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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

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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 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?" 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 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?" 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/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path LOADEDMODULES= LC_MEASUREMENT=fa_IR COMPIZ_CONFIG_PROFILE=ubuntu IM_CONFIG_PHASE=1 DAALROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/daal GDMSESSION=ubuntu MPM_LAUNCHER=/opt/intel/debugger_2017/mpm/mic/bin/start_mpm.sh INTEL_PYTHONHOME=/opt/intel/debugger_2017/python/intel64/ SESSIONTYPE=gnome-session GTK2_MODULES=overlay-scrollbar SHLVL=1 HOME=/home/a XDG_SEAT=seat0 LANGUAGE=en_US GNOME_DESKTOP_SESSION_ID=this-is-deprecated XDG_SESSION_DESKTOP=ubuntu LOGNAME=a CLASSPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/daal.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/daal.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-hW2Ws04x5W XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop QT4_IM_MODULE=xim MODULESHOME=/usr/share/modules LESSOPEN=| /usr/bin/lesspipe %s INFOPATH=/usr/local/texlive/2016/texmf-dist/doc/info:INFOPATH INSTANCE= XDG_RUNTIME_DIR=/run/user/1000 DISPLAY=:0 PATHONPATH=usr/local/lib: XDG_CURRENT_DESKTOP=Unity GTK_IM_MODULE=ibus LESSCLOSE=/usr/bin/lesspipe %s %s LC_TIME=fa_IR I_MPI_ROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi LC_NAME=fa_IR XAUTHORITY=/home/a/.Xauthority _=/usr/bin/env Re: installation error OpenMX ver 3.9 ( No.42 ) Date: 2020/01/30 00:53 Name: Naoya Yamaguchi Dear Asad, Please set the following again. MKLROOT = /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${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 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 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 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 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 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 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) 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 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 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 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 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 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 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 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 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 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 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 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 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 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? 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? 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 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. 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 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 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 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. 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 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 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 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 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 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 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) 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 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. 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 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: $: command not found Re: installation error OpenMX ver 3.9 ( No.81 ) Date: 2020/02/26 01:24 Name: Naoya Yamaguchi Dear Asad, Please try the following: CC = /usr/local/openmpi/bin/mpicc -O3 -fopenmp -ffast-math FC = /opt/openmpi/bin/mpif90 -O3 -fopenmp -ffast-math LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_mpifh Regards, Naoya Yamaguchi 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 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 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 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. 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

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