Re: [OMPI users] Strange behavior of OMPI 1.8.3
Hi Michael,
If you do not include --enable-ipv6 in the config line, do you still
observe the problem?
Is it possible that one or more interfaces on nodes H1 and H2 do not have
ipv6 enabled?
Howard
2014-10-06 16:51 GMT-06:00 Michael Thomadakis :
> Hello,
>
> I've configured OpenMPI1.8.3 with the following command line
>
>
>
> $ AXFLAGS="-xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2"
> $ myFLAGS="-O2 ${AXFLAGS}" ;
>
> $ ./configure --prefix=${proot} \
> --with-lsf \
> --with-cma \
> --enable-peruse --enable-branch-probabilities \
> --enable-mpi-fortran=all \
> --enable-cxx-exceptions \
> --enable-ipv6 \
> --enable-sparse-groups \
> --with-threads=posix \
> --enable-mpi-thread-multiple \
> --enable-openib-connectx-xrc \
> --enable-mtl-portals4-flow-control \
> --with-hwloc=internal \
> --enable-orterun-prefix-by-default \
> --with-ident-string="MikeT_15.0" \
> CC=icc CFLAGS="$myFLAGS" \
> CXX=icpc CXXFLAGS="$myFLAGS" \
> F77=ifort FFLAGS="$myFLAGS" FC=ifort FCFLAGS="$myFLAGS" \
> LIBS="-lnsl" \
> && make -j 8 && make install
>
> but when I run it with
>
> $ mpirun --bind-to core --map-by core -mca mpi_show_mca_params all --host
> H1,H2 -np 2
> ~/performance/analysis/networks/Intel64_SandyBridge/HPCI/OMB_4.3.0/ompi_1.8.2/cpu/osu-micro-benchmarks-4.3/libexec/osu-micro-benchmarks/mpi/one-sided/osu_put_bibw
> H H
>
> I am getting
> "
> [H1:33580] [[41149,0],0] ORTE_ERROR_LOG: Address family not supported by
> protocol in file oob_tcp_listener.c at line 120
> [h2:33580] [[41149,0],0] ORTE_ERROR_LOG: Address family not supported by
> protocol in file oob_tcp_component.c at line 584
>
> "
>
> Any suggestions ?
>
>
> Thanks !
> Michael
>
>
> ___
> users mailing list
> us...@open-mpi.org
> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
> Link to this post:
> http://www.open-mpi.org/community/lists/users/2014/10/25468.php
>
Re: [OMPI users] Strange behavior of OMPI 1.8.3
Hi Howard,
We have NOT defined IPv6 on the nodes.
Actually I was looking at the location of the code that complains and I
also saw references to IPv6 sockets.
Thanks a lot for the suggestion! I'll try this out tomorrow.
Regards
Michael
On Mon, Oct 6, 2014 at 11:07 PM, Howard Pritchard
wrote:
> Hi Michael,
>
> If you do not include --enable-ipv6 in the config line, do you still
> observe the problem?
> Is it possible that one or more interfaces on nodes H1 and H2 do not have
> ipv6 enabled?
>
> Howard
>
>
> 2014-10-06 16:51 GMT-06:00 Michael Thomadakis :
>
>> Hello,
>>
>> I've configured OpenMPI1.8.3 with the following command line
>>
>>
>>
>> $ AXFLAGS="-xSSE4.2 -axAVX,CORE-AVX-I,CORE-AVX2"
>> $ myFLAGS="-O2 ${AXFLAGS}" ;
>>
>> $ ./configure --prefix=${proot} \
>> --with-lsf \
>> --with-cma \
>> --enable-peruse --enable-branch-probabilities \
>> --enable-mpi-fortran=all \
>> --enable-cxx-exceptions \
>> --enable-ipv6 \
>> --enable-sparse-groups \
>> --with-threads=posix \
>> --enable-mpi-thread-multiple \
>> --enable-openib-connectx-xrc \
>> --enable-mtl-portals4-flow-control \
>> --with-hwloc=internal \
>> --enable-orterun-prefix-by-default \
>> --with-ident-string="MikeT_15.0" \
>> CC=icc CFLAGS="$myFLAGS" \
>> CXX=icpc CXXFLAGS="$myFLAGS" \
>> F77=ifort FFLAGS="$myFLAGS" FC=ifort FCFLAGS="$myFLAGS" \
>> LIBS="-lnsl" \
>> && make -j 8 && make install
>>
>> but when I run it with
>>
>> $ mpirun --bind-to core --map-by core -mca mpi_show_mca_params all --host
>> H1,H2 -np 2
>> ~/performance/analysis/networks/Intel64_SandyBridge/HPCI/OMB_4.3.0/ompi_1.8.2/cpu/osu-micro-benchmarks-4.3/libexec/osu-micro-benchmarks/mpi/one-sided/osu_put_bibw
>> H H
>>
>> I am getting
>> "
>> [H1:33580] [[41149,0],0] ORTE_ERROR_LOG: Address family not supported by
>> protocol in file oob_tcp_listener.c at line 120
>> [h2:33580] [[41149,0],0] ORTE_ERROR_LOG: Address family not supported by
>> protocol in file oob_tcp_component.c at line 584
>>
>> "
>>
>> Any suggestions ?
>>
>>
>> Thanks !
>> Michael
>>
>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
>> Link to this post:
>> http://www.open-mpi.org/community/lists/users/2014/10/25468.php
>>
>
>
> ___
> users mailing list
> us...@open-mpi.org
> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
> Link to this post:
> http://www.open-mpi.org/community/lists/users/2014/10/25472.php
>
Re: [OMPI users] Update/patch to check/opal_check_pmi.m4
I've poked at this a bit and think I have all the combinations covered - can you try the attached patch? I don't have a way to test it right now, so I don't want to put it in the trunk. Thanks Ralph On Mon, Oct 6, 2014 at 6:02 PM, Ralph Castain wrote: > I've looked at your patch, and it isn't quite right as it only looks for > libpmi and not libpmi2. We need to look for each of them as we could have > either or both. > > I'll poke a bit at this tonight and see if I can make this a little > simpler - the nesting is getting a little deep. > > > On Mon, Oct 6, 2014 at 5:33 PM, Timothy Brown < > timothy.brow...@colorado.edu> wrote: > >> Yes, I know. Sorry I might not have articulated myself fully earlier. >> >> Currently if I run configure as: >> >> $ ./configure --prefix=/curc/tools/x_86_64/rh6/openmpi/1.8.3/intel/13.0.0 >> \ >> --with-threads=posix --enable-mpi-thread-multiple \ >> --with-pmi=/curc/slurm/slurm/current/ --with-slurm >> >> I get the following error: >> >> --- MCA component common:pmi (m4 configuration macro) >> checking for MCA component common:pmi compile mode... dso >> checking if user requested PMI support... yes >> checking if PMI or PMI2 headers installed... Slurm PMI headers found >> checking for PMI2_Init in -lpmi2... no >> checking for PMI2_Init in -lpmi... no >> checking for PMI_Init in -lpmi... no >> checking PMI2 and/or PMI support enabled... no >> configure: WARNING: PMI support requested (via --with-pmi) but not found. >> configure: error: Aborting. >> >> As the test in config/opal_check_pmi.m4 contains: >> >> [AS_IF([test -d "$with_pmi/lib64"], >> [opal_check_pmi_$1_LDFLAGS="-L$with_pmi/lib64" >> opal_pmi_rpath="$with_pmi/lib64"], >> [opal_check_pmi_$1_LDFLAGS="-L$with_pmi/lib" >> opal_pmi_rpath="$with_pmi/lib”]) >> >> And in our SLURM installation directory: >> >> $ ls /curc/slurm/slurm/current/lib64/ >> perl5 >> $ ls /curc/slurm/slurm/current/lib/ >> libpmi.a libpmi.so.0 libslurmdb.a libslurmdb.so.27 >> libslurm.so slurm >> libpmi.la libpmi.so.0.0.0 libslurmdb.la libslurmdb.so.27.0.0 >> libslurm.so.27 >> libpmi.so libslurm.a libslurmdb.so libslurm.la >> libslurm.so.27.0.0 >> >> So the patch I am providing checks for the actual libpmi.so file, by >> 1) replacing the test -d with a test -f >> 2) appending the file we are looking for (libpmi.so) >> >> You do bring up an interesting point, I didn’t think of. If it is >> checking for libpmi2.so, that can be accounted for by adding another 2 test >> and run-if-true results to the AS_IF macro. If you deem my patch >> worthwhile, I am happy to modify it to meet this criteria. >> >> Regards >> Timothy >> >> >> On Oct 6, 2014, at 6:07 PM, Joshua Ladd wrote: >> >> > We only link in libpmi(2).so if specifically requested to do so via >> "--with-pmi" configure flag. It is not automatic. >> > >> > Josh >> > >> > On Mon, Oct 6, 2014 at 3:28 PM, Timothy Brown < >> timothy.brow...@colorado.edu> wrote: >> > Hi, >> > >> > I’m not too sure if this is the right list, or if I should be posting >> to the dev list. Please let me know if I’m in the wrong. >> > >> > We use SLURM (14.03.7) and have been trying to get OpenMPI (1.8.3) to >> work with `srun`. It seems that the M4 file to check for PMI doesn’t work >> in our situation. Where we have both a lib64 and lib directory within >> SLURM. The lib64 directory only contains perl modules, while the lib >> directory contains the PMI library. >> > >> > By changing the M4 AS_IF macro in config/opal_check_pmi.m4 to check for >> the library .so and to have an else if test. The configuration script finds >> the library. Which means OpenMPI builds with PMI support and now we have >> > - srun >> > - mpirun >> > - mpiexec >> > all working properly. >> > >> > I have created a patch against the git master and it’s attached. >> > >> > Regards >> > Timothy >> > >> > >> > >> > ___ >> > users mailing list >> > us...@open-mpi.org >> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> > Link to this post: >> http://www.open-mpi.org/community/lists/users/2014/10/25467.php >> > >> > ___ >> > users mailing list >> > us...@open-mpi.org >> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> > Link to this post: >> http://www.open-mpi.org/community/lists/users/2014/10/25469.php >> >> ___ >> users mailing list >> us...@open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2014/10/25470.php >> > > diff --git a/config/opal_check_pmi.m4 b/config/opal_check_pmi.m4 index e71202c..af60dbe 100644 --- a/config/opal_check_pmi.m4 +++ b/config/opal_check_pmi.m4 @@ -50,6 +50,11 @@ AC_DEFUN([OPAL_CHECK_PMI],[ opal_pmi_rpath=
[OMPI users] metis in fortran looking for an example
Dear all, I would like to use the METIS library to partitioning my domain. May domain is a structured mesh but I would like to use different cell, according to how many particles I have in each cell. Does someone tall me, please, where I can find a good example in FORTRAN and how link my program to the METIS? Diego
Re: [OMPI users] SENDRECV + MPI_TYPE_CREATE_STRUCT
Dear all, thanks a lot. I rewrote the code starting from the Nick's one. It's work I have still to think about the "-r8" things, I belive that less er type less we make error. Another questions about Nick's code: Why do I have to use MPIstatus(MPI_STATUS_SIZE) and not a simple MPI%ierror Thanks a lot Diego On 3 October 2014 21:55, Jeff Squyres (jsquyres) wrote: > On Oct 3, 2014, at 3:50 PM, George Bosilca wrote: > > > 1. I’m not a Fortran expert but I think that real is not > MPI_DOUBLE_RECISION but MPI_FLOAT. > > It's actually MPI_REAL. :-) (MPI_FLOAT is for the C "float" type) > > /me goes back in my Fortran hole... > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > ___ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2014/10/25461.php >
Re: [OMPI users] Update/patch to check/opal_check_pmi.m4
Ralph, Thanks for the patch. It cleaned up the pmi check nicely. Applied, configured and compiled without any problems! Great! The configure gave me: --- MCA component pubsub:pmi (m4 configuration macro) checking for MCA component pubsub:pmi compile mode... dso checking if user requested PMI support... yes checking if PMI installed... yes checking final added libraries... -lpmi checking if MCA component pubsub:pmi can compile…yes Regards Timothy On Oct 7, 2014, at 9:39 AM, Ralph Castain wrote: > I've poked at this a bit and think I have all the combinations covered - can > you try the attached patch? I don't have a way to test it right now, so I > don't want to put it in the trunk. > > Thanks > Ralph > > > On Mon, Oct 6, 2014 at 6:02 PM, Ralph Castain wrote: > I've looked at your patch, and it isn't quite right as it only looks for > libpmi and not libpmi2. We need to look for each of them as we could have > either or both. > > I'll poke a bit at this tonight and see if I can make this a little simpler - > the nesting is getting a little deep. > > > On Mon, Oct 6, 2014 at 5:33 PM, Timothy Brown > wrote: > Yes, I know. Sorry I might not have articulated myself fully earlier. > > Currently if I run configure as: > > $ ./configure --prefix=/curc/tools/x_86_64/rh6/openmpi/1.8.3/intel/13.0.0 \ > --with-threads=posix --enable-mpi-thread-multiple \ > --with-pmi=/curc/slurm/slurm/current/ --with-slurm > > I get the following error: > > --- MCA component common:pmi (m4 configuration macro) > checking for MCA component common:pmi compile mode... dso > checking if user requested PMI support... yes > checking if PMI or PMI2 headers installed... Slurm PMI headers found > checking for PMI2_Init in -lpmi2... no > checking for PMI2_Init in -lpmi... no > checking for PMI_Init in -lpmi... no > checking PMI2 and/or PMI support enabled... no > configure: WARNING: PMI support requested (via --with-pmi) but not found. > configure: error: Aborting. > > As the test in config/opal_check_pmi.m4 contains: > > [AS_IF([test -d "$with_pmi/lib64"], > [opal_check_pmi_$1_LDFLAGS="-L$with_pmi/lib64" > opal_pmi_rpath="$with_pmi/lib64"], > [opal_check_pmi_$1_LDFLAGS="-L$with_pmi/lib" > opal_pmi_rpath="$with_pmi/lib”]) > > And in our SLURM installation directory: > > $ ls /curc/slurm/slurm/current/lib64/ > perl5 > $ ls /curc/slurm/slurm/current/lib/ > libpmi.a libpmi.so.0 libslurmdb.a libslurmdb.so.27 libslurm.so >slurm > libpmi.la libpmi.so.0.0.0 libslurmdb.la libslurmdb.so.27.0.0 > libslurm.so.27 > libpmi.so libslurm.a libslurmdb.so libslurm.la > libslurm.so.27.0.0 > > So the patch I am providing checks for the actual libpmi.so file, by > 1) replacing the test -d with a test -f > 2) appending the file we are looking for (libpmi.so) > > You do bring up an interesting point, I didn’t think of. If it is checking > for libpmi2.so, that can be accounted for by adding another 2 test and > run-if-true results to the AS_IF macro. If you deem my patch worthwhile, I am > happy to modify it to meet this criteria. > > Regards > Timothy > > > On Oct 6, 2014, at 6:07 PM, Joshua Ladd wrote: > > > We only link in libpmi(2).so if specifically requested to do so via > > "--with-pmi" configure flag. It is not automatic. > > > > Josh > > > > On Mon, Oct 6, 2014 at 3:28 PM, Timothy Brown > > wrote: > > Hi, > > > > I’m not too sure if this is the right list, or if I should be posting to > > the dev list. Please let me know if I’m in the wrong. > > > > We use SLURM (14.03.7) and have been trying to get OpenMPI (1.8.3) to work > > with `srun`. It seems that the M4 file to check for PMI doesn’t work in our > > situation. Where we have both a lib64 and lib directory within SLURM. The > > lib64 directory only contains perl modules, while the lib directory > > contains the PMI library. > > > > By changing the M4 AS_IF macro in config/opal_check_pmi.m4 to check for the > > library .so and to have an else if test. The configuration script finds the > > library. Which means OpenMPI builds with PMI support and now we have > > - srun > > - mpirun > > - mpiexec > > all working properly. > > > > I have created a patch against the git master and it’s attached. > > > > Regards > > Timothy > > > > > > > > ___ > > users mailing list > > us...@open-mpi.org > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > Link to this post: > > http://www.open-mpi.org/community/lists/users/2014/10/25467.php > > > > ___ > > users mailing list > > us...@open-mpi.org > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > Link to this post: > > http://www.open-mpi.org/community/lists/users/2014/10/25469.php > > ___ > us
Re: [OMPI users] SENDRECV + MPI_TYPE_CREATE_STRUCT
You should redo it in terms of George's suggestion, in that way you should also circumvent the "manual" alignment of data. George's method is the best generic way of doing it. As for the -r8 thing, just do not use it :) And check the interface for the routines used to see why MPIstatus is used. 2014-10-07 18:00 GMT+02:00 Diego Avesani : > Dear all, > thanks a lot. I rewrote the code starting from the Nick's one. > It's work > > I have still to think about the "-r8" things, I belive that less er type > less we make error. > > Another questions about Nick's code: > > Why do I have to use MPIstatus(MPI_STATUS_SIZE) and not a simple MPI%ierror > > Thanks a lot > > > > Diego > > > On 3 October 2014 21:55, Jeff Squyres (jsquyres) > wrote: > >> On Oct 3, 2014, at 3:50 PM, George Bosilca wrote: >> >> > 1. I’m not a Fortran expert but I think that real is not >> MPI_DOUBLE_RECISION but MPI_FLOAT. >> >> It's actually MPI_REAL. :-) (MPI_FLOAT is for the C "float" type) >> >> /me goes back in my Fortran hole... >> >> -- >> Jeff Squyres >> jsquy...@cisco.com >> For corporate legal information go to: >> http://www.cisco.com/web/about/doing_business/legal/cri/ >> >> ___ >> users mailing list >> us...@open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2014/10/25461.php >> > > > ___ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2014/10/25476.php > -- Kind regards Nick
