"interference between the previously installed MPICH and the subsequent installation of OpenMPI" This is dealt with by using Modules It is common on HPC systems to have several MPI flavours installed. Also compilers etc. Please learn about the Modules environment.
Also take time to look at Spack and Easybuild. On Wed, 14 Jun 2023 at 01:59, 深空探测 <wude7826...@gmail.com> wrote: > Hello, > > As you mentioned before, I was initially puzzled by the inability to > generate the libmpicxx.so.12 and libmpi.so.12 files after installing > OpenMPI. When I attempted to run the command "mpirun -H wude,wude mpispeed > 1000 10s 1," I received the following error message: > > mpispeed: error while loading shared libraries: libmpicxx.so.12: cannot > open shared object file: No such file or directory > > Initially, I had installed mpich-4.0.3, but I have since uninstalled it > and reinstalled openmpi-1.6.5. However, even with the new installation, I > encountered the same issue where it still required the libmpicxx.so.12 file > to be loaded. I suspect that there might have been some remnants from the > previous installation that were not completely removed. > > I conducted a fresh installation of openmpi-1.6.5 on another system, using > the --enable-mpi-cxx flag added to the ./configure command to enable the > C++ bindings in Open MPI. After successfully installing openmpi-1.6.5, I > ran the program again with the command "mpirun -H localhost,localhost > mpispeed 1000 10s 1 | head" and it executed successfully on both nodes. My > username is "wude," and the displayed results were as follows: > > Processor = wude > Rank = 0/2 > [0] Starting > Processor = wude > Rank = 1/2 > [1] Starting > [0] Sent 0 -> 0 > [0] Sent 1 -> 0 > [0] Sent 2 -> 0 > [0] Sent 3 -> 0 > [wude:109888] mpirun: SIGPIPE detected on fd 13 - aborting > mpirun: killing job... > > However, I am unsure if the message "mpirun: killing job..." is considered > a normal occurrence. > > In conclusion, the root cause of the issue was the interference between > the previously installed MPICH and the subsequent installation of OpenMPI, > as you suggested. It is possible that mpirun and libmpi.so originated from > different vendors and/or significantly different versions. > > I would like to express my sincere appreciation for your patient > assistance throughout this troubleshooting process. Your guidance has been > invaluable in helping me understand and resolve the challenges I > encountered. > > Thank you once again for your support. > > Best regards, > De Wu > > John Hearns via users <users@lists.open-mpi.org> 于2023年6月13日周二 14:13写道： > >> You talk about adjusting your PATH and LD_LIBRARY_PATH in your .bashrc >> Jeff Squyres has given you some guidance on this. >> Please investigate the following. >> It is common to use Modules in an HPC environment >> https://www.admin-magazine.com/HPC/Articles/Lmod-Alternative-Environment-Modules >> >> For compiling software packages and creating Modules files investigate >> these frameworks: >> https://spack.io/ >> https://easybuild.io/ >> >> >> >> On Mon, 12 Jun 2023 at 22:44, Jeff Squyres (jsquyres) via users < >> users@lists.open-mpi.org> wrote: >> >>> Your steps are generally correct, but I cannot speak for whether your >>> /home/wude/.bashrc file is executed for both non-interactive and >>> interactive logins. If /home/wude is your $HOME, it *probably* is, but >>> I don't know about your specific system. >>> >>> Also, you should be aware that MPI applications built with Open MPI >>> v1.6.x will not be ABI compatible with Open MPI v4.1.x. Specifically: you >>> will need to re-compile / re-build your "mpispeed" application with Open >>> MPI v4.1.x. >>> >>> If you are using the MPI C++ bindings in your application: >>> >>> 1. I suggest you migrate away from them, because the MPI Forum >>> (i.e., the standards body that governs the MPI API) removed the C++ >>> bindings in version 3.0 of the MPI specification in 2012 -- over a decade >>> ago. >>> 2. That being said, the C++ bindings are still available in Open MPI >>> v4.1.x -- they're just not built and installed by default (frankly, to >>> discourage their use). You can enable the C++ bindings in Open MPI 4.1.x >>> with by adding --enable-mpi-cxx to the ./configure command that you use >>> to >>> build Open MPI. You will need to have a C++ compiler present to build >>> and >>> install the C++ bindings. >>> >>> Also note that in Open MPI, the C++ bindings library is named >>> "libmpi_cxx.so", not "libmpicxx.so" (I checked both Open MPI v1.6.5 and >>> 4.1.5). If your MPI executable is dependant upon a file named >>> "libmpicxx.so", then, as Gilles mentioned earlier in this thread, you might >>> accidentally be mixing the libraries between two different implmenetations >>> of MPI (e.g., Open MPI and MPICH are two entirely different implementations >>> of the same MPI API. They are written and maintained by different sets of >>> people, and are not binary compatible with each other). >>> >>> If you'e just starting out in MPI, I'd strongly suggest ensuring that >>> your system has exactly 1 implementation of MPI installed (e.g., Open MPI >>> v4.1.5). Ensure that no other versions of Open MPI or MPICH -- or any >>> other MPI implementation -- are installed. That way, you can avoid >>> confusing issues with libraries that are similar-but-different, ... etc. >>> >>> >>> ------------------------------ >>> *From:* users <users-boun...@lists.open-mpi.org> on behalf of 深空探测 via >>> users <users@lists.open-mpi.org> >>> *Sent:* Sunday, June 11, 2023 11:28 AM >>> *To:* Open MPI Users <users@lists.open-mpi.org> >>> *Cc:* 深空探测 <wude7826...@gmail.com> >>> *Subject:* Re: [OMPI users] Issue with Running MPI Job on CentOS 7 >>> >>> Subject: Open MPI Installation Issues >>> >>> Hello, >>> >>> Despite following your previous suggestions, I am still encountering >>> some problems. Below, I have outlined the specific challenges I am facing: >>> >>> 1. Installation with Updated Open MPI Version: >>> I attempted to install the latest version of Open MPI (v4.1.5) using the >>> following steps: >>> - Downloaded the package from >>> https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz >>> . >>> - Executed the installation commands: >>> ./configure --prefix=/usr/local/openmpi >>> make >>> sudo make install >>> - Added the environment variables to the "/home/wude/.bashrc" file: >>> export PATH=/usr/local/openmpi/bin:$PATH >>> export LD_LIBRARY_PATH=/usr/local/openmpi/lib:$LD_LIBRARY_PATH >>> - Ran the command: source /home/wude/.bashrc >>> >>> Could you please verify if these installation steps are correct? >>> >>> 2. Missing "libmpicxx.so.12" file after Open MPI 1.6.5 installation: >>> After reinstalling Open MPI 1.6.5, I noticed the existence of the >>> "mpirun" executable file in the "/usr/local/openmpi/bin" directory, as well >>> as the "libmpi.so" file in the "/usr/lib" directory. However, when I >>> executed the command "mpirun -n 2 -H wude,wude mpispeed 1000 10s 1", an >>> error occurred: "mpispeed: error while loading shared libraries: >>> libmpicxx.so.12: cannot open shared object file: No such file or >>> directory". It seems that the "libmpicxx.so.12" file was not generated >>> during the installation process. Could you please help me identify the >>> cause of this issue? >>> >>> 3. Missing "libmpixcc.so.12" file in CentOS 7 default Open MPI >>> installation: >>> In case I install the Open MPI version provided by CentOS 7 using the >>> command "sudo yum install openmpi-devel.x86_64", I encountered a similar >>> problem. Even after installation, I cannot find the "libmpixcc.so.12" file. >>> It appears that the "/usr/lib64/openmpi/lib" directory does not contain any >>> files related to "libmpixcc". Could you kindly advise on this matter? >>> >>> I greatly appreciate your time and assistance in resolving these issues. >>> Thank you in advance for your support. >>> >>> Best regards, >>> De Wu >>> >>> Zhéxué M. Krawutschke via users <users@lists.open-mpi.org> 于2023年6月1日周四 >>> 20:32写道： >>> >>> Hello together, >>> >>> regardless that CentOS 7.X already has EOL status, >>> I would recommend, for example, that you always build/compile OpenMPI >>> and the other tools yourself >>> compile OpenMPI and the other tools to one's needs. >>> >>> It is true that it is more effort, but in the end it pays off, because >>> the >>> distributions are sometimes very behind. >>> >>> I have already thought about providing something like this, how to do it >>> or how to make the whole process available in an automated way, so to speak. >>> >>> >>> If someone would like to help me develop this, I would be very happy. >>> Kind regards from Berlin.... >>> >>> Z. Matthias >>> >>> -- >>> Sent from Canary <https://canarymail.io> >>> >>> On Donnerstag, Juni 01, 2023 at 10:11 AM, Tru Huynh via users < >>> users@lists.open-mpi.org> wrote: >>> Hello, >>> >>> A few comments below: >>> >>> On Thu, Jun 01, 2023 at 09:09:32AM +0800, 深空探测 via users wrote: >>> <...> >>> >>> >>> To provide some context, I have successfully installed Open MPI version >>> 1.6.5 on my CentOS 7 system. However, when I attempted to run the >>> command >>> "mpirun -n 2 -H wude,wude mpispeed 1000 10s 1", where "wude" is my >>> hostname, I encountered unexpected results. Instead of running with two >>> processes as intended, it appears that only one process was executed. >>> The >>> output I received is as follows: >>> >>> ... >>> 1) Why not using one of the openmpi versions provided by CentOS-7? >>> $ yum list openmpi\* >>> <...> >>> Available Packages >>> openmpi.i686 1.10.7-5.el7 base >>> openmpi-devel.i686 1.10.7-5.el7 base >>> openmpi.x86_64 1.10.7-5.el7 base >>> openmpi-devel.x86_64 1.10.7-5.el7 base >>> openmpi3.i686 3.1.3-2.el7 base >>> openmpi3.x86_64 3.1.3-2.el7 base >>> openmpi3-devel.i686 3.1.3-2.el7 base >>> openmpi3-devel.x86_64 3.1.3-2.el7 base >>> >>> You have the choice of 1.x series or 3.1.y series.. >>> + environment setup are pre-filled for environment-modules. >>> >>> 2) maybe you have one of them installed and conflicting >>> with your self built openmpi 1.6.5 version? >>> >>> 3) CentOS-7 is nearing end-of-life >>> >>> Good luck. >>> >>> Tru >>> >>> -- >>> Tru Huynh (PhD) | mailto:t...@pasteur.fr | tel +33 1 45 68 87 37 >>> https://research.pasteur.fr/en/team/structural-bioinformatics/ >>> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France >>> >>>
