[mvapich-discuss] (no subject)

[Prasad Maddumage]

Hello Hari,

Thank you for your quick response. We have run two test jobs and 
following are the results. Both jobs get allocated with correct number 
of cores but uses half of the available cores.

Test 1:

$ cat submit.sh
#!/bin/sh

#SBATCH -N 2
#SBATCH --ntasks-per-node=4

export MV2_SHOW_CPU_BINDING=1
srun --cpu_bind=verbose ./mbp-gnu-mvapich2 primates.nex


$ cat slurm-732.out
cpu_bind=NULL - hpc-tc-2, task  6  2 [6819]: mask 0x20
cpu_bind=NULL - hpc-tc-1, task  3  3 [1691]: mask 0x80
cpu_bind=NULL - hpc-tc-2, task  5  1 [6818]: mask 0x8
cpu_bind=NULL - hpc-tc-2, task  7  3 [6820]: mask 0x80
cpu_bind=NULL - hpc-tc-2, task  4  0 [6817]: mask 0x2
cpu_bind=NULL - hpc-tc-1, task  0  0 [1688]: mask 0x2
cpu_bind=NULL - hpc-tc-1, task  1  1 [1689]: mask 0x8
cpu_bind=NULL - hpc-tc-1, task  2  2 [1690]: mask 0x20
-------------CPU AFFINITY-------------
RANK:0  CPU_SET:   1
RANK:1  CPU_SET:   3
RANK:2  CPU_SET:   1
RANK:3  CPU_SET:   3
-------------------------------------
                                MrBayes v3.1.2

                       (Bayesian Analysis of Phylogeny)

                              (Parallel version)
                          (8 processors available)


Test 2:

#!/bin/bash
#
#SBATCH --ntasks=8
#SBATCH --nodes=2
#SBATCH --core-spec=8
#SBATCH --ntasks-per-node=4
#SBATCH --ntasks-per-core=1
#SBATCH --ntasks-per-socket=4
#SBATCH --cpus-per-task=1
#SBATCH --extra-node-info=2:4:1
#SBATCH --job-name=mva_test
#SBATCH -p genacc_q
#SBATCH -t 00:30:00
#SBATCH --mail-type=ALL

module purge
module load gnu-mvapich2

echo$SLURM_NODELIST
export MV2_SHOW_CPU_BINDING=1
srun --cpu_bind=verbose,cores  ./micro_gnu_pich2
~




hpc-tc-[1-2]
cpu_bind_cores=UNK  - hpc-tc-1, task  1  1 [1579]: mask 0x4 set
cpu_bind_cores=UNK  - hpc-tc-2, task  6  2 [6797]: mask 0x10 set
cpu_bind_cores=UNK  - hpc-tc-1, task  0  0 [1578]: mask 0x1 set
cpu_bind_cores=UNK  - hpc-tc-1, task  2  2 [1580]: mask 0x10 set
cpu_bind_cores=UNK  - hpc-tc-1, task  3  3 [1581]: mask 0x40 set
cpu_bind_cores=UNK  - hpc-tc-2, task  4  0 [6795]: mask 0x1 set
cpu_bind_cores=UNK  - hpc-tc-2, task  5  1 [6796]: mask 0x4 set
cpu_bind_cores=UNK  - hpc-tc-2, task  7  3 [6798]: mask 0x40 set
-------------CPU AFFINITY-------------
RANK:0  CPU_SET:   0
RANK:1  CPU_SET:   2
RANK:2  CPU_SET:   0
RANK:3  CPU_SET:   2
-------------------------------------

Please note that no other jobs exist on this test cluster.

Best,
Prasad

On 06/08/2015 12:35 PM, Hari Subramoni wrote:
> Hello Prasad,
>
> It could be due to oversubscription of processes i.e multiple 
> processes getting bound to the same CPU core. Can you please run your 
> program after setting MV2_SHOW_CPU_BINDING=1 and see how the process 
> mapping is happening?
>
> Regards,
> Hari.
>
> On Mon, Jun 8, 2015 at 12:12 PM, Prasad Maddumage <MHEMANTHA at fsu.edu 
> <mailto:MHEMANTHA at fsu.edu>> wrote:
>
>     X-MS-Exchange-Transport-CrossTenantHeader
>     Hi,
>
>     I have installed mvapich2 latest version and getting 50% CPU
>     utilization. This is on a test cluster with no other jobs running. We
>     have hwloc 1.10 already installed and I did not make any changes
>     to the
>     hwloc 1.9 came with mvapich2. Could this be a problem? Is it
>     possible to
>     configure mvapich2 with (already available) hwloc 1.10?
>
>     Thank you
>     Prasad Maddumage
>
>     --
>     Prasad Maddumage
>     Application Specialist, Research Computing Center
>     150F, Dirac Science Library, Florida State University
>     Tallahassee Fl 32306-4120
>
>     _______________________________________________
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>
>

-- 
Prasad Maddumage
Application Specialist, Research Computing Center
150F, Dirac Science Library, Florida State University
Tallahassee Fl 32306-4120

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