compiling on centos~~ can't find Python.h

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Clicked A Few Times
Threads 2
Posts 7
12:28:29 PM PDT - Fri, Nov 4th 2016
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!

Gets Around
Threads 1
Posts 139
1:23:26 PM PDT - Fri, Nov 4th 2016
Is the package python-devel installed on your system?

Clicked A Few Times
Threads 2
Posts 7
4:41:15 PM PDT - Fri, Nov 4th 2016
Actually, I found Python.h under: "/usr/local/python/include/python2.7"

How does this change my .bashrc profile? Thanks for your prompt response!

Gets Around
Threads 1
Posts 139
7:42:47 AM PST - Tue, Nov 8th 2016
If you have the header file for python 2.7, I am assuming that version 2.7 is installed on your system as well, probably somewhere in /usr/local based on the location of the header file. Try changing your pythonhome variable to point to that version rather than the one in /usr/bin

Forum Vet
Threads 7
Posts 1336
10:45:44 AM PST - Tue, Nov 8th 2016
Quote:Zww9 Nov 4th 3:41 pm
Actually, I found Python.h under: "/usr/local/python/include/python2.7"

How does this change my .bashrc profile? Thanks for your prompt response!

You value of PYTHONHOME should be changed to /usr/local/python

export PYTHONHOME=/usr/local/python
Edited On 10:46:04 AM PST - Tue, Nov 8th 2016 by Edoapra

Clicked A Few Times
Threads 2
Posts 7
1:29:11 PM PST - Tue, Jan 17th 2017
Hi,
I have made this change in my setup script, as well as a few others. I am attempting compiling under the Intel Xeon Phi processors. The following is my setup script:

!#/bin/bash
export NWCHEM_TARGET=LINUX64
export NWCHEM_TOP=/work/zacharyw/recompile_nwchem6_6/nwchem-6.6
export ARMCI_NETWORK=OPENIB
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export PATH=/usr/local/intel-2015.2/impi/5.0.3.048/bin64/mpif90:$PATH #location of 'which mpif90'
export PYTHONHOME=/usr/local/python #defined in manual online
export PYTHONVERSION=2.7
export USE_PYTHONCONFIG=y
export USE_64TO32=y


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 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


export ARMCI_OPENIB_DEVICE=mlx4_0
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y



export MKLROOT=/usr/local/intel-2017/compilers_and_libraries_2017.0.098/linux/mkl

export USE_OPENMP=1
export USE_F90_ALLOCATABLE=T
export USE_FASTMEM=T
export SCALAPACK="-mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64"
export ELPA="-I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lelpa"
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH
export BLASOPT="-mkl -qopenmp"
export SCALAPACK_SIZE=4
export BLAS_SIZE=4
export OMP_NUM_THREADS=4
export MIC_USE_2MB_BUFFER=16k



export USE_INTERNALBLAS=y

cd $NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES="all python"
make 64_to_32
make FC=ifort CC=icc AR=xiar -j 8 |tee /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/nwchem_buil.log


However, I get the following error message:

DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DUSE_F90_ALLOCATABLE -DDEBUG_PRINT icsd_t2_neword.F
ifort -c -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O3 -unroll -ip -xHost -I. -I../include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DUSE_F90_ALLOCATABLE -DDEBUG_PRINT ccsd_kernels.F

Begin optimization report for: T2_P8

   Report from: OpenMP optimizations [openmp]

OpenMP Construct at ccsd_kernels.F(37,8)
  remark #16200: OpenMP DEFINED LOOP WAS PARALLELIZED
OpenMP Construct at ccsd_kernels.F(14,8)
  remark #16200: OpenMP DEFINED LOOP WAS PARALLELIZED
ifort -c -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O3 -unroll -ip -xHost -I. -I../include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DUSE_F90_ALLOCATABLE -DDEBUG_PRINT ccsd_t2_8.F
ccsd_t2_8.F(489): error #6404: This name does not have a type, and must have an explicit type. [L_A]
     if (e_a) call errquit("MA pops a",l_a,MA_ERR)
^
ccsd_t2_8.F(490): error #6404: This name does not have a type, and must have an explicit type. [L_T]
     if (e_t) call errquit("MA pops t",l_t,MA_ERR)
^
compilation aborted for ccsd_t2_8.F (code 1)
make[3]: *** [/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a(ccsd_t2_8.o)] Error 1
make[3]: *** Waiting for unfinished jobs....
===============================================================
make[3]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce/ccsd'
make[2]: *** [optimized] Error 2
make[2]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce/ccsd'
make[1]: *** [subdirs] Error 1
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce'
make: *** [libraries] Error 1


I do not understand what this means. Additionally, I am confused as to why I have to include the 64_to32 bit in my setup script. My initial assumption is something is wrong with the SCALAPATH or BLASOPT environment variable. Could someone please lend me some assistance? Thanks

Forum Vet
Threads 7
Posts 1336
1:47:15 PM PST - Tue, Jan 17th 2017
Please unset USE_F90_ALLOCATABLE and USE_FASTMEM (since they can be used only with the current development version of NWChem and not with version 6.6) and then recompile

unset USE_F90_ALLOCATABLE
unset USE_FASTMEM
rm $NWCHEM_TOP/lib/$NWCHEM_TARGET/libtce.a
cd $NWCHEM_TOP/src/tce
make FC=ifort
cd ..
make FC=ifort link

Clicked A Few Times
Threads 2
Posts 7
3:32:24 PM PST - Tue, Jan 17th 2017
Hi,
I made the changes you suggested, including manually deleting the libtce.a file. My setup bash script now reads:

!#/bin/bash
export NWCHEM_TARGET=LINUX64
export NWCHEM_TOP=/work/zacharyw/recompile_nwchem6_6/nwchem-6.6
export ARMCI_NETWORK=OPENIB
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export PATH=/usr/local/intel-2015.2/impi/5.0.3.048/bin64/mpif90:$PATH #location of 'which mpif90'
export PYTHONHOME=/usr/local/python #defined in manual online
export PYTHONVERSION=2.7
export USE_PYTHONCONFIG=y
export USE_64TO32=y


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 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


export ARMCI_OPENIB_DEVICE=mlx4_0
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
  1. changed **

    1. !!!!!!
export MKLROOT=/usr/local/intel-2017/compilers_and_libraries_2017.0.098/linux/mkl

export USE_OPENMP=1
  1. export USE_F90_ALLOCATABLE=T
  2. export USE_FASTMEM=T
export SCALAPACK="-mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64"
export ELPA="-I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lelpa"
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH
export BLASOPT="-mkl -qopenmp"
export SCALAPACK_SIZE=4
export BLAS_SIZE=4
export OMP_NUM_THREADS=4
export MIC_USE_2MB_BUFFER=16k



export USE_INTERNALBLAS=y
unset USE_F90_ALLOCATABLE
unset USE_FASTMEM
cd $NWCHEM_TOP/src/tce
make FC=ifort
cd ..
make FC=ifort link

However, this time I am getting an error that reads:

===============================================================
ifort -c -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O3 -unroll -ip -xHost -I. -I../include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG new_sort6.F
ifort -c -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O3 -unroll -ip -xHost -I. -I../include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG tce_sort8.F
ifort -c -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O3 -unroll -ip -xHost -I. -I../include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG tce_sortacc8.F
ifort -c -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O3 -unroll -ip -xHost tce_sort1.f
make[2]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce/sort'
make[2]: Entering directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce/sort'
Got lock on /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.lock
ar r /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a tce_sort_4kg.o tce_sort0.o tce_sortacc0.o new_sort2.o new_sort4.o new_sort6.o tce_sort8.o tce_sortacc8.o tce_sort1.o
echo /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a
/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a
make[2]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce/sort'
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce/sort'
make[1]: Entering directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce'
Got lock on /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.lock
ar r /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a tce_input.o tce_init.o tce_energy.o tce_energy_fragment.o tce_tile.o tce_ao1e.o tce_mo1e.o tce_ao2e.o tce_filename.o createfile.o deletefile.o reconcilefile.o dratoga.o gatodra.o gatoeaf.o get_block.o put_block.o add_block.o tce_tidy.o sf_test.o hbar.o tce_mo2e.o tce_mo1e_offset.o tce_mo2e_offset.o tce_e_offset.o tce_guess_t1.o tce_guess_t2.o tce_zero.o tce_print_x1.o tce_print_x2.o tce_residual_t1.o tce_residual_t2.o tce_residual_t3.o tce_residual_t4.o ma_pack.o sf_print.o ma_print_compact.o ma_scale.o copyfile.o ddotfile.o daxfile.o daxpyfile.o dscalfile.o tce_aod1.o tce_nud1.o tce_mod1.o tce_mod1_offset.o sym_abelian_axis.o tce_mod1_new.o tce_mod1_offset_new.o tce_eom_init.o tce_eom_tidy.o tce_eom_xdiagon.o tce_eom_ydiagon.o tce_t1_offset.o tce_t2_offset.o tce_t3_offset.o tce_t4_offset.o tce_x1_offset.o tce_x2_offset.o tce_x3_offset.o tce_x4_offset.o tce_y1_offset.o tce_y2_offset.o tce_y3_offset.o tce_y4_offset.o tce_mbpt2.o tce_restricted.o tce_hash.o get_hash_block.o put_hash_block.o add_hash_block.o tce_residual_t3a.o tce_t3a_offset.o tce_x3a_offset.o tce_cholesky.o tce_ao2e_cholesky.o tce_ao2e_cholesky_2d.o tce_ao2e_cholesky_4d.o e2_offset_2_offset.o get_block_ind.o get_block_ind_sf.o tce_hash_ind.o tce_mo2e_offset_intorb.o tce_mo2e_offset_size.o tce_mo2e_trans.o atpart_nalength.o tce_mo2e_zones_4a_disk_ga.o tce_mo2e_zones_4a_disk_ga_chop.o tce_mo2e_zones_4a_disk_2s_new.o tce_restart.o tce_restart_triples.o tce_restart_quadruples.o tce_dens_hh_offset.o tce_dens_hp_offset.o tce_dens_pp_offset.o tce_dens_ph_offset.o get_mo_rdm_hh.o get_mo_rdm_hp.o get_mo_rdm_ph.o get_mo_rdm_pp.o ao_rdm_write.o tce_prop_start.o tce_property.o tce_diagnose_t1.o tce_fourindex_driver.o tce_fock_create.o tce_multipole_create.o tce_reference_check.o tce_fourindex_cleanup.o tce_fock_destroy.o tce_multipole_destroy.o tce_create_t1.o tce_create_t2.o tce_create_t3.o tce_create_t4.o tce_create_x1.o tce_create_x2.o tce_create_x3.o tce_create_x4.o tce_create_y1.o tce_create_y2.o tce_create_y3.o tce_create_y4.o tce_clone_x1.o tce_clone_x2.o tce_clone_x3.o tce_clone_x4.o tce_clone_y1.o tce_clone_y2.o tce_clone_y3.o tce_clone_y4.o tce_t1_offset_new.o tce_t2_offset_new.o tce_t3_offset_new.o tce_t4_offset_new.o tce_x1_offset_new.o tce_x2_offset_new.o tce_x3_offset_new.o tce_x4_offset_new.o tce_y1_offset_new.o tce_y2_offset_new.o tce_y3_offset_new.o tce_y4_offset_new.o tce_ccsd_driver.o tce_ccsdt_driver.o tce_ccsdtq_driver.o tce_ccsd_perturbative.o tce_ccsd_lambda_perturbative.o tce_ccsd_lambda_driver.o tce_ccsdt_lambda_driver.o tce_ccsdtq_lambda_driver.o tce_ccsd_response_driver.o tce_ccsdt_response_driver.o tce_ccsdtq_response_driver.o tce_ccsd_symm_polar.o tce_ccsdt_symm_polar.o tce_ccsdtq_symm_polar.o tce_ccsd_lambda_response_driver.o tce_ccsd_asym_polar.o tce_ccsd_hyperpolar.o tce_ao2e_new.o tce_mo2e_new.o tce_tile_new.o tce_init_new.o tce_mo2e_zones_4a_disk_4s_new_patch.o tce_mo2e_zones_4a_disk_4s_new_patch_m2.o tce_mo2e_zones_4a_disk_4s_new_patch_m3.o tce_ao2e_disk.o tce_mo2e_disk.o tce_mo2e_disk_2eorb.o tce_mo2e_incore_2eorb.o tce_mo2e_incore_2eorb_split.o tce_mo2e_hybrid_2eorb_split.o tce_mo2e_offset_intorb_hybrid.o tce_mo2e_2emet3.o tce_mo2e_2emet3_n5.o tce_mo2e_2emet4.o tce_mo2e_2emet4_n5.o get_hash_block_ma.o ccsd_energy_loc.o cc2_energy.o ccsd_lambda.o ccsd_imaginary.o ccsd_lr_alpha.o ccsd_qr_beta.o tce_dgeev.o tce_schmidt.o tensor_read_write.o tce_diis_act.o tce_mo2e_zones_4a_disk_ga_act.o tce_mo2e_zones_4a_disk_ga_chop_act.o tce_t2a_offset.o tce_x2a_offset.o new_ga4ind_N5.o tce_mo2e_zones_4a_disk_ga_N5.o tce_mo2e_zones_4a_disk_ga_chop_N5.o tce_eom_xguess.o tce_eom_yguess.o ma_transpose.o
echo /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a
/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64/libtce.a
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tce'
+ cd ..
+ make FC=ifort link
make nwchem.o stubs.o
make[1]: Entering directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--export-dynamic -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64 -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/lib -o /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/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 -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lelpa -mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -l64to32 -mkl -qopenmp -lnwclapack -lnwcblas -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib/release_mt -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -libverbs -libumad -lpthread -lrt -L/usr/lib64 -lrt -lpthread -lnwcutil -lpthread -ldl -lutil -lm -lpython2.7 -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic
ld: cannot find -ldangchang
make: *** [link] Error 1


Any ideas, I am again at a loss? Thanks for your understanding and patience of these seemingly trivial questions!

Clicked A Few Times
Threads 2
Posts 7
8:04:32 AM PST - Wed, Jan 18th 2017
I tried starting over by completely removing the nwchem-6.6 directory, untarring the nwchem tar file and recompiling just to see if I would get the same error message. Instead I get another error message shown in the following:

ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--export-dynamic -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64 -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/lib -o /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/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 -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -mkl -qopenmp -lnwclapack -lnwcblas -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib/release_mt -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lnwcutil -lpthread -ldl -lutil -lm -lpython2.7 -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic
ld: cannot find -lpython2.7
make: *** [all] Error 1

I notice that this linker file 'L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib' shows up in both error messages. I assume there is an issue here, and I feel like perhaps python is an issue? There is a similar path '/usr/local/intel-2017/impi/2017.0.098/intel64/lib' that exists. My question is: how do I know which path to include in my setup script? It seems like the HPC I am attempting to compile this in puts me in this predicament a lot--- another example is that python2.7 and python3.4 are in my /usr/local path, but only python2.6 exists in my /usr/bin path. How do I know what are the correct versions of mpi and python to reference in my setup script?

Forum Vet
Threads 7
Posts 1336
10:16:51 AM PST - Wed, Jan 18th 2017
Since I am not sure yet how to deal with your Python environment, may I suggest you the following: first, try to build a NWChem binary and test it and then try to create a build with python?

In order to exclude Python from the build, please execute the following commands:

cd $NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES="all"
make FC=ifort link

PS#1 I see mention of OpenMPI in your env. settings and -- at the same time -- your are using Intel MPI, this is likely to cause problems. Please remove anything mention of OpenMPI in your settings

PS#2 You defined BLAS_SIZE=4, while your definition of SCALAPACK uses ILP64, a.k.a 64-bit integers, therefore you should set BLAS_SIZE=8. I would suggest you the following

export BLAS_SIZE=8
cd $NWCHEM_TOP/src/64to32blas
make clean
make FC=ifort
cd ../tools
make clean
make FC=ifort
cd ..
make FC=ifort link

Clicked A Few Times
Threads 2
Posts 7
12:36:18 PM PST - Wed, Jan 18th 2017
I have made the changes you have suggested, and everything runs smoothly (i.e. no discernable error messages). Here is the setup script I used, with your modifications for clarification purposes:

!#/bin/bash
export NWCHEM_TARGET=LINUX64
export NWCHEM_TOP=/work/zacharyw/recompile_nwchem6_6/nwchem-6.6
export ARMCI_NETWORK=OPENIB
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export PATH=/usr/local/intel-2015.2/impi/5.0.3.048/bin64/mpif90:$PATH #location of 'which mpif90'
export PYTHONHOME=/usr/local/python #defined in manual online
export PYTHONVERSION=2.7
export USE_PYTHONCONFIG=y
export USE_64TO32=y


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 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


export ARMCI_OPENIB_DEVICE=mlx4_0
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y

export MKLROOT=/usr/local/intel-2017/compilers_and_libraries_2017.0.098/linux/mkl

export USE_OPENMP=1
export SCALAPACK="-mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64"
export BLASOPT="-mkl -qopenmp"
export SCALAPACK_SIZE=4
export BLAS_SIZE=8
export OMP_NUM_THREADS=4
export MIC_USE_2MB_BUFFER=16k



export USE_INTERNALBLAS=y
unset USE_F90_ALLOCATABLE
unset USE_FASTMEM

cd $NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES="all"
make FC=ifort link
cd $NWCHEM_TOP/src/64to32blas
make clean
make FC=ifort
cd ../tools
make clean
make FC=ifort
cd ..
make FC=ifort link

The last few lines of output looks something like:

Libraries have been installed in:
  /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
  - add LIBDIR to the `LD_LIBRARY_PATH' environment variable

    during execution

  - add LIBDIR to the `LD_RUN_PATH' environment variable

    during linking

  - use the `-Wl,-rpath -Wl,LIBDIR' linker flag

  - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.

/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'

 /bin/sh ./libtool   --mode=install /usr/bin/install -c global/trace/adjust.x global/trace/collisions.x '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'
libtool: install: /usr/bin/install -c global/trace/adjust.x /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin/adjust.x
libtool: install: /usr/bin/install -c global/trace/collisions.x /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin/collisions.x
/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'

/usr/bin/install -c tools/ga-config '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'

/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'

/usr/bin/install -c -m 644 ../ga-5-4/ma/error.h ../ga-5-4/ma/macdecls.h ../ga-5-4/ma/macommon.h ../ga-5-4/ma/maf2c.fh ma/mafdecls.fh ma/matypes.h ../ga-5-4/ma/scope.h ../ga-5-4/ma/string-util.h ../ga-5-4/ma/table.h ../ga-5-4/global/src/gacommon.h ../ga-5-4/global/src/ga.h global/src/global.fh ../ga-5-4/global/src/ga-papi.h ../ga-5-4/global/src/ga-mpi.h ../ga-5-4/global/src/ga-mpi.fh ../ga-5-4/pario/dra/dra.fh ../ga-5-4/pario/dra/dra.h ../ga-5-4/pario/eaf/eaf.fh ../ga-5-4/pario/eaf/eaf.h ../ga-5-4/pario/elio/chemio.h ../ga-5-4/pario/elio/elio.h ../ga-5-4/pario/sf/coms.h ../ga-5-4/pario/sf/sf.fh ../ga-5-4/pario/sf/sf.h gaf2c/typesf2c.h gaf2c/farg.h ../ga-5-4/tcgmsg/tcgmsg.fh ../ga-5-4/tcgmsg/tcgmsg.h ../ga-5-4/tcgmsg/tcgmsg-mpi/msgtypesc.h ../ga-5-4/tcgmsg/tcgmsg-mpi/msgtypesf.h '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'

/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'

/usr/bin/install -c -m 644 global/src/ga-wapi.h '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'
make[4]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
make[3]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
make[2]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
+ cd ..
+ make FC=ifort link
make nwchem.o stubs.o
make[1]: Entering directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64 -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/lib -o /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/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 -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -l64to32 -mkl -qopenmp -lnwclapack -lnwcblas -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib/release_mt -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -libverbs -libumad -lpthread -lrt -L/usr/lib64 -lrt -lm -lpthread

This leads us to assume that, providing my corrections to 'BLAS_SIZE' env variable and omitting references to openMPI, the python env variables I used in earlier setup scripts are the issue. How should I proceed?

Curiously, there is no specific reference to nwchem-6.6 in my /usr/local directory. I was going to see if the executable linked successfully using 'ldd' command; but as the directory is not present this is not possible. There is, however, a directory to nwchem-6.5 (containing an executable that is not completely linked), as well as a 'nwchem' symbolic link to the path '/usr/local/server/x86_64-RedHat6/nwchem' which also contains an executable that is not completely linked. I find this odd; any thoughts?

Thanks


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