Intel Xeon Phi compilation error

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Forum >> NWChem's corner >> Compiling NWChem

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4:31:28 AM PST - Sun, Jan 25th 2015
My script for compilation is as following :

  1. !/bin/bash
export NWCHEM_TARGET=LINUX64
export NWCHEM_TOP=/work/mmh568/software/nwchem
export ARMCI_NETWORK=OPENIB
export ARMCI_OPENIB_DEVICE=mlx4_0

export IB_HOME="/usr"
export IB_INCLUDE="$IB_HOME/include/infiniband"
export IB_LIB="$IB_HOME/lib64"
export IB_LIB_NAME="-libverbs -libumad -lpthread -lrt"

export ARMCI_DEFAULT_SHMMAX_UBOUND=65536
export USE_MPI=y
export NWCHEM_MODULES=all\ python
export USE_MPIF=y
export USE_MPIF4=y
export MPI_HOME=/usr/local/intel-2015/impi/5.0.1.035/intel64/
export MPI_INCLUDE="$MPI_HOME"/include
export MPI_LIB="$MPI_HOME"/lib
export LIBMPI="-lmpi -lmpigf -lmpigi -lrt -lpthread"
export MKLROOT=/usr/local/intel-2015/composer_xe_2015.0.090/mkl/
export SCALAPACK_LIB=" -mkl -openmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"
export SCALAPACK="$SCALAPACK_LIB"
export LAPACK_LIB="-mkl -openmp -lpthread -lm"
export BLAS_LIB="$LAPACK_LIB"
export BLASOPT="$LAPACK_LIB"
export USE_SCALAPACK=y
export SCALAPACK_SIZE=8
export BLAS_SIZE=8
export LAPACK_SIZE=8
export PYTHONHOME=/usr
export PYTHONVERSION=2.6
export PYTHONLIBTYPE=so
export USE_PYTHON64=y
export USE_CPPRESERVE=y
export USE_NOFSCHECK=y
export USE_OPENMP=1
export USE_OFFLOAD=1
cd $NWCHEM_TOP/src
patch -p0 < Xlmpoles_ifort15.patch
make nwchem_config
make FC=ifort CC=icc AR=xiar |tee /work/mmh568/software/nwchem_buil.log



I ended up with the following error. Please anybody help me

ifort -i8 -align -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qopt-report-phase=offload -qoffload-option,mic,compiler,"-align array64byte" -align array64byte -qoffload-option,mic,compiler," -Wl,-zmuldefs" -watch=mic_cmd -fimf-arch-consistency=true -O2 -g -fp-model source -Wl,--export-dynamic -L/work/mmh568/software/nwchem-6.5/lib/LINUX64 -L/work/mmh568/software/nwchem-6.5/src/tools/install/lib -o /work/mmh568/software/nwchem-6.5/bin/LINUX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil /usr/lib64/python2.6/config/libpython2.6.so -mkl -openmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -mkl -openmp -lpthread -lm -L/usr/local/intel-2015/impi/5.0.1.035/intel64//lib -lmpi -lmpigf -lmpigi -lrt -lpthread -libverbs -loffload -lnwcutil -lpthread -lutil -ldl -lz
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/mpss/3.1.4/sysroots/x86_64-mpsssdk-linux/usr/lib/k1om-mpss-linux/../libz.so.1)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/mpss/3.1.4/sysroots/x86_64-mpsssdk-linux/usr/lib/k1om-mpss-linux/../libz.so.1)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/mpss/3.1.4/sysroots/x86_64-mpsssdk-linux/usr/lib/k1om-mpss-linux/../libz.so.1)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar)
/usr/linux-k1om-4.7/linux-k1om/../bin/x86_64-k1om-linux-ar: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /opt/mpss/3.1.4/sysroots/x86_64-mpsssdk-linux/usr/lib/k1om-mpss-linux/../libz.so.1)
/work/mmh568/software/nwchem-6.5/lib/LINUX64/libnwcutil.a(util_mic_support.o): In function `offload_master_':
/work/mmh568/software/nwchem/src/util/util_mic_support.c:48: multiple definition of `offload_master_'
/work/mmh568/software/nwchem-6.5/lib/LINUX64/libnwcutil.a(util_getenv.o):/work/mmh568/software/nwchem/src/util/util_getenv.F:59: first defined here
make: *** [all] Error 1
Edited On 9:47:52 PM PST - Sun, Jan 25th 2015 by Masrul

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11:51:06 AM PST - Mon, Jan 26th 2015
Masrul
I need more information about your compilation environment in order to help you.
Please post the output of the following commands

ifort -V

env | grep LIBRARY_PATH

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4:07:06 PM PST - Mon, Jan 26th 2015
ifort -V
Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.0.090 Build 20140723
Copyright (C) 1985-2014 Intel Corporation. All rights reserved

env | grep LIBRARY_PATH
LIBRARY_PATH=/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4
MIC_LD_LIBRARY_PATH=/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/mic
LD_LIBRARY_PATH=/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4:/usr/local/mpi-intel/x86_64/openmpi/lib:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/ipp/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/mkl/lib/intel64:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4:/usr/local/intel-2015/impi/5.0.1.035/lib64:/lib64:/usr/lib64:/lib:/usr/lib:/usr/lib64/qt-3.3/lib:/usr/local/torque/lib
MIC_LIBRARY_PATH=/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/compiler/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/mpirt/lib/mic:/usr/local/intel-2015/composer_xe_2015.0.090/tbb/lib/mic

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4:52:36 PM PST - Mon, Jan 26th 2015
What is the output of
ls -l /usr/linux-k1om-4.7/linux-k1om/lib64
ls -l /usr/linux-k1om-4.7/linux-k1om/lib64/libc.so.6



PS: By the way, do you happen to have the variable MIC_ENV_PREFIX set or not?

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6:07:44 PM PST - Mon, Jan 26th 2015
ls -l /usr/linux-k1om-4.7/linux-k1om/lib64
lrwxrwxrwx 1 root root 46 Jun 19 2014 /usr/linux-k1om-4.7/linux-k1om/lib64 -> /opt/mpss/3.1.4/sysroots/k1om-mpss-linux/lib64/

ls -l /usr/linux-k1om-4.7/linux-k1om/lib64/libc.so.6
lrwxrwxrwx 1 root root 15 Jun 19 2014 /usr/linux-k1om-4.7/linux-k1om/lib64/libc.so.6 -> libc-2.14.90.so*

i did not set MIC_ENV_PREFIX variable

thanks for your support
Edited On 8:23:28 AM PST - Tue, Jan 27th 2015 by Masrul

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11:25:38 AM PST - Tue, Jan 27th 2015
I would try the following (not sure if it is going to work, I have to admit ...)

export MIC_LIBRARY_PATH=/usr/linux-k1om-4.7/linux-k1om/lib64:$MIC_LIBRARY_PATH
export MIC_LD_LIBRARY_PATH=/usr/linux-k1om-4.7/linux-k1om/lib64:$MIC_LD_LIBRARY_PATH

Clicked A Few Times
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Posts 8
11:52:28 PM PST - Thu, Jan 29th 2015
Finally successful compiled in intel Xeon phi. Actually i was failing for a weird use, i named untar file 'nwchem' and it failed but when i named it 'nwchem-6.5' then worked. Would you explain the reason


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