[OMPI users] Open MPI installation problem

2019-01-23 Thread Serdar Hiçdurmaz 
Hi All,

I try to install Open MPI, which is prerequiste for liggghts (DEM
software). Some info about my current linux version :

NAME="SLED"
VERSION="12-SP3"
VERSION_ID="12.3"
PRETTY_NAME="SUSE Linux Enterprise Desktop 12 SP3"
ID="sled"

I installed Open MPI 1.6 by typing

./configure --prefix=$HOME/openmpi
make all
make install

Here, it is discussed that openmpi 1.6 is compatible with OpenSuse 12.3
https://public.kitware.com/pipermail/paraview/2014-February/030487.html
https://build.opensuse.org/package/show/openSUSE:12.3/openmpi

To add OpenMPI to my path and LD_LIBRARY_PATH, I execute the following
comands on terminal:

export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpi/gcc/openmpi/lib64

Then, in /liggghts/src directory, I execute make auto, this appears :

Creating list of contact models completed.
make[1]: Entering directory
'/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
Makefile:456: *** 'Could not compile a simple MPI example. Test was done
with MPI_INC="" and MPICXX="mpicxx"'. Stop.
make[1]: Leaving directory
'/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
Makefile:106: recipe for target 'auto' failed
make: *** [auto] Error 2

Do you have any idea what the problem is here ? I went through the
"makefile" but it looks like quite complicated as linux beginner like me.

Thanks in advance. Regards,

Serdar
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Re: [OMPI users] Open MPI installation problem

2019-01-23 Thread Ralph H Castain 
Your PATH and LD_LIBRARY_PATH setting is incorrect. You installed OMPI into 
$HOME/openmpi, so you should have done:

PATH=$HOME/openmpi/bin:$PATH
LD_LIBRARY_PATH=$HOME/openmpi/lib:$LD_LIBRARY_PATH

Ralph


> On Jan 23, 2019, at 6:36 AM, Serdar Hiçdurmaz  
> wrote:
> 
> Hi All,
> 
> I try to install Open MPI, which is prerequiste for liggghts (DEM software). 
> Some info about my current linux version :
> 
> NAME="SLED"
> VERSION="12-SP3"
> VERSION_ID="12.3"
> PRETTY_NAME="SUSE Linux Enterprise Desktop 12 SP3"
> ID="sled"
> 
> I installed Open MPI 1.6 by typing
> 
> ./configure --prefix=$HOME/openmpi
> make all
> make install
> 
> Here, it is discussed that openmpi 1.6 is compatible with OpenSuse 12.3 
> https://public.kitware.com/pipermail/paraview/2014-February/030487.html 
>  
> https://build.opensuse.org/package/show/openSUSE:12.3/openmpi 
> 
> To add OpenMPI to my path and LD_LIBRARY_PATH, I execute the following 
> comands on terminal:
> 
> export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpi/gcc/openmpi/lib64
> 
> Then, in /liggghts/src directory, I execute make auto, this appears :
> 
> Creating list of contact models completed.
> make[1]: Entering directory 
> '/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
> Makefile:456: *** 'Could not compile a simple MPI example. Test was done with 
> MPI_INC="" and MPICXX="mpicxx"'. Stop.
> make[1]: Leaving directory 
> '/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
> Makefile:106: recipe for target 'auto' failed
> make: *** [auto] Error 2
> 
> Do you have any idea what the problem is here ? I went through the "makefile" 
> but it looks like quite complicated as linux beginner like me.
> 
> Thanks in advance. Regards,
> 
> Serdar
> 
> 
> 
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Re: [OMPI users] Open MPI installation problem

2019-01-23 Thread John Hearns via users 
Sorry if I am being stupid, Serdar might also have to set the location for
the includes by setting MPI_INC

On Wed, 23 Jan 2019 at 14:47, Ralph H Castain  wrote:

> Your PATH and LD_LIBRARY_PATH setting is incorrect. You installed OMPI
> into $HOME/openmpi, so you should have done:
>
> PATH=$HOME/openmpi/bin:$PATH
> LD_LIBRARY_PATH=$HOME/openmpi/lib:$LD_LIBRARY_PATH
>
> Ralph
>
>
> On Jan 23, 2019, at 6:36 AM, Serdar Hiçdurmaz 
> wrote:
>
> Hi All,
>
> I try to install Open MPI, which is prerequiste for liggghts (DEM
> software). Some info about my current linux version :
>
> NAME="SLED"
> VERSION="12-SP3"
> VERSION_ID="12.3"
> PRETTY_NAME="SUSE Linux Enterprise Desktop 12 SP3"
> ID="sled"
>
> I installed Open MPI 1.6 by typing
>
> ./configure --prefix=$HOME/openmpi
> make all
> make install
>
> Here, it is discussed that openmpi 1.6 is compatible with OpenSuse 12.3
> https://public.kitware.com/pipermail/paraview/2014-February/030487.html
> https://build.opensuse.org/package/show/openSUSE:12.3/openmpi
>
> To add OpenMPI to my path and LD_LIBRARY_PATH, I execute the following
> comands on terminal:
>
> export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpi/gcc/openmpi/lib64
>
> Then, in /liggghts/src directory, I execute make auto, this appears :
>
> Creating list of contact models completed.
> make[1]: Entering directory
> '/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
> Makefile:456: *** 'Could not compile a simple MPI example. Test was done
> with MPI_INC="" and MPICXX="mpicxx"'. Stop.
> make[1]: Leaving directory
> '/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
> Makefile:106: recipe for target 'auto' failed
> make: *** [auto] Error 2
>
> Do you have any idea what the problem is here ? I went through the
> "makefile" but it looks like quite complicated as linux beginner like me.
>
> Thanks in advance. Regards,
>
> Serdar
>
> ___
> users mailing list
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> https://lists.open-mpi.org/mailman/listinfo/users
>
>
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Re: [OMPI users] Open MPI installation problem

2019-01-23 Thread Serdar Hiçdurmaz 
Thanks Ralph. It worked.

Serdar

Ralph H Castain , 23 Oca 2019 Çar, 15:48 tarihinde şunu
yazdı:

> Your PATH and LD_LIBRARY_PATH setting is incorrect. You installed OMPI
> into $HOME/openmpi, so you should have done:
>
> PATH=$HOME/openmpi/bin:$PATH
> LD_LIBRARY_PATH=$HOME/openmpi/lib:$LD_LIBRARY_PATH
>
> Ralph
>
>
> On Jan 23, 2019, at 6:36 AM, Serdar Hiçdurmaz 
> wrote:
>
> Hi All,
>
> I try to install Open MPI, which is prerequiste for liggghts (DEM
> software). Some info about my current linux version :
>
> NAME="SLED"
> VERSION="12-SP3"
> VERSION_ID="12.3"
> PRETTY_NAME="SUSE Linux Enterprise Desktop 12 SP3"
> ID="sled"
>
> I installed Open MPI 1.6 by typing
>
> ./configure --prefix=$HOME/openmpi
> make all
> make install
>
> Here, it is discussed that openmpi 1.6 is compatible with OpenSuse 12.3
> https://public.kitware.com/pipermail/paraview/2014-February/030487.html
> https://build.opensuse.org/package/show/openSUSE:12.3/openmpi
>
> To add OpenMPI to my path and LD_LIBRARY_PATH, I execute the following
> comands on terminal:
>
> export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpi/gcc/openmpi/lib64
>
> Then, in /liggghts/src directory, I execute make auto, this appears :
>
> Creating list of contact models completed.
> make[1]: Entering directory
> '/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
> Makefile:456: *** 'Could not compile a simple MPI example. Test was done
> with MPI_INC="" and MPICXX="mpicxx"'. Stop.
> make[1]: Leaving directory
> '/home/serdarhd/liggghts/LIGGGHTS-PUBLIC/src/Obj_auto'
> Makefile:106: recipe for target 'auto' failed
> make: *** [auto] Error 2
>
> Do you have any idea what the problem is here ? I went through the
> "makefile" but it looks like quite complicated as linux beginner like me.
>
> Thanks in advance. Regards,
>
> Serdar
>
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> users mailing list
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>
>
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Re: [OMPI users] Help Getting Started with Open MPI and PMIx and UCX

2019-01-23 Thread Matt Thompson 
_MAC, et al,

Things are looking up. By specifying, --with-verbs=no, things are looking
up. I can run helloworld. But in a new-for-me wrinkle, I can only run on
*more* than one node. Not sure I've ever seen that. Using 40 core nodes,
this:

mpirun -np 41 ./helloWorld.mpi3.SLES12.OMPI400.exe

works, and -np 40 fails:

(1027)(master) $ mpirun -np 40 ./helloWorld.mpi3.SLES12.OMPI400.exe
[borga033:05598] *** An error occurred in MPI_Barrier
[borga033:05598] *** reported by process [140735567101953,140733193388034]
[borga033:05598] *** on communicator MPI_COMM_WORLD
[borga033:05598] *** MPI_ERR_OTHER: known error not in list
[borga033:05598] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
will now abort,
[borga033:05598] ***and potentially your MPI job)
Compiler Version: Intel(R) Fortran Intel(R) 64 Compiler for applications
running on Intel(R) 64, Version 18.0.5.274 Build 20180823
MPI Version: 3.1
MPI Library Version: Open MPI v4.0.0, package: Open MPI mathomp4@discover21
Distribution, ident: 4.0.0, repo rev: v4.0.0, Nov 12, 2018
forrtl: error (78): process killed (SIGTERM)
Image  PCRoutineLineSource
helloWorld.mpi3.S  0040A38E  for__signal_handl Unknown  Unknown
libpthread-2.22.s  2B9CCB20  Unknown   Unknown  Unknown
libpthread-2.22.s  2B9CC3ED  __nanosleep   Unknown  Unknown
libopen-rte.so.40  2C3C5854  orte_show_help_no Unknown  Unknown
libopen-rte.so.40  2C3C5595  orte_show_helpUnknown  Unknown
libmpi.so.40.20.0  2B3BADC5  ompi_mpi_errors_a Unknown  Unknown
libmpi.so.40.20.0  2B3B99D9  ompi_errhandler_i Unknown  Unknown
libmpi.so.40.20.0  2B3E4586  MPI_Barrier   Unknown  Unknown
libmpi_mpifh.so.4  2B15EE53  MPI_Barrier_f08   Unknown  Unknown
libmpi_usempif08.  2ACE7742  mpi_barrier_f08_  Unknown  Unknown
helloWorld.mpi3.S  0040939F  Unknown   Unknown  Unknown
helloWorld.mpi3.S  0040915E  Unknown   Unknown  Unknown
libc-2.22.so   2BBF96D5  __libc_start_main Unknown  Unknown
helloWorld.mpi3.S  00409069  Unknown   Unknown  Unknown

So, I'm getting closer but I have to admit I've never built an MPI stack
before where running on a single node was the broken bit!

On Tue, Jan 22, 2019 at 1:31 PM Cabral, Matias A 
wrote:

> Hi Matt,
>
>
>
> There seem to be two different issues here:
>
> a)  The warning message comes from the openib btl. Given that
> Omnipath has verbs API and you have the necessary libraries in your system,
> openib btl finds itself as a potential transport and prints the warning
> during its init (openib btl is its way to deprecation). You may try to
> explicitly ask for vader btl given you are running on shared mem: -mca btl
> self,vader -mca pml ob1. Or better, explicitly build without openib:
> ./configure --with-verbs=no …
>
> b)  Not my field of expertise, but you may be having some conflict
> with the external components you are using:
> --with-pmix=/usr/nlocal/pmix/2.1 --with-libevent=/usr . You may try not
> specifying these and using the ones provided by OMPI.
>
>
>
> _MAC
>
>
>
> *From:* users [mailto:users-boun...@lists.open-mpi.org] *On Behalf Of *Matt
> Thompson
> *Sent:* Tuesday, January 22, 2019 6:04 AM
> *To:* Open MPI Users 
> *Subject:* Re: [OMPI users] Help Getting Started with Open MPI and PMIx
> and UCX
>
>
>
> Well,
>
>
>
> By turning off UCX compilation per Howard, things get a bit better in that
> something happens! It's not a good something, as it seems to die with an
> infiniband error. As this is an Omnipath system, is OpenMPI perhaps seeing
> libverbs somewhere and compiling it in? To wit:
>
>
>
> (1006)(master) $ mpirun -np 4 ./helloWorld.mpi3.SLES12.OMPI400.exe
>
> --
>
> By default, for Open MPI 4.0 and later, infiniband ports on a device
>
> are not used by default.  The intent is to use UCX for these devices.
>
> You can override this policy by setting the btl_openib_allow_ib MCA
> parameter
>
> to true.
>
>
>
>   Local host:  borgc129
>
>   Local adapter:   hfi1_0
>
>   Local port:  1
>
>
>
> --
>
> --
>
> WARNING: There was an error initializing an OpenFabrics device.
>
>
>
>   Local host:   borgc129
>
>   Local device: hfi1_0
>
> --
>
> Compiler Version: Intel(R) Fortran Intel(R) 64 Compiler for applications
> running on Intel(R) 64, Version 18.0.5.274 Build 20180823
>
> MPI Version: 3.1
>
> MPI Library Version: Open MPI v4.0.0, package: Open MPI mathomp4@discover23
> Distribution, ident: 4.0.0, repo rev: v4.0.0, Nov 12, 2018
>
> [borgc129:260830] *** An error occur

[OMPI users] please fix RMA before you ship 4.0.0

2019-01-23 Thread Jeff Hammond 
I am very sad to see that RMA has reverted to a state of brokenness ala
Open-MPI 1.x when it comes to the use of datatypes.  Open-MPI 3.x worked
great for me and I had started to use Open-MPI by default on some platforms.

https://github.com/open-mpi/ompi/issues/6275 has details.  The issues
appear with shared-memory, which is a pretty important conduit.

Jeff

-- 
Jeff Hammond
jeff.scie...@gmail.com
http://jeffhammond.github.io/
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