On Wed, May 8, 2019 at 8:22 AM CHRISTINA-ANNA GATSIOU <[email protected]> wrote: > > Yes I understand this but I what I do not understand why or where it fails to > generate this. It should be generated by csg_stat. Just look for the last csg_stat execution in the log file before the error occurs.
Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > On 8 May 2019, at 4:00 PM, Christoph Junghans <[email protected]> wrote: > > > > On Wed, May 8, 2019, 01:43 CHRISTINA-ANNA GATSIOU > <[email protected]> wrote: >> >> Hi, >> >> Thanks for the help! The error message I get now looks like this: >> Running subscript 'update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new >> P4_P4.pot.cur P4_P4.dpot.pure_ibi' (from tags update ibi_pot) dir /usr/s >> hare/votca/scripts/inverse >> readin_table: could not open file P4_P4.dist.new >> >> Callstack: >> D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/inverse.sh - linenumber >> 301 >> do_external - linenumber 240 in >> D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/functions_common.sh >> /usr/share/votca/scripts/inverse/update_ibi.sh - linenumber 32 >> for_all - linenumber 22 (see 'csg_call --cat function for_all') >> do_external - linenumber 19 (see 'csg_call --cat >> function do_external') >> >> /usr/share/votca/scripts/inverse/update_ibi_single.sh - linenumber 39 >> do_external - linenumber 22 (see 'csg_call --cat >> function do_external') >> die - linenumber 2 (see 'csg_call --cat >> function die') >> ###################################################################################################################### >> # >> # >> # ERROR: >> # >> # do_external: subscript >> # >> # /usr/share/votca/scripts/inverse/update_ibi_pot.pl P4_P4.dist.tgt >> P4_P4.dist.new P4_P4.pot.cur P4_P4.dpot.pure_ibi # >> # (from tags update ibi_pot) failed >> # >> # For details see the logfile /d/MAPS/DEMO2/CG_urea_water_2/inverse.log >> # >> # >> # >> ###################################################################################################################### >> die: (called from 5888) CSG_MASTER_PID is 12388 >> die: pids to kill: 0 >> >> Do you have ideas on what might be the problem. > > The error message says it all: could not open file P4_P4.dist.new > > This file is missing. > > Christoph > >> >> Best regards, >> Christianna >> >> On 28 Apr 2019, at 9:31 PM, Christoph Junghans <[email protected]> wrote: >> >> I found it, it was actually a bug in the code, when using multiple >> mapping files, which I fixed here: >> https://github.com/votca/csg/pull/371 >> >> As a workaround apply the patch or revert the order of the mapping >> files in your settings.xml for now: >> --- settings.xml.orig 2019-04-27 19:42:45.434237893 -0600 >> +++ settings.xml 2019-04-27 19:43:08.314463798 -0600 >> @@ -122,7 +122,7 @@ >> <pot_max>1000000</pot_max> >> <table_end>2.4</table_end> >> </gromacs> >> - <map>p4_topol.xml p2p1_topol.xml</map> >> + <map>p2p1_topol.xml p4_topol.xml</map> >> <filelist>grompp.mdp topol.top conf.gro index.ndx table.xvg</filelist> >> <iterations_max>30</iterations_max> >> <convergence_check> >> >> Christoph >> >> On Sat, Apr 27, 2019 at 6:48 PM CHRISTINA-ANNA GATSIOU >> <[email protected]> wrote: >> >> >> The error message looks like this >> for_all: run 'do_external prepare_single ibi' for interaction named 'P2-P1' >> Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) >> dir /scratch/cgatsiou/votca/share/votca/scripts/inverse >> >> Callstack: >> /scratch/cgatsiou/votca/share/votca/scripts/inverse/inverse.sh - linenumber >> 156 >> do_external - linenumber 176 in >> /scratch/cgatsiou/votca/share/votca/scripts/inverse/functions_common.sh >> >> /scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic.sh - >> linenumber 31 >> for_all - linenumber 22 (see 'csg_call --cat function for_all') >> do_external - linenumber 19 (see 'csg_call --cat function >> do_external') >> >> /scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic_single.sh >> - linenumber 34 >> csg_get_interaction_property - linenumber 44 (see >> 'csg_call --cat function csg_get_interaction_property') >> has_duplicate - linenumber 1 (see 'csg_call >> --cat function has_duplicate') >> die - linenumber 2 (see 'csg_call --cat >> function die') >> ######################################################################## >> # # >> # ERROR: # >> # has_duplicate: Missing argument # >> # For details see the logfile /home/cgatsiou/CG_urea_water/inverse.log # >> # # >> ######################################################################## >> die: (called from 14553) CSG_MASTER_PID is 13536 >> die: pids to kill: 13536 14455 14538 14553 >> Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p' >> Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p’ >> >> The has_duplicate signifies the existence of a duplicate interaction, or >> option somewhere in the input but I cannot find an error in the inputs. >> >> Best regards, >> >> Christianna >> >> On 27 Apr 2019, at 7:11 PM, Christoph Junghans <[email protected]> wrote: >> >> >> >> On Fri, Apr 26, 2019, 07:52 <[email protected]> wrote: >> >> >> Hi, >> >> >> I have attached the neccessary files. IBI seems to be failing before the >> inversion of the initial distributions! Some help would be very much >> appreciated. >> >> >> What is the error message? >> >> Christoph >> >> >> >> >> Best regards, >> Christianna >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/5A96003C-4D45-48E5-9DA5-6A9D03023606%40gmail.com. >> For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e5_MeTvn%2BwU7B6q_D6To7ER7J2V%3DhY0uZdQJ4bE42Gh%3Dw%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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