Re: [OMPI users] Linkage problem
I solved my problem. I uninstalled all the mpi software that were on the computer reinstalled openmpi. It was still not working so I uninstalled it again and reinstalled it again and it is working now. Apparently there was a problem with the installation. Thanks for the help. Quentin > On 4 Apr 2018, at 11:30, Jeff Squyres (jsquyres) <jsquy...@cisco.com> wrote: > >> On Apr 4, 2018, at 12:58 PM, Quentin Faure <quentin...@hotmail.fr> wrote: >> >> Sorry, I did not see my autocorrect changed some word. >> >> I added the -l and it did not change anything. Also the mpicxx —showme does >> not work. It says that the option —showme does not exist > > If 'mpicxx --showme' (with 2 dashes) does not work, then you are not using > Open MPI's mpicxx. You should check to make sure you are testing what you > think you are testing. > > Note, too, that Nathan was pointing out a missing capital "i" (as in > "include") not a missing capital "l" (as in "link"). Depending on the font > in your mail client, it can be difficult to tell the two apart. > > He is correct that what you showed was not an *error* -- it was a warning > that the C++ compiler was telling you that it ignored an argument on the > command line. Specifically, you did: > >>>>> mpicxx -g -O3 -DLAMMPS_GZIP -DLMP_USER_INTEL -DLMP_MPIIO >>>>> /usr/lib/openmpi/include -pthread -DFFT_FFTW3 -DFFT_SINGLE >>>>> -I../../lib/molfile -c ../create_atoms.cpp > > But you missed the -I (capital I, as in indigo, not capital L, as in Llama). > It should have been: > >>>>> mpicxx -g -O3 -DLAMMPS_GZIP -DLMP_USER_INTEL -DLMP_MPIIO -I >>>>> /usr/lib/openmpi/include -pthread -DFFT_FFTW3 -DFFT_SINGLE >>>>> -I../../lib/molfile -c ../create_atoms.cpp > > That being said, you shouldn't need to mention /usr/lib/openmpi/include at > all (even with the -I), because mpicxx will automatically insert that for > you. Specifically: mpicxx is not a compiler itself -- it's just a "wrapper" > around the underlying C++ compiler. All mpicxx does is add some additional > command line arguments and then invoke the underlying C++ compiler. When you > run "mpicxx --showme" (with Open MPI's mpicxx command), it will show you the > underlying C++ compiler command that it would have invoked. > > Similarly, the "ompi_info: error while loading shared libraries: > libmpi.so.40: cannot open shared object file: No such file or directory" > error means that you do not have Open MPI's libmpi at the front of your > searchable library path. See > https://www.open-mpi.org/faq/?category=running#adding-ompi-to-path. > > -- > Jeff Squyres > jsquy...@cisco.com > > ___ > 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
Re: [OMPI users] Linkage problem
Sorry, I did not see my autocorrect changed some word. I added the -l and it did not change anything. Also the mpicxx —showme does not work. It says that the option —showme does not exist Quentin On Apr 4, 2018, at 10:45, Quentin Faure <quentin...@hotmail.fr<mailto:quentin...@hotmail.fr>> wrote: I had the -l but it did not change anything. Also the mlicxx —showme does not work, it says that the option —showmen does not exist. Quentin On Apr 3, 2018, at 14:25, Nathan Hjelm <hje...@me.com<mailto:hje...@me.com>> wrote: I guess I should point out the reason the compiler thought you had linker input was a missing -I on /usr/lib/openmpi/include . Though that include shouldn't be needed as the wrapper will do that for you. You can see what the wrapper passes to gcc by running: mpicxx --showme. -Nathan On Apr 03, 2018, at 02:16 PM, Quentin Faure <quentin...@hotmail.fr<mailto:quentin...@hotmail.fr>> wrote: Hello, Date: Fri, 30 Mar 2018 14:29:57 + From: "Jeff Squyres (jsquyres)" <jsquy...@cisco.com<mailto:jsquy...@cisco.com>> To: "Open MPI User's List" <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> Subject: Re: [OMPI users] Linkage problem Message-ID: <fc668c2e-a403-47ef-bac2-81caabb41...@cisco.com<mailto:fc668c2e-a403-47ef-bac2-81caabb41...@cisco.com>> Content-Type: text/plain; charset="utf-8" On Mar 29, 2018, at 11:19 AM, Quentin Faure <quentin...@hotmail.fr<mailto:quentin...@hotmail.fr>> wrote: I would like to use openmpi with a software called LAMMPS. I know it is possible when compiling the software to indicate it to use it with openmpi. However when I do that I have a warning message telling me that the linkage could not have been done (I specified the path for openmpi library and name like it is done in LAMMPS manual). What error message are you getting? The error I get is: /usr/lib/openmpi/include: linker input file unused because linking not done mpicxx -g -O3 -DLAMMPS_GZIP -DLMP_USER_INTEL -DLMP_MPIIO /usr/lib/openmpi/include -pthread -DFFT_FFTW3 -DFFT_SINGLE -I../../lib/molfile -c ../create_atoms.cpp I tried to reinstall openmpi in two different ways (following the advices of people that had LAMMPS and openmpi works together) but it still does not work. Also I don?t know if this is part of my problem or not but, the option ?showme does not work (command: mpicc ?showme). What error message are you getting? It's quite possible that you're using a different mpicc (e.g., from a different MPI installation on your same machine), and not using the mpicc from the Open MPI that you just installed. I do not have any errors when I install openmpi, i just have an error when I tried to compile my other software with openmpi. Concerning the mpicc command, normally there is no other MPI software install on this computer. Can you send all the information listed here: https://www.open-mpi.org/community/help/ I am enclosing the config log file. I tried the command ompi_info —all and I got: ompi_info: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory. I tried to install the software hwloc and used the command stoop -v but I got an error: lstopo: error while loading shared libraries: libhwloc.so15: cannot open shared object file: No such file or directory. One thing that I did not specify about the computer is that it has been build and all the software have been install manually, it is not a computer already built when it was bought. -- Jeff Squyres jsquy...@cisco.com<mailto:jsquy...@cisco.com> Quentin ___ users mailing list users@lists.open-mpi.org<mailto:users@lists.open-mpi.org> 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 ___ users mailing list users@lists.open-mpi.org<mailto: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
Re: [OMPI users] Linkage problem
I had the -l but it did not change anything. Also the mlicxx —showme does not work, it says that the option —showmen does not exist. Quentin On Apr 3, 2018, at 14:25, Nathan Hjelm <hje...@me.com<mailto:hje...@me.com>> wrote: I guess I should point out the reason the compiler thought you had linker input was a missing -I on /usr/lib/openmpi/include . Though that include shouldn't be needed as the wrapper will do that for you. You can see what the wrapper passes to gcc by running: mpicxx --showme. -Nathan On Apr 03, 2018, at 02:16 PM, Quentin Faure <quentin...@hotmail.fr<mailto:quentin...@hotmail.fr>> wrote: Hello, Date: Fri, 30 Mar 2018 14:29:57 + From: "Jeff Squyres (jsquyres)" <jsquy...@cisco.com<mailto:jsquy...@cisco.com>> To: "Open MPI User's List" <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> Subject: Re: [OMPI users] Linkage problem Message-ID: <fc668c2e-a403-47ef-bac2-81caabb41...@cisco.com<mailto:fc668c2e-a403-47ef-bac2-81caabb41...@cisco.com>> Content-Type: text/plain; charset="utf-8" On Mar 29, 2018, at 11:19 AM, Quentin Faure <quentin...@hotmail.fr<mailto:quentin...@hotmail.fr>> wrote: I would like to use openmpi with a software called LAMMPS. I know it is possible when compiling the software to indicate it to use it with openmpi. However when I do that I have a warning message telling me that the linkage could not have been done (I specified the path for openmpi library and name like it is done in LAMMPS manual). What error message are you getting? The error I get is: /usr/lib/openmpi/include: linker input file unused because linking not done mpicxx -g -O3 -DLAMMPS_GZIP -DLMP_USER_INTEL -DLMP_MPIIO /usr/lib/openmpi/include -pthread -DFFT_FFTW3 -DFFT_SINGLE -I../../lib/molfile -c ../create_atoms.cpp I tried to reinstall openmpi in two different ways (following the advices of people that had LAMMPS and openmpi works together) but it still does not work. Also I don?t know if this is part of my problem or not but, the option ?showme does not work (command: mpicc ?showme). What error message are you getting? It's quite possible that you're using a different mpicc (e.g., from a different MPI installation on your same machine), and not using the mpicc from the Open MPI that you just installed. I do not have any errors when I install openmpi, i just have an error when I tried to compile my other software with openmpi. Concerning the mpicc command, normally there is no other MPI software install on this computer. Can you send all the information listed here: https://www.open-mpi.org/community/help/ I am enclosing the config log file. I tried the command ompi_info —all and I got: ompi_info: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory. I tried to install the software hwloc and used the command stoop -v but I got an error: lstopo: error while loading shared libraries: libhwloc.so15: cannot open shared object file: No such file or directory. One thing that I did not specify about the computer is that it has been build and all the software have been install manually, it is not a computer already built when it was bought. -- Jeff Squyres jsquy...@cisco.com<mailto:jsquy...@cisco.com> Quentin ___ users mailing list users@lists.open-mpi.org<mailto:users@lists.open-mpi.org> 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 ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
[OMPI users] Linkage problem
Hello, I would like to use openmpi with a software called LAMMPS. I know it is possible when compiling the software to indicate it to use it with openmpi. However when I do that I have a warning message telling me that the linkage could not have been done (I specified the path for openmpi library and name like it is done in LAMMPS manual). I tried to reinstall openmpi in two different ways (following the advices of people that had LAMMPS and openmpi works together) but it still does not work. Also I don’t know if this is part of my problem or not but, the option —showme does not work (command: mpicc —showme). I looked at many forums and could not find anything to solve my problem and this is the reason why I am using this email list. The computer I am using have Ubuntu on it. Does anyone have idea how to solve my problem? Quentin ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
