Top Page > Browsing
installation error OpenMX ver 3.9
Date: 2020/01/06 08:01
Name: Maedeh

Dear OpenMX developers,

I am getting this error while trying to install the new version (3.9) of OpenMX:

In file included from TRAN_DFT.c:25:
openmx_common.h:75: error: redefinition of typedef ‘Type_Orbs_Grid’
tran_prototypes.h:36: note: previous declaration of ‘Type_Orbs_Grid’ was here
make: *** [TRAN_DFT.o] Error 1

it looks like the error previously had mentioned in this link for the version 3.8:
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=1951

but I couldn't figure out how to solve it.

here are my Settings:

MKLROOT = /opt/intel/composerxe-2011.2.137/mkl/
CC = /opt/openmpi/bin/mpicc -O3 -fopenmp -I/opt/intel/composerxe-2011.2.137/mkl/include/fftw -I/opt/intel/mkl/lib/intel64/include
FC = /opt/openmpi/bin/mpif90 -O3 -fopenmp -I/opt/intel/mkl/lib/intel64/include
LIB = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4/lib -lgfortran -L/opt/openmpi/lib/lib -lmpi -libverbs -ldat -lrt -lnsl -lutil -lm -ldl -lm


any help will be appreciated.

Thanks

Best regards,
Maedeh
メンテ
Page: [1] [2]

Re: installation error OpenMX ver 3.9 ( No.37 )
Date: 2020/01/29 22:27
Name: Mitsuaki Kawamura  <mkawamura@issp.u-tokyo.ac.jp>

Dear Asad

Could you check whether your compiler works fine as follows?

$ cat > test.c << EOF
#include "pthread.h"
void *func_thread(void* a) {}
int main(void) {
pthread_t pthread;
pthread_create( &pthread, NULL, &func_thread, NULL);
}
EOF
$ icc test.c -lpthread

Best regards,
Mitsuaki Kawamura
メンテ
Re: installation error OpenMX ver 3.9 ( No.38 )
Date: 2020/01/29 22:32
Name: asad  <bafekry.asad@gmail.com>

what means Naoya "Could you show us the output of env command if you can?"
メンテ
Re: installation error OpenMX ver 3.9 ( No.39 )
Date: 2020/01/29 23:01
Name: Naoya Yamaguchi

Dear Asad,

e.g. $ env

Output for this command shows the environment variables to help us to know your environment.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.40 )
Date: 2020/01/29 23:05
Name: asad  <bafekry.asad@gmail.com>

what means Naoya "Could you show us the output of env command if you can?"
メンテ
Re: installation error OpenMX ver 3.9 ( No.41 )
Date: 2020/01/29 23:09
Name: asad  <bafekry.asad@gmail.com>

$ env

MKLROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
XDG_VTNR=7
LC_PAPER=fa_IR
MODULE_VERSION_STACK=3.2.10
MANPATH=/usr/local/texlive/2016/texmf-dist/doc/man:/usr/local/openmpi/share/man:/opt/intel/man/common:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/man:/opt/intel/documentation_2017/en/debugger//gdb-ia/man/:/opt/intel/documentation_2017/en/debugger//gdb-mic/man/:/opt/intel/documentation_2017/en/debugger//gdb-igfx/man/:/opt/intel/man/common:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/man:/opt/intel/documentation_2017/en/debugger//gdb-ia/man/:/opt/intel/documentation_2017/en/debugger//gdb-mic/man/:/opt/intel/documentation_2017/en/debugger//gdb-igfx/man/:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/man:/usr/local/texlive/2016/bin/x86_64-linux/man:/usr/share/man:/usr/local/man:/usr/local/share/man::
LC_ADDRESS=fa_IR
XDG_SESSION_ID=c2
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/a
LC_MONETARY=fa_IR
CLUTTER_IM_MODULE=xim
SESSION=ubuntu
INTEL_LICENSE_FILE=/opt/intel/compilers_and_libraries_2017.4.196/linux/licenses:/opt/intel/licenses:/home/a/intel/licenses:/opt/intel/compilers_and_libraries_2017.4.196/linux/licenses:/opt/intel/licenses:/home/a/intel/licenses
IPPROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp
GPG_AGENT_INFO=/home/a/.gnupg/S.gpg-agent:0:1
TERM=xterm-256color
VTE_VERSION=4205
XDG_MENU_PREFIX=gnome-
SHELL=/bin/bash
GDBSERVER_MIC=/opt/intel/debugger_2017/gdb/targets/mic/bin/gdbserver
LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/../tbb/lib/intel64_lin/gcc4.4
QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1
WINDOWID=60817418
LC_NUMERIC=fa_IR
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/2349
GNOME_KEYRING_CONTROL=
MIC_LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic
GTK_MODULES=gail:atk-bridge:unity-gtk-module
USER=a
LD_LIBRARY_PATH=/usr/local/openmpi/lib:/usr/local/openmpi/lib:/usr/local/openmpi/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/opt/intel/debugger_2017/iga/lib:/opt/intel/debugger_2017/libipt/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/opt/intel/debugger_2017/iga/lib:/opt/intel/debugger_2017/libipt/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017/linux/mkl:/opt/acml5.3.0/gfortran64_mp/lib:/usr/local/openmpi/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=00: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:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=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:*.jpg=01;35:*.jpeg=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=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
QT_ACCESSIBILITY=1
LC_TELEPHONE=fa_IR
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
MIC_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/include
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SESSION_MANAGER=local/a-System-Product-Name:@/tmp/.ICE-unix/2593,unix/a-System-Product-Name:/tmp/.ICE-unix/2593
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
MPIROOT=/usr/local/openmpi
NLSPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/locale/%l_%t/%N:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/locale/%l_%t/%N:/opt/intel/debugger_2017/gdb/intel64_mic/share/locale/%l_%t/%N:/opt/intel/debugger_2017/gdb/intel64/share/locale/%l_%t/%N:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/locale/%l_%t/%N:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/locale/%l_%t/%N:/opt/intel/debugger_2017/gdb/intel64_mic/share/locale/%l_%t/%N:/opt/intel/debugger_2017/gdb/intel64/share/locale/%l_%t/%N
DESKTOP_SESSION=ubuntu
MODULE_VERSION=3.2.10
PATH=/home/a/ins/quantum-honeycomp-0.15.0/bin:/home/a/ins/wannier_tools-2.3.1/bin:/home/a/ins/wannier_tools-2.3.1/bin:/home/a/ins/omxtool:/usr/local/openmpi/bin:/usr/local/bin/:/usr/local/bin/nanocap:/home/a/ins/vaspkit.0.62/bin:/home/a/ins/siesta-4.1-gfort/siesta:/home/a/ins/phonopy-1.12.2.12/PHONOPY/phonopy:/home/a/OMXTool-1.5.5/omxtool:/home/a/ins/openmx3.8/work/DosMain:/home/a/ins/openmx3.8/work/bandgnu13:/home/a/ins/openmx3.8/work/openmx:/usr/local/texlive/2016/bin/x86_64-linux:usr/local/bin:/home/a/ins/visualize/xcrysden-1.5.60-bin-semishared:/home/a/ins/VESTA-x86_64:/home/a/ins/cif2cell-1.2.10:/usr/local/openmpi/bin:/opt/intel/compilers_and_libraries_2017.4.196/linux/bin/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin:/opt/intel/debugger_2017/gdb/intel64_mic/bin:/opt/intel/compilers_and_libraries_2017.4.196/linux/bin/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin:/opt/intel/debugger_2017/gdb/intel64_mic/bin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin:/opt/intel/compilers_and_libraries_2017/linux/mpi/intel64/bin:/home/a/bin:/home/a/.local/bin:/usr/local/texlive/2016/bin/x86_64-linux:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/intel/inspector_xe_2017:/home/a/ins/visualize/xcrysden-1.5.60-bin-semishared/xcrysden:/home/a/ins/boltztrap-1.2.5/src
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
TBBROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb
LC_IDENTIFICATION=fa_IR
XDG_SESSION_TYPE=x11
PWD=/home/a/ins/openmx3.9/source
JOB=dbus
XMODIFIERS=@im=ibus
QHROOT=/home/a/ins/quantum-honeycomp-0.15.0
GDB_CROSS=/opt/intel/debugger_2017/gdb/intel64_mic/bin/gdb-mic
GNOME_KEYRING_PID=
LANG=en_US.UTF-8
GDM_LANG=en_US
MODULEPATH=/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
LOADEDMODULES=
LC_MEASUREMENT=fa_IR
COMPIZ_CONFIG_PROFILE=ubuntu
IM_CONFIG_PHASE=1
DAALROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/daal
GDMSESSION=ubuntu
MPM_LAUNCHER=/opt/intel/debugger_2017/mpm/mic/bin/start_mpm.sh
INTEL_PYTHONHOME=/opt/intel/debugger_2017/python/intel64/
SESSIONTYPE=gnome-session
GTK2_MODULES=overlay-scrollbar
SHLVL=1
HOME=/home/a
XDG_SEAT=seat0
LANGUAGE=en_US
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
XDG_SESSION_DESKTOP=ubuntu
LOGNAME=a
CLASSPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/daal.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/daal.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-hW2Ws04x5W
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop
QT4_IM_MODULE=xim
MODULESHOME=/usr/share/modules
LESSOPEN=| /usr/bin/lesspipe %s
INFOPATH=/usr/local/texlive/2016/texmf-dist/doc/info:INFOPATH
INSTANCE=
XDG_RUNTIME_DIR=/run/user/1000
DISPLAY=:0
PATHONPATH=usr/local/lib:
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_TIME=fa_IR
I_MPI_ROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi
LC_NAME=fa_IR
XAUTHORITY=/home/a/.Xauthority
_=/usr/bin/env
メンテ
Re: installation error OpenMX ver 3.9 ( No.42 )
Date: 2020/01/30 00:53
Name: Naoya Yamaguchi

Dear Asad,

Please set the following again.

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore

And execute the following command.

$ LD_LIBRARY_PATH="" make

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.43 )
Date: 2020/01/30 02:12
Name: asad  <bafekry.asad@gmail.com>

Dear Naoya.
I performed that work but see same error:

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.44 )
Date: 2020/01/30 02:38
Name: Naoya Yamaguchi

Dear Asad,

Next,

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -ldl

And,
$ make clean && LD_LIBRARY_PATH="" make

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.45 )
Date: 2020/01/30 02:46
Name: asad  <bafekry.asad@gmail.com>

AGAIN:


/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.46 )
Date: 2020/01/30 10:39
Name: T.V.T. Duy  <duy.truong@aisin.co.jp>

Hi Asad,

Could you please add -lpthread after -liomp5 of LIB in the latest attempt suggested by Naoya?

Duy
メンテ
Re: installation error OpenMX ver 3.9 ( No.47 )
Date: 2020/01/30 10:55
Name: Naoya Yamaguchi

Dear Asad,

Next, please try the following:

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -L/lib64 -lpthread -ldl

And,
$ make clean && LD_LIBRARY_PATH="" make

In addition, please execute the following and show the output to get information of the setting for the previous version, that is, OpenMX 3.8.

$ ldd `which openmx`

PS

Just in case, before my suggestion, please try the suggestion in No. 46 by Dr. Duy although you may have tried the similar one suggested in No. 25 by Dr. Kawamura.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.48 )
Date: 2020/01/30 19:48
Name: asad  <bafekry.asad@gmail.com>

Thanks Naoya for helping and comments.
With:

MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -L/lib64 -lpthread -ldl

I see this error again:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1

for other:
$ ldd `which openmx`
linux-vdso.so.1 => (0x00007ffde3784000)
libmkl_intel_lp64.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so (0x00007f4c26379000)
libmkl_intel_thread.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so (0x00007f4c248b4000)
libmkl_core.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_core.so (0x00007f4c22d82000)
libifcore.so.5 => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libifcore.so.5 (0x00007f4c22a21000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4c22804000)
libmpi_mpifh.so.2 => /usr/local/openmpi/lib/libmpi_mpifh.so.2 (0x00007f4c2259b000)
libmpi_usempif08.so.0 => /usr/local/openmpi/lib/libmpi_usempif08.so.0 (0x00007f4c2236c000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f4c22063000)
libmpi.so.1 => /usr/local/openmpi/lib/libmpi.so.1 (0x00007f4c21d56000)
libiomp5.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libiomp5.so (0x00007f4c219b2000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f4c2179c000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f4c213d2000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f4c211ce000)
libimf.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libimf.so (0x00007f4c20ce1000)
libsvml.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libsvml.so (0x00007f4c1fdc8000)
libintlc.so.5 => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libintlc.so.5 (0x00007f4c1fb5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007f4c26db0000)
libopen-rte.so.7 => /usr/local/openmpi/lib/libopen-rte.so.7 (0x00007f4c1f8c7000)
libopen-pal.so.6 => /usr/local/openmpi/lib/libopen-pal.so.6 (0x00007f4c1f5b9000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f4c1f3b1000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f4c1f1ae000)
libirng.so => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libirng.so (0x00007f4c1ee39000)
libifport.so.5 => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libifport.so.5 (0x00007f4c1ec0a000)
libifcoremt.so.5 => /opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/libifcoremt.so.5 (0x00007f4c1e87a000)
メンテ
Re: installation error OpenMX ver 3.9 ( No.49 )
Date: 2020/01/30 20:17
Name: Naoya Yamaguchi

Dear Asad,

How about the following:

CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -lpthread -ldl

And,
$ make clean && LD_LIBRARY_PATH="/lib/x86_64-linux-gnu" make

And, you can omit "MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl".

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.50 )
Date: 2020/01/30 21:50
Name: asad  <bafekry.asad@gmail.com>


Naoya
look

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.51 )
Date: 2020/01/30 22:31
Name: Naoya Yamaguchi  <n-yamaguchi@cphys.s.kanazawa-u.ac.jp>

Dear Asad,

Could you try 'make' for openmx3.8 and report the result?
I recommend the backup of the directory openmx3.8 in advance.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.52 )
Date: 2020/01/30 22:58
Name: asad  <bafekry.asad@gmail.com>

with this:

CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -L/lib64 -lpthread -ldl

And,
$ make clean && LD_LIBRARY_PATH="" make

######################for 3.8
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:121: recipe for target 'openmx' failed
make: *** [openmx] Error 1
######################for 3.9

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.53 )
Date: 2020/01/31 01:20
Name: Naoya Yamaguchi

Dear Asad,

I guess that your system is Ubuntu.
If so, have you ever upgraded your Ubuntu without clean install?

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.54 )
Date: 2020/01/31 02:10
Name: asad  <bafekry.asad@gmail.com>

Naoya, system is upgraded and again see :

/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_create.o): In function `allocate_stack':
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:475: undefined reference to `_dl_stack_flags'
/build/glibc-LK5gWL/glibc-2.23/nptl/allocatestack.c:613: undefined reference to `_dl_stack_flags'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(pthread_getattr_np.o): In function `pthread_getattr_np':
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:97: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/pthread_getattr_np.c:133: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(elision-lock.o): In function `elision_init':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/sysv/linux/x86/elision-conf.c:65: undefined reference to `_dl_x86_cpu_features'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_initialize_minimal_internal':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:305: undefined reference to `__libc_setup_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:322: undefined reference to `_dl_cpuclock_offset'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:457: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:466: undefined reference to `_dl_pagesize'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:486: undefined reference to `_dl_init_static_tls'
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:488: undefined reference to `_dl_wait_lookup_done'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(nptl-init.o): In function `__pthread_get_minstack':
/build/glibc-LK5gWL/glibc-2.23/nptl/nptl-init.c:509: undefined reference to `_dl_pagesize'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-write.o): In function `__write_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-read.o): In function `__read_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o): In function `__close_nocancel':
/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: undefined reference to `__syscall_error'
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libpthread.a(ptw-close.o):/build/glibc-LK5gWL/glibc-2.23/nptl/../sysdeps/unix/syscall-template.S:84: more undefined references to `__syscall_error' follow
makefile:183: recipe for target 'openmx' failed
make: *** [openmx] Error 1


I am confused really, due to the differnet versions is installed in previously
メンテ
Re: installation error OpenMX ver 3.9 ( No.55 )
Date: 2020/01/31 03:18
Name: Naoya Yamaguchi

Dear Asad,

Upgrading the system sometimes breaks the environment, and I guess that in your case, ld command to link libraries may be broken at least in the case of using MKL.
If you upgraded it after the successful installation of OpenMX 3.8, I can believe that the upgrade may cause this problem.
In addition, you might have changed the environment too much and the system is not normal.
Therefore, my final suggestion is doing clean install as shown in Solution C.

So, I leave options to solve it as follows, and please try them in alphabetical order until the installation is successful.

Solution A -> Preparing a clean environment to install OpenMX
1. Prepare a new user
2. Login the system as the new user.
3. Download OpenMX 3.9, and apply a patch of 3.9.1.
4. Install OpenMX 3.9 by editing makefile and execute "make".
Please paste the following into makefile:
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore
5. Check if a binary "openmx" can run normally.

Solution B (if A fails) -> Using packages from apt to install OpenMX
1. Execute $ sudo apt install libscalapack-openmpi-dev -y
2. Download OpenMX 3.9, and apply a patch of 3.9.1.
3. Install OpenMX 3.9 by editing makefile and execute "make".
Please paste the following into makefile:
CC = mpicc -O3 -fopenmp -ffast-math
FC = mpif90 -O3 -fopenmp -ffast-math
LIB= -llapack -lblas -lfftw3 -lmpi -lmpi_mpifh -lgfortran -lscalapack
4. Check if a binary "openmx" can run normally.

Solution C (if B fails) -> Doing clean install Ubuntu to install OpenMX
0. Backup all your data if necessary
1. Do clean install of Ubuntu
2. Do settings for Ubuntu
3. Install the required packages for OpenMX 3.9 by apt as follows:
$ sudo apt install libscalapack-openmpi-dev -y
4. Download OpenMX 3.9, and apply a patch of 3.9.1.
5. Install OpenMX 3.9 by editing makefile and execute "make".
CC = mpicc -O3 -fopenmp -ffast-math
FC = mpif90 -O3 -fopenmp -ffast-math
LIB= -llapack -lblas -lfftw3 -lmpi -lmpi_mpifh -lgfortran -lscalapack
6. Check if a binary "openmx" can run normally.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.56 )
Date: 2020/02/01 02:06
Name: Naoya Yamaguchi

Dear Asad,

If you have not done Solution C-1 yet, that is, clean install, could you try the following commands and paste outputs?

$ locate libpthread.a

$ history | grep libpthread | grep -v grep

If you have already done C-1, please continue it without executing the above commands.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.57 )
Date: 2020/02/01 04:20
Name: asad  <bafekry.asad@gmail.com>

Hi dear Naoya.
Thanks a lot for your comments for solution this problem.
The Solution A, need to instalation of more things and i have not time for performing that.
I performed, Solution B and received again error.
Solution C, is impossible for me, with this conditions.

#########
$ locate libpthread.a
opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a
/usr/lib/x86_64-linux-gnu/libpthread.a


$ history | grep libpthread | grep -v grep
1076 locate libpthread
1384 locate libpthread.a
1618 locate libpthread.a
1619 cd /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a
1650 locate libpthread.a
1658 locate libpthread.a
1704 locate libpthread.a
1783 locate libpthread.a
1798 locate libpthread.a
1854 locate libpthread.a
1875 locate libpthread.a
1877 locate libpthread.a
1913 locate libpthread.a
1937 locate libpthread.a
1979 locate libpthread.a
#########3





メンテ
Re: installation error OpenMX ver 3.9 ( No.58 )
Date: 2020/02/01 13:20
Name: Naoya Yamaguchi

Dear Asad,

Please execute the following command:
$ sudo rm /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libpthread.a

After that, do make again as follows.
CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw
FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lifcore -lpthread -ldl

$ make clean && LD_LIBRARY_PATH="" make

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.59 )
Date: 2020/02/02 19:48
Name: asad  <bafekry.asad@gmail.com>

Hi dear Naoya.
Hope you are fine.
Thanks a lot for your spending time and comments for solution of problem.
With last your comments, the code installed successfully.
Best wishes.
Asad
メンテ
Re: installation error OpenMX ver 3.9 ( No.60 )
Date: 2020/02/02 20:36
Name: Naoya Yamaguchi

Dear Asad,

I am grad to hear that, and if you follow my setting completely and installed by make with LD_LIBRARY_PATH="", in some cases, your binary of OpenMX might require LD_LIBRARY_PATH="" before "openmx": For example,
$ LD_LIBRARY_PATH="" ./openmx input.dat
or
$ LD_LIBRARY_PATH="" mpirun ./openmx input.dat
So, if you get any error on executing OpenMX, please try the above first.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.61 )
Date: 2020/02/02 21:28
Name: asad  <bafekry.asad@gmail.com>

Dear Naoya.
I tested some input files successfully and without need to LD_LIBRARY_PATH="" .
Thanks a lot, i am happy from this.
My goal is that show to all the powerment of OpenMX code in comparison other codes. I published so much papers in the high journal that this case proof this case.
I am happy that OpenMX team, implemented the optic and other options for new version. I hope that soon implement the phonon properties.
Best wishes for Taisuke, Naoya and OpenMX team.
Asad
メンテ
Re: installation error OpenMX ver 3.9 ( No.62 )
Date: 2020/02/05 17:45
Name: asad  <bafekry.asad@gmail.com>

Hi dear Naoya.
Hope you are well.
I tested the optical calculation for Si2_k50x50x50.dat, based on the manual OpenMX 3.9.
But after finishing the calculation, there are not any optical out put similar:

Si2_k50x50x50.cd_re real part of optical conductivity tensor
Si2_k50x50x50.cd_im imaginary part of optical conductivity tensor
Si2_k50x50x50.df_re real part of dielectric function tensor
Si2_k50x50x50.df_im

I changed more options, but ...

Why?
メンテ
Re: installation error OpenMX ver 3.9 ( No.63 )
Date: 2020/02/06 22:29
Name: asad

Hi dear Naoya.
Hope you are well.
I tested the optical calculation for Si2_k50x50x50.dat, based on the manual OpenMX 3.9.
But after finishing the calculation, there are not any optical out put similar:

Si2_k50x50x50.cd_re real part of optical conductivity tensor
Si2_k50x50x50.cd_im imaginary part of optical conductivity tensor
Si2_k50x50x50.df_re real part of dielectric function tensor
Si2_k50x50x50.df_im

I changed more options, but ...

Why?
メンテ
Re: installation error OpenMX ver 3.9 ( No.64 )
Date: 2020/02/07 00:49
Name: T. Ozaki

Hi,

Did you find the following lines in the standard output?

<Optical calculation start>
CDDF.KGrids1: -0.49000 -0.47000 ....

If not, I wonder that you used the older version of OpenMX.

Regards,

TO
メンテ
Re: installation error OpenMX ver 3.9 ( No.65 )
Date: 2020/02/07 16:30
Name: asad

Hi
thanks your reply.
I couldn't find that line for optical calculation.
I used from Si_PBE19 in input file and its clear that only OpenMX 3.9 create out put not older version.
メンテ
Re: installation error OpenMX ver 3.9 ( No.66 )
Date: 2020/02/07 17:07
Name: asad

Thanks your reply Taisuke.
The problem is solved.
Best regards
メンテ
Re: installation error OpenMX ver 3.9 ( No.67 )
Date: 2020/02/07 17:18
Name: T. Ozaki

Hi Asad,

To share your experience with other users, could you explain what your problem was briefly?

Regards.

TO
メンテ
Re: installation error OpenMX ver 3.9 ( No.68 )
Date: 2020/02/11 19:38
Name: asad

Hi Taisuke.
Hope You are fine.
I used from older version of OpenMX that defined in ".bashrc", and defined a new path for new version.
Regards.
TO
メンテ
Re: installation error OpenMX ver 3.9 ( No.69 )
Date: 2020/02/14 01:17
Name: asad

Hi
I want to calculate the thermoelectric with BoltzTrap and i performed based on command in manual:

#! /bin/csh
echo -e "=========================Outputfile List==========================\n"
ls -c *out
echo -e "==================================================================\n"
echo -n 'Please enter the outputfile name ; Outputfile name = ZnSb_BoltzTraP.out '
read outputfile #input

but after performing of MX_TRAP.sh, i received this

$..../MX_TRAP.sh
-e =========================Outputfile List==========================\n
ZnSb_BoltzTraP.out
-e ==================================================================\n
Please enter the outputfile name ; Outputfile name = ZnSb_BoltzTraP.out read: Command not found.
[: No match.
メンテ
Re: installation error OpenMX ver 3.9 ( No.70 )
Date: 2020/02/14 02:48
Name: Naoya Yamaguchi

Dear Asad,

Please try the following:
$ bash ..../MX_TRAP.sh

Perhaps a command "read" is expected to be a built-in command of "bash".
And, if this is solution, "/bin/csh" should not be specified as the shebang, and "/bin/bash" should be required.

In addition, If you have any problems else as you emailed me, please report it here, but I cannot provide solution for optical calculations.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.71 )
Date: 2020/02/14 03:21
Name: asad

Hi Naoya.
Thanks your comment.
With "$ bash ..../MX_TRAP.sh", it solved.

Regards
メンテ
Re: installation error OpenMX ver 3.9 ( No.72 )
Date: 2020/02/22 18:58
Name: asad

Dears.
I want to install OpenMX3.9 in new cluster and this is my setting:

MKLROOT = /usr/local/intel/composer_xe_2015.2.164/mkl
CC = /usr/local/openmpi/bin/mpicc -O3 -fopenmp -I/opt/openmpi/include -I/$(MKLROOT)/include
FC = /usr/local/openmpi/bin/mpif90 -O3 -fopenmp -I/opt/openmpi/include -I/$(MKLROOT)/include
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -liomp5 -L/usr/local/lib64 -lgfortran -L/opt/openmpi/lib -lmpi_f77 -lmpi_f90 -lmpi -L/usr/lib64 -lpthread -L/opt/openmpi/lib -lmpi -libverbs -ldat -lrt -lnsl -lutil -lm -ldl

##############################################################
but this is my error:
.
.
.
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x17d8): undefined reference to `for_stop_core'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x17fd): undefined reference to `for_errmsg'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1864): undefined reference to `for_concat'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x18ad): undefined reference to `for_write_seq_lis'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x18d8): undefined reference to `for_stop_core'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x18fd): undefined reference to `for_errmsg'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x196a): undefined reference to `for_concat'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x19b3): undefined reference to `for_write_seq_lis'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x19de): undefined reference to `for_stop_core'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1a1f): undefined reference to `for_errmsg'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1ae6): undefined reference to `for_check_mult_overflow64'
./elpa-2018.05.001/elpa_solve_evp_complex_2stage_double_impl.F90:(.text+0x1b25): undefined reference to `for_alloc_allocatable'
collect2: error: ld returned 1 exit status
make: *** [openmx] Error 1


メンテ
Re: installation error OpenMX ver 3.9 ( No.73 )
Date: 2020/02/24 01:45
Name: Naoya Yamaguchi

Dear Asad,

Please try the following if you use OpenMPI+GCC+MKL.
CC = /usr/local/openmpi/bin/mpicc -O3 -fopenmp -ffast-math
FC = /usr/local/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_mpifh
If you don't use the combination, please tell us more information of the environment on your new machine.

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.74 )
Date: 2020/02/24 18:17
Name: asad

Dear Naoya.
Thanks your reply.

The error is now:
elpa1.o: In function `elpa1_mp_tridiag_real_':
elpa1.f90:(.text+0x42a): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0x473): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0x4fd): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0x546): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0x5c8): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0x60d): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0x697): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0x6e0): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0x764): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0x7ad): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0x7d7): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0x801): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0x82b): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0x855): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0x87f): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0x92d): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0x96f): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0xa1d): undefined reference to `for_check_mult_overflow64'
elpa1.f90:(.text+0xa5f): undefined reference to `for_alloc_allocatable'
elpa1.f90:(.text+0xa84): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0xa96): undefined reference to `_intel_fast_memset'
elpa1.f90:(.text+0xaa8): undefined reference to `_intel_fast_memset'

####################################
The environment is:

$ env

LC_PAPER=fa_IR
MANPATH=/opt/torque/man:/opt/torque/man:
PDSHROOT=/opt/pdsh
LC_ADDRESS=fa_IR
LC_MONETARY=fa_IR
BIOROLL=/opt/bio
SHELL=/bin/bash
TERM=xterm-256color
SSH_CLIENT=172.16.21.225 55198 22
HMMER_DB=/home/farjami/bio/hmmer/db
CONDOR_IDS=407.407
SGE_ARCH=linux-x64
SGE_CELL=default
LC_NUMERIC=fa_IR
MPICH_PROCESS_GROUP=no
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
SSH_TTY=/dev/pts/2
ROCKSROOT=/opt/rocks/share/devel
ANT_HOME=/opt/rocks
USER=farjami
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lz=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.bz=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.rar=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
LC_TELEPHONE=fa_IR
LD_LIBRARY_PATH=/opt/gridengine/lib/linux-x64:/opt/gridengine/lib/linux-x64:/opt/openmpi/lib:/opt/python/lib
ROCKS_ROOT=/opt/rocks
PATH=/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/maven/bin:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condor/sbin:/opt/gridengine/bin/linux-x64:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin
MAIL=/var/mail/farjami
MAVEN_HOME=/opt/maven
LC_IDENTIFICATION=fa_IR
CONDOR_CONFIG=/opt/condor/etc/condor_config
PWD=/home/farjami/MIX/source
JAVA_HOME=/usr/java/latest
_LMFILES_=/usr/share/Modules/modulefiles/rocks-openmpi
SGE_EXECD_PORT=537
LANG=en_US.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
SGE_QMASTER_PORT=536
LC_MEASUREMENT=fa_IR
LOADEDMODULES=rocks-openmpi
CONDOR_ROOT=/opt/condor
SGE_ROOT=/opt/gridengine
BLASTDB=/home/farjami/bio/ncbi/db
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
HOME=/home/farjami
SHLVL=1
ROLLSROOT=/opt/rocks/share/devel/src/roll
MPIHOME=/opt/openmpi
LOGNAME=farjami
CVS_RSH=ssh
QTLIB=/usr/lib64/qt-3.3/lib
SSH_CONNECTION=172.16.21.225 55198 192.168.23.30 22
MODULESHOME=/usr/share/Modules
LESSOPEN=||/usr/bin/lesspipe.sh %s
BLASTMAT=/opt/bio/ncbi/data
LC_TIME=fa_IR
G_BROKEN_FILENAMES=1
OMPI_MCA_btl=self,sm,tcp
LC_NAME=fa_IR
BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`
}
_=/bin/env

メンテ
Re: installation error OpenMX ver 3.9 ( No.75 )
Date: 2020/02/24 18:45
Name: Naoya Yamaguchi

Dear Asad,

What are output for the following commands?
$ /usr/local/openmpi/bin/mpif90 -v

$ /usr/local/openmpi/bin/mpicc -v

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.76 )
Date: 2020/02/24 18:55
Name: asad

Dear Naoya.

$ /usr/local/openmpi/bin/mpif90 -v
ifort version 15.0.2

$ /usr/local/openmpi/bin/mpicc -v
Using built-in specs.
COLLECT_GCC=/usr/local/bin/gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-pc-linux-gnu/7.1.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ./configure --prefix=/usr/local/ --with-gmp=/usr/local/gmp/ --with-mpfr=/usr/local/mpfr/ --with-mpc=/usr/local/mpc/ --disable-multilib
Thread model: posix
gcc version 7.1.0 (GCC)

メンテ
Re: installation error OpenMX ver 3.9 ( No.77 )
Date: 2020/02/25 01:18
Name: Naoya Yamaguchi

Dear Asad,

Can you reinstall mpicc with icc instead of gcc?

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.78 )
Date: 2020/02/25 17:15
Name: asad

Dera Naoya.
I cant reinstall mpicc with icc instead of gcc, due to that the cluster environment is unavailable for me.
メンテ
Re: installation error OpenMX ver 3.9 ( No.79 )
Date: 2020/02/25 17:20
Name: Naoya Yamaguchi

Dear Asad,

Next, please show output for the following commands:

$ mpif90 -v

$ mpicc -v

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.80 )
Date: 2020/02/25 20:23
Name: asad

Dera Naoya.


$ mpif90 -v
Using built-in specs.
COLLECT_GCC=/usr/local/bin/gfortran
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-pc-linux-gnu/7.1.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ./configure --prefix=/usr/local/ --with-gmp=/usr/local/gmp/ --with-mpfr=/usr/local/mpfr/ --with-mpc=/usr/local/mpc/ --disable-multilib
Thread model: posix
gcc version 7.1.0 (GCC)

$ mpicc -v
bash: $: command not found

メンテ
Re: installation error OpenMX ver 3.9 ( No.81 )
Date: 2020/02/26 01:24
Name: Naoya Yamaguchi

Dear Asad,

Please try the following:

CC = /usr/local/openmpi/bin/mpicc -O3 -fopenmp -ffast-math
FC = /opt/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_mpifh

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.82 )
Date: 2020/02/26 02:02
Name: asad

Thanks Naoya.
.
.
.
Cluster_DFT_Optical_ScaLAPACK.c:542:3: warning: implicit declaration of function ‘Cblacs_barrier’; did you mean ‘PMPI_Ibarrier’? [-Wimplicit-function-declaration]
Cblacs_barrier(ictxt1,"A");
^~~~~~~~~~~~~~
PMPI_Ibarrier
In file included from openmx_common.h:123:0,
from Cluster_DFT_Optical_ScaLAPACK.c:18:
Cluster_DFT_Optical_ScaLAPACK.c:543:12: warning: implicit declaration of function ‘pdgemm_’ [-Wimplicit-function-declaration]
F77_NAME(pdgemm,PDGEMM)("N","N",&n,&n,&n,&alpha,Hs,&ONE,&ONE,descH,Ss,&ONE,&ONE,descS,&beta,Cs,&ONE,&ONE,descC);
^
f77func.h:63:27: note: in definition of macro ‘F77_NAME’
#define F77_NAME(a,A) a ## _
^
In file included from Cluster_DFT_Optical_ScaLAPACK.c:18:0:
Cluster_DFT_Optical_ScaLAPACK.c: At top level:
openmx_common.h:3536:13: warning: inline function ‘Spherical_Bessel’ declared but never defined
inline void Spherical_Bessel( double x, int lmax, double *sb, double *dsb ) ;
^~~~~~~~~~~~~~~~
/opt/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math -I./elpa-2018.05.001 -c ./elpa-2018.05.001/mod_precision.F90
/opt/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math -I./elpa-2018.05.001 -c ./elpa-2018.05.001/elpa_utilities.F90
/opt/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math -I./elpa-2018.05.001 -c ./elpa-2018.05.001/elpa1_compute_real.F90
./elpa-2018.05.001/elpa1_compute_real.F90:57:6:

use mpi
1
Fatal Error: Cannot read module file ‘mpi.mod’ opened at (1), because it was created by a different version of GNU Fortran
compilation terminated.
make: *** [elpa1_compute_real.o] Error 1
メンテ
Re: installation error OpenMX ver 3.9 ( No.83 )
Date: 2020/02/26 02:46
Name: Naoya Yamaguchi

Dear Asad,

What is output for the following:

$ module list

$ module avail

Regards,
Naoya Yamaguchi
メンテ
Re: installation error OpenMX ver 3.9 ( No.84 )
Date: 2020/02/26 02:59
Name: asad

$ module list
bash: $: command not found

$ module avail
bash: $: command not found
メンテ
Re: installation error OpenMX ver 3.9 ( No.85 )
Date: 2020/02/26 03:15
Name: asad

Dear Naoya.
Thanks your comments.
I will to try for the error solution in another time.
Best regards.

メンテ
Re: installation error OpenMX ver 3.9 ( No.86 )
Date: 2020/02/26 13:12
Name: Naoya Yamaguchi

Dear Asad,

>I will to try for the error solution in another time.

OK, so I leave the next ones as below, and please post the results in the next time.

What is output for the followings:

$ locate mpi.mod

$ locate mpicc

$ locate mpif90

And, please try the following:

CC = /usr/local/openmpi/bin/mpicc -O3 -fopenmp -ffast-math
FC = /opt/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math -I/opt/openmpi/lib
LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -L/opt/openmpi/lib -lmpi_mpifh

Regards,
Naoya Yamaguchi
メンテ

Page: [1] [2]

Thread Title (must) Move the thread to the top
Your Name (must)
E-Mail (must)
URL
Password (used in modification of the submitted text)
Comment (must)

   Save Cookie