[OMPI users] openmpi-2.0.1
Hi I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 intel compilers and I an having problems. The configure script with CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make all install this fails with the output: Making all in tools/ompi_info make[2]: Entering directory `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' CCLD ompi_info ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o) is referenced by DSO ld: final link failed: Bad value make[2]: *** [ompi_info] Error 1 make[2]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi' make: *** [all-recursive] Error 1 Does anyone have suggestions for fixing this problem? Thanks Bill -- Professor W P Jones, FREng Department of Mechanical Engineering Imperial College London Exhibition Road London SW7 2AZ Tel:+44 (0)20 7594 7037/7033 Mobile +44 (0)776 495 9702 Fax:+44 (0)20 7594 5702 E-mail: w.jo...@imperial.ac.uk web site: http://www.imperial.ac.uk/me ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
Re: [OMPI users] openmpi-2.0.1
On 11/17/2016 8:45 AM, Professor W P Jones wrote: > Hi > > I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 > intel compilers and I an having problems. The configure script with > CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make > all install this fails with the output: > > > Making all in tools/ompi_info > make[2]: Entering directory > `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' > CCLD ompi_info > ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not > found (try using -rpath or -rpath-link) > ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not > found (try using -rpath or -rpath-link) > ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not > found (try using -rpath or -rpath-link) > ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, > not found (try using -rpath or -rpath-link) > ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in > /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o) > is referenced by DSO > ld: final link failed: Bad value > make[2]: *** [ompi_info] Error 1 > make[2]: Leaving directory > `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi' > make: *** [all-recursive] Error 1 > Do you have the Intel compilervars.[c]sh sourced (and associated library files visible) on each node where you expect to install? -- Tim Prince ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
Re: [OMPI users] openmpi-2.0.1
Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2 (gcc version 4.8.0 compatibility) Bill Professor W P Jones, FREng Department of Mechanical Engineering Imperial College London Exhibition Road London SW7 2AZ Tel:+44 (0)20 7594 7037/7033 Mobile +44 (0)776 495 9702 Fax:+44 (0)20 7594 5702 E-mail: w.jo...@imperial.ac.uk web site: http://www.imperial.ac.uk/me On 17/11/16 14:02, Tim Prince via users wrote: On 11/17/2016 8:45 AM, Professor W P Jones wrote: Hi I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 intel compilers and I an having problems. The configure script with CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make all install this fails with the output: Making all in tools/ompi_info make[2]: Entering directory `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' CCLD ompi_info ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o) is referenced by DSO ld: final link failed: Bad value make[2]: *** [ompi_info] Error 1 make[2]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi' make: *** [all-recursive] Error 1 Do you have the Intel compilervars.[c]sh sourced (and associated library files visible) on each node where you expect to install? ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
Re: [OMPI users] openmpi-2.0.1
Can you include your entire ./configure line? Also, it would be useful, perhaps to look at the output of $ printenv | grep LIBRARY to make sure that all Intel library paths made it into the appropriate variables. When I build 1.10.2, I had these: LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64 LD_LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64_lin and those sufficed. I have not tried OMPI 2.x. -- bennet On Thu, Nov 17, 2016 at 9:20 AM, Professor W P Jones wrote: > Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2 > (gcc version 4.8.0 compatibility) > > Bill > > Professor W P Jones, FREng > Department of Mechanical Engineering > Imperial College London > Exhibition Road > London SW7 2AZ > Tel:+44 (0)20 7594 7037/7033 > Mobile +44 (0)776 495 9702 > Fax:+44 (0)20 7594 5702 > E-mail: w.jo...@imperial.ac.uk > web site: http://www.imperial.ac.uk/me > > On 17/11/16 14:02, Tim Prince via users wrote: >> >> >> On 11/17/2016 8:45 AM, Professor W P Jones wrote: >>> >>> Hi >>> >>> I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 >>> intel compilers and I an having problems. The configure script with >>> CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make >>> all install this fails with the output: >>> >>> >>> Making all in tools/ompi_info >>> make[2]: Entering directory >>> `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' >>>CCLD ompi_info >>> ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not >>> found (try using -rpath or -rpath-link) >>> ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not >>> found (try using -rpath or -rpath-link) >>> ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not >>> found (try using -rpath or -rpath-link) >>> ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, >>> not found (try using -rpath or -rpath-link) >>> ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in >>> >>> /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o) >>> is referenced by DSO >>> ld: final link failed: Bad value >>> make[2]: *** [ompi_info] Error 1 >>> make[2]: Leaving directory >>> `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi' >>> make: *** [all-recursive] Error 1 >>> >> Do you have the Intel compilervars.[c]sh sourced (and associated library >> files visible) on each node where you expect to install? >> > > ___ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
Re: [OMPI users] openmpi-2.0.1
The .configure is: ./configure PREFIX=/opt/openmpi-2.0.1-intel-14.0.2 CC=icc CXX=icpc F77=ifort FC=ifort and the output from printenv | grep LIBRARY is: LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4 MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic LD_LIBRARY_PATH=/opt/lf6481/lib64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4:/opt/lf6481/lib64:/usr/StorMan:/usr/StorMan/ssl/lib:/usr/StorMan/pegasus/lib: MIC_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic Bill Professor W P Jones, FREng Department of Mechanical Engineering Imperial College London Exhibition Road London SW7 2AZ Tel:+44 (0)20 7594 7037/7033 Mobile +44 (0)776 495 9702 Fax:+44 (0)20 7594 5702 E-mail: w.jo...@imperial.ac.uk web site: http://www.imperial.ac.uk/me On 17/11/16 14:33, Bennet Fauber wrote: Can you include your entire ./configure line? Also, it would be useful, perhaps to look at the output of $ printenv | grep LIBRARY to make sure that all Intel library paths made it into the appropriate variables. When I build 1.10.2, I had these: LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64 LD_LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64_lin and those sufficed. I have not tried OMPI 2.x. -- bennet On Thu, Nov 17, 2016 at 9:20 AM, Professor W P Jones wrote: Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2 (gcc version 4.8.0 compatibility) Bill Professor W P Jones, FREng Department of Mechanical Engineering Imperial College London Exhibition Road London SW7 2AZ Tel:+44 (0)20 7594 7037/7033 Mobile +44 (0)776 495 9702 Fax:+44 (0)20 7594 5702 E-mail: w.jo...@imperial.ac.uk web site: http://www.imperial.ac.uk/me On 17/11/16 14:02, Tim Prince via users wrote: On 11/17/2016 8:45 AM, Professor W P Jones wrote: Hi I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 intel compilers and I an having problems. The configure script with CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make all install this fails with the output: Making all in tools/ompi_info make[2]: Entering directory `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' CCLD ompi_info ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, not found (try using -rpath or -rpath-link) ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o) is referenced by DSO ld: final link failed: Bad value make[2]: *** [ompi_info] Error 1 make[2]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi' make: *** [all-recursive] Error 1 Do you have the Intel compilervars.[c]sh sourced (and associated library files visible) on each node where you expect to install? ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
Re: [OMPI users] openmpi-2.0.1
That's a stumper. Only thing I can think of is that the LD_LIBRARY_PATH is being overwritten somewhere inside the Makefile, or perhaps that it isn't properly exported...? As a graspable straw, try $ set -a to export all variables, then $ source /opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh (I may have the path to your compilervars.sh wrong). That should insure that everything is properly exported. It sure looks to me like the compilers aren't finding the right library paths. -- bennet On Thu, Nov 17, 2016 at 9:44 AM, Professor W P Jones wrote: > The .configure is: > > ./configure PREFIX=/opt/openmpi-2.0.1-intel-14.0.2 CC=icc CXX=icpc F77=ifort > FC=ifort > > and the output from printenv | grep LIBRARY is: > > LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4 > MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic > LD_LIBRARY_PATH=/opt/lf6481/lib64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4:/opt/lf6481/lib64:/usr/StorMan:/usr/StorMan/ssl/lib:/usr/StorMan/pegasus/lib: > MIC_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic > > Bill > > > Professor W P Jones, FREng > Department of Mechanical Engineering > Imperial College London > Exhibition Road > London SW7 2AZ > Tel:+44 (0)20 7594 7037/7033 > Mobile +44 (0)776 495 9702 > Fax:+44 (0)20 7594 5702 > E-mail: w.jo...@imperial.ac.uk > web site: http://www.imperial.ac.uk/me > > On 17/11/16 14:33, Bennet Fauber wrote: >> >> Can you include your entire ./configure line? Also, it would be >> useful, perhaps to look at the output of >> >> $ printenv | grep LIBRARY >> >> to make sure that all Intel library paths made it into the appropriate >> variables. >> >> When I build 1.10.2, I had these: >> >> >> LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64 >> >> >> LD_LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64_lin >> >> and those sufficed. I have not tried OMPI 2.x. >> >> -- bennet >> >> >> >> On Thu, Nov 17, 2016 at 9:20 AM, Professor W P Jones >> wrote: >>> >>> Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version >>> 14.0.2 >>> (gcc version 4.8.0 compatibility) >>> >>> Bill >>> >>> Professor W P Jones, FREng >>> Department of Mechanical Engineering >>> Imperial College London >>> Exhibition Road >>> London SW7 2AZ >>> Tel:+44 (0)20 7594 7037/7033 >>> Mobile +44 (0)776 495 9702 >>> Fax:+44 (0)20 7594 5702 >>> E-mail: w.jo...@imperial.ac.uk >>> web site: http://www.imperial.ac.uk/me >>> >>> On 17/11/16 14:02, Tim Prince via users wrote: On 11/17/2016 8:45 AM, Professor W P Jones wrote: > > Hi > > I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 > intel compilers and I an having problems. The configure script with > CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make > all install this fails with the output: > > > Making all in tools/ompi_info > make[2]: Entering directory > `/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info' > CCLD ompi_info > ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not > found (try using -rpath or -rpath-link) > ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not > found (try using -rpath or -rpath-link) > ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not > found (try using -rpath or -rpath-link) > ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, > not found (try using -rpath or -rpath-link) > ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in > > > /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o) > is referenced by DSO > ld: final link failed: Bad va
[OMPI users] malloc related crash inside openmpi
Hi - we’ve started seeing over the last few days crashes and hangs in openmpi, in a code that hasn’t been touched in months, and an openmpi installation (v. 1.8.5) that also hasn’t been touched in months. The symptoms are either a hang, with a stack trace (from attaching to the one running process that’s got 0% CPU usage) that looks like this: (gdb) where #0 0x00358980f00d in nanosleep () from /lib64/libpthread.so.0 #1 0x2af19a8758de in opal_memory_ptmalloc2_free () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6 #2 0x02bca106 in for__free_vm () #3 0x02b8cf62 in for__exit_handler () #4 0x02b89782 in for__issue_diagnostic () #5 0x02b90a50 in for__signal_handler () #6 #7 0x2af19a8746fc in malloc_consolidate () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6 #8 0x2af19a876e69 in opal_memory_ptmalloc2_int_malloc () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6 #9 0x2af19a877c4f in opal_memory_ptmalloc2_int_memalign () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6 #10 0x2af19a8788a3 in opal_memory_ptmalloc2_memalign () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6 #11 0x2af19a29e0f4 in ompi_free_list_grow () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi.so.1 #12 0x2af1a0718546 in append_frag_to_list () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_pml_ob1.so #13 0x2af1a0718cbe in match_one () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_pml_ob1.so #14 0x2af1a07190f3 in mca_pml_ob1_recv_frag_callback_match () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_pml_ob1.so #15 0x2af19fab4a48 in btl_openib_handle_incoming () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_btl_openib.so #16 0x2af19fab5e1f in poll_device () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_btl_openib.so #17 0x2af19fab618c in btl_openib_component_progress () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_btl_openib.so #18 0x2af19a801f8a in opal_progress () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6 #19 0x2af19a2b7a0d in ompi_request_default_wait_all () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi.so.1 #20 0x2af1a17afef2 in ompi_coll_tuned_sendrecv_nonzero_actual () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_coll_tuned.so #21 0x2af1a17b7542 in ompi_coll_tuned_alltoallv_intra_pairwise () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_coll_tuned.so #22 0x2af19a2c9419 in PMPI_Alltoallv () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi.so.1 #23 0x2af19a05f2a2 in pmpi_alltoallv__ () from /usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi_mpifh.so.2 #24 0x00416213 in m_alltoall_i (comm=..., xsnd=..., psnd=Cannot access memory at address 0x51 ) at mpi.F:1906 #25 0x029ca135 in mapset (grid=...) at fftmpi_map.F:267 #26 0x02a15c62 in vamp () at main.F:2002 #27 0x0041281e in main () #28 0x00358941ed1d in __libc_start_main () from /lib64/libc.so.6 #29 0x00412729 in _start () (gdb) quit Or segfault that looks like this forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource vasp.gamma_para.i 02C7B031 Unknown Unknown Unknown vasp.gamma_para.i 02C7916B Unknown Unknown Unknown vasp.gamma_para.i 02BECFF4 Unknown Unknown Unknown vasp.gamma_para.i 02BECE06 Unknown Unknown Unknown vasp.gamma_para.i 02B89827 Unknown Unknown Unknown vasp.gamma_para.i 02B90A50 Unknown Unknown Unknown libpthread-2.12.s 003FED60F7E0 Unknown Unknown Unknown libopen-pal.so.6. 2AF7775346FC Unknown Unknown Unknown libopen-pal.so.6. 2AF777536E69 opal_memory_ptmal Unknown Unknown libopen-pal.so.6. 2AF777537C4F opal_memory_ptmal Unknown Unknown libopen-pal.so.6. 2AF7775388A3 opal_memory_ptmal Unknown Unknown libmlx4-rdmav2.so 2AF77EE87242 Unknown Unknown Unknown libmlx4-rdmav2.so 2AF77EE8979F Unknown Unknown Unknown libmlx4-rdmav2.so 2AF77EE89AD6 Unknown Unknown Unknown libibverbs.so.1.0 2AF77CBFFDD2 ibv_create_qp Unknown Unknown mca_btl_openib.so 2AF77C7D15C5 Unknown Unknown Unknown mca_btl_openib.so 2AF77C7D4088 Unknown Unknown Unknown mca_btl_openib.so 2AF77C7C6CAD mca_btl_openib_en Unknown Unknown mca_pml_ob1.so 2AF77D42D7F6 mca_pml_ob1_send_ Unk
Re: [OMPI users] openmpi-2.0.1
Hi, at first, you might want to remove path related to Intel MPI runtime (e.g. /opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64) from your environment if you are using bash, double check you export LD_LIBRARY_PATH (otherwise echo $LD_LIBRARY_PATH and the linker see different things) then you can file ompi/.libs/libmpi.so file ompi/tools/.libs/ompi_info.o and they are both 64 bits x86_64 (e.g. no 32 bits, nor MIC binaries) ldd ompi/.libs/libmpi.so should resolve all intel runtime libs. then i recommend you restart configure from a clean directory if it still does not work, you can cd ompi/tools make V=1 and post the output Cheers, Gilles On Thu, Nov 17, 2016 at 8:12 AM, Bennet Fauber wrote: > That's a stumper. Only thing I can think of is that the > LD_LIBRARY_PATH is being overwritten somewhere inside the Makefile, or > perhaps that it isn't properly exported...? > > As a graspable straw, try > > $ set -a > > to export all variables, then > > $ source /opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh > > (I may have the path to your compilervars.sh wrong). That should > insure that everything is properly exported. > > It sure looks to me like the compilers aren't finding the right library paths. > > -- bennet > > > > On Thu, Nov 17, 2016 at 9:44 AM, Professor W P Jones > wrote: >> The .configure is: >> >> ./configure PREFIX=/opt/openmpi-2.0.1-intel-14.0.2 CC=icc CXX=icpc F77=ifort >> FC=ifort >> >> and the output from printenv | grep LIBRARY is: >> >> LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4 >> MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic >> LD_LIBRARY_PATH=/opt/lf6481/lib64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4:/opt/lf6481/lib64:/usr/StorMan:/usr/StorMan/ssl/lib:/usr/StorMan/pegasus/lib: >> MIC_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic >> >> Bill >> >> >> Professor W P Jones, FREng >> Department of Mechanical Engineering >> Imperial College London >> Exhibition Road >> London SW7 2AZ >> Tel:+44 (0)20 7594 7037/7033 >> Mobile +44 (0)776 495 9702 >> Fax:+44 (0)20 7594 5702 >> E-mail: w.jo...@imperial.ac.uk >> web site: http://www.imperial.ac.uk/me >> >> On 17/11/16 14:33, Bennet Fauber wrote: >>> >>> Can you include your entire ./configure line? Also, it would be >>> useful, perhaps to look at the output of >>> >>> $ printenv | grep LIBRARY >>> >>> to make sure that all Intel library paths made it into the appropriate >>> variables. >>> >>> When I build 1.10.2, I had these: >>> >>> >>> LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64 >>> >>> >>> LD_LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64_lin >>> >>> and those sufficed. I have not tried OMPI 2.x. >>> >>> -- bennet >>> >>> >>> >>> On Thu, Nov 17, 2016 at 9:20 AM, Professor W P Jones >>> wrote: Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2 (gcc version 4.8.0 compatibility) Bill Professor W P Jones, FREng Department of Mechanical Engineering Imperial College London Exhibition Road London SW7 2AZ Tel:+44 (0)20 7594 7037/7033 Mobile +44 (0)776 495 9702 Fax:+44 (0)20 7594 5702 E-mail: w.jo...@imperial.ac.uk web site: http://www.imperial.ac.uk/me On 17/11/16 14:02, Tim Prince via users wrote: > > > On 11/17/2016 8:45 AM, Professor W P Jones wrote: >> >> Hi >> >> I am trying to install openmpi-2.0.1 togeter with the version 14.0.2 >> intel compilers and I an having problems. The configure script with >> CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make >> all install this fails with the output: >> >> >> Making all in tools/ompi_info >> make[2]: En
[OMPI users] Using custom version of gfortran in mpifort
Hi, The mpifort wrapper uses the default gfortran compiler on the system. How can I give it another version of gfortran which has been installed in another folder? Regards, Mahmood ___ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users