Hi, I would like to ask a slightly different question. In case I want to run a
parallel lammps job. What would be the entry in settings.xml?
I tried
<program>lammps</program>
<lammps>
<command> mpirun lammps</command>
<opts>-nt 4</opts>
But it does not seem to work. I get the error message that the command is not
found.
> On 8 May 2019, at 8:33 PM, Christoph Junghans <[email protected]> wrote:
>
> On Wed, May 8, 2019 at 10:40 AM CHRISTINA-ANNA GATSIOU
> <[email protected] <mailto:[email protected]>> wrote:
>>
>> Hi,
>> I would like to ask one additional question. So the csg_stat during IBI is
>> calculated by the following scripts:
>> 1)calc_rdf_generic.sh
>> 2)calc_target_rdf_generic.sh
>>
>> I guess the second one is not used during inversion. Are there any
>> additional scripts used.
> It is 1.) [2.) is used for the optimizer method, when the rdf is a
> target property).
>
> The log file should tell you, which exact command got run, e.g.
> csg_stat --options ..., so you can run this manually to see why
> P4_P4.dist.new didn't get generated. The log file should also tell
> you, which files csg_stat did write.
>
> Christoph
>
>> Christianna
>>
>> On 8 May 2019, at 5:37 PM, Christoph Junghans <[email protected]> wrote:
>>
>> 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.
>> 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/CAHG27e6-O%3DSDGFZS-RP8CAfvUNurigDM0NpsFnYE6ySQpxUw0w%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]
>> <mailto:[email protected]>.
>> To post to this group, send email to [email protected]
>> <mailto:[email protected]>.
>> Visit this group at https://groups.google.com/group/votca
>> <https://groups.google.com/group/votca>.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/votca/F7860F64-884D-4A9A-AB18-281A6C279AAC%40gmail.com
>>
>> <https://groups.google.com/d/msgid/votca/F7860F64-884D-4A9A-AB18-281A6C279AAC%40gmail.com>.
>> For more options, visit https://groups.google.com/d/optout
>> <https://groups.google.com/d/optout>.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de <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]
> <mailto:[email protected]>.
> To post to this group, send email to [email protected]
> <mailto:[email protected]>.
> Visit this group at https://groups.google.com/group/votca
> <https://groups.google.com/group/votca>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e6ooBaDwoB%2BA7Bhixwf-_57H9Q0K7t5CY%2B2O06YXud76w%40mail.gmail.com
>
> <https://groups.google.com/d/msgid/votca/CAHG27e6ooBaDwoB%2BA7Bhixwf-_57H9Q0K7t5CY%2B2O06YXud76w%40mail.gmail.com>.
> For more options, visit https://groups.google.com/d/optout
> <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/F3F0FBBA-1DB7-4544-BBB3-0499E5703BC1%40gmail.com.
For more options, visit https://groups.google.com/d/optout.
