Yes, I also had this problem when compiling with the Intel compiler. I have made a bug report for this now: https://github.com/hashdist/hashstack/issues/886. My current solution is to disable ipython in the hashdist profile.
Johannes On Tue, Nov 17, 2015 at 3:08 PM Guy Moebs <[email protected]> wrote: > Thank you for your message. > It works fine for this problem and the compilation goes further. > > Now I have a compilation error with the "zmq" package > > =========================] 100.0% (2.0MB of 2.0MB) 1.405MB/s ETA 0s > [zmq] Building zmq/32k234mmpyhn, follow log with: > [zmq] tail -f > /work/mdsip/fenics/1.6.0_intel/tmp/zmq-32k234mmpyhn/_hashdist/build.log > [zmq|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned > non-zero exit status 2 > [zmq|ERROR] command failed (code=2); raising > > > > The end of its "build.log" file is : > > 2015/11/17 14:58:37 - INFO: [package:run_job] make[2]: Entering directory > `/work/mdsip/fenics/1.6.0_intel/tmp/zmq-32k234mmpyhn/src' > 2015/11/17 14:58:37 - INFO: [package:run_job] CXX libzmq_la-address.lo > 2015/11/17 14:58:37 - INFO: [package:run_job] CXX libzmq_la-clock.lo > 2015/11/17 14:58:37 - INFO: [package:run_job] CXX libzmq_la-ctx.lo > 2015/11/17 14:58:37 - INFO: [package:run_job] CXX libzmq_la-decoder.lo > 2015/11/17 14:58:38 - INFO: [package:run_job] CXX libzmq_la-devpoll.lo > 2015/11/17 14:58:38 - INFO: [package:run_job] CXX libzmq_la-dist.lo > 2015/11/17 14:58:39 - INFO: [package:run_job] CXX libzmq_la-encoder.lo > 2015/11/17 14:58:39 - INFO: [package:run_job] CXX libzmq_la-epoll.lo > 2015/11/17 14:58:39 - INFO: [package:run_job] CXX libzmq_la-err.lo > 2015/11/17 14:58:40 - INFO: [package:run_job] CXX libzmq_la-fq.lo > 2015/11/17 14:58:40 - INFO: [package:run_job] CXX > libzmq_la-io_object.lo > 2015/11/17 14:58:40 - INFO: [package:run_job] CXX > libzmq_la-io_thread.lo > 2015/11/17 14:58:40 - INFO: [package:run_job] CXX libzmq_la-ip.lo > 2015/11/17 14:58:40 - INFO: [package:run_job] CXX > libzmq_la-ipc_address.lo > 2015/11/17 14:58:41 - INFO: [package:run_job] CXX > libzmq_la-ipc_connecter.lo > 2015/11/17 14:58:41 - INFO: [package:run_job] CXX > libzmq_la-ipc_listener.lo > 2015/11/17 14:58:41 - INFO: [package:run_job] CXX libzmq_la-kqueue.lo > 2015/11/17 14:58:41 - INFO: [package:run_job] In file included from > ipc_connecter.cpp(28): > 2015/11/17 14:58:41 - INFO: [package:run_job] stream_engine.hpp(97): error > #82: storage class is not first > 2015/11/17 14:58:41 - INFO: [package:run_job] const static > size_t greeting_size = 12; > 2015/11/17 14:58:41 - INFO: [package:run_job] ^ > 2015/11/17 14:58:41 - INFO: [package:run_job] > 2015/11/17 14:58:41 - INFO: [package:run_job] compilation aborted for > ipc_connecter.cpp (code 2) > 2015/11/17 14:58:41 - INFO: [package:run_job] make[2]: *** > [libzmq_la-ipc_connecter.lo] Error 1 > 2015/11/17 14:58:41 - INFO: [package:run_job] make[2]: *** Waiting for > unfinished jobs.... > 2015/11/17 14:58:41 - INFO: [package:run_job] In file included from > ipc_listener.cpp(29): > 2015/11/17 14:58:41 - INFO: [package:run_job] stream_engine.hpp(97): error > #82: storage class is not first > 2015/11/17 14:58:41 - INFO: [package:run_job] const static > size_t greeting_size = 12; > 2015/11/17 14:58:41 - INFO: [package:run_job] ^ > 2015/11/17 14:58:41 - INFO: [package:run_job] > 2015/11/17 14:58:41 - INFO: [package:run_job] compilation aborted for > ipc_listener.cpp (code 2) > 2015/11/17 14:58:41 - INFO: [package:run_job] make[2]: *** > [libzmq_la-ipc_listener.lo] Error 1 > 2015/11/17 14:58:42 - INFO: [package:run_job] make[2]: Leaving directory > `/work/mdsip/fenics/1.6.0_intel/tmp/zmq-32k234mmpyhn/src' > 2015/11/17 14:58:42 - INFO: [package:run_job] make[1]: *** [all] Error 2 > 2015/11/17 14:58:42 - INFO: [package:run_job] make[1]: Leaving directory > `/work/mdsip/fenics/1.6.0_intel/tmp/zmq-32k234mmpyhn/src' > 2015/11/17 14:58:42 - INFO: [package:run_job] make: *** [all-recursive] > Error 1 > 2015/11/17 14:58:42 - ERROR: [package:run_job] Command '[u'/bin/bash', > '_hashdist/build.sh']' returned non-zero exit status 2 > 2015/11/17 14:58:42 - ERROR: [package:run_job] command failed (code=2); > raising > > > Regards, > Guy > > > > Le 17/11/2015 13:59, Johannes Ring a écrit : > > Sourcing compilervars_global.sh should set the correct paths > (LD_LIBRARY_PATH, etc.). I would try with the following in your local.yaml: > > parameters: > PROLOGUE: | > . > /ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/bin/compilervars_global.sh > intel64; . > /ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/mpi/intel64/bin/mpivars.sh; > echo "setting default compilers"; export CC=icc; export CXX=icpc; export > FC=ifort; export F77=ifort; export F90=ifort > > Johannes > > On Tue, Nov 17, 2015 at 1:42 PM Guy Moebs <[email protected]> > wrote: > > Hello Johannes, >> >> I do agree with you. >> The Intel's environment is set by using Intel's scripts in my ".bashrc" >> file. >> >> . >> /ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/bin/compilervars_global.sh >> intel64 >> . >> /ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/mpi/intel64/bin/mpivars.sh >> >> I have changed the "config.yaml" file : "build_dirs" are not in my home >> but elsewhere on a shared filesystem. >> >> I have changed the local.yaml file by looking what I did some weeks ago : >> parameters: >> PROLOGUE: | >> export >> FC=/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/bin/intel64/ifort >> ; export >> CC=/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/bin/intel64/icc >> ; export >> CXX=/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/bin/intel64/icpc >> >> Should I set "the LD_LIBRARY_PATH" and the "PATH" env. variables as "FC", >> "CC", "CXX" juste above at the end of the "local.yaml" file ? >> >> Regards, >> Guy. >> > _______________________________________________ >>> fenics-support mailing list >>> [email protected] >>> http://fenicsproject.org/mailman/listinfo/fenics-support >>> >>
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