quick Q about atom/data/top.lib

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imp-dev meeting today at 1pm

simple transformation test fails

Keren Lasker

2 Jan 2010 2 Jan '10

4:27 p.m.

hi,

running IMP on a mac. trying to use add_radius , which requires reading force field parameters. however, IMP keeps compiling that it can not file top.lib. can someone please help ( guessing it has to do something with paths / install ) ?

thanks, keren,

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Daniel Russel

2 Jan 2 Jan

4:59 p.m.

How are you running imp? Using imppy.sh? Or have you installed it?

On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote:

> hi, > > running IMP on a mac. > trying to use add_radius , which requires reading force field parameters. > however, IMP keeps compiling that it can not file top.lib. > can someone please help ( guessing it has to do something with paths / install ) ? > > thanks, > keren, > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Keren Lasker

5:01 p.m.

> imppy.sh thanks! On Jan 2, 2010, at 4:59 PM, Daniel Russel wrote:

> How are you running imp? Using imppy.sh? Or have you installed it? > > On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote: > >> hi, >> >> running IMP on a mac. >> trying to use add_radius , which requires reading force field >> parameters. >> however, IMP keeps compiling that it can not file top.lib. >> can someone please help ( guessing it has to do something with >> paths / install ) ? >> >> thanks, >> keren, >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Daniel Russel

5:07 p.m.

Does the file exist in build/data/atom? Have you moved the IMP dir since you last did built "all"?

On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote:

>> imppy.sh > thanks! > On Jan 2, 2010, at 4:59 PM, Daniel Russel wrote: > >> How are you running imp? Using imppy.sh? Or have you installed it? >> >> On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote: >> >>> hi, >>> >>> running IMP on a mac. >>> trying to use add_radius , which requires reading force field parameters. >>> however, IMP keeps compiling that it can not file top.lib. >>> can someone please help ( guessing it has to do something with paths / install ) ? >>> >>> thanks, >>> keren, >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Keren Lasker

5:14 p.m.

yes On Jan 2, 2010, at 5:07 PM, Daniel Russel wrote:

> Does the file exist in build/data/atom? Have you moved the IMP dir > since you last did built "all"? > > > On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote: > >>> imppy.sh >> thanks! >> On Jan 2, 2010, at 4:59 PM, Daniel Russel wrote: >> >>> How are you running imp? Using imppy.sh? Or have you installed it? >>> >>> On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote: >>> >>>> hi, >>>> >>>> running IMP on a mac. >>>> trying to use add_radius , which requires reading force field >>>> parameters. >>>> however, IMP keeps compiling that it can not file top.lib. >>>> can someone please help ( guessing it has to do something with >>>> paths / install ) ? >>>> >>>> thanks, >>>> keren, >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Daniel Russel

5:09 p.m.

And do you have a real boost install or just headers?

On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote:

Keren Lasker

5:14 p.m.

just headers On Jan 2, 2010, at 5:09 PM, Daniel Russel wrote:

> And do you have a real boost install or just headers? > > On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote: > >>> imppy.sh >> thanks! >> On Jan 2, 2010, at 4:59 PM, Daniel Russel wrote: >> >>> How are you running imp? Using imppy.sh? Or have you installed it? >>> >>> On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote: >>> >>>> hi, >>>> >>>> running IMP on a mac. >>>> trying to use add_radius , which requires reading force field >>>> parameters. >>>> however, IMP keeps compiling that it can not file top.lib. >>>> can someone please help ( guessing it has to do something with >>>> paths / install ) ? >>>> >>>> thanks, >>>> keren, >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Daniel Russel

5:19 p.m.

Does the updated directories code produce an error message? What does it say?

On Jan 2, 2010, at 8:14 PM, Keren Lasker wrote:

> just headers > On Jan 2, 2010, at 5:09 PM, Daniel Russel wrote: > >> And do you have a real boost install or just headers? >> >> On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote: >> >>>> imppy.sh >>> thanks! >>> On Jan 2, 2010, at 4:59 PM, Daniel Russel wrote: >>> >>>> How are you running imp? Using imppy.sh? Or have you installed it? >>>> >>>> On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote: >>>> >>>>> hi, >>>>> >>>>> running IMP on a mac. >>>>> trying to use add_radius , which requires reading force field parameters. >>>>> however, IMP keeps compiling that it can not file top.lib. >>>>> can someone please help ( guessing it has to do something with paths / install ) ? >>>>> >>>>> thanks, >>>>> keren, >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Daniel Russel

5:21 p.m.

I would suggest installing the libs if you are using macports. Just do "sudo ports install boost" (or /opt/local/bin/ports). And make sure you don't use the old headers any more.

On Jan 2, 2010, at 8:14 PM, Keren Lasker wrote:

Keren Lasker

5:23 p.m.

I will try and get back to you later - have to leave .... thanks :) On Jan 2, 2010, at 5:21 PM, Daniel Russel wrote:

> I would suggest installing the libs if you are using macports. Just > do "sudo ports install boost" (or /opt/local/bin/ports). And make > sure you don't use the old headers any more. > > > On Jan 2, 2010, at 8:14 PM, Keren Lasker wrote: > >> just headers >> On Jan 2, 2010, at 5:09 PM, Daniel Russel wrote: >> >>> And do you have a real boost install or just headers? >>> >>> On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote: >>> >>>>> imppy.sh >>>> thanks! >>>> On Jan 2, 2010, at 4:59 PM, Daniel Russel wrote: >>>> >>>>> How are you running imp? Using imppy.sh? Or have you installed it? >>>>> >>>>> On Jan 2, 2010, at 7:27 PM, Keren Lasker wrote: >>>>> >>>>>> hi, >>>>>> >>>>>> running IMP on a mac. >>>>>> trying to use add_radius , which requires reading force field >>>>>> parameters. >>>>>> however, IMP keeps compiling that it can not file top.lib. >>>>>> can someone please help ( guessing it has to do something with >>>>>> paths / install ) ? >>>>>> >>>>>> thanks, >>>>>> keren, >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Daniel Russel

5:11 p.m.

I just committed a change to kernel/src/internal/directories.cpp which will print out where it is looking for the data file if it can't be found. The change should not depend on any other changes so the file should be updatable independently.

On Jan 2, 2010, at 8:01 PM, Keren Lasker wrote:

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Daniel Russel
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