[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"
I see now that the symbols are actually there, but they are dynamic symbols which don't seem to get picked up (Though I don't really know what the difference is). -Kyle -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"
Hi Kyle On Friday, January 25, 2019 at 9:11:35 AM UTC+1, ky...@math.uh.edu wrote: > > Hi Denis, > > I did see both of the issues raised on github before I posted, but it > wasn't really clear what the resolution was other than its a gsl dependency > problem. > I would say from our side we tried to pick up `gslcblas` to fix part of the issue with Linux provided GSL > > nm -g /usr/lib64/libgslcblas.so > nm -g /usr/lib64/libgsl.so > both tell me there are no symbols, even without grepping for the one in > question. > > Does this mean that if I do need GSL I should install from source instead? > (as pointed out in the other response, I don't need GSL for the work i will > be doing). > Yes, I would say so. But given that you won't need this functionality, you can safely disable GSL as recommended by David. In recent years I tend to prefer build everything from sources using https://github.com/dealii/dealii/wiki/deal.II-in-Spack for all environments (macOS and HPC). Regards, Denis. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"
Hi Denis, I did see both of the issues raised on github before I posted, but it wasn't really clear what the resolution was other than its a gsl dependency problem. nm -g /usr/lib64/libgslcblas.so nm -g /usr/lib64/libgsl.so both tell me there are no symbols, even without grepping for the one in question. Does this mean that if I do need GSL I should install from source instead? (as pointed out in the other response, I don't need GSL for the work i will be doing). -Kyle -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"
Hi Kyle, According to your config, deal.II picked up gslcblas.so: GSL_LIBRARIES = /usr/lib64/libgsl.so;/usr/lib64/libgslcblas.so Could you check if it contains the missing symbol, something like: $ nm -g ~/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/gsl-2.5-3xp3xgxrby4oihswo2f7ve2hywzbxvjx/lib/libgslcblas.dylib | grep cblas_ctrmv 000316c0 T _cblas_ctrmv p.s. FYI https://github.com/dealii/dealii/issues/2881#issuecomment-235790839 and also https://github.com/JuliaMath/GSL.jl/issues/70#issuecomment-402674809 Looks like this is really an issue with GSL as natively provided by Linux package manager. Denis. On Thursday, January 24, 2019 at 10:43:14 PM UTC+1, ky...@math.uh.edu wrote: > > Hi all, > > I'm having trouble installing deal.II. cmake seems to find gsl just fine, > but it looks like there is trouble when linking against it. As you can see > in the quicktests.log, the error it gives is that "symbol lookup error: > /lib64/libgsl.so.23: undefined symbol: cblas_ctrmv" > > I also see that a similar issue had bee reported here > https://github.com/dealii/dealii/issues/2757, but this was a couple years > ago and a patch was merged. > > The logs you see are for installing the master branch from github, > although I got similar errors when trying to install version 8.5 as well. > > -Kyle Williams > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"
Thank you very much, this will work fine. -Kyle williams -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"
Hi Kyle, deal.II only uses GSL in two places: the Functions::CSpline class (which interpolates provided data with splines) and in FESeries::Legendre, (which is used in some regularity estimators). Unless you plan on using either of these classes directly I suggest just disabling GSL with the cmake flag -DDEAL_II_WITH_GSL=OFF. Does this work for you? If not we can try to work out a way to get your GSL installation working. Thanks, David Wells On Thursday, January 24, 2019 at 4:43:14 PM UTC-5, ky...@math.uh.edu wrote: > > Hi all, > > I'm having trouble installing deal.II. cmake seems to find gsl just fine, > but it looks like there is trouble when linking against it. As you can see > in the quicktests.log, the error it gives is that "symbol lookup error: > /lib64/libgsl.so.23: undefined symbol: cblas_ctrmv" > > I also see that a similar issue had bee reported here > https://github.com/dealii/dealii/issues/2757, but this was a couple years > ago and a patch was merged. > > The logs you see are for installing the master branch from github, > although I got similar errors when trying to install version 8.5 as well. > > -Kyle Williams > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
