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11
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by Anders Blom on September 18, 2023, 21:13 »
More info, but not clue. Now please add the -v option to mpiexec.hydra also, but post the results in an attachment text file, rather, as it will be very long.
12
General Questions and Answers / QuantumATK and Wannier90 Hamiltonian
« Last post by m_spin on September 17, 2023, 23:41 »
Hello,

I currently have a tight-binding Hamiltonian generated by Wannier90 for a 2D tellurium system, and I was wondering if the tight-binding parameters I've generated can be input into QuantumATK (e.g. through atkpython) to be used in conjunction with the Semi-Empirical Calculator.

I'd ultimately like to perform a device-level NEGF simulation in QuantumATK using the tight-binding Hamiltonian I've generated.

Thanks for your assistance!
13
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by rebacoo on September 16, 2023, 12:13 »
Thank you professor Anders, here is the results:
[atk@cluster ~]$ mpiexec.hydra -n 4 -genv I_MPI_HYDRA_DEBUG=1 -genv I_MPI_DEBUG=5 atkpython A5AO2-opt.py
host: cluster

==================================================================================================
mpiexec options:
----------------
  Base path: /home/atk/software/QuantumATK2022/libexec/
  Launcher: ssh
  Debug level: 1
  Enable X: -1

  Global environment:
  -------------------
    LD_LIBRARY_PATH=/home/atk/software/QuantumATK2022/lib
    LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.m4a=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.oga=01;36:*.opus=01;36:*.spx=01;36:*.xspf=01;36:
    SSH_CONNECTION=192.168.0.3 14188 192.168.0.202 22
    MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD
    LANG=en_US.UTF-8
    HISTCONTROL=ignoredups
    HOSTNAME=cluster
    S_COLORS=auto
    which_declare=declare -f
    XDG_SESSION_ID=19
    MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl
    USER=atk
    SELINUX_ROLE_REQUESTED=
    PWD=/home/atk
    SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
    HOME=/home/atk
    SSH_CLIENT=192.168.0.3 14188 22
    SELINUX_LEVEL_REQUESTED=
    XDG_DATA_DIRS=/home/atk/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
    LOADEDMODULES=
    SSH_TTY=/dev/pts/2
    MAIL=/var/spool/mail/atk
    TERM=xterm
    SHELL=/bin/bash
    SELINUX_USE_CURRENT_RANGE=
    SHLVL=1
    MANPATH=:
    GDK_BACKEND=x11
    MODULEPATH=/etc/scl/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles
    LOGNAME=atk
    DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-qciD5xJKGf,guid=1da0234fcdd78505b1ab234365039c04
    XDG_RUNTIME_DIR=/run/user/1000
    MODULEPATH_modshare=/usr/share/Modules/modulefiles:2:/etc/modulefiles:2:/usr/share/modulefiles:2
    PATH=/home/atk/software/QuantumATK2022/bin:/home/atk/software/QuantumATK2022/libexec:/home/atk/software/QuantumATK2022/bin:/home/atk/.local/bin:/home/atk/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
    DEBUGINFOD_URLS=https://debuginfod.centos.org/
    MODULESHOME=/usr/share/Modules
    HISTSIZE=1000
    LESSOPEN=||/usr/bin/lesspipe.sh %s
    BASH_FUNC_which%%=() {  ( alias;
 eval ${which_declare} ) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@
}
    BASH_FUNC_module%%=() {  _module_raw "$@" 2>&1
}
    BASH_FUNC__module_raw%%=() {  unset _mlshdbg;
 if [ "${MODULES_SILENT_SHELL_DEBUG:-0}" = '1' ]; then
 case "$-" in
 *v*x*)
 set +vx;
 _mlshdbg='vx'
 ;;
 *v*)
 set +v;
 _mlshdbg='v'
 ;;
 *x*)
 set +x;
 _mlshdbg='x'
 ;;
 *)
 _mlshdbg=''
 ;;
 esac;
 fi;
 unset _mlre _mlIFS;
 if [ -n "${IFS+x}" ]; then
 _mlIFS=$IFS;
 fi;
 IFS=' ';
 for _mlv in ${MODULES_RUN_QUARANTINE:-};
 do
 if [ "${_mlv}" = "${_mlv##*[!A-Za-z0-9_]}" -a "${_mlv}" = "${_mlv#[0-9]}" ]; then
 if [ -n "`eval 'echo ${'$_mlv'+x}'`" ]; then
 _mlre="${_mlre:-}${_mlv}_modquar='`eval 'echo ${'$_mlv'}'`' ";
 fi;
 _mlrv="MODULES_RUNENV_${_mlv}";
 _mlre="${_mlre:-}${_mlv}='`eval 'echo ${'$_mlrv':-}'`' ";
 fi;
 done;
 if [ -n "${_mlre:-}" ]; then
 eval `eval ${_mlre} /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash '"$@"'`;
 else
 eval `/usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash "$@"`;
 fi;
 _mlstatus=$?;
 if [ -n "${_mlIFS+x}" ]; then
 IFS=$_mlIFS;
 else
 unset IFS;
 fi;
 unset _mlre _mlv _mlrv _mlIFS;
 if [ -n "${_mlshdbg:-}" ]; then
 set -$_mlshdbg;
 fi;
 unset _mlshdbg;
 return $_mlstatus
}
    BASH_FUNC_switchml%%=() {  typeset swfound=1;
 if [ "${MODULES_USE_COMPAT_VERSION:-0}" = '1' ]; then
 typeset swname='main';
 if [ -e /usr/share/Modules/libexec/modulecmd.tcl ]; then
 typeset swfound=0;
 unset MODULES_USE_COMPAT_VERSION;
 fi;
 else
 typeset swname='compatibility';
 if [ -e /usr/share/Modules/libexec/modulecmd-compat ]; then
 typeset swfound=0;
 MODULES_USE_COMPAT_VERSION=1;
 export MODULES_USE_COMPAT_VERSION;
 fi;
 fi;
 if [ $swfound -eq 0 ]; then
 echo "Switching to Modules $swname version";
 source /usr/share/Modules/init/bash;
 else
 echo "Cannot switch to Modules $swname version, command not found";
 return 1;
 fi
}
    BASH_FUNC_scl%%=() {  if [ "$1" = "load" -o "$1" = "unload" ]; then
 eval "module $@";
 else
 /usr/bin/scl "$@";
 fi
}
    BASH_FUNC_ml%%=() {  module ml "$@"
}
    _=/home/atk/software/QuantumATK2022/libexec/mpiexec.hydra

  Hydra internal environment:
  ---------------------------
    MPIR_CVAR_NEMESIS_ENABLE_CKPOINT=1
    GFORTRAN_UNBUFFERED_PRECONNECTED=y
    I_MPI_HYDRA_UUID=be640200-572b-9016-7705-060000cac0a8
    DAPL_NETWORK_PROCESS_NUM=4

  User set environment:
  ---------------------
    I_MPI_HYDRA_DEBUG=1
    I_MPI_DEBUG=5

  Intel(R) MPI Library specific variables:
  ----------------------------------------
    I_MPI_HYDRA_UUID=be640200-572b-9016-7705-060000cac0a8
    I_MPI_HYDRA_DEBUG=1
    I_MPI_DEBUG=5


    Proxy information:
    *********************
      [1] proxy: cluster (48 cores)
      Exec list: atkpython (4 processes);


==================================================================================================

[mpiexec@cluster] Timeout set to -1 (-1 means infinite)
[mpiexec@cluster] Got a control port string of cluster:45541

Proxy launch args: /home/atk/software/QuantumATK2022/libexec/pmi_proxy --control-port cluster:45541 --debug --pmi-connect alltoall --pmi-aggregate -s 0 --rmk user --launcher ssh --demux poll --pgid 0 --enable-stdin 1 --retries 10 --control-code 2105394070 --usize -2 --proxy-id

Arguments being passed to proxy 0:
--version 3.2 --iface-ip-env-name MPIR_CVAR_CH3_INTERFACE_HOSTNAME --hostname cluster --global-core-map 0,48,48 --pmi-id-map 0,0 --global-process-count 4 --auto-cleanup 1 --pmi-kvsname kvs_156862_0 --pmi-process-mapping (vector,(0,1,48)) --topolib ipl --ckpointlib blcr --ckpoint-prefix /tmp --ckpoint-preserve 1 --ckpoint off --ckpoint-num -1 --global-inherited-env 45 'LD_LIBRARY_PATH=/home/atk/software/QuantumATK2022/lib' 'LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.m4a=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.oga=01;36:*.opus=01;36:*.spx=01;36:*.xspf=01;36:' 'SSH_CONNECTION=192.168.0.3 14188 192.168.0.202 22' 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' 'LANG=en_US.UTF-8' 'HISTCONTROL=ignoredups' 'HOSTNAME=cluster' 'S_COLORS=auto' 'which_declare=declare -f' 'XDG_SESSION_ID=19' 'MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl' 'USER=atk' 'SELINUX_ROLE_REQUESTED=' 'PWD=/home/atk' 'SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass' 'HOME=/home/atk' 'SSH_CLIENT=192.168.0.3 14188 22' 'SELINUX_LEVEL_REQUESTED=' 'XDG_DATA_DIRS=/home/atk/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share' 'LOADEDMODULES=' 'SSH_TTY=/dev/pts/2' 'MAIL=/var/spool/mail/atk' 'TERM=xterm' 'SHELL=/bin/bash' 'SELINUX_USE_CURRENT_RANGE=' 'SHLVL=1' 'MANPATH=:' 'GDK_BACKEND=x11' 'MODULEPATH=/etc/scl/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles' 'LOGNAME=atk' 'DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-qciD5xJKGf,guid=1da0234fcdd78505b1ab234365039c04' 'XDG_RUNTIME_DIR=/run/user/1000' 'MODULEPATH_modshare=/usr/share/Modules/modulefiles:2:/etc/modulefiles:2:/usr/share/modulefiles:2' 'PATH=/home/atk/software/QuantumATK2022/bin:/home/atk/software/QuantumATK2022/libexec:/home/atk/software/QuantumATK2022/bin:/home/atk/.local/bin:/home/atk/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin' 'DEBUGINFOD_URLS=https://debuginfod.centos.org/ ' 'MODULESHOME=/usr/share/Modules' 'HISTSIZE=1000' 'LESSOPEN=||/usr/bin/lesspipe.sh %s' 'BASH_FUNC_which%%=() {  ( alias;
 eval ${which_declare} ) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@
}' 'BASH_FUNC_module%%=() {  _module_raw "$@" 2>&1
}' 'BASH_FUNC__module_raw%%=() {  unset _mlshdbg;
 if [ "${MODULES_SILENT_SHELL_DEBUG:-0}" = '1' ]; then
 case "$-" in
 *v*x*)
 set +vx;
 _mlshdbg='vx'
 ;;
 *v*)
 set +v;
 _mlshdbg='v'
 ;;
 *x*)
 set +x;
 _mlshdbg='x'
 ;;
 *)
 _mlshdbg=''
 ;;
 esac;
 fi;
 unset _mlre _mlIFS;
 if [ -n "${IFS+x}" ]; then
 _mlIFS=$IFS;
 fi;
 IFS=' ';
 for _mlv in ${MODULES_RUN_QUARANTINE:-};
 do
 if [ "${_mlv}" = "${_mlv##*[!A-Za-z0-9_]}" -a "${_mlv}" = "${_mlv#[0-9]}" ]; then
 if [ -n "`eval 'echo ${'$_mlv'+x}'`" ]; then
 _mlre="${_mlre:-}${_mlv}_modquar='`eval 'echo ${'$_mlv'}'`' ";
 fi;
 _mlrv="MODULES_RUNENV_${_mlv}";
 _mlre="${_mlre:-}${_mlv}='`eval 'echo ${'$_mlrv':-}'`' ";
 fi;
 done;
 if [ -n "${_mlre:-}" ]; then
 eval `eval ${_mlre} /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash '"$@"'`;
 else
 eval `/usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash "$@"`;
 fi;
 _mlstatus=$?;
 if [ -n "${_mlIFS+x}" ]; then
 IFS=$_mlIFS;
 else
 unset IFS;
 fi;
 unset _mlre _mlv _mlrv _mlIFS;
 if [ -n "${_mlshdbg:-}" ]; then
 set -$_mlshdbg;
 fi;
 unset _mlshdbg;
 return $_mlstatus
}' 'BASH_FUNC_switchml%%=() {  typeset swfound=1;
 if [ "${MODULES_USE_COMPAT_VERSION:-0}" = '1' ]; then
 typeset swname='main';
 if [ -e /usr/share/Modules/libexec/modulecmd.tcl ]; then
 typeset swfound=0;
 unset MODULES_USE_COMPAT_VERSION;
 fi;
 else
 typeset swname='compatibility';
 if [ -e /usr/share/Modules/libexec/modulecmd-compat ]; then
 typeset swfound=0;
 MODULES_USE_COMPAT_VERSION=1;
 export MODULES_USE_COMPAT_VERSION;
 fi;
 fi;
 if [ $swfound -eq 0 ]; then
 echo "Switching to Modules $swname version";
 source /usr/share/Modules/init/bash;
 else
 echo "Cannot switch to Modules $swname version, command not found";
 return 1;
 fi
}' 'BASH_FUNC_scl%%=() {  if [ "$1" = "load" -o "$1" = "unload" ]; then
 eval "module $@";
 else
 /usr/bin/scl "$@";
 fi
}' 'BASH_FUNC_ml%%=() {  module ml "$@"
}' '_=/home/atk/software/QuantumATK2022/libexec/mpiexec.hydra' --global-user-env 2 'I_MPI_HYDRA_DEBUG=1' 'I_MPI_DEBUG=5' --global-system-env 4 'MPIR_CVAR_NEMESIS_ENABLE_CKPOINT=1' 'GFORTRAN_UNBUFFERED_PRECONNECTED=y' 'I_MPI_HYDRA_UUID=be640200-572b-9016-7705-060000cac0a8' 'DAPL_NETWORK_PROCESS_NUM=4' --proxy-core-count 48 --mpi-cmd-env mpiexec.hydra -n 4 -genv I_MPI_HYDRA_DEBUG=1 -genv I_MPI_DEBUG=5 atkpython A5AO2-opt.py  --exec --exec-appnum 0 --exec-proc-count 4 --exec-local-env 0 --exec-wdir /home/atk --exec-args 2 atkpython A5AO2-opt.py

[mpiexec@cluster] Launch arguments: /home/atk/software/QuantumATK2022/libexec/pmi_proxy --control-port cluster:45541 --debug --pmi-connect alltoall --pmi-aggregate -s 0 --rmk user --launcher ssh --demux poll --pgid 0 --enable-stdin 1 --retries 10 --control-code 2105394070 --usize -2 --proxy-id 0
[proxy:0:0@cluster] Start PMI_proxy 0
[proxy:0:0@cluster] STDIN will be redirected to 1 fd(s): 17
[proxy:0:0@cluster] got pmi command (from 16): init
pmi_version=1 pmi_subversion=1
[proxy:0:0@cluster] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0
[proxy:0:0@cluster] got pmi command (from 12): init
pmi_version=1 pmi_subversion=1
[proxy:0:0@cluster] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0
[proxy:0:0@cluster] got pmi command (from 14): init
pmi_version=1 pmi_subversion=1
[proxy:0:0@cluster] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0
[proxy:0:0@cluster] got pmi command (from 21): init
pmi_version=1 pmi_subversion=1
[proxy:0:0@cluster] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0
[proxy:0:0@cluster] got pmi command (from 12): get_maxes

[proxy:0:0@cluster] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=1024
[proxy:0:0@cluster] got pmi command (from 14): get_maxes

[proxy:0:0@cluster] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=1024
[proxy:0:0@cluster] got pmi command (from 16): get_maxes

[proxy:0:0@cluster] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=1024
[proxy:0:0@cluster] got pmi command (from 12): barrier_in

[proxy:0:0@cluster] got pmi command (from 14): barrier_in

[proxy:0:0@cluster] got pmi command (from 21): get_maxes

[proxy:0:0@cluster] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=1024
[proxy:0:0@cluster] got pmi command (from 16): barrier_in

[proxy:0:0@cluster] got pmi command (from 21): barrier_in

[proxy:0:0@cluster] forwarding command (cmd=barrier_in) upstream
[mpiexec@cluster] [pgid: 0] got PMI command: cmd=barrier_in
[mpiexec@cluster] PMI response to fd 8 pid 21: cmd=barrier_out
[proxy:0:0@cluster] PMI response: cmd=barrier_out
[proxy:0:0@cluster] PMI response: cmd=barrier_out
[proxy:0:0@cluster] PMI response: cmd=barrier_out
[proxy:0:0@cluster] PMI response: cmd=barrier_out
[proxy:0:0@cluster] got pmi command (from 12): get_ranks2hosts

[proxy:0:0@cluster] PMI response: put_ranks2hosts 21 1
7 cluster 0,1,2,3,
[proxy:0:0@cluster] got pmi command (from 14): get_ranks2hosts

[proxy:0:0@cluster] PMI response: put_ranks2hosts 21 1
7 cluster 0,1,2,3,
[proxy:0:0@cluster] got pmi command (from 16): get_ranks2hosts

[proxy:0:0@cluster] PMI response: put_ranks2hosts 21 1
7 cluster 0,1,2,3,
[proxy:0:0@cluster] got pmi command (from 21): get_ranks2hosts

[proxy:0:0@cluster] PMI response: put_ranks2hosts 21 1
7 cluster 0,1,2,3,
[proxy:0:0@cluster] got pmi command (from 12): get_appnum

[proxy:0:0@cluster] PMI response: cmd=appnum appnum=0
[proxy:0:0@cluster] got pmi command (from 14): get_appnum

[proxy:0:0@cluster] PMI response: cmd=appnum appnum=0
[proxy:0:0@cluster] got pmi command (from 16): get_appnum

[proxy:0:0@cluster] PMI response: cmd=appnum appnum=0
[proxy:0:0@cluster] got pmi command (from 12): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
[proxy:0:0@cluster] got pmi command (from 14): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
[proxy:0:0@cluster] got pmi command (from 21): get_appnum

[proxy:0:0@cluster] PMI response: cmd=appnum appnum=0
[proxy:0:0@cluster] got pmi command (from 12): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
[proxy:0:0@cluster] got pmi command (from 14): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
[proxy:0:0@cluster] got pmi command (from 16): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
[proxy:0:0@cluster] got pmi command (from 21): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
  • MPI startup(): Multi-threaded optimized library
[proxy:0:0@cluster] got pmi command (from 16): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0
[proxy:0:0@cluster] got pmi command (from 21): get_my_kvsname

[proxy:0:0@cluster] PMI response: cmd=my_kvsname kvsname=kvs_156862_0

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 156869 RUNNING AT cluster
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
   Intel(R) MPI Library troubleshooting guide:
      https://software.intel.com/node/561764
===================================================================================
Please help me, thank you
14
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by Anders Blom on September 15, 2023, 19:27 »
The use of localonly might be specific to Linux vs Windows. I use it all the time on Windows if I launch from the command line to avoid having to set up ssh keys or an MPI service, or give my password to each ssh process. Perhaps there is a smarter way to do it, but there is no indication this keyword is deprecated on Windows at least (https://www.intel.com/content/www/us/en/docs/mpi-library/developer-reference-windows/2021-10/global-hydra-options.html).

But you use Linux, rebacoo, so indeed you can skip it.

Did you try the -v version (mpiexec.hydra -v -np 4 ...)? Also, you can try

mpiexec.hydra -n 4 -genv I_MPI_HYDRA_DEBUG=1 -genv I_MPI_DEBUG=5 atkpython script.py

to generate a LOT of debug info that might help
15
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by rebacoo on September 15, 2023, 13:33 »
A5AO2-opt.py is a test file, and when i use atkpython A5AO2-opt.py, it works well
16
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by filipr on September 15, 2023, 11:15 »
Can you share with us your input script A5AO2-opt.py?
17
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by rebacoo on September 15, 2023, 10:59 »
Thank you professor filipr, the mpiexec.hydra is from the software of QuantumATK2022, when i run:    mpiexec.hydra -np 8 echo "Hello"      it work well,  when i run atkpython **.py > ***.log    it work well
but when i run: mpiexec.hydra -np 4 atkpython A5AO2-opt.py      it does't work   
***********************************************************************
[atk@cluster ~]$ mpiexec.hydra -np 4 atkpython A5AO2-opt.py

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 108659 RUNNING AT cluster
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
   Intel(R) MPI Library troubleshooting guide:
      https://software.intel.com/node/561764
===================================================================================
[atk@cluster ~]$ mpiexec.hydra -np 8 echo "Hello"
Hello
Hello
Hello
Hello
Hello
Hello
Hello
Hello
************************************
18
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by filipr on September 15, 2023, 08:32 »
Remove the '-localonly' option from the command, it was only available for older versions of Intel MPI.
19
General Questions and Answers / Re: error in mpiexec.hydra
« Last post by rebacoo on September 15, 2023, 02:07 »
Thank you professor Anders, the QuantumATK2022 is installed in single node server, and the path of mpiexec.hydra and atkpython is correct.
 ([atk@cluster ~]$ which atkpython
~/software/QuantumATK2022/bin/atkpython             
 [atk@cluster ~]$ which mpiexec.hydra
~/software/QuantumATK2022/libexec/mpiexec.hydra)

According to your suggestion, when i run: mpiexec.hydra -np 4 -localonly echo "hello", the  message is as follows:
*********************************
[atk@cluster ~]$ mpiexec.hydra -np 4 -localonly echo "hello"
[mpiexec@cluster] match_arg (../../utils/args/args.c:254): unrecognized argument localonly
[mpiexec@cluster] HYDU_parse_array (../../utils/args/args.c:269): argument matching returned error
[mpiexec@cluster] parse_args (../../ui/mpich/utils.c:4770): error parsing input array
[mpiexec@cluster] HYD_uii_mpx_get_parameters (../../ui/mpich/utils.c:5106): unable to parse user arguments

Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local opts] : ...

Global options (passed to all executables):

  Global environment options:
    -genv {name} {value}             environment variable name and value
    -genvlist {env1,env2,...}        environment variable list to pass
    -genvnone                        do not pass any environment variables
    -genvall                         pass all environment variables not managed
                                          by the launcher (default)

  Other global options:
    -f {name} | -hostfile {name}     file containing the host names
    -hosts {host list}               comma separated host list
    -configfile {name}               config file containing MPMD launch options
    -machine {name} | -machinefile {name}
                                     file mapping procs to machines
    -pmi-connect {nocache|lazy-cache|cache}
                                     set the PMI connections mode to use
    -pmi-aggregate                   aggregate PMI messages
    -pmi-noaggregate                 do not  aggregate PMI messages
    -trace {<libraryname>}           trace the application using <libraryname>
                                     profiling library; default is libVT.so
    -trace-imbalance {<libraryname>} trace the application using <libraryname>
                                     imbalance profiling library; default is libVTim.so
    -check-mpi {<libraryname>}       check the application using <libraryname>
                                     checking library; default is libVTmc.so
    -ilp64                           Preload ilp64 wrapper library for support default size of
                                     integer 8 bytes
    -mps                             start statistics gathering for MPI Performance Snapshot (MPS)
    -aps                             start statistics gathering for Application Performance Snapshot (APS)
    -trace-pt2pt                     collect information about
                                     Point to Point operations
    -trace-collectives               collect information about
                                     Collective operations
    -tune [<confname>]               apply the tuned data produced by
                                     the MPI Tuner utility
    -use-app-topology <statfile>     perform optimized rank placement based statistics
                                     and cluster topology
    -noconf                          do not use any mpiexec's configuration files
    -branch-count {leaves_num}       set the number of children in tree
    -gwdir {dirname}                 working directory to use
    -gpath {dirname}                 path to executable to use
    -gumask {umask}                  mask to perform umask
    -tmpdir {tmpdir}                 temporary directory for cleanup input file
    -cleanup                         create input file for clean up
    -gtool {options}                 apply a tool over the mpi application
    -gtoolfile {file}                apply a tool over the mpi application. Parameters specified in the file


Local options (passed to individual executables):

  Local environment options:
    -env {name} {value}              environment variable name and value
    -envlist {env1,env2,...}         environment variable list to pass
    -envnone                         do not pass any environment variables
    -envall                          pass all environment variables (default)

  Other local options:
    -host {hostname}                 host on which processes are to be run
    -hostos {OS name}                operating system on particular host
    -wdir {dirname}                  working directory to use
    -path {dirname}                  path to executable to use
    -umask {umask}                   mask to perform umask
    -n/-np {value}                   number of processes
    {exec_name} {args}               executable name and arguments


Hydra specific options (treated as global):

  Bootstrap options:
    -bootstrap                       bootstrap server to use
     (ssh rsh pdsh fork slurm srun ll llspawn.stdio lsf blaunch sge qrsh persist service pbsdsh)
    -bootstrap-exec                  executable to use to bootstrap processes
    -bootstrap-exec-args             additional options to pass to bootstrap server
    -prefork                         use pre-fork processes startup method
    -enable-x/-disable-x             enable or disable X forwarding

  Resource management kernel options:
    -rmk                             resource management kernel to use (user slurm srun ll llspawn.stdio lsf blaunch sge qrsh pbs cobalt)

  Processor topology options:
    -binding                         process-to-core binding mode
  Extended fabric control options:
    -rdma                            select RDMA-capable network fabric (dapl). Fallback list is ofa,tcp,tmi,ofi
    -RDMA                            select RDMA-capable network fabric (dapl). Fallback is ofa
    -dapl                            select DAPL-capable network fabric. Fallback list is tcp,tmi,ofa,ofi
    -DAPL                            select DAPL-capable network fabric. No fallback fabric is used
    -ib                              select OFA-capable network fabric. Fallback list is dapl,tcp,tmi,ofi
    -IB                              select OFA-capable network fabric. No fallback fabric is used
    -tmi                             select TMI-capable network fabric. Fallback list is dapl,tcp,ofa,ofi
    -TMI                             select TMI-capable network fabric. No fallback fabric is used
    -mx                              select Myrinet MX* network fabric. Fallback list is dapl,tcp,ofa,ofi
    -MX                              select Myrinet MX* network fabric. No fallback fabric is used
    -psm                             select PSM-capable network fabric. Fallback list is dapl,tcp,ofa,ofi
    -PSM                             select PSM-capable network fabric. No fallback fabric is used
    -psm2                            select Intel* Omni-Path Fabric. Fallback list is dapl,tcp,ofa,ofi
    -PSM2                            select Intel* Omni-Path Fabric. No fallback fabric is used
    -ofi                             select OFI-capable network fabric. Fallback list is tmi,dapl,tcp,ofa
    -OFI                             select OFI-capable network fabric. No fallback fabric is used

  Checkpoint/Restart options:
    -ckpoint {on|off}                enable/disable checkpoints for this run
    -ckpoint-interval                checkpoint interval
    -ckpoint-prefix                  destination for checkpoint files (stable storage, typically a cluster-wide file system)
    -ckpoint-tmp-prefix              temporary/fast/local storage to speed up checkpoints
    -ckpoint-preserve                number of checkpoints to keep (default: 1, i.e. keep only last checkpoint)
    -ckpointlib                      checkpointing library (blcr)
    -ckpoint-logfile                 checkpoint activity/status log file (appended)
    -restart                         restart previously checkpointed application
    -ckpoint-num                     checkpoint number to restart

  Demux engine options:
    -demux                           demux engine (poll select)

  Debugger support options:
    -tv                              run processes under TotalView
    -tva {pid}                       attach existing mpiexec process to TotalView
    -gdb                             run processes under GDB
    -gdba {pid}                      attach existing mpiexec process to GDB
    -gdb-ia                          run processes under Intel IA specific GDB

  Other Hydra options:
    -v | -verbose                    verbose mode
    -V | -version                    show the version
    -info                            build information
    -print-rank-map                  print rank mapping
    -print-all-exitcodes             print exit codes of all processes
    -iface                           network interface to use
    -help                            show this message
    -perhost <n>                     place consecutive <n> processes on each host
    -ppn <n>                         stand for "process per node"; an alias to -perhost <n>
    -grr <n>                         stand for "group round robin"; an alias to -perhost <n>
    -rr                              involve "round robin" startup scheme
    -s <spec>                        redirect stdin to all or 1,2 or 2-4,6 MPI processes (0 by default)
    -ordered-output                  avoid data output intermingling
    -profile                         turn on internal profiling
    -l | -prepend-rank               prepend rank to output
    -prepend-pattern                 prepend pattern to output
    -outfile-pattern                 direct stdout to file
    -errfile-pattern                 direct stderr to file
    -localhost                       local hostname for the launching node
    -nolocal                         avoid running the application processes on the node where mpiexec.hydra started

Intel(R) MPI Library for Linux* OS, Version 2018 Update 1 Build 20171011 (id: 17941)
Copyright (C) 2003-2017, Intel Corporation. All rights reserved.
****************************
when i run: mpiexec.hydra -np 4 echo "hello"
it seems work:
[atk@cluster ~]$ mpiexec.hydra -np 4 echo "hello"
hello
hello
hello
hello

How to deal with this problem?  Thank you
20
General Questions and Answers / Re: How to bring up a suitable ESDP or MEP plot with color variation in Quantum ATK?
« Last post by Anders Blom on September 14, 2023, 21:09 »
Well, actually an isosurface by definition only has 1 color (or 2, which is why I asked about the phase). The isosurface consists of all the points in space where the quantity you are plotting are equal to a certain value. The only way it can have "many" colors is if we then color it by a different quantity. The reason we sometimes see 2 colors is that we can pick the points by absolute value and color by sign, or phase.

If you want to see the potential variation in a plane, use cut planes instead.
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