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Subject: Re: [OMPI devel] OpenMPI and R
From: Benedict Holland (benedict.m.holland_at_[hidden])
Date: 2012-04-05 19:59:04


So I am now back on this full time as I need this to work. OpenMPI 1.4.3 is
deadlocking with Rmpi and I need the latest code. I still get the exact
same problem. I configured it with a --prefix=/usr to get it to install
everything in default directories and added /usr/lib/openmpi to my
ldconfig. I don't have a LD_LIBRARY_PATH global variable on ubuntu 11.10.

ldconfig -p |grep mpi
libvt-mpi.so.0 (libc6,x86-64) => /usr/lib/libvt-mpi.so.0
libvt-mpi.so (libc6,x86-64) => /usr/lib/libvt-mpi.so
libvt-mpi-unify.so.0 (libc6,x86-64) => /usr/lib/libvt-mpi-unify.so.0
libvt-mpi-unify.so (libc6,x86-64) => /usr/lib/libvt-mpi-unify.so
libopenmpi_malloc.so.0 (libc6,x86-64) => /usr/lib/libopenmpi_malloc.so.0
libompitrace.so.0 (libc6,x86-64) => /usr/lib/libompitrace.so.0
libompitrace.so (libc6,x86-64) => /usr/lib/libompitrace.so
libompi_dbg_msgq.so (libc6,x86-64) => /usr/lib/openmpi/libompi_dbg_msgq.so
libmpi_f90.so.1 (libc6,x86-64) => /usr/lib/libmpi_f90.so.1
libmpi_f90.so.0 (libc6,x86-64) => /usr/lib/libmpi_f90.so.0
libmpi_f90.so (libc6,x86-64) => /usr/lib/libmpi_f90.so
libmpi_f77.so.1 (libc6,x86-64) => /usr/lib/libmpi_f77.so.1
libmpi_f77.so.0 (libc6,x86-64) => /usr/lib/libmpi_f77.so.0
libmpi_f77.so (libc6,x86-64) => /usr/lib/libmpi_f77.so
libmpi_cxx.so.1 (libc6,x86-64) => /usr/lib/libmpi_cxx.so.1
libmpi_cxx.so.0 (libc6,x86-64) => /usr/lib/libmpi_cxx.so.0
libmpi_cxx.so (libc6,x86-64) => /usr/lib/libmpi_cxx.so
libmpi.so.1 (libc6,x86-64) => /usr/lib/libmpi.so.1
libmpi.so.0 (libc6,x86-64) => /usr/lib/libmpi.so.0
libmpi.so (libc6,x86-64) => /usr/lib/libmpi.so
libexempi.so.3 (libc6,x86-64) => /usr/lib/libexempi.so.3
libcompizconfig.so.0 (libc6,x86-64) => /usr/lib/libcompizconfig.so.0

Compiling Rmpi from inside R gives me:

* installing *source* package ‘Rmpi’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** Creating default NAMESPACE file
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI -fpic -O3
-pipe -g -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI -fpic -O3
-pipe -g -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI -fpic -O3
-pipe -g -c conversion.c -o conversion.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2 -DOPENMPI -fpic -O3
-pipe -g -c internal.c -o internal.o
gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o
-L/usr/lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
[ben-Inspiron-1764:18216] mca: base: component_find: unable to open
/usr/lib/openmpi/mca_paffinity_hwloc:
/usr/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol:
opal_hwloc_topology (ignored)
[ben-Inspiron-1764:18216] mca: base: component_find: unable to open
/usr/lib/openmpi/mca_shmem_posix: /usr/lib/openmpi/mca_shmem_posix.so:
undefined symbol: opal_shmem_base_output (ignored)
[ben-Inspiron-1764:18216] mca: base: component_find: unable to open
/usr/lib/openmpi/mca_ess_hnp: /usr/lib/openmpi/mca_ess_hnp.so: undefined
symbol: orte_timing_output (ignored)
[ben-Inspiron-1764:18216] mca: base: component_find: unable to open
/usr/lib/openmpi/mca_ess_singleton: /usr/lib/openmpi/mca_ess_singleton.so:
undefined symbol: orte_local_cpu_model (ignored)
[ben-Inspiron-1764:18216] mca: base: component_find: unable to open
/usr/lib/openmpi/mca_ess_slurm: /usr/lib/openmpi/mca_ess_slurm.so:
undefined symbol: orte_orted_exit_with_barrier (ignored)
[ben-Inspiron-1764:18216] mca: base: component_find: unable to open
/usr/lib/openmpi/mca_ess_slurmd: /usr/lib/openmpi/mca_ess_slurmd.so:
undefined symbol: orte_pmap_t_class (ignored)
[ben-Inspiron-1764:18216] [[INVALID],INVALID] ORTE_ERROR_LOG: Unknown
error: -1 in file ../../../orte/runtime/orte_globals.c at line 176
input in flex scanner failed
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/Rmpi’
* restoring previous ‘/usr/local/lib/R/site-library/Rmpi’

Notice that the libRmpi actually does compile but can't be installed. Other
than the --prefix option I added nothing new to the ./configure script. It
now knows by default where everything should be and I think I have every
required package installed. Anyone have any ideas? Do you need any other
files attached?

Thanks,
~Ben

On Tue, Apr 3, 2012 at 1:39 AM, Ralph Castain <rhc_at_[hidden]> wrote:

> Looks like you didn't set your LD_LIBRARY_PATH to point to where OMPI was
> installed, so the individual component libs couldn't be loaded. From the
> below, it looks like you need to add /usr/local to your path.
>
> On Mon, Apr 2, 2012 at 7:26 PM, Benedict Holland <
> benedict.m.holland_at_[hidden]> wrote:
>
>> Hi All,
>>
>> I am on ubuntu 11.10 and the only package that they have for OpenMPI is
>> 1.4.3 and I noticed the latest was 1.5.5 and I decided to try to use it to
>> get the Rmpi R package compiled against it. I failed. My R version is 2.15,
>> the OpenMPI is 1.5.5. I compiled it and installed it but when I tried to
>> compile Rmpi I get the result below. I can try to run this stuff again but
>> I had to use the base packages because they worked and I need to get some
>> stuff done. I can always recompile though, install and run the Rmpi package
>> against the installed OpenMPI stuff. Any ideas what I need to do? Also, is
>> there an Ubuntu or Debian package available with the latest and greatest
>> and if not, how can I make one?
>>
>> Thanks,
>> ~Ben
>>
>> checking for gcc... gcc -std=gnu99
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc -std=gnu99 accepts -g... yes
>> checking for gcc -std=gnu99 option to accept ISO C89... none needed
>> I am here /usr/local and it is OpenMPI
>> Trying to find mpi.h ...
>> Found in /usr/local/include
>> Trying to find libmpi.so or libmpich.a ...
>> Found libmpi in /usr/local/lib
>> checking for openpty in -lutil... yes
>> checking for main in -lpthread... yes
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** Creating default NAMESPACE file
>> ** libs
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic
>> -O3 -pipe -g -c RegQuery.c -o RegQuery.o
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic
>> -O3 -pipe -g -c Rmpi.c -o Rmpi.o
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic
>> -O3 -pipe -g -c conversion.c -o conversion.o
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
>> -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic
>> -O3 -pipe -g -c internal.c -o internal.o
>> gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o
>> internal.o -L/usr/local/lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR
>> installing to /usr/local/lib/R/site-library/Rmpi/libs
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>> [ben-Inspiron-1764:26048] mca: base: component_find: unable to open
>> /usr/local/lib/openmpi/mca_paffinity_hwloc:
>> /usr/local/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol:
>> opal_hwloc_topology (ignored)
>> [ben-Inspiron-1764:26048] mca: base: component_find: unable to open
>> /usr/local/lib/openmpi/mca_carto_auto_detect:
>> /usr/local/lib/openmpi/mca_carto_auto_detect.so: undefined symbol:
>> opal_carto_base_graph_get_host_graph_fn (ignored)
>> [ben-Inspiron-1764:26048] mca: base: component_find: unable to open
>> /usr/local/lib/openmpi/mca_carto_file:
>> /usr/local/lib/openmpi/mca_carto_file.so: undefined symbol:
>> opal_carto_base_graph_get_host_graph_fn (ignored)
>> [ben-Inspiron-1764:26048] mca: base: component_find: unable to open
>> /usr/local/lib/openmpi/mca_shmem_mmap:
>> /usr/local/lib/openmpi/mca_shmem_mmap.so: undefined symbol: opal_show_help
>> (ignored)
>> [ben-Inspiron-1764:26048] mca: base: component_find: unable to open
>> /usr/local/lib/openmpi/mca_shmem_posix:
>> /usr/local/lib/openmpi/mca_shmem_posix.so: undefined symbol:
>> opal_shmem_base_output (ignored)
>> [ben-Inspiron-1764:26048] mca: base: component_find: unable to open
>> /usr/local/lib/openmpi/mca_shmem_sysv:
>> /usr/local/lib/openmpi/mca_shmem_sysv.so: undefined symbol: opal_show_help
>> (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
>> --------------------------------------------------------------------------
>> [ben-Inspiron-1764:26048] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in
>> file runtime/orte_init.c at line 79
>> --------------------------------------------------------------------------
>> It looks like MPI_INIT failed for some reason; your parallel process is
>> likely to abort. There are many reasons that a parallel process can
>> fail during MPI_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):
>>
>> ompi_mpi_init: orte_init failed
>> --> Returned "Error" (-1) instead of "Success" (0)
>> --------------------------------------------------------------------------
>> *** An error occurred in MPI_Init
>> *** on a NULL communicator
>> *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
>> [ben-Inspiron-1764:26048] Local abort before MPI_INIT completed
>> successfully; not able to aggregate error messages, and not able to
>> guarantee that all other processes were killed!
>>
>>
>> _______________________________________________
>> devel mailing list
>> devel_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>
>
>
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