.pl --help'
Running subscript 'table_to_xvg.pl smooth_A-A.pot.cur
table_A_A.xvg'(from tags convert_potential xvg)
for_all: run 'do_external convert_potential gromacs'
Running critical command '/usr/local/share/votca/scripts/inverse/
potential_to_gromacs.sh --help'
Running subscript 'potential_to_gromacs.sh '(from tags
convert_potential gromacs)
Convert B-B.pot.cur to table_B_B.xvg
Running critical command 'csg_resample --in B-B.pot.cur --out smooth_B-
B.pot.cur --grid 0:0.002:1.38 --comment Created on Fri May 27 01:20:35
WEST 2011 by sacha@ubuntu
called from potential_to_gromacs.sh, version 1.1.2
settings file: /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
settings.xml
working directory: /home/sacha/Documents/votca-tutorials-1.1/propane/
ibm/step_001'
Running critical command '/usr/local/share/votca/scripts/inverse/
table_to_xvg.pl --help'
Running subscript 'table_to_xvg.pl smooth_B-B.pot.cur
table_B_B.xvg'(from tags convert_potential xvg)
for_all: run 'do_external convert_potential gromacs'
Running critical command '/usr/local/share/votca/scripts/inverse/
potential_to_gromacs.sh --help'
Running subscript 'potential_to_gromacs.sh '(from tags
convert_potential gromacs)
Convert A-B.pot.cur to table_A_B.xvg
Running critical command 'csg_resample --in A-B.pot.cur --out smooth_A-
B.pot.cur --grid 0:0.002:1.36 --comment Created on Fri May 27 01:20:35
WEST 2011 by sacha@ubuntu
called from potential_to_gromacs.sh, version 1.1.2
settings file: /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
settings.xml
working directory: /home/sacha/Documents/votca-tutorials-1.1/propane/
ibm/step_001'
Running critical command '/usr/local/share/votca/scripts/inverse/
table_to_xvg.pl --help'
Running subscript 'table_to_xvg.pl smooth_A-B.pot.cur
table_A_B.xvg'(from tags convert_potential xvg)
awk: line 1: syntax error at or near *
##########################
# #
# ERROR: #
# check_temp: awk failed #
# #
##########################
For details see /home/sacha/Documents/votca-tutorials-1.1/propane/ibm/
inverse.log
die: (called from 22529) CSG_MASTER_PID is 22177
die: pids to kill: 22177 22458 22529
Thanks so much for the quick reply.
Siceraly,
Sacha
On May 27, 8:05 am, Christoph Junghans<[email protected]> wrote:
Hi Sacha,
can you please post the last 100 lines of the logfile (inverse.log or so)?
Cheers,
Christoph
Am 05/27/2011 02:50 AM, schrieb Sacha Mould:
Hello all,
i've tryed to run IBM and IMC examples given by the tutorial and i got
an error concearning "awk":
-------------------------------
Doing iteration 1 (dir step_001)
-------------------------------
Incomplete step 1
##########################
# #
# ERROR: #
# check_temp: awk failed #
# #
##########################
I'm wondering if someone already had this issue and managed to solve
it, i will be very grateful if someone can help me.
Best regards,
Sacha
--
Dr. Christoph Junghans
Votca Core Developer
Web:http://www.votca.org
--
Dr. Christoph Junghans
Votca Core Developer
Web: http://www.votca.org
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