On Tue, Sep 22, 2015 at 3:43 PM Guy Moebs <[email protected]> wrote:
> Hi Johannes, > > I'd like our users to be able to run fenics on our cluster. So a runable > version first, and next a maybe more optimized one. > > "gcc", /usr/bin/gcc, is version 4.3 of the GNU compiler. > > We have version 4.7 as /usr/bin/gcc-4.7 > Where is the hashdist profile file in order to modify the gcc default name > ? > You will have to create the hashdist profile, either from scratch or by modifying an existing profile. There are profiles that you can use in hashstack and in fenics-developer-tools. You can for example do the following: git clone https://bitbucket.org/fenics-project/fenics-developer-tools.git cd fenics-developer-tools cp install/profiles/fenics.Linux.yaml local.yaml Now, open local.yaml and add something like the following: parameters: PROLOGUE: | export CC=/usr/bin/gcc-4.7; export CXX=/usr/bin/g++-4.7; export FC=/usr/bin/gfortran-4.7 To use OpenMPI instead of MPICH, replace mpi: use: mpich with this: mpi: use: openmpi When you are satisfied with your profile, run ./install/fenics-install.sh The fenics-install.sh script will detect and use your local.yaml profile. Note that you should set the same variables when compiling/running FEniCS programs as you do in the PROLOGUE. In the case above, this will be source fenics.custom export CC=/usr/bin/gcc-4.7 export CXX=/usr/bin/g++-4.7 export FC=/usr/bin/gfortran-4.7 Johannes Regards, > Guy Moebs > > > Le 22/09/2015 15:25, Johannes Ring a écrit : > > [missed the list] > > Hi Guy, > > Please see comments below. > > On Tue, Sep 22, 2015 at 2:21 PM Guy Moebs <[email protected]> > wrote: > >> >> Hello, >> >> Thank you for your responses. >> I'm the person who tries to install fenics for Katerina Sladkova on our >> cluster in Nantes. >> >> As you explained it, I put the source cache mirror in the >> ~/.hashdist/config.yaml and it works better, i.e. : >> >> source_caches: >> - dir: ./src >> ## For additional source cache mirror: >> - url: http://fenicsproject.org/pub/hashdist/src >> >> >> >> >> >> Now, the script fenics-install.sh goes further but stops with the >> following error : >> >> Downloading >> http://fenicsproject.org/pub/hashdist/src/packs/tar.gz/6lm2emnxz6l7d7xg5dewmmit5p3meqgu >> ... >> [=========================] 100.0% (5.3MB of 5.3MB) 2.626MB/s ETA 0s >> [parmetis] Building parmetis/3fq73xu4m2bo, follow log with: >> [parmetis] tail -f >> /ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/_hashdist/build.log >> [parmetis|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned >> non-zero exit status 2 >> [parmetis|ERROR] command failed (code=2); raising >> >> >> >> I look at the file build.log and it ends with the following lines >> >> 2015/09/22 11:57:21 - INFO: [package:run_job] Building C object >> libmetis/CMakeFiles/metis.dir/__/GKlib/error.c.o >> 2015/09/22 11:57:21 - INFO: [package:run_job] cd >> /ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/_build_metis/libmetis >> && /ccipl/users/gmoebs/.hashdist/bld/mpi/gmkx3ftk3tz2/bin/mpicc >> -Dmetis_EXPORTS -DLINUX -D_FILE_OFFSET_BITS=64 -std=c99 >> -fno-strict-aliasing -fPIC -Wall -pedantic -Wno-unused-but-set-variable >> -Wno-unused-variable -Wno-unknown-pragmas -DNDEBUG -DNDEBUG2 >> -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -fPIC >> -I/ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/metis/GKlib >> -I/ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/metis/include >> -I/ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/metis/libmetis/. >> -o CMakeFiles/metis.dir/__/GKlib/error.c.o -c >> /ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/metis/GKlib/error.c >> 2015/09/22 11:57:21 - INFO: [package:run_job] cc1: error: unrecognized >> command line option "-Wno-unused-but-set-variable" >> 2015/09/22 11:57:21 - INFO: [package:run_job] cc1: error: unrecognized >> command line option "-Wno-unused-but-set-variable" >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[2]: *** >> [libmetis/CMakeFiles/metis.dir/__/GKlib/blas.c.o] Error 1 >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[2]: *** Waiting for >> unfinished jobs.... >> 2015/09/22 11:57:21 - INFO: [package:run_job] cc1: error: unrecognized >> command line option "-Wno-unused-but-set-variable" >> 2015/09/22 11:57:21 - INFO: [package:run_job] cc1: error: unrecognized >> command line option "-Wno-unused-but-set-variable" >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[2]: *** >> [libmetis/CMakeFiles/metis.dir/__/GKlib/b64.c.o] Error 1 >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[2]: *** >> [libmetis/CMakeFiles/metis.dir/__/GKlib/csr.c.o] Error 1 >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[2]: *** >> [libmetis/CMakeFiles/metis.dir/__/GKlib/error.c.o] Error 1 >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[1]: *** >> [libmetis/CMakeFiles/metis.dir/all] Error 2 >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[2]: Leaving directory >> `/ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/_build_metis' >> 2015/09/22 11:57:21 - INFO: [package:run_job] make[1]: Leaving directory >> `/ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/_build_metis' >> 2015/09/22 11:57:21 - INFO: [package:run_job] make: *** [all] Error 2 >> 2015/09/22 11:57:21 - INFO: [package:run_job] make: Leaving directory >> `/ccipl/users/gmoebs/.hashdist/tmp/parmetis-3fq73xu4m2bo/_build_metis' >> 2015/09/22 11:57:21 - ERROR: [package:run_job] Command '[u'/bin/bash', >> '_hashdist/build.sh']' returned non-zero exit status 2 >> 2015/09/22 11:57:21 - ERROR: [package:run_job] command failed (code=2); >> raising >> > > It looks like you have an old version of GCC. You will need at least > version 4.6. Are there other GCC versions available on the cluster? In that > case you will have to modify the hashdist profile such that it will use the > correct compiler. > > >> >> >> >> >> I have an other question : >> how can I tell fenics that I have some softwares already installed and >> that I want to use them instead of downloaded ones ? For instance, if I >> want to use Intel's compilers (icc/ifort/icpc), Intel's MPI (wrappers and >> compilation options, libs), Intel's scientific library (mkl) for blas, >> lapack, etc. , what and where should I change things ? >> > > Unfortunately, building FEniCS with Intel compilers/MPI/MKL has not been > tested with hashdist and will therefore not work with the fenics-install.sh > script. To make it work, we will have to make changes in hashstack. This is > on my TODO list, but it will probably not happen in the near future. > > So, your current options are to either build with GCC using hashdist or > with Intel and build everything from source manually. > > Johannes > > >> Thank you in advance for your advices. >> >> Regards, >> Guy Moebs >> >> >> >> Ok. I have modified fenics-install.sh now such that it adds a source >> cache mirror to fenicsproject.org in ~/.hashdist/config.yaml if this >> file does not exist. If you already have ~/.hashdist/config.yaml, you will >> have to add it manually. >> >> Johannes >> >> On Tue, Sep 22, 2015 at 10:48 AM Anders Logg <[email protected]> >> wrote: >> >>> I just want to add that we also experienced the problem with OpenSSL >>> download just now at Chalmers. >>> >>> -- >>> Anders >>> >>> >>> tis 22 sep. 2015 kl 09:41 skrev Johannes Ring < <[email protected]> >>> [email protected]>: >>> >>>> Hi, >>>> >>>> It may look like it starts from the beginning, because the >>>> fenics-install.sh script will download hashdist, hashstack and >>>> fenics-developer-tools every time you run it. However, the other packages >>>> will be stored in ~/.hashdist (unless you modify ~/.hashdist/config.yaml) >>>> and it will not build them again unless you change the hashdist profile. I >>>> see from your terminal output that there is a problem downloading openssl. >>>> This problem can be fixed by adding a source cache mirror to >>>> fenicsproject.org. To do this, add the following line under >>>> source_caches in ~/.hashdist/config.yaml: >>>> >>>> - url: <http://fenicsproject.org/pub/hashdist/src> >>>> http://fenicsproject.org/pub/hashdist/src >>>> >>>> Note that on a cluster it might be better to download hashdist and >>>> hashstack manually instead of using the fenics-install.sh script. This >>>> gives you better control and you can setup a hashdist profile to use >>>> modules from the cluster, like compiler and MPI modules. See for instance >>>> the fenics.abel.gnu.yaml example in hashstack. >>>> >>>> Johannes >>>> >>>> On Tue, Sep 22, 2015 at 8:00 AM Sladkova < >>>> <[email protected]> >>>> [email protected]> wrote: >>>> >>> Hi, >>>>> >>>>> I am an PhD student using Fenics for my thesis and we are trying to >>>>> installing FEnics also on our cluster (LPGN, University of Nantes). I >>>>> would like to ask you a question regarding this installation. >>>>> >>>>> Exist there a way how to tell Fenics that he doesn't have to start the >>>>> installation from beginning? And that he can start the installation >>>>> from >>>>> the point where he stopped the last time by for example giving him >>>>> what's still missing? >>>>> >>>>> For example: fenics-install.sh downloads lot of thing, most of them >>>>> already exists on the cluster. But he doesn't look for them, he just >>>>> starts from the beginning. However sometimes the distant server doesn't >>>>> respond quickly enough and everything stops. At this point we would >>>>> like >>>>> to start from the point where we stopped before. >>>>> >>>>> I am also attaching a text file with an example of this problem. >>>>> >>>>> Thank you very much for your time, >>>>> Katerina Sladkova >>>>> >>>> _______________________________________________ >>>>> fenics-support mailing list >>>>> [email protected] >>>>> http://fenicsproject.org/mailman/listinfo/fenics-support >>>>> >>>> >> >> >> -- >> Ingénieur de Recherche CNRS >> Laboratoire de Mathématiques Jean Leray >> UMR 6629 CNRS - Université de [email protected] --- 02 51 12 59 >> 40 >> >> > -- > Ingénieur de Recherche CNRS > Laboratoire de Mathématiques Jean Leray > UMR 6629 CNRS - Université de [email protected] --- 02 51 12 59 > 40 > >
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