Re: [votca] No *rc.bash matches found in VOTCASHARE on macOS
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Christoph Junghans
Apr 1, 2020, 3:23:14 PM4/1/20
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On Wed, Apr 1, 2020 at 1:14 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I installed VOTCA on macOS but when I source /usr/local/votca/bin/VOTCARC.bash I get this error:
>
> /usr/local/votca/bin/VOTCARC.bash:29: no matches found: /usr/local/votca/share/votca/rc/*rc.bash
How did you install VOTCA? What version?
Christoph
>
> Thanks,
>
> Ramón
>
> --
> 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 votca+un...@googlegroups.com.
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--
Christoph Junghans
Web: http://www.compphys.de
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I installed VOTCA on macOS but when I source /usr/local/votca/bin/VOTCARC.bash I get this error:
>
> /usr/local/votca/bin/VOTCARC.bash:29: no matches found: /usr/local/votca/share/votca/rc/*rc.bash
How did you install VOTCA? What version?
Christoph
>
> Thanks,
>
> Ramón
>
> --
> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c19d41b6-7295-41d3-8fac-1366431f7601%40googlegroups.com.
--
Christoph Junghans
Web: http://www.compphys.de
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Christoph Junghans
Apr 1, 2020, 3:56:05 PM4/1/20
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On Wed, Apr 1, 2020 at 1:30 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> v1.4.1 through:
>
> sudo rm -rf /usr/local/votca
>
> prefix=/usr/local/votca
>
> version=v1.4.1
>
> git clone -b ${version} --recursive https://github.com/votca/votca.git
>
> cd votca
>
> mkdir build
>
> cd build
>
> cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_SQLITE3=OFF -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.dylib ..
>
> sudo make -j5
No sudo needed here.
>
> sudo make install
I did exactly that on Linux and I get the following file:
$ ls /usr/local/votca/share/votca/rc/
csg-completion.bash
Christoph
<gonzale...@licifug.ugto.mx> wrote:
>
> v1.4.1 through:
>
> sudo rm -rf /usr/local/votca
>
> prefix=/usr/local/votca
>
> version=v1.4.1
>
> git clone -b ${version} --recursive https://github.com/votca/votca.git
>
> cd votca
>
> mkdir build
>
> cd build
>
> cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_SQLITE3=OFF -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.dylib ..
>
> sudo make -j5
No sudo needed here.
>
> sudo make install
I did exactly that on Linux and I get the following file:
$ ls /usr/local/votca/share/votca/rc/
csg-completion.bash
Christoph
>
>
> On Wednesday, April 1, 2020 at 1:23:14 PM UTC-6, Christoph Junghans wrote:
>>
>> On Wed, Apr 1, 2020 at 1:14 PM Ramon Gonzalez Perez
>> <gonzale...@licifug.ugto.mx> wrote:
>> >
>> > Hello,
>> >
>> > I installed VOTCA on macOS but when I source /usr/local/votca/bin/VOTCARC.bash I get this error:
>> >
>> > /usr/local/votca/bin/VOTCARC.bash:29: no matches found: /usr/local/votca/share/votca/rc/*rc.bash
>> How did you install VOTCA? What version?
>>
>> Christoph
>> >
>> > Thanks,
>> >
>> > Ramón
>> >
>> > --
>> > 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 vo...@googlegroups.com.
>
> On Wednesday, April 1, 2020 at 1:23:14 PM UTC-6, Christoph Junghans wrote:
>>
>> On Wed, Apr 1, 2020 at 1:14 PM Ramon Gonzalez Perez
>> <gonzale...@licifug.ugto.mx> wrote:
>> >
>> > Hello,
>> >
>> > I installed VOTCA on macOS but when I source /usr/local/votca/bin/VOTCARC.bash I get this error:
>> >
>> > /usr/local/votca/bin/VOTCARC.bash:29: no matches found: /usr/local/votca/share/votca/rc/*rc.bash
>> How did you install VOTCA? What version?
>>
>> Christoph
>> >
>> > Thanks,
>> >
>> > Ramón
>> >
>> > --
>> > You received this message because you are subscribed to the Google Groups "votca" group.
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c19d41b6-7295-41d3-8fac-1366431f7601%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/10085817-cd1a-45e6-8054-8e570f7ec1ea%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
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Christoph Junghans
Apr 1, 2020, 4:41:43 PM4/1/20
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On Wed, Apr 1, 2020 at 2:36 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> I'm also getting that file. Did the installation work, then?
>
> Because when I try to use csg_stat I get the following message:
>
> dyld: Library not loaded: @rpath/libmkl_core.dylib
> Referenced from: /usr/local/votca/bin/csg_stat
> Reason: image not found
> zsh: abort csg_stat
<gonzale...@licifug.ugto.mx> wrote:
>
> I'm also getting that file. Did the installation work, then?
>
> Because when I try to use csg_stat I get the following message:
>
> dyld: Library not loaded: @rpath/libmkl_core.dylib
> Referenced from: /usr/local/votca/bin/csg_stat
> Reason: image not found
> zsh: abort csg_stat
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/10085817-cd1a-45e6-8054-8e570f7ec1ea%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/23598d8a-56eb-4a45-a796-5e95a13c469d%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
Christoph Junghans
Apr 1, 2020, 4:52:39 PM4/1/20
to vo...@googlegroups.com
On Wed, Apr 1, 2020 at 2:36 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> I'm also getting that file. Did the installation work, then?
>
> Because when I try to use csg_stat I get the following message:
>
> dyld: Library not loaded: @rpath/libmkl_core.dylib
> Referenced from: /usr/local/votca/bin/csg_stat
You could try to adding -DENABLE_RPATH_INJECT=ON on your cmake comment.
<gonzale...@licifug.ugto.mx> wrote:
>
> I'm also getting that file. Did the installation work, then?
>
> Because when I try to use csg_stat I get the following message:
>
> dyld: Library not loaded: @rpath/libmkl_core.dylib
> Referenced from: /usr/local/votca/bin/csg_stat
Alternatively, set the DYLD_LIBRARY_PATH variable to where your libmkl
is located.
> Reason: image not found
> zsh: abort csg_stat
I guess, you could try "setopt NULL_GLOB" in zsh to make the bash file work.
Christoph
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/10085817-cd1a-45e6-8054-8e570f7ec1ea%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/23598d8a-56eb-4a45-a796-5e95a13c469d%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
Christoph Junghans
Apr 1, 2020, 10:41:08 PM4/1/20
to vo...@googlegroups.com
On Wed, Apr 1, 2020 at 2:52 PM Christoph Junghans <jung...@votca.org> wrote:
>
> On Wed, Apr 1, 2020 at 2:36 PM Ramon Gonzalez Perez
> <gonzale...@licifug.ugto.mx> wrote:
> >
> > I'm also getting that file. Did the installation work, then?
> >
> > Because when I try to use csg_stat I get the following message:
> >
> > dyld: Library not loaded: @rpath/libmkl_core.dylib
> > Referenced from: /usr/local/votca/bin/csg_stat
> You could try to adding -DENABLE_RPATH_INJECT=ON on your cmake comment.
> Alternatively, set the DYLD_LIBRARY_PATH variable to where your libmkl
> is located.
>
> > Reason: image not found
> > zsh: abort csg_stat
> Oh, you are using zsh, so the VOTCA.bash won't work for you as it is for bash.
> I guess, you could try "setopt NULL_GLOB" in zsh to make the bash file work.
Also fixed in the next release: https://github.com/votca/tools/pull/220
>
> On Wed, Apr 1, 2020 at 2:36 PM Ramon Gonzalez Perez
> <gonzale...@licifug.ugto.mx> wrote:
> >
> > I'm also getting that file. Did the installation work, then?
> >
> > Because when I try to use csg_stat I get the following message:
> >
> > dyld: Library not loaded: @rpath/libmkl_core.dylib
> > Referenced from: /usr/local/votca/bin/csg_stat
> You could try to adding -DENABLE_RPATH_INJECT=ON on your cmake comment.
> Alternatively, set the DYLD_LIBRARY_PATH variable to where your libmkl
> is located.
>
> > Reason: image not found
> > zsh: abort csg_stat
> Oh, you are using zsh, so the VOTCA.bash won't work for you as it is for bash.
> I guess, you could try "setopt NULL_GLOB" in zsh to make the bash file work.
Christoph
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Christoph Junghans
Apr 3, 2020, 1:36:55 PM4/3/20
to vo...@googlegroups.com
On Fri, Apr 3, 2020 at 11:29 AM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I added -DENABLE_RPATH_INJECT=ON and moved from zsh to bash but got a new error when running make:
>
> error:
> no member named 'nmolblock' in 'gmx_mtop_t'
> for(int iblock=0; iblock<mtop.nmolblock; ++iblock)
> ~~~~ ^
Yea, VOTCA-1.4* doesn't support newer versions of gromacs. What
version of gromacs are you using?
>
> I tried the stable version and the installation seemed to work but when running csg_stat it says:
>
> dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
> Abort trap: 6
Did you source VOTCARC.bash and GMXRC.bash?
Alternatively, do "export
DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib"
Christoph
>
> This is the procedure I'm following:
>
> sudo rm -rf /usr/local/votca
> sudo rm -rf votca
> prefix=/usr/local/votca
> version=stable
> make -j5
> sudo make install
> source /usr/local/votca/bin/VOTCARC.bash
>
> And this is the content of the directories where the libraries are located:
>
> ls /usr/local/gromacs/lib/
> libgromacs.4.0.0.dylib libgromacs.4.dylib libgromacs.dylib pkgconfig
>
> ls /usr/local/votca/lib/
> cmake libvotca_csg.6.dylib libvotca_csg.dylib libvotca_tools.6.dylib libvotca_tools.dylib
>
> Am I missing something?
>
> Ramón
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I added -DENABLE_RPATH_INJECT=ON and moved from zsh to bash but got a new error when running make:
>
> error:
> no member named 'nmolblock' in 'gmx_mtop_t'
> for(int iblock=0; iblock<mtop.nmolblock; ++iblock)
> ~~~~ ^
Yea, VOTCA-1.4* doesn't support newer versions of gromacs. What
version of gromacs are you using?
>
> I tried the stable version and the installation seemed to work but when running csg_stat it says:
>
> dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
> Abort trap: 6
Did you source VOTCARC.bash and GMXRC.bash?
Alternatively, do "export
DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib"
Christoph
>
> This is the procedure I'm following:
>
> sudo rm -rf /usr/local/votca
> sudo rm -rf votca
> prefix=/usr/local/votca
> version=stable
> git clone -b ${version} --recursive https://github.com/votca/votca.git
> cd votca
> mkdir build
> cd build
> cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_SQLITE3=OFF -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.4.dylib -DENABLE_RPATH_INJECT=ON -DYLD_LIBRARY_PATH=/usr/local/votca/lib/libvotca_csg.6.dylib ..
> cd votca
> mkdir build
> cd build
> make -j5
> sudo make install
> source /usr/local/votca/bin/VOTCARC.bash
>
> And this is the content of the directories where the libraries are located:
>
> ls /usr/local/gromacs/lib/
> libgromacs.4.0.0.dylib libgromacs.4.dylib libgromacs.dylib pkgconfig
>
> ls /usr/local/votca/lib/
> cmake libvotca_csg.6.dylib libvotca_csg.dylib libvotca_tools.6.dylib libvotca_tools.dylib
>
> Am I missing something?
>
> Ramón
>> > > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/23598d8a-56eb-4a45-a796-5e95a13c469d%40googlegroups.com.
>> >
>> >
>> >
>> > --
>> > Christoph Junghans
>> > Web: http://www.compphys.de
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/9fb7768d-cc06-4e3b-bf93-5c9d227c49ff%40googlegroups.com.
>> >
>> >
>> >
>> > --
>> > Christoph Junghans
>> > Web: http://www.compphys.de
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
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Christoph Junghans
Apr 3, 2020, 9:40:54 PM4/3/20
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On Fri, Apr 3, 2020 at 6:49 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I'm using GROMACS 2019.
>
> I did "export DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib" and csg_stat and csg_map seem to work but when I run "csg_settings --options settings.xml" on the hexane/ibi_all tutorial I get:
Do you mean csg_inverse? Try "csg_inverse --debug --options
settings.xml" and post the end of the output here.
Christoph
>
> Terminated: 15
>
> Thanks,
>
> Ramón
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I'm using GROMACS 2019.
>
> I did "export DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib" and csg_stat and csg_map seem to work but when I run "csg_settings --options settings.xml" on the hexane/ibi_all tutorial I get:
Do you mean csg_inverse? Try "csg_inverse --debug --options
settings.xml" and post the end of the output here.
Christoph
>
> Terminated: 15
>
> Thanks,
>
> Ramón
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/9fb7768d-cc06-4e3b-bf93-5c9d227c49ff%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c80e6e02-10c2-4cb6-a871-de091895798e%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
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Christoph Junghans
Apr 3, 2020, 10:21:49 PM4/3/20
to vo...@googlegroups.com
On Fri, Apr 3, 2020 at 7:44 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Yes, I meant csg_inverse. Here's the output:
>
> + [[ --debug = \-\-\h\e\l\p ]]
> + source /usr/local/votca/share/votca/scripts/inverse/start_framework.sh
> ++ '[' --debug = --help ']'
> ++ [[ -n /usr/local/votca/share/votca ]]
> ++ [[ -d /usr/local/votca/share/votca ]]
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/inverse.sh ]]
> ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/functions_common.sh ]]
> ++ source /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> +++ [[ --debug = \-\-\h\e\l\p ]]
> +++ export BASH
> +++ shopt -s extglob
> +++ export -f msg
> +++ export -f show_callstack
> +++ unset -f die
> +++ export -f die
> +++ export -f cat_external
> +++ export -f do_external
> +++ export -f critical
> +++ export -f for_all
> +++ export -f csg_get_interaction_property
> +++ export -f csg_get_property
> +++ export -f trim_all
> +++ export -f mark_done
> +++ export -f is_done
> +++ export -f is_int
> +++ export -f to_int
> +++ export -f is_part
> +++ export -f has_duplicate
> +++ export -f remove_duplicate
> +++ export -f is_num
> +++ export -f get_stepname
> +++ export -f update_stepnames
> +++ export -f get_current_step_dir
> +++ export -f get_last_step_dir
> +++ export -f get_main_dir
> +++ export -f get_current_step_nr
> +++ export -f get_step_nr
> +++ export -f cp_from_main_dir
> +++ export -f cp_from_last_step
> +++ export -f get_time
> +++ export -f get_number_tasks
> +++ export -f get_table_comment
> +++ export -f csg_inverse_clean
> +++ export -f check_path_variable
> +++ export -f add_to_csgshare
> +++ export -f globalize_dir
> +++ export -f globalize_file
> +++ export -f source_function
> +++ export -f csg_banner
> +++ export -f csg_calc
> +++ export -f show_csg_tables
> +++ export -f get_command_from_csg_tables
> +++ export -f source_wrapper
> +++ export -f find_in_csgshare
> ++++ type -p mktemp
> +++ '[' -z /usr/bin/mktemp ']'
> +++ export -f enable_logging
> +++ export -f get_restart_file
> +++ export -f check_for_obsolete_xml_options
> +++ export -f command_not_found_handle
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
> +++ eval 'simulation_finish()' '{' command_not_found_handle 'simulation_finish;' '}'
> +++ eval export -f simulation_finish
> ++++ export -f simulation_finish
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
> +++ eval 'checkpoint_exist()' '{' command_not_found_handle 'checkpoint_exist;' '}'
> +++ eval export -f checkpoint_exist
> ++++ export -f checkpoint_exist
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
> +++ eval 'get_simulation_setting()' '{' command_not_found_handle 'get_simulation_setting;' '}'
> +++ eval export -f get_simulation_setting
> ++++ export -f get_simulation_setting
> +++ unset i
> ++ export CSG_MASTER_PID=65637
> ++ CSG_MASTER_PID=65637
> ++ export CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all
> ++ CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all
> ++ [[ -n '' ]]
> ++ export VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml
> ++ VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml
> ++ [[ -f /usr/local/votca/share/votca/xml/csg_defaults.xml ]]
> ++ add_to_csgshare --at-the-end /usr/local/votca/share/votca/scripts/inverse
> ++ local dir end=no
> ++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]]
> ++ end=yes
> ++ shift
> ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> ++ for dirlist in '"$@"'
> ++ old_IFS='
> '
> ++ IFS=:
> ++ for dir in '$dirlist'
> ++ eval dir=/usr/local/votca/share/votca/scripts/inverse
> +++ dir=/usr/local/votca/share/votca/scripts/inverse
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> +++ globalize_dir /usr/local/votca/share/votca/scripts/inverse
> +++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> +++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> +++ cd /usr/local/votca/share/votca/scripts/inverse
> +++ pwd
> ++ dir=/usr/local/votca/share/votca/scripts/inverse
> ++ [[ yes = \y\e\s ]]
> ++ export CSGSHARE=/usr/local/votca/share/votca/scripts/inverse
> ++ CSGSHARE=/usr/local/votca/share/votca/scripts/inverse
> ++ export PERL5LIB=/usr/local/votca/share/votca/scripts/inverse
> ++ PERL5LIB=/usr/local/votca/share/votca/scripts/inverse
> ++ IFS='
> '
> ++ check_path_variable CSGSHARE PERL5LIB
> ++ local old_IFS dir
> ++ [[ -z CSGSHARE ]]
> ++ for var in '"$@"'
> ++ [[ -z CSGSHARE ]]
> ++ old_IFS='
> '
> ++ IFS=:
> ++ for dir in '${!var}'
> ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]]
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> ++ IFS='
> '
> ++ for var in '"$@"'
> ++ [[ -z PERL5LIB ]]
> ++ old_IFS='
> '
> ++ IFS=:
> ++ for dir in '${!var}'
> ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]]
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> ++ IFS='
> '
> + do_iterations=
> + waittime=10
> + unset CSGXMLFILE CSGENDING CSGDEBUG
> + shopt -s extglob
> + [[ -debug != --debug ]]
> + [[ debug = --debug ]]
> + case $1 in
> + export CSGDEBUG=yes
> + CSGDEBUG=yes
> + shift
> + [[ -options != --options ]]
> + [[ options = --options ]]
> + case $1 in
> + CSGXMLFILE=
> + [[ -f '' ]]
> + die 'options xml file '\'''\'' not found'
> + local pid pids c place
> + echo -e '\nCallstack:'
>
> Callstack:
> + show_callstack
> + local space line
> + [[ -n '' ]]
> + space=
> + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = *\b\a\s\h ]]
> + echo '/usr/local/votca/share/votca/scripts/inverse/inverse.sh - linenumber 82'
> /usr/local/votca/share/votca/scripts/inverse/inverse.sh - linenumber 82
> + (( c=3-1 ))
> + (( c>0 ))
> + [[ main = main ]]
> + continue
> + (( c-- ))
> + (( c>0 ))
> + [[ die = main ]]
> + space+=' '
> + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = *csg_call ]]
> + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = *inverse.sh ]]
> + echo ' die - linenumber 109 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh'
> die - linenumber 109 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> + (( c-- ))
> + (( c>0 ))
> + [[ '' = \-\-\e\x\t\r\a ]]
> + return 0
> + [[ -z '' ]]
> + place='Details can be found above'
> ++ csg_banner ERROR: 'options xml file '\'''\'' not found' 'Details can be found above'
> ++ list=()
> ++ local i l=0 list
> ++ [[ -z ERROR: ]]
> ++ for i in '"$@"'
> ++ [[ -n ERROR: ]]
> ++ [[ -z ERROR: ]]
> ++ list[$l]=ERROR:
> ++ (( l++ ))
> ++ for i in '"$@"'
> ++ [[ -n options xml file '' not found ]]
> ++ [[ -z options xml file '' not found ]]
> ++ list[$l]='options xml file '\'''\'' not found'
> ++ (( l++ ))
> ++ for i in '"$@"'
> ++ [[ -n Details can be found above ]]
> ++ [[ -z Details can be found above ]]
> ++ list[$l]='Details can be found above'
> ++ (( l++ ))
> ++ l=1
> ++ for i in '"${list[@]}"'
> ++ [[ 1 -lt 6 ]]
> ++ l=ERROR:
> ++ for i in '"${list[@]}"'
> ++ [[ 6 -lt 29 ]]
> ++ l='options xml file '\'''\'' not found'
> ++ for i in '"${list[@]}"'
> ++ [[ 29 -lt 26 ]]
> ++ echo '#################################'
> ++ echo '# #'
> ++ for i in '"${list[@]}"'
> ++ printf '# %-29s #\n' ERROR:
> ++ for i in '"${list[@]}"'
> ++ printf '# %-29s #\n' 'options xml file '\'''\'' not found'
> ++ for i in '"${list[@]}"'
> ++ printf '# %-29s #\n' 'Details can be found above'
> ++ echo '# #'
> ++ echo '#################################'
> + msg --color red --to-stderr '#################################
> # #
> # ERROR: #
> # options xml file '\'''\'' not found #
> # Details can be found above #
> # #
> #################################'
> + local color 'colors=blue cyan cyann green red purp'
> + [[ -z '' ]]
> + local 'blue='
> + local 'cyan='
> + local 'cyann='
> + local 'green='
> + local 'red='
> + local 'purp='
> + local 'off='
> + [[ --color = \-\-\c\o\l\o\r ]]
> + [[ -z red ]]
> + is_part red 'blue cyan cyann green red purp'
> + [[ -z red ]]
> + [[ -z blue cyan cyann green red purp ]]
> + [[ blue cyan cyann green red purp = *\ \r\e\d\ * ]]
> + color=''
> + shift 2
> + [[ --to-stderr = \-\-\t\o\-\s\t\d\e\r\r ]]
> + shift
> + [[ -z ################################# # # # ERROR: # # options xml file '' not found # # Details can be found above # # # ################################# ]]
> + [[ -n '' ]]
> + echo -e '#################################
> # #
> # ERROR: #
> # options xml file '\'''\'' not found #
> # Details can be found above #
> # #
> #################################'
> #################################
> # #
> # ERROR: #
> # options xml file '' not found #
> # Details can be found above #
> # #
> #################################
> + [[ -n 65637 ]]
> + pid=65637
> + pids=65637
> + c=0
> + [[ 65637 -eq 65637 ]]
> + [[ -n '' ]]
> + kill 65637
> Terminated: 15
The error is "options xml file '' not found", between '' should be the
filename. I am really not sure why that is.
Is the settings.xml file there and readable?
Christoph
<gonzale...@licifug.ugto.mx> wrote:
>
> Yes, I meant csg_inverse. Here's the output:
>
> + [[ --debug = \-\-\h\e\l\p ]]
> + source /usr/local/votca/share/votca/scripts/inverse/start_framework.sh
> ++ '[' --debug = --help ']'
> ++ [[ -n /usr/local/votca/share/votca ]]
> ++ [[ -d /usr/local/votca/share/votca ]]
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/inverse.sh ]]
> ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/functions_common.sh ]]
> ++ source /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> +++ [[ --debug = \-\-\h\e\l\p ]]
> +++ export BASH
> +++ shopt -s extglob
> +++ export -f msg
> +++ export -f show_callstack
> +++ unset -f die
> +++ export -f die
> +++ export -f cat_external
> +++ export -f do_external
> +++ export -f critical
> +++ export -f for_all
> +++ export -f csg_get_interaction_property
> +++ export -f csg_get_property
> +++ export -f trim_all
> +++ export -f mark_done
> +++ export -f is_done
> +++ export -f is_int
> +++ export -f to_int
> +++ export -f is_part
> +++ export -f has_duplicate
> +++ export -f remove_duplicate
> +++ export -f is_num
> +++ export -f get_stepname
> +++ export -f update_stepnames
> +++ export -f get_current_step_dir
> +++ export -f get_last_step_dir
> +++ export -f get_main_dir
> +++ export -f get_current_step_nr
> +++ export -f get_step_nr
> +++ export -f cp_from_main_dir
> +++ export -f cp_from_last_step
> +++ export -f get_time
> +++ export -f get_number_tasks
> +++ export -f get_table_comment
> +++ export -f csg_inverse_clean
> +++ export -f check_path_variable
> +++ export -f add_to_csgshare
> +++ export -f globalize_dir
> +++ export -f globalize_file
> +++ export -f source_function
> +++ export -f csg_banner
> +++ export -f csg_calc
> +++ export -f show_csg_tables
> +++ export -f get_command_from_csg_tables
> +++ export -f source_wrapper
> +++ export -f find_in_csgshare
> ++++ type -p mktemp
> +++ '[' -z /usr/bin/mktemp ']'
> +++ export -f enable_logging
> +++ export -f get_restart_file
> +++ export -f check_for_obsolete_xml_options
> +++ export -f command_not_found_handle
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
> +++ eval 'simulation_finish()' '{' command_not_found_handle 'simulation_finish;' '}'
> +++ eval export -f simulation_finish
> ++++ export -f simulation_finish
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
> +++ eval 'checkpoint_exist()' '{' command_not_found_handle 'checkpoint_exist;' '}'
> +++ eval export -f checkpoint_exist
> ++++ export -f checkpoint_exist
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
> +++ eval 'get_simulation_setting()' '{' command_not_found_handle 'get_simulation_setting;' '}'
> +++ eval export -f get_simulation_setting
> ++++ export -f get_simulation_setting
> +++ unset i
> ++ export CSG_MASTER_PID=65637
> ++ CSG_MASTER_PID=65637
> ++ export CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all
> ++ CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all
> ++ [[ -n '' ]]
> ++ export VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml
> ++ VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml
> ++ [[ -f /usr/local/votca/share/votca/xml/csg_defaults.xml ]]
> ++ add_to_csgshare --at-the-end /usr/local/votca/share/votca/scripts/inverse
> ++ local dir end=no
> ++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]]
> ++ end=yes
> ++ shift
> ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> ++ for dirlist in '"$@"'
> ++ old_IFS='
> '
> ++ IFS=:
> ++ for dir in '$dirlist'
> ++ eval dir=/usr/local/votca/share/votca/scripts/inverse
> +++ dir=/usr/local/votca/share/votca/scripts/inverse
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> +++ globalize_dir /usr/local/votca/share/votca/scripts/inverse
> +++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> +++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> +++ cd /usr/local/votca/share/votca/scripts/inverse
> +++ pwd
> ++ dir=/usr/local/votca/share/votca/scripts/inverse
> ++ [[ yes = \y\e\s ]]
> ++ export CSGSHARE=/usr/local/votca/share/votca/scripts/inverse
> ++ CSGSHARE=/usr/local/votca/share/votca/scripts/inverse
> ++ export PERL5LIB=/usr/local/votca/share/votca/scripts/inverse
> ++ PERL5LIB=/usr/local/votca/share/votca/scripts/inverse
> ++ IFS='
> '
> ++ check_path_variable CSGSHARE PERL5LIB
> ++ local old_IFS dir
> ++ [[ -z CSGSHARE ]]
> ++ for var in '"$@"'
> ++ [[ -z CSGSHARE ]]
> ++ old_IFS='
> '
> ++ IFS=:
> ++ for dir in '${!var}'
> ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]]
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> ++ IFS='
> '
> ++ for var in '"$@"'
> ++ [[ -z PERL5LIB ]]
> ++ old_IFS='
> '
> ++ IFS=:
> ++ for dir in '${!var}'
> ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]]
> ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]]
> ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]]
> ++ IFS='
> '
> + do_iterations=
> + waittime=10
> + unset CSGXMLFILE CSGENDING CSGDEBUG
> + shopt -s extglob
> + [[ -debug != --debug ]]
> + [[ debug = --debug ]]
> + case $1 in
> + export CSGDEBUG=yes
> + CSGDEBUG=yes
> + shift
> + [[ -options != --options ]]
> + [[ options = --options ]]
> + case $1 in
> + CSGXMLFILE=
> + [[ -f '' ]]
> + die 'options xml file '\'''\'' not found'
> + local pid pids c place
> + echo -e '\nCallstack:'
>
> Callstack:
> + show_callstack
> + local space line
> + [[ -n '' ]]
> + space=
> + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = *\b\a\s\h ]]
> + echo '/usr/local/votca/share/votca/scripts/inverse/inverse.sh - linenumber 82'
> /usr/local/votca/share/votca/scripts/inverse/inverse.sh - linenumber 82
> + (( c=3-1 ))
> + (( c>0 ))
> + [[ main = main ]]
> + continue
> + (( c-- ))
> + (( c>0 ))
> + [[ die = main ]]
> + space+=' '
> + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = *csg_call ]]
> + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = *inverse.sh ]]
> + echo ' die - linenumber 109 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh'
> die - linenumber 109 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> + (( c-- ))
> + (( c>0 ))
> + [[ '' = \-\-\e\x\t\r\a ]]
> + return 0
> + [[ -z '' ]]
> + place='Details can be found above'
> ++ csg_banner ERROR: 'options xml file '\'''\'' not found' 'Details can be found above'
> ++ list=()
> ++ local i l=0 list
> ++ [[ -z ERROR: ]]
> ++ for i in '"$@"'
> ++ [[ -n ERROR: ]]
> ++ [[ -z ERROR: ]]
> ++ list[$l]=ERROR:
> ++ (( l++ ))
> ++ for i in '"$@"'
> ++ [[ -n options xml file '' not found ]]
> ++ [[ -z options xml file '' not found ]]
> ++ list[$l]='options xml file '\'''\'' not found'
> ++ (( l++ ))
> ++ for i in '"$@"'
> ++ [[ -n Details can be found above ]]
> ++ [[ -z Details can be found above ]]
> ++ list[$l]='Details can be found above'
> ++ (( l++ ))
> ++ l=1
> ++ for i in '"${list[@]}"'
> ++ [[ 1 -lt 6 ]]
> ++ l=ERROR:
> ++ for i in '"${list[@]}"'
> ++ [[ 6 -lt 29 ]]
> ++ l='options xml file '\'''\'' not found'
> ++ for i in '"${list[@]}"'
> ++ [[ 29 -lt 26 ]]
> ++ echo '#################################'
> ++ echo '# #'
> ++ for i in '"${list[@]}"'
> ++ printf '# %-29s #\n' ERROR:
> ++ for i in '"${list[@]}"'
> ++ printf '# %-29s #\n' 'options xml file '\'''\'' not found'
> ++ for i in '"${list[@]}"'
> ++ printf '# %-29s #\n' 'Details can be found above'
> ++ echo '# #'
> ++ echo '#################################'
> + msg --color red --to-stderr '#################################
> # #
> # ERROR: #
> # options xml file '\'''\'' not found #
> # Details can be found above #
> # #
> #################################'
> + local color 'colors=blue cyan cyann green red purp'
> + [[ -z '' ]]
> + local 'blue='
> + local 'cyan='
> + local 'cyann='
> + local 'green='
> + local 'red='
> + local 'purp='
> + local 'off='
> + [[ --color = \-\-\c\o\l\o\r ]]
> + [[ -z red ]]
> + is_part red 'blue cyan cyann green red purp'
> + [[ -z red ]]
> + [[ -z blue cyan cyann green red purp ]]
> + [[ blue cyan cyann green red purp = *\ \r\e\d\ * ]]
> + color=''
> + shift 2
> + [[ --to-stderr = \-\-\t\o\-\s\t\d\e\r\r ]]
> + shift
> + [[ -z ################################# # # # ERROR: # # options xml file '' not found # # Details can be found above # # # ################################# ]]
> + [[ -n '' ]]
> + echo -e '#################################
> # #
> # ERROR: #
> # options xml file '\'''\'' not found #
> # Details can be found above #
> # #
> #################################'
> #################################
> # #
> # ERROR: #
> # options xml file '' not found #
> # Details can be found above #
> # #
> #################################
> + [[ -n 65637 ]]
> + pid=65637
> + pids=65637
> + c=0
> + [[ 65637 -eq 65637 ]]
> + [[ -n '' ]]
> + kill 65637
> Terminated: 15
The error is "options xml file '' not found", between '' should be the
filename. I am really not sure why that is.
Is the settings.xml file there and readable?
Christoph
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c80e6e02-10c2-4cb6-a871-de091895798e%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/218b0088-3272-4c9e-ad5f-7e92942ac3e5%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
Message has been deleted
Message has been deleted
Christoph Junghans
Apr 4, 2020, 9:38:22 AM4/4/20
to vo...@googlegroups.com
Try to run "csg_call --debug --options settings.xml function
csg_get_property cg.inverse.log_file" ? And post the output here.
Christoph
On Fri, Apr 3, 2020 at 8:35 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Actually, I don't know what changed but I tried it again and the output is:
> ++ export CSG_MASTER_PID=11337
> ++ CSG_MASTER_PID=11337
> + CSGXMLFILE=settings.xml
> + [[ -f settings.xml ]]
> ++ globalize_file settings.xml
> ++ [[ -z settings.xml ]]
> ++ [[ -f settings.xml ]]
> ++ local dir
> ++ [[ settings.xml = settings.xml ]]
> ++ dir=.
> +++ globalize_dir .
> +++ [[ -z . ]]
> +++ [[ -d . ]]
> +++ cd .
> +++ pwd
> ++ echo /Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml
> + export CSGXMLFILE=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml
> + CSGXMLFILE=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml
> + shift 2
> + [[ '' != '' ]]
> + [[ -z /Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml ]]
> + [[ '' = \c\l\e\a\n ]]
> + enable_logging
> + local log
> + [[ -z '' ]]
> ++ csg_get_property cg.inverse.log_file
> Terminated: 15
>
>
>
> On Friday, April 3, 2020 at 8:30:16 PM UTC-6, Ramon Gonzalez Perez wrote:
>>
>> Yes, here's what I get if I do «ls -l»:
>>
>> -rw-r--r-- 1 ramongonzalezperez staff 4536 Apr 3 12:11 settings.xml
>>
>> Ramón
csg_get_property cg.inverse.log_file" ? And post the output here.
Christoph
On Fri, Apr 3, 2020 at 8:35 PM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Actually, I don't know what changed but I tried it again and the output is:
> ++ CSG_MASTER_PID=11337
> + [[ -f settings.xml ]]
> ++ globalize_file settings.xml
> ++ [[ -z settings.xml ]]
> ++ [[ -f settings.xml ]]
> ++ local dir
> ++ [[ settings.xml = settings.xml ]]
> ++ dir=.
> +++ globalize_dir .
> +++ [[ -z . ]]
> +++ [[ -d . ]]
> +++ cd .
> +++ pwd
> ++ echo /Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml
> + export CSGXMLFILE=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml
> + CSGXMLFILE=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml
> + shift 2
> + [[ '' != '' ]]
> + [[ -z /Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml ]]
> + [[ '' = \c\l\e\a\n ]]
> + enable_logging
> + local log
> + [[ -z '' ]]
> ++ csg_get_property cg.inverse.log_file
> Terminated: 15
>
>
>
> On Friday, April 3, 2020 at 8:30:16 PM UTC-6, Ramon Gonzalez Perez wrote:
>>
>> Yes, here's what I get if I do «ls -l»:
>>
>> -rw-r--r-- 1 ramongonzalezperez staff 4536 Apr 3 12:11 settings.xml
>>
>> Ramón
>>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/218b0088-3272-4c9e-ad5f-7e92942ac3e5%40googlegroups.com.
>>>
>>>
>>>
>>> --
>>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/f43e6426-fe77-4745-a39a-c6f2a6924864%40googlegroups.com.
>>>
>>>
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>
> --
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Christoph Junghans
Apr 4, 2020, 11:10:28 AM4/4/20
to vo...@googlegroups.com
The issue is:
> csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, trying /usr/local/votca/share/votca/xml/csg_defaults.xml
> Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property cg.inverse.log_filedyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
It basically cannot find your gromacs library. Like I said in an
earlier email you need to run "export
DYLD_LIBRARY_PATH=/usr/local/gromacs/lib"
before sourcing VOTCARC.bash ( For convenience you can also add this
line to your VOTCARC.bash somewhere in the top.)
And you will have to do this for every new terminal you open unless
you add these commands to your ~/.bashrc
Alternatively you can change LD_LIBRARY_PATH to DYLD_LIBRARY_PATH in
/usr/local/gromacs/bin/GMXRC.bash and source GMXRC.bash before
VOTCARC.bash. As a second alternative you can install gromacs and
votca in the same prefix path.
Also, didn't we have the exact same discussion on this mailing list a
year ago already:
https://groups.google.com/d/topic/votca/QpoDsXf56bg/discussion ?
I looked up the solution myself right there.
Christoph
On Sat, Apr 4, 2020 at 8:45 AM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I get a loop of this:
>
> Callstack:
> /usr/local/votca/bin/csg_call - linenumber 165
> csg_get_property - linenumber 338 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> critical - linenumber 187 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> Terminated: 15
> csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, trying /usr/local/votca/share/votca/xml/csg_defaults.xml
> Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property cg.inverse.log_filedyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
>
> Callstack:
> /usr/local/votca/bin/csg_call - linenumber 165
> csg_get_property - linenumber 344 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> critical - linenumber 187 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 136: kill: (45887) - No such process
>
> Ramón
> csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, trying /usr/local/votca/share/votca/xml/csg_defaults.xml
> Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property cg.inverse.log_filedyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
> /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: 45917 Abort trap: 6 "$@"
> Reason: image not found
It basically cannot find your gromacs library. Like I said in an
earlier email you need to run "export
DYLD_LIBRARY_PATH=/usr/local/gromacs/lib"
before sourcing VOTCARC.bash ( For convenience you can also add this
line to your VOTCARC.bash somewhere in the top.)
And you will have to do this for every new terminal you open unless
you add these commands to your ~/.bashrc
Alternatively you can change LD_LIBRARY_PATH to DYLD_LIBRARY_PATH in
/usr/local/gromacs/bin/GMXRC.bash and source GMXRC.bash before
VOTCARC.bash. As a second alternative you can install gromacs and
votca in the same prefix path.
Also, didn't we have the exact same discussion on this mailing list a
year ago already:
https://groups.google.com/d/topic/votca/QpoDsXf56bg/discussion ?
I looked up the solution myself right there.
Christoph
On Sat, Apr 4, 2020 at 8:45 AM Ramon Gonzalez Perez
<gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I get a loop of this:
>
> dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
> /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: 45909 Abort trap: 6 "$@"
> dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
>
> Callstack:
> /usr/local/votca/bin/csg_call - linenumber 165
> csg_get_property - linenumber 338 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> critical - linenumber 187 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> die - linenumber 109 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> ######################################################################################################
> # #
> # ERROR: #
> # critical: 'csg_property --file settings.xml --path cg.inverse.scriptpath --short --print .' failed #
> # ERROR: #
> # Details can be found above #
> # #
> ######################################################################################################
> # #
> Terminated: 15
> csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, trying /usr/local/votca/share/votca/xml/csg_defaults.xml
> Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property cg.inverse.log_filedyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
> /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: 45917 Abort trap: 6 "$@"
> Reason: image not found
>
> Callstack:
> /usr/local/votca/bin/csg_call - linenumber 165
> csg_get_property - linenumber 344 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> critical - linenumber 187 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> die - linenumber 109 in /usr/local/votca/share/votca/scripts/inverse/functions_common.sh
> ###########################################################################################################################################
> # #
> # ERROR: #
> # critical: 'csg_property --file /usr/local/votca/share/votca/xml/csg_defaults.xml --path cg.inverse.scriptpath --short --print .' failed #
> # ERROR: #
> # Details can be found above #
> # #
> ###########################################################################################################################################
> # #
> /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 136: kill: (45887) - No such process
>
> Ramón
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/votca/f43e6426-fe77-4745-a39a-c6f2a6924864%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/9390608a-d38e-4053-8cc6-051b8bf5bbe7%40googlegroups.com.
>>
>>
>>
>> --
>> 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 votca+un...@googlegroups.com.
Christoph Junghans
Apr 12, 2020, 5:37:44 PM4/12/20
to vo...@googlegroups.com
On Sat, Apr 4, 2020, 09:10 Christoph Junghans <jung...@votca.org> wrote:
The issue is:
> csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, trying /usr/local/votca/share/votca/xml/csg_defaults.xml
> Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property cg.inverse.log_filedyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib
> Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib
> Reason: image not found
> /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: 45917 Abort trap: 6 "$@"
It basically cannot find your gromacs library. Like I said in an
earlier email you need to run "export
DYLD_LIBRARY_PATH=/usr/local/gromacs/lib"
before sourcing VOTCARC.bash ( For convenience you can also add this
line to your VOTCARC.bash somewhere in the top.)
And you will have to do this for every new terminal you open unless
you add these commands to your ~/.bashrc
Alternatively you can change LD_LIBRARY_PATH to DYLD_LIBRARY_PATH in
/usr/local/gromacs/bin/GMXRC.bash and
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