Thanks a lot. Installing the headers worked like a charm ! I have a question though. Why does configuration says:
Version: 3.0.1 Build MPI C bindings: yes Build MPI C++ bindings (deprecated): no Build MPI Fortran bindings: mpif.h, use mpi MPI Build Java bindings (experimental): no Build Open SHMEM support: yes Debug build: no Platform file: (none) Miscellaneous ----------------------- *CUDA support: no* I have a single GPU on my machine. Do I need to define it manually while configuring openmpi? On Tue, Apr 3, 2018 at 11:21 AM, Gilles Gouaillardet <gil...@rist.or.jp> wrote: > It looks like kernel-headers is required too > > > Cheers, > > > Gilles > > > On 4/3/2018 2:28 PM, abhisek Mondal wrote: > >> Hello, >> >> Installing glibc moved the installation little bit but again stuck at >> sanity check. >> Location of config.log: https://drive.google.com/drive >> /u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVW >> FjajR0UFFHNk5aYlhoSHVTWkU >> >> $ cpp --version >> cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) >> Copyright (C) 2015 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> PURPOSE. >> >> I have gcc and gcc-c++ installed. >> >> On Tue, Apr 3, 2018 at 10:08 AM, Gilles Gouaillardet <gil...@rist.or.jp >> <mailto:gil...@rist.or.jp>> wrote: >> >> This is the relevant part related to this error >> >> configure:6620: checking whether we are cross compiling >> configure:6628: gcc -o conftest conftest.c >&5 >> conftest.c:10:19: fatal error: stdio.h: No such file or directory >> #include <stdio.h> >> ^ >> compilation terminated. >> configure:6632: $? = 1 >> configure:6639: ./conftest >> ../configure: line 6641: ./conftest: No such file or directory >> configure:6643: $? = 127 >> >> >> at the very least, you need to install the glibc-headers package >> >> >> Cheers, >> >> >> Gilles >> >> >> On 4/3/2018 1:22 PM, abhisek Mondal wrote: >> >> Hello, >> >> I have uploaded the config.log here: >> https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4 >> N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU >> <https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ >> 4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU> >> >> >> >> >> On Tue, Apr 3, 2018 at 9:47 AM, Gilles Gouaillardet >> <gil...@rist.or.jp <mailto:gil...@rist.or.jp> >> <mailto:gil...@rist.or.jp <mailto:gil...@rist.or.jp>>> wrote: >> >> Can you please compress and attach your config.log ? >> >> >> You might also want to double check you can compile *and* >> run a >> simple C hello world program >> >> >> Cheers, >> >> >> Gilles >> >> >> On 4/3/2018 1:06 PM, abhisek Mondal wrote: >> >> Hi, >> >> I need some help regarding compiling Openmpi-3.0. I have >> perfectly working C compiler, however, during >> configuration >> I'm keep getting this error: >> >> >> /=========================================================== >> =================/ >> /== Configuring Open MPI/ >> >> /=========================================================== >> =================/ >> / >> / >> /*** Startup tests/ >> /checking build system type... x86_64-unknown-linux-gnu/ >> /checking host system type... x86_64-unknown-linux-gnu/ >> /checking target system type... x86_64-unknown-linux-gnu/ >> /checking for gcc... gcc/ >> /checking whether the C compiler works... yes/ >> /checking for C compiler default output file name... >> a.out/ >> /checking for suffix of executables... / >> /*checking whether we are cross compiling... >> configure: error: >> in `/home/user/openmpi-2.0.4':*/ >> /configure: error: cannot run C compiled programs./ >> /If you meant to cross compile, use `--host'./ >> /See `config.log' for more details/ >> >> I do not know waht is cross compiling but how can I >> avoid this >> error ? >> Please help me out here. >> >> Thanks >> >> -- Abhisek Mondal >> /Senior Research Fellow >> / >> /Structural Biology and Bioinformatics Division >> / >> /CSIR-Indian Institute of Chemical Biology/ >> /Kolkata 700032 >> / >> /INDIA >> / >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> <https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users>> >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> <https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users>> >> >> >> >> >> -- Abhisek Mondal >> /Senior Research Fellow >> / >> /Structural Biology and Bioinformatics Division >> / >> /CSIR-Indian Institute of Chemical Biology/ >> /Kolkata 700032 >> / >> /INDIA >> / >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> >> >> >> >> -- >> Abhisek Mondal >> /Senior Research Fellow >> / >> /Structural Biology and Bioinformatics Division >> / >> /CSIR-Indian Institute of Chemical Biology/ >> /Kolkata 700032 >> / >> /INDIA >> / >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users >> > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users > -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*
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