Hi Gus: Can you review the procedures I went through to install and let me know where it went wrong?
Procedures: Step 1: Download Open link http://www.open-mpi.org/software/ompi/v1.6/ You will see Click openmpi-1.6.5.tar.gz And download the tar file. Step 2: prepare to install $ cd ~ysun/Codes $ mkdir OpenMpi $ cd ~ysun/Codes/OpenMpi $ mv ../openmpi-1.6.5.tar.gz . $ gunzip openmpi-1.6.5.tar.gz $ tar -xvf openmpi-1.6.5.tar; gzip *.tar $ ./configure --prefix=/usr/local/openmpi165 FC=`which ifort ` F77=`which ifort` --disable-shared # this is the same process: to use configure to produce a localized Makefile. Here we have to use --disble-shared! #here prefix is used to specify the install location #FC is used to indicate the path of fortran compiler, here ifort is used #F77 is used to indicate the path of F77, here ifort is used $ make -j8 #here we execute make using 8 processors we have on this machine. Then we need to use root to install $ su root $ cd ~ysun/Codes/OpenMpi/openmpi-1.6.5 $ make install If possible, would you list the procedures you went through to install openmpi-1.6.5? Thank you. Have a good night. Yuping -----Original Message----- From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa Sent: Thursday, July 25, 2013 9:40 PM To: Open MPI Users Subject: Re: [OMPI users] errors testing openmpi1.6.5 ---- Hi Yuping Hmmm... I think the last release in the 1.4.X series was 1.4.5. I don't remember any 1.4.7. Is it a typo in your email. In any case, I always install OpenMPI from source code. It works like a charm, and is trouble-free. I am not familiar to the OpenMPI packages from the various Linux distributions. So, I am afraid I can't help you with this. Gus Correa On 07/25/2013 08:15 PM, Yuping Sun wrote: > Hi Gus: > > I use yum install to install openmpi 1.4.7 and it went through. Then I tested > a small code, hello world, and it worked. > Now I have two questions for you: > > 1. do we have a openmpi 1.6.5 rpm package so I can use rpm or yum to install? > 2. do you know how to specify the directory to install openmpi when using yum > install? > > Thank you. > > Best regards, > > Yuping > > > > > -----Original Message----- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] > On Behalf Of Gus Correa > Sent: Thursday, July 25, 2013 7:22 PM > To: Open MPI Users > Subject: Re: [OMPI users] errors testing openmpi1.6.5 ---- > > Hi Yuping > > Something seems to be broken in the way you set your environment variables. > We use .bashrc/.tcshrc for this. > For what is worth, the bash man page says: > > *** > "When bash is invoked as an interactive login shell, or as a non-inter- > active shell with the --login option, it first reads and executes com- mands > from the file /etc/profile, if that file exists. After reading that file, > it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile, in that order, > and reads and executes commands from the first one that exists and is > readable. The --noprofile option may be used when the shell is started to > inhibit this behavior. > > When a login shell exits, bash reads and executes commands from the file > ~/.bash_logout, if it exists. > > When an interactive shell that is not a login shell is started, bash reads > and executes commands from ~/.bashrc, if that file exists. This may be > inhibited by using the --norc option. The --rcfile file option will force > bash to read and execute commands from file instead of ~/.bashrc. " > *** > > Notice the difference between interactive login shells, and interactive shell > that is not a login shell. > > However, it is hard to guess what it is going on. > We (the OMPI list) don't even know if you are running the job in a single > machine, or on a cluster, or on a few networked workstations. > It would help if you tell more. > > Anyway, you could try to pass along the environment variables the mpiexec > command line. > > Something like this: > > *** > export PATH=... (whatever you use) > export LD_LIBRARY_PATH=... (whatever you use) mpiexec -x PATH -x > LD_LIBRARY_PATH -np 4 ./my_program > > *** > > See 'man mpiexec" for details. > > ** > > In any case, in my humble opinion, > the best approach is to fix for good the problems with your environment. > They will haunt you sooner or later. > > I hope this helps, > Gus Correa > > > > On 07/25/2013 05:58 PM, Yuping Sun wrote: >> >> Hi Gus: >> >> Thank you. I did these as I use .bash_profile to add the path and LD, but it >> did not help. Thank you. >> Is there anything else you can think of? >> >> Best regards, >> >> Yuping >> >> -----Original Message----- >> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] >> On Behalf Of Gus Correa >> Sent: Thursday, July 25, 2013 4:51 PM >> To: Open MPI Users >> Subject: Re: [OMPI users] errors testing openmpi1.6.5 ---- >> >> Hi Yuping >> >> A simple way to do it is to put in your initialization files, which are >> hidden ("dot files") in your home directory. >> >> It depends on the shell you use (do 'echo $SHELL' to see). >> >> If bash, >> .bashrc >> >> export PATH=/usr/local/openmpi1.6.5/bin:${PATH} >> export LD_LIBRARY_PATH=/usr/local/openmpi1.6.5/lib:${LD_LIBRARY_PATH} >> >> If csh/tcsh >> .cshrc/.tcshrc >> >> setenv PATH /usr/local/openmpi1.6.5/bin:${PATH} >> setenv LD_LIBRARY_PATH >> /usr/local/openmpi1.6.5/lib:${LD_LIBRARY_PATH} >> >> Are you running the programs in a single machine, or is it a cluster or some >> farm or networked machines? >> In the second case, you need to make sure your home directory is shared >> across the machines, or if it is not shared, you need to make the >> modifications above in each machine. >> >> I hope this helps. >> >> Gus Correa >> >> On 07/25/2013 03:11 PM, Yuping Sun wrote: >>> Hi Gus: >>> >>> I went back and set the PATH and LD_LIBRARY_PATH following the FAQ answer. >>> However, it did not change anything. >>> >>> What else can you suggest? >>> >>> Thank you. >>> >>> Yuping >>> >>> -----Original Message----- >>> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] >>> On Behalf Of Gus Correa >>> Sent: Wednesday, July 24, 2013 8:28 PM >>> To: Open MPI Users >>> Subject: Re: [OMPI users] errors testing openmpi1.6.5 ---- >>> >>> Hi Yuping >>> >>> Did you set your PATH and LD_LIBRARY_PATH? >>> Please, see these FAQ: >>> http://www.open-mpi.org/faq/?category=running#run-prereqs >>> http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path >>> >>> I hope this helps, >>> Gus Correa >>> >>> On 07/24/2013 08:09 PM, Yuping Sun wrote: >>>> Dear All: >>>> >>>> I downloaded openmpi1.5.6 and installed on my linux workstation >>>> with the help of NASA engineer. Then I tried to test the openmpi >>>> installation, but get the following error message: >>>> >>>> [ysun@ysunrh mpi]$ which mpiexec >>>> >>>> /usr/local/openmpi1.6.5/bin/mpiexec >>>> >>>> [ysun@ysunrh mpi]$ mpiexec utils/MPIcheck/mpicheck >>>> >>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_paffinity_hwloc: >>>> lt_dlerror() returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_carto_auto_detect: >>>> lt_dlerror() returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_carto_file: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_shmem_mmap: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_shmem_posix: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24905] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_shmem_sysv: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> ------------------------------------------------------------------- >>>> - >>>> - >>>> - >>>> ---- >>>> >>>> It looks like opal_init failed for some reason; your parallel >>>> process is >>>> >>>> likely to abort. There are many reasons that a parallel process can >>>> >>>> fail during opal_init; some of which are due to configuration or >>>> >>>> environment problems. This failure appears to be an internal >>>> failure; >>>> >>>> here's some additional information (which may only be relevant to >>>> an >>>> >>>> Open MPI developer): >>>> >>>> opal_shmem_base_select failed >>>> >>>> --> Returned value -1 instead of OPAL_SUCCESS >>>> >>>> ------------------------------------------------------------------- >>>> - >>>> - >>>> - >>>> ---- >>>> >>>> [ysunrh.fdwt.com:24905] [[INVALID],INVALID] ORTE_ERROR_LOG: Error >>>> in file runtime/orte_init.c at line 79 >>>> >>>> [ysunrh.fdwt.com:24905] [[INVALID],INVALID] ORTE_ERROR_LOG: Error >>>> in file orterun.c at line 694 >>>> >>>> I also try the use ompi_info to get more information, and it give >>>> me a lot error messages and I listed some below: >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_osc_pt2pt: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_osc_rdma: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_btl_self: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_btl_sm: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_btl_tcp: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_topo_unity: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_pubsub_orte: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> [ysunrh.fdwt.com:24920] mca: base: component_find: unable to open >>>> /usr/local/openmpi1.6.5/lib/openmpi/mca_dpm_orte: lt_dlerror() >>>> returned NULL! (ignored) >>>> >>>> MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.6.5) >>>> >>>> MCA memory: linux (MCA v2.0, API v2.0, Component v1.6.5) >>>> >>>> MCA timer: linux (MCA v2.0, API v2.0, Component v1.6.5) >>>> >>>> MCA installdirs: env (MCA v2.0, API v2.0, Component v1.6.5) >>>> >>>> MCA installdirs: config (MCA v2.0, API v2.0, Component v1.6.5) >>>> >>>> MCA hwloc: hwloc132 (MCA v2.0, API v2.0, Component v1.6.5) >>>> >>>> Could anyone of you give me some help, and tell me what I need to >>>> do to install openmpi correctly or give me some instructions to >>>> make it working? Thank you. >>>> >>>> */Yuping Sun/* >>>> >>>> >>>> FloDesign Wind Turbine Corp >>>> >>>> 242 Sturbridge Road >>>> >>>> Charlton, MA 01507 >>>> Direct: 508-434-1507 >>>> >>>> Cell: 713-456-9420 >>>> y...@fdwt.com<mailto:y...@fdwt.com> >>>> >>>> Description: cid:3300779197_294562 >>>> _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
