you need to set PATH and LD_LIBRARY_PATH to point to the right places to find it
On Aug 29, 2013, at 6:30 AM, Federico Carotenuto <caroten...@ibimet.cnr.it> wrote: > That's really weird: I know that mpirun works (at least the old mpirun coming > with PGI's compiler's MPICH1), and I've make installed the new Openmp 1.6.5. > I've installed it in a custom folder (under /home/Software/) so it may be > that it's not a path in which the OS looks for the MPI libraries: should I > set some environmental variable and/or source commands for pointing the bash > shell to the installed Openmp? > > Ralph Castain <r...@open-mpi.org> ha scritto: > >> Given what you report, you don't even have MPI installed on your machine. >> The output you provided indicates that no mpicc and no mpiexec have been >> installed on your machine, and so none of the MPI implementations have >> actually been installed. >> >> >> On Aug 29, 2013, at 2:49 AM, Reuti <re...@staff.uni-marburg.de> wrote: >> >>> Am 29.08.2013 um 10:41 schrieb Federico Carotenuto: >>> >>>> Kind Reuti, >>>> >>>> the output of which mpicc is that such program may be found in various >>>> packages (which can be installed with apt-get), while which mpiexec >>>> outputs nothing (goes back to the prompt). >>> >>> You can compile and install Open MPI directly from source - even without >>> being root. You are not limited to what the distribution offers at all. >>> >>> -- Reuti >>> >>> >>>> Seems like no mpicc and mpiexec are set on the system... >>>> >>>> >>>> Reuti <re...@staff.uni-marburg.de> ha scritto: >>>> >>>>> Hi, >>>>> >>>>> Am 26.08.2013 um 18:10 schrieb Federico Carotenuto: >>>>> >>>>>> Kind Reuti, >>>>>> >>>>>> as you suggested I proceeded to install Openmpi 1.6.5 >>>>> >>>>> Good. >>>>> >>>>> >>>>>> and changed the environmental variable MPI_ROOT >>>>> >>>>> No, there is no such variable necessary to be set (at least from Open MPI >>>>> points of view). >>>>> >>>>> >>>>>> to the new folder, should I know source the commands in .bashrc to be >>>>>> sure to be able to execute the right mpirun and mpiexec (something like >>>>>> source >>>>> >>>>> Please check with: >>>>> >>>>> which mpicc >>>>> which mpiexec >>>>> >>>>> which you are using. It's also necessary to recompile the application >>>>> with the new MPI library. >>>>> >>>>> -- Reuti >>>>> >>>>> >>>>>> /home/modelstation/Software/openmpi1.6.5/mpirun, where the directory is >>>>>> the installation directory)? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> Reuti <re...@staff.uni-marburg.de> ha scritto: >>>>>> >>>>>>> Am 26.08.2013 um 14:33 schrieb Federico Carotenuto: >>>>>>> >>>>>>>> Kind Reuti, >>>>>>>> >>>>>>>> I'm start thinking I've got some compilation issue with MPI: I'm >>>>>>>> afraid I've got the MPICH 1 coming with the PGI compiler installation, >>>>>>>> because if I try to run mpiexec the terminal answers with "The program >>>>>>>> 'mpiexec' can be found in the following packages: *lam-runtime *mpich2 >>>>>>>> *openmpi-bin *openmpi1.6-bin. Try: sudo apt-get install <selected >>>>>>>> package>". >>>>>>>> >>>>>>>> I've also tried to modify the machinefile that comes by default under >>>>>>>> /opt/pgi/linux86-64/13.4/mpi/mpich/share/machinefile.LINUX adding the >>>>>>>> line "modelstation:8", but still mpirun prompts for the password 8 >>>>>>>> times. >>>>>>> >>>>>>> This was normal at that time: one rsh/ssh per parallel instance. >>>>>>> Nowadays Open MPI and MPICH2/3 will use only one `rsh`/`ssh` per host >>>>>>> and start all other parallel tasks as thread (i.e: on a local machine >>>>>>> they don't need a local `rsh` or `ssh` at all). Although you could >>>>>>> either adjust `rsh` to disregard passwords (deprecated) or route `rsh` >>>>>>> to `ssh` and enable passphraseless login: >>>>>>> >>>>>>> MPICH(1) is outdated (released 2005) and I suggested already to >>>>>>> Portland to exclude it from the package. IMO this adds more confusion >>>>>>> than it help. >>>>>>> >>>>>>> Hence, please install a recent version of Open MPI or MPICH2/3 and then >>>>>>> we can look into it again on the appropriate list. >>>>>>> >>>>>>> -- Reuti >>>>>>> >>>>>>> PS: The above mentioned LAM/MPI is outdated too. >>>>>>> >>>>>>> >>>>>>>> Thanks for your help and patience >>>>>>>> >>>>>>>> >>>>>>>> Reuti <re...@staff.uni-marburg.de> ha scritto: >>>>>>>> >>>>>>>>> Am 26.08.2013 um 12:53 schrieb Federico Carotenuto: >>>>>>>>> >>>>>>>>>> Kind Reuti, >>>>>>>>>> >>>>>>>>>> Thanks for your quick reply! >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I'm afraid I didn't set a machinefile...that may be the problem: I'm >>>>>>>>>> fairly new to MPI and SSH and I'm still quite confused even after >>>>>>>>>> reading some tutorials. >>>>>>>>> >>>>>>>>> There is a default. But you can also specify it on the command line >>>>>>>>> to test it: >>>>>>>>> >>>>>>>>> mpiexec -host modelstation -np 2 mpihello >>>>>>>>> >>>>>>>>> -- Reuti >>>>>>>>> >>>>>>>>> >>>>>>>>>> My etc/hosts contains: 127.0.0.1 localhost and 127.0.1.1 >>>>>>>>>> modelstation (modelstation is the machine name I was mentioning in >>>>>>>>>> the previous mail) >>>>>>>>>> >>>>>>>>>> if I type hostname the terminal returns modelstation >>>>>>>>>> >>>>>>>>>> Cheers >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Reuti <re...@staff.uni-marburg.de> ha scritto: >>>>>>>>>> >>>>>>>>>>> Am 26.08.2013 um 12:15 schrieb Federico Carotenuto: >>>>>>>>>>> >>>>>>>>>>>> I'm currently having this issue with mpirun: I want to launch a >>>>>>>>>>>> program only on the cores of the local machine, but every time I >>>>>>>>>>>> run an mpi program it says that the host 127.0.0.1 >>>>>>>>>>>> <local_machine_name> with it's associated key is unkown and asks >>>>>>>>>>>> me if I want to add it to the list of ssh known hosts. >>>>>>>>>>>> >>>>>>>>>>>> By chowing/chmodding the .ssh file I was able to permanently add >>>>>>>>>>>> this "host" to the list of known hosts, but my problem is that >>>>>>>>>>>> every program that I try to run ask me to insert a password (the >>>>>>>>>>>> actual local user password) n times where n is equal to the -np >>>>>>>>>>>> parameter (i.e.: if I run the program on 8 cores I receive 8 >>>>>>>>>>>> successive password pronts). >>>>>>>>>>>> >>>>>>>>>>>> If I insert the password everything runs fine, but it's quite >>>>>>>>>>>> annoying and I wish to bypass such step: is there a way to have >>>>>>>>>>>> mpirun memorize the password? Or make him understand that the 8 >>>>>>>>>>>> nodes are actually 8 cores on the local machine and not 8 >>>>>>>>>>>> different hosts? >>>>>>>>>>> >>>>>>>>>>> Which hostname do you specify in your machinefile? >>>>>>>>>>> Which hostnames are set in /etc/hosts for your local machine? >>>>>>>>>>> What is the output of `hostname`? Does it match the one in the >>>>>>>>>>> machinefile? >>>>>>>>>>> >>>>>>>>>>> For systemd there is a new command `hostnamectl --static >>>>>>>>>>> set-hostname [NAME]` to set it. >>>>>>>>>>> >>>>>>>>>>> -- Reuti >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> users mailing list >>>>>>>>>>> us...@open-mpi.org >>>>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ---------------------------------------------------------------- >>>>>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> users mailing list >>>>>>>>>> us...@open-mpi.org >>>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> users mailing list >>>>>>>>> us...@open-mpi.org >>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------- >>>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> users mailing list >>>>>>>> us...@open-mpi.org >>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>>> >>>>>>> _______________________________________________ >>>>>>> users mailing list >>>>>>> us...@open-mpi.org >>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ---------------------------------------------------------------- >>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>> >>>>>> _______________________________________________ >>>>>> users mailing list >>>>>> us...@open-mpi.org >>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> >>>>> _______________________________________________ >>>>> users mailing list >>>>> us...@open-mpi.org >>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> >>>> >>>> >>>> >>>> ---------------------------------------------------------------- >>>> This message was sent using IMP, the Internet Messaging Program. >>>> >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
