On 04 Aug 2014, at 18:52, Johannes Ring <[email protected]> wrote: > 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
Great, that’s all I needed, thanks:-) > > If you want to build your own copy of dolfin-dev, I can tell you how > to do that with HashDist later. Looking forward to it. Mikael > > 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
