Dear Kamil,

The first error is simply that more memory was needed than the amount you allocated to the job (as you probably realised). The second error is a segmentation fault.

Can you reproduce the problem using a (much) smaller job?

Cheers,
Chris


On 30/11/14 21:41, Kamil ÖZDEN wrote:

Dear Dr. Cantwell,

Thanks for your help. I'll try this and inform you about the result.

Meanwhile I made another installation with ACML on the same cluster with
the following ACML and MPI configuration

****************
/* ACML /truba/sw/centos6.4/lib/acml/4.4.0/gfortran64/lib/libacml.so *//*
*//* ACML_INCLUDE_PATH
/truba/sw/centos6.4/lib/acml/4.4.0/gfortran64/include *//*
*//* ACML_SEARCH_PATHS
/truba/sw/centos6.4/lib/acml/4.4.0/gfortran64/include *//*
*//* ACML_USE_OPENMP_LIBRARIES OFF *//*
*//* ACML_USE_SHARED_LIBRARIES        ON */
**********************
/*MPIEXEC /usr/mpi/gcc/openmpi-1.6.5/bin/mpiexec *//*
*//* MPIEXEC_MAX_NUMPROCS 2 *//*
*//* MPIEXEC_NUMPROC_FLAG -np *//*
*//* MPIEXEC_POSTFLAGS *//*
*//* MPIEXEC_PREFLAGS *//*
*//* MPI_CXX_COMPILER /usr/mpi/gcc/openmpi-1.6.5/bin/mpicxx *//*
*//* MPI_CXX_COMPILE_FLAGS *//*
*//* MPI_CXX_INCLUDE_PATH /usr/mpi/gcc/openmpi-1.6.5/include *//*
*//* MPI_CXX_LIBRARIES
/usr/mpi/gcc/openmpi-1.6.5/lib64/libmpi_cxx.so;/usr/mpi/gcc/openmpi-1.6.5/lib64/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
*//*
*//* MPI_CXX_LINK_FLAGS -Wl,--export-dynamic *//*
*//* MPI_C_COMPILER /usr/mpi/gcc/openmpi-1.6.5/bin/mpicc *//*
*//* MPI_C_COMPILE_FLAGS *//*
*//* MPI_C_INCLUDE_PATH /usr/mpi/gcc/openmpi-1.6.5/include *//*
*//* MPI_C_LIBRARIES
/usr/mpi/gcc/openmpi-1.6.5/lib64/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
*//*
*//* MPI_C_LINK_FLAGS -Wl,--export-dynamic *//*
*//* MPI_EXTRA_LIBRARY
/usr/mpi/gcc/openmpi-1.6.5/lib64/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
*//*
*//* MPI_LIBRARY /usr/mpi/gcc/openmpi-1.6.5/lib64/libmpi_cxx.so
***********************

*/Nektar seems to be installed successfully. However when I try to
submit a job by using mpirun command with a script to the AMD processors
of cluster (cluster uses SLURM resource manager) I face with such an issue.

When I tried to run with 4 processors.Initial conditons are read and
first .chk directory is started to write as seen below:

/*=======================================================================*/

/**/

/*EquationType: UnsteadyNavierStokes*/

/**/

/*Session Name: Re_1_v2_N6*/

/**/

/*Spatial Dim.: 3*/

/**/

/*Max SEM Exp. Order: 7*/

/**/

/*Expansion Dim.: 3*/

/**/

/*Projection Type: Continuous Galerkin*/

/**/

/*Advection: explicit*/

/**/

/*Diffusion: explicit*/

/**/

/*Time Step: 0.01*/

/**/

/*No. of Steps: 300*/

/**/

/*Checkpoints (steps): 30*/

/**/

/*Integration Type: IMEXOrder1*/

/**/

/*=======================================================================*/

/**/

/*Initial Conditions:*/

/**/

/*- Field u: 0*/

/**/

/*- Field v: 0*/

/**/

/*- Field w: 0.15625*/

/**/

/*- Field p: 0*/

/**/

/*Writing: Re_1_v2_N6_0.chk
*/


/**/

/**/But after that the analysis is ended by giving the error below:

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*slurmd[mercan115]: Job 405433 exceeded memory limit (22245156 >
20480000), being killed*/

/**/

/*slurmd[mercan115]: Exceeded job memory limit*/

/**/

/*slurmd[mercan115]: *** JOB 405433 CANCELLED AT 2014-11-30T23:15:28 ****/

However when I try to run the analysis with 8 processors, the analysis
directly ends by giving the error below:

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*Warning: Conflicting CPU frequencies detected, using: 2300.000000.*/

/**/

/*--------------------------------------------------------------------------*/

/**/

/*mpirun noticed that process rank 2 with PID 24004 on node
mercan146.yonetim exited on signal 11 (Segmentation fault).*/


What may be the reason for this problem?

Regards,
Kamil

/**/
30.11.2014 13:08 tarihinde, Chris Cantwell yazdı:

Dear Kamil,

This still seems to suggest that the version in your home directory is
not compiled with -fPIC.

Try deleting all library files (*.a) and all compiled object code
(*.o) from within the LAPACK source tree and try compiling from fresh
again. Also note that you need to add the -fPIC flag to both the OPTS
and NOOPT variables in your LAPACK make.inc file (which presumably is
what your system administrator altered).

Cheers,
Chris