[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]>: >> >>> 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 >>> >>> 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]> 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 > >
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