<div dir="ltr"><div><div><div>Dear PWSCF,<br><br></div>I am trying new 6.1 version of PWSCF for phonon calculations.<br><br></div>I am trying to run the examples inside PHonon/tetra_example for aluminium.<br><br></div>Here i am giving my complete input.<br><br>#!/bin/bash<br>#PBS -N teat_al <br>#PBS -q workq<br>#PBS -l select=1:ncpus=1:mpiprocs=16:ompthreads=1<br><br>DEVICE="mlx4_0" #connectX3<br>PORT="1"<br><br># FCA<br>#export OMPI_MCA_coll_fca_enable="1"<br>#export OMPI_MCA_coll_fca_np="0"<br>#FCAOPTIONS="-x fca_ib_dev_name=${DEVICE}"<br><br><br>export OMPI_MCA_btl_openib_if_include="${DEVICE}:${PORT}"<br>export OMPI_MCA_mpi_paffinity_alone="1"<br>export OMPI_MCA_rmaps_base_schedule_policy="slot"<br>export OMPI_MCA_btl_openib_use_message_coalescing="1"<br>export OMPI_MCA_rmaps_base_dist_hca="${DEVICE}:${PORT}"<br>export OMPI_MCA_btl="self,openib,sm"<br><br># MXM<br>export OMPI_MCA_pml="cm"<br>export OMPI_MCA_mtl="mxm"<br>export OMPI_MCA_mtl_mxm_np="0"<br><br>MXMOPTIONS="-x MXM_RDMA_PORTS=${DEVICE}:${PORT}"<br>MXMOPTIONS="$MXMOPTIONS -x MXM_TLS=ud,shm,self -x MXM_SHM_RNDV_THRESH=32768 -x KMP_BLOCKTIME=0"<br><br>cd $PBS_O_WORKDIR<br><br>cat $PBS_NODEFILE | sort > hostfile.pbs<br>cat $PBS_NODEFILE | sort -u > nodefile.pbs<br>sed -e "s/.bmc.pdb.local//g" -i nodefile.pbs<br>HOSTFILE=nodefile.pbs<br><br>PPN=1<br>TMP_DIR=/home/kanchana/sreenivas/pwscf/SnP/PH_test_with_6.1/tetra_example/test1/TMP<br>mpirun=/opt/apps/openmpi/intel/bin/mpirun<br>exe_pw=/home/kanchana/QE_6.1/qe-6.1/bin/pw.x<br>exe_ph=/home/kanchana/QE_6.1/qe-6.1/bin/ph.x<br>exe_dy=/home/kanchana/QE_6.1/qe-6.1/bin/dynmat.x<br>exe_al2f=/home/kanchana/QE_6.1/qe-6.1/bin/alpha2f.x<br>number_of_cores=1<br><br><br>#<br># SCF at k-mesh good enough for phonons<br>#<br>cat > <a href="http://al.scf.in">al.scf.in</a> << EOF<br>&CONTROL<br> calculation = 'scf' ,<br> prefix='aluminum',<br> pseudo_dir = '/opt/apps/pseudo',<br> outdir='$TMP_DIR/'<br>/<br>&SYSTEM<br> ibrav = 2,<br> celldm(1) = 7.628216862d0,<br> nat = 1,<br> ntyp = 1,<br> ecutwfc = 40.0 ,<br> ecutrho = 150 ,<br> occupations = 'tetrahedra_opt' ,<br>/<br> &ELECTRONS<br>/<br>ATOMIC_SPECIES<br> Al 26.98000 Al.pbe-n-rrkjus_psl.0.1.UPF<br>ATOMIC_POSITIONS alat <br> Al 0.000000000 0.000000000 0.000000000 <br>K_POINTS automatic <br> 8 8 8 0 0 0<br>EOF<br>time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \<br> -x MLX5_SINGLE_THREADED=1 \<br> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \<br> ${exe_pw} -input <a href="http://al.scf.in">al.scf.in</a> > al.scf.out 2>&1<br><br>#<br># Phonon calculation<br>#<br>cat > <a href="http://al.ph.in">al.ph.in</a> << EOF<br>Al phonon<br>&INPUTPH<br> prefix = 'aluminum',<br> outdir = '$TMP_DIR/',<br> fildyn = 'al.dyn'<br> fildvscf = 'dv',<br> fildrho = 'drho',<br> ldisp = .true.,<br> lshift_q = .true.,<br> nq1 = 2, <br> nq2 = 2,<br> nq3 = 2,<br>/<br>EOF<br><br>time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \<br> -x MLX5_SINGLE_THREADED=1 \<br> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \<br> ${exe_ph} -input <a href="http://al.ph.in">al.ph.in</a> > al.ph.out 2>&1<br><br>#<br># Electron-phonon calculation<br>#<br>cat > <a href="http://al.elph.in">al.elph.in</a> << EOF<br>Al electron-phonon<br>&INPUTPH<br> prefix = 'aluminum',<br> outdir = '$TMP_DIR/',<br> fildyn = 'al.dyn'<br> fildvscf = 'dv',<br> fildrho = 'drho',<br> ldisp = .true.,<br> lshift_q = .true.,<br> nq1 = 4, <br> nq2 = 4,<br> nq3 = 4,<br> electron_phonon = "lambda_tetra"<br> nk1 = 16,<br> nk2 = 16,<br> nk3 = 16,<br>/<br>EOF<br>time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \<br> -x MLX5_SINGLE_THREADED=1 \<br> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \<br> ${exe_ph} -input <a href="http://al.elph.in">al.elph.in</a> > al.elph.out 2>&1<br><br><br>#<br># Eliashberg function<br>#<br>cat > <a href="http://lambda.in">lambda.in</a> << EOF<br>&input<br> ne = 500, <br> ltetra = 2, <br> fildyn = "al.dyn", <br> mustar = 0.1, <br> prefix = "$TMP_DIR/aluminum",<br>/<br>EOF<br>time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \<br> -x MLX5_SINGLE_THREADED=1 \<br> -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \<br> ${exe_al2f} -input <a href="http://lambda.in">lambda.in</a> > lambda.out 2>&1<br><br><div><div><div><div><div>----------------------------<br></div><div>it works fine for pw.x and it created al.scf.out file. But when it came to run <a href="http://al.ph.in">al.ph.in</a> file it is giving error like bellow.<br><br><br> Program PHONON v.6.1 (svn rev. 13369) starts on 25Apr2017 at 9:25:11 <br><br> This program is part of the open-source Quantum ESPRESSO suite<br> for quantum simulation of materials; please cite<br> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br> URL <a href="http://www.quantum-espresso.org">http://www.quantum-espresso.org</a>", <br> in publications or presentations arising from this work. More details at<br> <a href="http://www.quantum-espresso.org/quote">http://www.quantum-espresso.org/quote</a><br><br> Parallel version (MPI), running on 1 processors<br><br> Reading data from directory:<br> /home/kanchana/sreenivas/pwscf/SnP/PH_test_with_6.1/tetra_example/test1/TMP/aluminum.save<br><br> Info: using nr1, nr2, nr3 values from input<br><br> Info: using nr1, nr2, nr3 values from input<br>MXM: Got signal 11 (Segmentation fault)<br>==== backtrace ====<br> 0 /lib64/libc.so.6(+0x32920) [0x2adc149bd920]<br> 1 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x8f8b0d]<br> 2 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6c1add]<br> 3 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6be3ec]<br> 4 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6c9aa3]<br> 5 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x48617b]<br> 6 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f5b9]<br> 7 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f53c]<br> 8 /lib64/libc.so.6(__libc_start_main+0xfd) [0x2adc149a9cdd]<br> 9 /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f439]<br>===================<br>--------------------------------------------------------------------------<br>mpirun noticed that process rank 0 with PID 25670 on node compute0 exited on signal 11 (Segmentation fault).<br>--------------------------------------------------------------------------<br><br></div><div>it seems to be fail to read the previous output files from TMP folder.<br><br></div><div>I am using the same input as given in the example. but still getting errors.<br><br></div><div>Please suggest any suggestions?<br><br><br></div><div>Thanking you.<br></div><div><br></div><div><br clear="all"><div><div><div><div><div><br>-- <br><div class="gmail_signature"><i>P.V.SREENIVASA REDDY</i><br><i>Research Scholar<br>Department of Physics</i><br><div><i>Indian Institute of Technology</i></div><div><i>Hyderabad</i></div></div>
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