[maker-devel] Maker-Error when started with IMPI : CORRECTED MAIL : SEE THIS ONE

[Rainer Rutka]

Sorry, sent wrong e-mail :-(

IGNORE THE FIRST MAIL I SENT!

Am 01.03.2017 um 13:30 schrieb Rainer Rutka:
Hi Carson.
  
Again THANK YOU for your efforts :-)
  
  
Am 24.02.2017 um 18:30 schrieb Carson Holt:
> Specific things.
>
> 1. Do not set LD_PRELOAD. That is only for OpenMPI, but it will cause
> problems with other MPI's.

OK, I deleted this envirnoment. Not set any more.
  
> 2. Make sure you recompiled MAKER for Intel MPI (MPI code always has
> to be compiled for the flavor you are using, so make sure you have a
> separate installation of MAKER for Intel MPI). Also validate that the
> mpicc and libmpi.h listed during the MAKER install belong to Intel
> MPI. Don’t just assume they do because you loaded the module. Manually
> verify the paths during MAKER’s setup.

I validated:
  
UC:[kn at uc1n996 bwhpc-examples]$ module list
Currently Loaded Modulefiles:
1) compiler/intel/16.0(default)
2) mpi/impi/5.1.3-intel-16.0(default)
  
FOR MPICC:
UC:[kn at uc1n996 bwhpc-examples]$ type mpicc
mpicc is
/opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64/bin/mpicc
  
  
FOR LIBMPI:
UC:[kn at uc1n996 bwhpc-examples]$ echo $MPIDIR
/opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64
UC:[kn at uc1n996 bwhpc-examples]$ find $MPIDIR -name '*'mpi.h -print
/opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64/include/mpi.h
  
  
Here i can find a mpi.h but not a libmpi.h. But I thinks this is o.k.,
because the SW was  compiled and linkes without any errors or missing libs.
  
> 3. The error you got previously should not even be possible with the
> current version of Intel MPI,
> which is why I say that when you called mpiexec, something else (that
> was not Intel MPI) was launched.
> Easy solution is to give the full path of mpiexec in your job, so are
> not relying on PATH to be unaltered in your job.

mpiexec is in the PATH and the right one is/was used, too:
  
MPIXEC:
UC:[kn at uc1n996 bwhpc-examples]$ type mpiexec
mpiexec is
/opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64/bin/mpiexec

> Do not do —>  mpiexec -nc 1 maker
> Do this for example —>
> /opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64/bin/mpiexec
> -nc maker
  
OK, so i did:
  
[...]
#MSUB -l nodes=1:ppn=1
#MSUB -l mem=20gb
[...]
echo " "
echo "### Runing Maker example"
echo " "
export OMPI_MCA_mpi_warn_on_fork=0
/opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64/bin/mpiexec
-nc maker
[...]
  
> 4. Build and run on the same node for your test. If you build on one
> node and run on another, you may
> be changing your environment in ways you don’t realize that break
> things. So if you can build and test on
> the same node and it works, then it fails when you test it elsewhere,
> then you have to track down how your
> environment is changing.

OK I did. Same node: uc1n996
  
  
UNFORTUNATELY I GOT THE SAME ERROR:
  
  [...]
Currently Loaded Modulefiles:
   1) compiler/intel/16.0(default)
   2) mpi/impi/5.1.3-intel-16.0(default)
   3) bio/maker/2.31.8_impi


### Display internal Maker/bwHPC environments...

MAKER_BIN_DIR  = /opt/bwhpc/common/bio/maker/2.31.8_impi/bin
MAKER_EXA_DIR  = /opt/bwhpc/common/bio/maker/2.31.8_impi/bwhpc-examples


### Runing Maker example
OMPI_MCA_mpi_warn_on_fork=0
I_MPI_CPUINFO=proc
I_MPI_PMI_LIBRARY=/opt/bwhpc/common/compiler/intel/compxe.2016.4.258/impi/5.1.3.223/intel64/lib/libmpi.so
I_MPI_PIN_DOMAIN=node
I_MPI_FABRICS=shm:tcp
I_MPI_HYDRA_IFACE=ib0
mpiexec_uc1n326.localdomain: cannot connect to local mpd (/scratch/mpd2.console_uc1n326.localdomain_kn_pop235844); possible causes:
   1. no mpd is running on this host
   2. an mpd is running but was started without a "console" (-n option)
### Cleaning up files ... removing unnecessary scratch files ...
  [...]
  
  
> —Carson
  
  tbc. ? :-)
  
  THANX
  

-- 
Rainer Rutka
Universität Konstanz
Kommunikations-, Informations-, Medienzentrum (KIM)
* KIM Ausbildung
* Wissenschaftliches Rechnen/bwHPC-C5
* KIM Basisdienste, KIM Support
Raum: V511
78457 Konstanz
+49 7531 88-5413

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