<div dir="ltr"><div><div><div>Dear Dr. Mitsuaki Kawamura,<br><br></div>Thank you very much for your quick response.<br><br></div>I will try your suggestion and get back to you.<br><br></div>Thanking you.<br><div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 25, 2017 at 10:12 AM, Mitsuaki Kawamura <span dir="ltr"><<a href="mailto:mkawamura@issp.u-tokyo.ac.jp" target="_blank">mkawamura@issp.u-tokyo.ac.jp</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Dr. P.V.SREENIVASA REDDY<br>
<br>
The tetrahedron method in the DFPT calculation works only together with the "New XML I/O" module.<br>
However this I/O module is not activated in the default configuration. Therefore, please build QE as<br>
$ ./configure --enable-xml<br>
$ make<br>
I am sorry for my too short information in the previous e-mail.<br>
<br>
Activation of the new XML I/O will become the default setting in the next version which will be released sooner or later.<br>
<br>
Best regards,<br>
Mitsuaki Kawamura<br>
<br>
--<br>
------------------------------<wbr>------------------------<br>
Dr. Mitsuaki Kawamura<br>
Software Advancement Team<br>
Supercomputer Section<br>
Materials Design and Characterization Laboratory<br>
The Institute for Solid State Physics, Kashiwa, Japan<br>
e-mail : <a href="mailto:mkawamura@issp.u-tokyo.ac.jp">mkawamura@issp.u-tokyo.ac.jp</a><br>
------------------------------<wbr>------------------------<br>
<br>
From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> [mailto:<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@<wbr>pwscf.org</a>] On Behalf Of Peram sreenivasa reddy<br>
Sent: Tuesday, April 25, 2017 1:07 PM<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Subject: [Pw_forum] Reg: error while running tetra_example in PHonon examples in 6.1 version<br>
<div><div class="h5"><br>
Dear PWSCF,<br>
I am trying new 6.1 version of PWSCF for phonon calculations.<br>
I am trying to run the examples inside PHonon/tetra_example for aluminium.<br>
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:<wbr>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=${DEVICE}"<br>
<br>
<br>
export OMPI_MCA_btl_openib_if_<wbr>include="${DEVICE}:${PORT}"<br>
export OMPI_MCA_mpi_paffinity_alone="<wbr>1"<br>
export OMPI_MCA_rmaps_base_schedule_<wbr>policy="slot"<br>
export OMPI_MCA_btl_openib_use_<wbr>message_coalescing="1"<br>
export OMPI_MCA_rmaps_base_dist_hca="<wbr>${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}:${<wbr>PORT}"<br>
MXMOPTIONS="$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 $PBS_NODEFILE | sort -u > nodefile.pbs<br>
sed -e "s/.bmc.pdb.local//g" -i nodefile.pbs<br>
HOSTFILE=nodefile.pbs<br>
<br>
PPN=1<br>
TMP_DIR=/home/kanchana/<wbr>sreenivas/pwscf/SnP/PH_test_<wbr>with_6.1/tetra_example/test1/<wbr>TMP<br>
mpirun=/opt/apps/openmpi/<wbr>intel/bin/mpirun<br>
exe_pw=/home/kanchana/QE_6.1/<wbr>qe-6.1/bin/pw.x<br>
exe_ph=/home/kanchana/QE_6.1/<wbr>qe-6.1/bin/ph.x<br>
exe_dy=/home/kanchana/QE_6.1/<wbr>qe-6.1/bin/dynmat.x<br>
exe_al2f=/home/kanchana/QE_6.<wbr>1/qe-6.1/bin/alpha2f.x<br>
number_of_cores=1<br>
<br>
<br>
#<br>
# SCF at k-mesh good enough for phonons<br>
#<br>
cat > <a href="http://al.scf.in" rel="noreferrer" target="_blank">al.scf.in</a> << EOF<br>
&CONTROL<br>
calculation = 'scf' ,<br>
prefix='aluminum',<br>
pseudo_dir = '/opt/apps/pseudo',<br>
outdir='$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>
${exe_pw} -input <a href="http://al.scf.in" rel="noreferrer" target="_blank">al.scf.in</a> > al.scf.out 2>&1<br>
<br>
#<br>
# Phonon calculation<br>
#<br>
cat > <a href="http://al.ph.in" rel="noreferrer" target="_blank">al.ph.in</a> << EOF<br>
Al phonon<br>
&INPUTPH<br>
prefix = 'aluminum',<br>
outdir = '$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>
${exe_ph} -input <a href="http://al.ph.in" rel="noreferrer" target="_blank">al.ph.in</a> > al.ph.out 2>&1<br>
<br>
#<br>
# Electron-phonon calculation<br>
#<br>
cat > <a href="http://al.elph.in" rel="noreferrer" target="_blank">al.elph.in</a> << EOF<br>
Al electron-phonon<br>
&INPUTPH<br>
prefix = 'aluminum',<br>
outdir = '$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>
${exe_ph} -input <a href="http://al.elph.in" rel="noreferrer" target="_blank">al.elph.in</a> > al.elph.out 2>&1<br>
<br>
<br>
#<br>
# Eliashberg function<br>
#<br>
cat > <a href="http://lambda.in" rel="noreferrer" target="_blank">lambda.in</a> << EOF<br>
&input<br>
ne = 500,<br>
ltetra = 2,<br>
fildyn = "al.dyn",<br>
mustar = 0.1,<br>
prefix = "$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" rel="noreferrer" target="_blank">lambda.in</a> > lambda.out 2>&1<br>
----------------------------<br>
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" rel="noreferrer" target="_blank">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" rel="noreferrer" target="_blank">http://www.quantum-espresso.<wbr>org</a>",<br>
in publications or presentations arising from this work. More details at<br>
<a href="http://www.quantum-espresso.org/quote" rel="noreferrer" target="_blank">http://www.quantum-espresso.<wbr>org/quote</a><br>
<br>
Parallel version (MPI), running on 1 processors<br>
<br>
Reading data from directory:<br>
/home/kanchana/sreenivas/<wbr>pwscf/SnP/PH_test_with_6.1/<wbr>tetra_example/test1/TMP/<wbr>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/<wbr>bin/ph.x() [0x8f8b0d]<br>
2 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x6c1add]<br>
3 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x6be3ec]<br>
4 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x6c9aa3]<br>
5 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x48617b]<br>
6 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x40f5b9]<br>
7 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x40f53c]<br>
8 /lib64/libc.so.6(__libc_start_<wbr>main+0xfd) [0x2adc149a9cdd]<br>
9 /home/kanchana/QE_6.1/qe-6.1/<wbr>bin/ph.x() [0x40f439]<br>
===================<br>
------------------------------<wbr>------------------------------<wbr>--------------<br>
mpirun noticed that process rank 0 with PID 25670 on node compute0 exited on signal 11 (Segmentation fault).<br>
------------------------------<wbr>------------------------------<wbr>--------------<br>
it seems to be fail to read the previous output files from TMP folder.<br>
I am using the same input as given in the example. but still getting errors.<br>
Please suggest any suggestions?<br>
<br>
Thanking you.<br>
<br>
<br>
<br>
<br>
--<br>
P.V.SREENIVASA REDDY<br>
Research Scholar<br>
Department of Physics<br>
Indian Institute of Technology<br>
Hyderabad<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="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>
</div>