| 12:28:29 PM PDT - Fri, Nov 4th 2016 |
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Hi all,
I am having issues compiling nwchem-6.6 on HPC. I followed the Documentation regarding setting environment variables for Intel Xeon Phi processors.
These are the relevant environment variables I have declared in my ~/.bashrc profile:
export PATH="$JAVA_HOME/bin:usr/bin/cc:/usr/local/intel-2015.2/impi/5.0.3.048/bin64/mpif90:$PATH"
export NWCHEM_TOP=/work/zacharyw/nwchem-6.6
export NWCHEM_TARGET="LINUX64" ##changed from just LINUX
export NWCHEM_MODULES="all"
export ARMCI_NETWORK="OPENIB"
export USE_64TO32=y
export BLAS_SIZE=4
export BLASOPT="-mkl -openmp -lpthread -lm"
export SCALAPACK="-mkl -openmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"
export OMP_NUM_THREADS=4
export MIC_USE_2MB_BUFFER=16k
export ARMCI_OPENIB_DEVICE=mlx4_0
export LD_LIBRARY_PATH=/usr/local/intel-2015.2/impi/5.0.3.048/bin64/mpif90:$LD_LIBRARY_PATH
export USE_INTERNALBLAS=y
export USE_MPI=y
export LIBMPI="-lmpich -lopa -lmpl -lpthread -lmpichf90 -lfmpich -lmpich"
export USE_MPIF=y
export USE_MPIF4=y
export USE_OPENMP=1
export USE_OFFLOAD=1
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.6
export PYTHONHOME=/usr
This is the corresponding error message I get after I attempt to compile:
Got lock on /work/zacharyw/nwchem-6.6/lib/LINUX64/libpfft.lock
xiar r /work/zacharyw/nwchem-6.6/lib/LINUX64/libpfft.a nwfft3d.o
xiar: executing 'ar'
echo /work/zacharyw/nwchem-6.6/lib/LINUX64/libpfft.a
/work/zacharyw/nwchem-6.6/lib/LINUX64/libpfft.a
make[3]: Leaving directory `/work/zacharyw/nwchem-6.6/src/fft/pfftwrap'
make[2]: Leaving directory `/work/zacharyw/nwchem-6.6/src/fft/pfftwrap'
make[2]: Entering directory `/work/zacharyw/nwchem-6.6/src/fft'
make[2]: Leaving directory `/work/zacharyw/nwchem-6.6/src/fft'
make[1]: Leaving directory `/work/zacharyw/nwchem-6.6/src/fft'
Making libraries in python
make[1]: Entering directory `/work/zacharyw/nwchem-6.6/src/python'
icc -c -I. -I/usr/include/python2.6 -I/usr/include -I/usr/Include -I/usr -I/work/zacharyw/nwchem-6.6/src/include -I/work/zacharyw/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DUSE_OFFLOAD -DINTEL_64ALIGN -DIFCV8 -DIFCLINUX -DPARALLEL_DIAG -qopenmp -qopt-report-phase=offload -xHOST -ftz -qopt-report-phase=vec -qopt-report-file=stderr -qopenmp -qopt-report-phase:openmp -g -o task_python.o task_python.c
icc -c -I. -I/usr/include/python2.6 -I/usr/include -I/usr/Include -I/usr -I/work/zacharyw/nwchem-6.6/src/include -I/work/zacharyw/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DUSE_OFFLOAD -DINTEL_64ALIGN -DIFCV8 -DIFCLINUX -DPARALLEL_DIAG -qopenmp -qopt-report-phase=offload -xHOST -ftz -qopt-report-phase=vec -qopt-report-file=stderr -qopenmp -qopt-report-phase:openmp -g -o nwchem_wrap.o nwchem_wrap.c
icc -c -I. -I/usr/include/python2.6 -I/usr/include -I/usr/Include -I/usr -I/work/zacharyw/nwchem-6.6/src/include -I/work/zacharyw/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DUSE_OFFLOAD -DINTEL_64ALIGN -DIFCV8 -DIFCLINUX -DPARALLEL_DIAG -qopenmp -qopt-report-phase=offload -xHOST -ftz -qopt-report-phase=vec -qopt-report-file=stderr -qopenmp -qopt-report-phase:openmp -g -o nw_inp_from_string.o nw_inp_from_string.c
task_python.c(4): catastrophic error: cannot open source file "Python.h"
#include <Python.h>
^
compilation aborted for task_python.c (code 4)
make[1]: *** [/work/zacharyw/nwchem-6.6/lib/LINUX64/libnwpython.a(task_python.o)] Error 4
make[1]: *** Waiting for unfinished jobs....
nwchem_wrap.c(4): catastrophic error: cannot open source file "Python.h"
#include <Python.h>
^
compilation aborted for nwchem_wrap.c (code 4)
make[1]: *** [/work/zacharyw/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o)] Error 4
make[1]: Leaving directory `/work/zacharyw/nwchem-6.6/src/python'
make: *** [libraries] Error 1
I try using the 'find' UNIX command to find this Python.h file. Unfortunately, I can't seem to find this file, so my attempts at solving this problem are proving unsuccessful. The results of 'which python' is /usr/bin/python. Python 2.6 is being used.
Additionally, I attempt to compile (while in /src folder) the make file using the syntax:
make FC=ifort CC=icc -j 8
I have found similar issues upon google searching but nothing that appears directly relevant to this problem I am facing. I am new to this, so please bear with me. If there are any questions please let me know and I would be happy to answer. Anything that could illuminate this issue would be much appreciated. Thanks!
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