[Pw_forum] Reg: error while running tetra_example in PHonon examples in 6.1 version
Peram sreenivasa reddy
peramsreenivas at gmail.com
Tue Apr 25 07:04:59 CEST 2017
Dear Dr. Mitsuaki Kawamura,
Thank you very much for your quick response.
I will try your suggestion and get back to you.
Thanking you.
On Tue, Apr 25, 2017 at 10:12 AM, Mitsuaki Kawamura <
mkawamura at issp.u-tokyo.ac.jp> wrote:
> Dear Dr. P.V.SREENIVASA REDDY
>
> The tetrahedron method in the DFPT calculation works only together with
> the "New XML I/O" module.
> However this I/O module is not activated in the default configuration.
> Therefore, please build QE as
> $ ./configure --enable-xml
> $ make
> I am sorry for my too short information in the previous e-mail.
>
> Activation of the new XML I/O will become the default setting in the next
> version which will be released sooner or later.
>
> Best regards,
> Mitsuaki Kawamura
>
> --
> ------------------------------------------------------
> Dr. Mitsuaki Kawamura
> Software Advancement Team
> Supercomputer Section
> Materials Design and Characterization Laboratory
> The Institute for Solid State Physics, Kashiwa, Japan
> e-mail : mkawamura at issp.u-tokyo.ac.jp
> ------------------------------------------------------
>
> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
> Behalf Of Peram sreenivasa reddy
> Sent: Tuesday, April 25, 2017 1:07 PM
> To: PWSCF Forum <pw_forum at pwscf.org>
> Subject: [Pw_forum] Reg: error while running tetra_example in PHonon
> examples in 6.1 version
>
> Dear PWSCF,
> I am trying new 6.1 version of PWSCF for phonon calculations.
> I am trying to run the examples inside PHonon/tetra_example for aluminium.
> Here i am giving my complete input.
>
> #!/bin/bash
> #PBS -N teat_al
> #PBS -q workq
> #PBS -l select=1:ncpus=1:mpiprocs=16:ompthreads=1
>
> DEVICE="mlx4_0" #connectX3
> PORT="1"
>
> # FCA
> #export OMPI_MCA_coll_fca_enable="1"
> #export OMPI_MCA_coll_fca_np="0"
> #FCAOPTIONS="-x fca_ib_dev_name=${DEVICE}"
>
>
> export OMPI_MCA_btl_openib_if_include="${DEVICE}:${PORT}"
> export OMPI_MCA_mpi_paffinity_alone="1"
> export OMPI_MCA_rmaps_base_schedule_policy="slot"
> export OMPI_MCA_btl_openib_use_message_coalescing="1"
> export OMPI_MCA_rmaps_base_dist_hca="${DEVICE}:${PORT}"
> export OMPI_MCA_btl="self,openib,sm"
>
> # MXM
> export OMPI_MCA_pml="cm"
> export OMPI_MCA_mtl="mxm"
> export OMPI_MCA_mtl_mxm_np="0"
>
> MXMOPTIONS="-x MXM_RDMA_PORTS=${DEVICE}:${PORT}"
> MXMOPTIONS="$MXMOPTIONS -x MXM_TLS=ud,shm,self -x
> MXM_SHM_RNDV_THRESH=32768 -x KMP_BLOCKTIME=0"
>
> cd $PBS_O_WORKDIR
>
> cat $PBS_NODEFILE | sort > hostfile.pbs
> cat $PBS_NODEFILE | sort -u > nodefile.pbs
> sed -e "s/.bmc.pdb.local//g" -i nodefile.pbs
> HOSTFILE=nodefile.pbs
>
> PPN=1
> TMP_DIR=/home/kanchana/sreenivas/pwscf/SnP/PH_test_
> with_6.1/tetra_example/test1/TMP
> mpirun=/opt/apps/openmpi/intel/bin/mpirun
> exe_pw=/home/kanchana/QE_6.1/qe-6.1/bin/pw.x
> exe_ph=/home/kanchana/QE_6.1/qe-6.1/bin/ph.x
> exe_dy=/home/kanchana/QE_6.1/qe-6.1/bin/dynmat.x
> exe_al2f=/home/kanchana/QE_6.1/qe-6.1/bin/alpha2f.x
> number_of_cores=1
>
>
> #
> # SCF at k-mesh good enough for phonons
> #
> cat > al.scf.in << EOF
> &CONTROL
> calculation = 'scf' ,
> prefix='aluminum',
> pseudo_dir = '/opt/apps/pseudo',
> outdir='$TMP_DIR/'
> /
> &SYSTEM
> ibrav = 2,
> celldm(1) = 7.628216862d0,
> nat = 1,
> ntyp = 1,
> ecutwfc = 40.0 ,
> ecutrho = 150 ,
> occupations = 'tetrahedra_opt' ,
> /
> &ELECTRONS
> /
> ATOMIC_SPECIES
> Al 26.98000 Al.pbe-n-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS alat
> Al 0.000000000 0.000000000 0.000000000
> K_POINTS automatic
> 8 8 8 0 0 0
> EOF
> time -p ${mpirun} --bind-to core -n $number_of_cores --map-by
> ppr:$PPN:node \
> -x MLX5_SINGLE_THREADED=1 \
> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS}
> ${FCAOPTIONS} \
> ${exe_pw} -input al.scf.in > al.scf.out 2>&1
>
> #
> # Phonon calculation
> #
> cat > al.ph.in << EOF
> Al phonon
> &INPUTPH
> prefix = 'aluminum',
> outdir = '$TMP_DIR/',
> fildyn = 'al.dyn'
> fildvscf = 'dv',
> fildrho = 'drho',
> ldisp = .true.,
> lshift_q = .true.,
> nq1 = 2,
> nq2 = 2,
> nq3 = 2,
> /
> EOF
>
> time -p ${mpirun} --bind-to core -n $number_of_cores --map-by
> ppr:$PPN:node \
> -x MLX5_SINGLE_THREADED=1 \
> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS}
> ${FCAOPTIONS} \
> ${exe_ph} -input al.ph.in > al.ph.out 2>&1
>
> #
> # Electron-phonon calculation
> #
> cat > al.elph.in << EOF
> Al electron-phonon
> &INPUTPH
> prefix = 'aluminum',
> outdir = '$TMP_DIR/',
> fildyn = 'al.dyn'
> fildvscf = 'dv',
> fildrho = 'drho',
> ldisp = .true.,
> lshift_q = .true.,
> nq1 = 4,
> nq2 = 4,
> nq3 = 4,
> electron_phonon = "lambda_tetra"
> nk1 = 16,
> nk2 = 16,
> nk3 = 16,
> /
> EOF
> time -p ${mpirun} --bind-to core -n $number_of_cores --map-by
> ppr:$PPN:node \
> -x MLX5_SINGLE_THREADED=1 \
> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS}
> ${FCAOPTIONS} \
> ${exe_ph} -input al.elph.in > al.elph.out 2>&1
>
>
> #
> # Eliashberg function
> #
> cat > lambda.in << EOF
> &input
> ne = 500,
> ltetra = 2,
> fildyn = "al.dyn",
> mustar = 0.1,
> prefix = "$TMP_DIR/aluminum",
> /
> EOF
> time -p ${mpirun} --bind-to core -n $number_of_cores --map-by
> ppr:$PPN:node \
> -x MLX5_SINGLE_THREADED=1 \
> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS}
> ${FCAOPTIONS} \
> ${exe_al2f} -input lambda.in > lambda.out 2>&1
> ----------------------------
> it works fine for pw.x and it created al.scf.out file. But when it came to
> run al.ph.in file it is giving error like bellow.
>
>
> Program PHONON v.6.1 (svn rev. 13369) starts on 25Apr2017 at 9:25:11
>
> This program is part of the open-source Quantum ESPRESSO suite
> for quantum simulation of materials; please cite
> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
> URL http://www.quantum-espresso.org",
> in publications or presentations arising from this work. More details
> at
> http://www.quantum-espresso.org/quote
>
> Parallel version (MPI), running on 1 processors
>
> Reading data from directory:
> /home/kanchana/sreenivas/pwscf/SnP/PH_test_with_6.1/
> tetra_example/test1/TMP/aluminum.save
>
> Info: using nr1, nr2, nr3 values from input
>
> Info: using nr1, nr2, nr3 values from input
> MXM: Got signal 11 (Segmentation fault)
> ==== backtrace ====
> 0 /lib64/libc.so.6(+0x32920) [0x2adc149bd920]
> 1 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x8f8b0d]
> 2 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6c1add]
> 3 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6be3ec]
> 4 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6c9aa3]
> 5 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x48617b]
> 6 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f5b9]
> 7 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f53c]
> 8 /lib64/libc.so.6(__libc_start_main+0xfd) [0x2adc149a9cdd]
> 9 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f439]
> ===================
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 25670 on node compute0 exited
> on signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
> it seems to be fail to read the previous output files from TMP folder.
> I am using the same input as given in the example. but still getting
> errors.
> Please suggest any suggestions?
>
> Thanking you.
>
>
>
>
> --
> P.V.SREENIVASA REDDY
> Research Scholar
> Department of Physics
> Indian Institute of Technology
> Hyderabad
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
*P.V.SREENIVASA REDDY*
*Research ScholarDepartment of Physics *
*Indian Institute of Technology*
*Hyderabad*
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