[Hpc-forum] MPI problemak

[etele molnar]

Kedves Gabor es tobbiek

Eloszor is koszonom szepen a valaszokat es segitseget,
mindjart mindjart ott vagyunk..

module use /opt/nce/modulefiles
bizony segitett es most lefut a program 12, 24, 48 slotton is, de most 
van egy ujabb hiba,
ami meg a program futasa elott jon, azutan lefut a program (sikeresen) 
de mar a kovetkezo hivasra
nem indul be es a job is megszakad.

A mostani teszt programokat igy hivtam bash-bol

mpirun -np 48 ./ program ... ;
mpirun -np 48 ./ program ... ;
...
wait


Error: NCE_PACKAGES not set
...
Error: NCE_PACKAGES not set

real    11m7.497s
user    39m5.807s
sys    0m1.416s
[r1i0n6:09241] opal_os_dirpath_create: Error: Unable to create the 
sub-directory 
(/scratch/tmp/425790.1.parallel.q/openmpi-sessions-emolnar at r1i0n6_0/39007) 
of 
(/scratch/tmp/425790.1.parallel.q/openmpi-sessions-emolnar at r1i0n6_0/39007/0/0), 
mkdir failed [1]
[r1i0n6:09241] [[39007,0],0] ORTE_ERROR_LOG: Error in file 
util/session_dir.c at line 106
[r1i0n6:09241] [[39007,0],0] ORTE_ERROR_LOG: Error in file 
util/session_dir.c at line 399
[r1i0n6:09241] [[39007,0],0] ORTE_ERROR_LOG: Error in file 
ess_hnp_module.c at line 320
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_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):

   orte_session_dir failed
   --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
[r1i0n6:09241] [[39007,0],0] ORTE_ERROR_LOG: Error in file 
runtime/orte_init.c at line 128
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_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):

   orte_ess_set_name failed
   --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
[r1i0n6:09241] [[39007,0],0] ORTE_ERROR_LOG: Error in file orterun.c at 
line 694


elore is koszonom
udv
e

On 25-Sep-13 11:17 AM, Rőczei Gábor wrote:
> Kedves Etele!
>
>> Leforditottam ujra a programot, mpicxx vagy mpic++ (gcc)
>> es futtatni probalom de sajnos most is hibauzenetet kapok
>>
>> mpirun-t adtam meg 1 job  8G memoria np=12:
>>
>> Warning: Permanently added '[r1i1n3.ice.debrecen.hpc.niif.hu]:58158,[10.148.0.21]:58158' (RSA) to the list of known hosts.
>> Warning: Permanently added '[r1i0n15.ice.debrecen.hpc.niif.hu]:45141,[10.148.0.17]:45141' (RSA) to the list of known hosts.
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'openmpi/1.6.3-gcc-4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'openmpi/1.6.3-gcc-4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'gcc/4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'gcc/4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'openmpi/1.6.3-gcc-4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'gcc/4.7.2'
>> --------------------------------------------------------------------------
>> WARNING: It appears that your OpenFabrics subsystem is configured to only
>> allow registering part of your physical memory.  This can cause MPI jobs to
>> run with erratic performance, hang, and/or crash.
>>
>> This may be caused by your OpenFabrics vendor limiting the amount of
>> physical memory that can be registered.  You should investigate the
>> relevant Linux kernel module parameters that control how much physical
>> memory can be registered, and increase them to allow registering all
>> physical memory on your machine.
>>
>> See this Open MPI FAQ item for more information on these Linux kernel module
>> parameters:
>>
>>      http://www.open-mpi.org/faq/?category=openfabrics#ib-locked-pages
>>
>>    Local host:              r1i0n14
>>    Registerable memory:     32768 MiB
>>    Total memory:            49143 MiB
>>
>> Your MPI job will continue, but may be behave poorly and/or hang.
>> --------------------------------------------------------------------------
>> [r1i0n14:21422] 47 more processes have sent help message help-mpi-btl-openib.txt / reg mem limit low
>> [r1i0n14:21422] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> Sikerült rájönnöm, hogy mi volt a baj. A debreceni CN gépek mlx4_core kernel modul konfigurációjánál meg kell adni ezt a paramétert:
>
> options mlx4_core log_mtts_per_seg=5
>
> Mivel sok párhuzamos job nem futott ma reggel Debrecenben, ezért lehetőségem volt arra, hogy a CN gépek nagy részét újraindítsam annak érdekében hogy ez a beállítás aktiválódjon. Amiket még nem tudtam újraindítani azokat most disabled állapotba tettem addig amíg a rajta lévő jobok le nem futnak.
>
>> Tovabba ha ugyanezt a programot
>>
>> mpirun.sge probalom futtatni (nem lett ujraforditva, maradt a gcc's forditas) akkor szinten
>> ugyan ezt a hibaunzenetet kapom csak sokkal hosszabbat es azonnal le is all a job...
> mpirun.sge-t légyszives ne használj OpenMPI-os job esetén, ez csak SGI MPT-nél lesz jó.
>
> OpenMPI-nál mpirun-t kell használni. Példa:
>
> #!/bin/bash
> #$ -N CONNECTIVITY
> #$ -pe mpi 120
>
> mpirun -np $NSLOTS ./connectivity -v
>
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'openmpi/1.6.3-gcc-4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'gcc/4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'openmpi/1.6.3-gcc-4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'openmpi/1.6.3-gcc-4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'gcc/4.7.2'
>> ModuleCmd_Load.c(199):ERROR:105: Unable to locate a modulefile for 'gcc/4.7.2'
> Ezt meg kellene adni a .bashrc fájlodban:
>
> module use /opt/nce/modulefiles
>
>> Meg 2 utolso "elmeleti" kerdes
>> Peldaul; egy program 4 Gb memoriat ker, ha parallel 2 programot szeretnek futtatni (./ program & ./ program &)
>> akkor 2*4 Gb memoriat kerjek vagy csak 4-et ?
>>> #$ -l h_vmem=8G vagy 4Gb
> h_vmem esetén azt adod meg, hogy 1 slot számára mennyi memóriára van szükség. Tehát: #$ -l h_vmem=4G
>
>> Ugyanez a program MPI-s verzioval tegyuk fel 6 slotton
>> mpirun -np 6 program
>>
>> akkor
>>> #$ -l h_vmem=4G vagy 6*4=24Gb
> Megoldás:
>
>   #$ -l h_vmem=4G
>
> Gábor