On Fri, Aug 1, 2014 at 9:54 PM, Mikael Mortensen <[email protected]> wrote: > > On 01 Aug 2014, at 21:48, Jan Blechta <[email protected]> wrote: > > On Fri, 1 Aug 2014 20:23:04 +0100 > "Garth N. Wells" <[email protected]> wrote: > > > On 1 Aug 2014, at 19:54, Mikael Mortensen > <[email protected]> wrote: > > Thank you both for the tips. I’ll look into it some more. BTW, do > you create your own modules for all dependencies Garth? The module > system is used on our cluster, but I have never tried to create > modules of my own. > > > I haven’t done it, but have seen colleagues do it for FEniCS (on > workstations and on clusters). It’s easy. > > > Yes, that's like a fenics.conf file but just in different language. And > it may handle dependencies. > > But creating a module does not resolve these linking problems. You > should solve there an original issue - FEniCS stable and libraries > (which could be reused) are installed in the same place. > > Currently we are thinking here in Prague before ugrading to Ubuntu > Trusty how to handle installation and usage of packages. Our homobrewn > system written in Make is getting out of hands with growing number of > different PETScs, FEniCSes, BLAS, debug/nodebug combinations... Not > talking how to handle smart pulling dev versions by pushing a button. > > We've heard about hashdist https://github.com/hashdist/hashdist, > https://github.com/hashdist/hashstack. I think Johannes is somewhat > involved. Do you have some experience with this? > > > Johannes has been using hashdist/hashstack on Abel, but I don’t really > understand it. So I guess the smart thing to do right now is just to wait > for the build engineer himself to comment and I think he’s on vacation.
I have built fenics-dev on Abel and you can use it by running source ~johannr/fenics-dev.abel.gnu.conf If you want to build your own copy of dolfin-dev, I can tell you how to do that with HashDist later. Johannes > Mikael > > > Other alternative seems to be http://hpcugent.github.io/easybuild/. > > Jan > > > Dorsal should create module files. > > Garth > > > Best regards > > Mikael > > On 01 Aug 2014, at 18:20, Garth N. Wells <[email protected]> wrote: > > Use the 'module' system to support multiple installations on a > cluster. > > Garth > > On Fri, 1 Aug, 2014 at 3:36 PM, Jan Blechta > <[email protected]> wrote: > > On Fri, 1 Aug 2014 16:16:38 +0200 > Mikael Mortensen <[email protected]> wrote: > > Hi, > I'm trying to install master version of fenics on top of a stable > version installed by Johannes on the Abel cluster. Johannes has > more or less everything, including dolfin, installed under > /usit/abel/u1/johannr/nobackup/src/hashstack/default/, which is > on my path. The stable version here works just fine. I now want > to use all the dependencies here and build a master version, so > I'm using dorsal with unstable for fiat/ffc/ufl/instant, and > install in my own folder. I then clone dolfin in a different > directory and run cmake.local. It stops at > MultiMeshAssembler.cpp because for some reason it picks up ufc.h > from the stable and not the unstable branch, even though the > unstable is sourced last. From my .bashrc: > source /usit/abel/u1/johannr/fenics-1.4.0-gcc.conf # stable > everything > source /usit/abel/u1/mikaem/Fenics/fenics-1.4/share/fenics/fenics.conf > # unstable fiat/ffc/ufl/instant/ufc.h With some hacking of paths > I am able to fix MultiMeshAssembler and everything compiles just > fine. However, the python version still does not work and I find > that it is because the module-libraries are picking up the > stable dolfin version. Here is ldd of dolfin/cpp/_common.so: > [mikaem@login-0-0 ~]$ ldd > /usit/abel/u1/mikaem/Fenics/dolfin/local.master/lib/python2.7/site-packages/dolfin/cpp/_common.so > linux-vdso.so.1 => (0x00007fff7816d000) > libdolfin.so.1.4 => > /usit/abel/u1/johannr/nobackup/src/hashstack/default/lib/libdolfin.so.1.4 > (0x00007fb14c5ee000) > libpython2.7.so.1.0 => > /usit/abel/u1/johannr/nobackup/src/hashstack/default/lib/libpython2.7.so.1.0 > (0x00007fb14c1e7000) > ... > Evidently _common.so has picked up the stable libdolfin.so.1.4. > Any hints at how this can be fixed? An alternative I don't like > is to give up Johannes' dependencies all together and install > everything for myself. > > You should not use Johannes' fenics.conf, it probably sets > LD_LIBRARY_PATH. Linker can't distinguish between stable and > unstable as they have same name libdolfin.so.1.4. Rather you > should tell to DOLFIN's CMake about all the dependencies which > you want to use from Johannes. Or maybe try a little bit messy > solution, keep the build you have and then get rid of Johannes' > LD_LIBRARY_PATH in your own fenics.conf a check what linker says. > Generally, it will be everytime tricky. You should convince > Johannes to install dependencies you need separately from stable > FEniCS. (You could simulate this with symlinks.) > Jan > > Thanks for any help. > Best regards > Mikael > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support > > > > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support > > _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
