Hi Arnau there is one tip I forgot to tell you in my previous email.
By default easybuild doesn't enable support for any queuing system in OpenMPI. I know at CRG you use SGE so I would recommend you to edit the openmpi easyconfig (if you are using goolf-1.4.10 that would be OpenMPI-1.6.4-GCC-4.7.2.eb) and modify the OpenMPI configopts to enable the SGE support in openmpi. You just need to edit the easyconfig file and modify configopts to add "--with-sge" flag, something like this: configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-sge ' regards, Pablo. 2014-07-02 14:00 GMT+02:00 Jens Timmerman <[email protected]>: > Hi Arnau, > > On 07/01/2014 10:31 AM, Arnau Bria wrote: > > Hi all, > > my name is Arnau Bria and I'm a sysadmin at CRG (Barcelona). > I'm really interested in EB as seems a good option for providing new > software to our users in a easy way. > > But eb fails with the error: > > ERROR: EasyBuild crashed with an error (at > easybuild/framework/easyconfig/tools.py:223 in resolve_dependencies): > Irresolvable dependencies encountered: [('gompi/1.4.10', {'dummy': > True, 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': > 'gompi', 'versionsuffix': '', 'version': '1.4.10', 'parsed': True})] > > > eb knows the toolchain: > > $ eb --list-toolchains > List of known toolchains (toolchainname: module[,module...]): > ClangGCC: Clang, GCC > GCC: GCC > [...] > gompi: GCC, OpenMPI > [...] > > Question 1: > - For each compiler toolchain, the constituent elements (compiler + > libraries) are printed, which provides the necessary information to select a > toolchain. > > so, If I have successfully installed gcc + openmpi gompi should be a > valid toolchain...am I right? > > you will still need to create a modulefile for the gompi toolchain, this > is done as explained later in the step by step guide, but I have added this > now as step 3.2 > > eb gompi-1.4.10.eb > > This will create a module which does nothing more then load the 2 > dependencies, so after this easybuild will be able to actually use the > gompi toolchain. > > $ module av > > ------------------------------------------------------------------ > /software/as/el6.3/EasyBuild/modules/all > ------------------------------------------------------------------- > EasyBuild/1.13.0 GCC/4.6.3 > LAPACK/3.4.0-GCC-4.6.3 OpenMPI/1.4.5-GCC-4.6.3-no-OFED > > ----------------------------------------------------------------------- > /usr/share/Modules/modulefiles > ------------------------------------------------------------------------ > dot module-cvs module-info modules null use.own > > ------------------------------------------------------------------------------ > /etc/modulefiles > ------------------------------------------------------------------------------- > compat-openmpi-x86_64 openmpi-x86_64 > > > > I've uploaded the eb installation log to pastebin:http://pastebin.com/f5tzUsai > > So, which is the Irresolvable dependencies encountered? How may I solve > it? > > the gompi module is not listed there, so easybuild can not use it yet. > However, easybuild could easily create it for you if you use the `-r` or > `--robot` option (but we don't show this in the step by step guide, since > this guide shows you all the steps instead of letting easybuild do > everything for you) > > if you run > > eb OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb > <https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb> > -r > EasyBuild will doe a recursive build, so figure out all the modules it > needs to build, and build them for you, so you don't have to do the step by > step thing. > > So this is why the quick demo will also work, it will build al needed > dependencies for you without any of your intervention since it has the > --robot option > > Regards, > > Bests, > Arnau > > > -- > Jens Timmerman > > Flemish Supercomputer Center > Ghent University High Performance Computing Team > Krijgslaan 281 Building S9 > B-9000 Gent > Belgium+32 9 264 96 [email protected] > > -- Pablo Escobar López HPC systems engineer Biozentrum, University of Basel Swiss Institute of Bioinformatics SIB Email: [email protected] Phone: +41 61 267 15 82 http://www.biozentrum.unibas.ch
