ld: cannot find -lpython2.7

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Forum >> NWChem's corner >> Compiling NWChem

Clicked A Few Times
Threads 1
Posts 8
10:45:42 AM PST - Tue, Feb 2nd 2016
Hi all,

nwchem-6.6

OS Scientific Linux release 6.2 (Carbon)

Relevant python bits in build script --

export PYTHONHOME=/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda
export PYTHONVERSION=2.7
export USE_PYTHONCONFIG=y

output from make


make[1]: Leaving directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--export-dynamic -L/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64 -L/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/tools/install/lib -o /afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/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 -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -l64to32 -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm -lnwcblas -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib/release -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lrt -lpthread -lnwcutil -lpython2.7 -lpthread -ldl -lutil -lm -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic
ld: cannot find -lpython2.7
make: *** [all] Error 1


Note that my build is successful if I eliminate the python bits.

Suggestions??

Thanks

GW

Forum Vet
Threads 9
Posts 1570
12:02:09 PM PST - Tue, Feb 2nd 2016
I would recommend using the default python 2.6 that Scientific Linux 6 should have under /usr

What are the outputs of the following commands on your system

/usr/bin/python-config --libs

rpm -q -l python-devel | grep config

Clicked A Few Times
Threads 1
Posts 8
12:43:29 PM PST - Tue, Feb 2nd 2016
I'm compiling on a node and the node does not have the python-devel libraries. Is there any specific reason the anaconda python doesn't work

Forum Vet
Threads 9
Posts 1570
12:51:32 PM PST - Tue, Feb 2nd 2016
It could be that the python-config --libs output from anaconda python is not correctly pointing to the installation directory.
What is the output of 
python-config --libs
find /afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda -name "libpy*"

Clicked A Few Times
Threads 1
Posts 8
1:06:02 PM PST - Tue, Feb 2nd 2016
[16:01] % python-config --libs
-lpython2.7 -lpthread -ldl -lutil -lm

[16:01] % find /afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda -name "libpy*"
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/cython-0.21-py27_0/lib/python2.7/site-packages/Cython/Debugger/libpython.py
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/cython-0.21-py27_0/lib/python2.7/site-packages/Cython/Debugger/libpython.pyc
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.8-1/lib/libpython2.7.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.8-1/lib/libpython2.7.so.1.0
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.8-1/lib/python2.7/config/libpython2.7.a
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/pyqt-4.10.4-py27_0/plugins/designer/libpyqt4.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.9-2/lib/libpython2.7.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.9-2/lib/libpython2.7.so.1.0
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.9-2/lib/python2.7/config/libpython2.7.a
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.10-0/lib/libpython2.7.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.10-0/lib/libpython2.7.so.1.0
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.10-0/lib/python2.7/config/libpython2.7.a
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.10-2/lib/libpython2.7.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.10-2/lib/libpython2.7.so.1.0
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/python-2.7.10-2/lib/python2.7/config/libpython2.7.a
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/pkgs/pyqt-4.11.4-py27_0/plugins/designer/libpyqt4.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/site-packages/Cython/Debugger/libpython.py
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/site-packages/Cython/Debugger/libpython.pyc
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/libpython2.7.so
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/libpython2.7.so.1.0
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/plugins/designer/libpyqt4.so

Forum Vet
Threads 9
Posts 1570
1:59:45 PM PST - Tue, Feb 2nd 2016
The following settings should work
unset USE_PYTHONCONFIG
export PYTHONHOME=/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda
export PYTHONVERSION=2.7
export PYTHONLIBTYPE=a
export EXTRA_LIBS=-lnwcutil

Clicked A Few Times
Threads 1
Posts 8
3:42:21 PM PST - Tue, Feb 2nd 2016
Tried this suggestion but it did not help.

Forum Vet
Threads 9
Posts 1570
4:10:02 PM PST - Tue, Feb 2nd 2016
Please post the full output of the command

cd $NWCHEM_TOP/src; make EXTRA_LIBS=-lnwcutil link
Edited On 4:13:13 PM PST - Tue, Feb 2nd 2016 by Edoapra

Clicked A Few Times
Threads 1
Posts 8
4:54:01 PM PST - Tue, Feb 2nd 2016
make nwchem.o stubs.o
make[1]: Entering directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/afs
Intel(R) Advisor can now assist with vectorization and show optimization
 report messages with your source code.
See "https://software.intel.com/en-us/intel-advisor-xe" for details.


   Report from: Interprocedural optimizations [ipo]

INLINING OPTION VALUES:
 -inline-factor: 100

 -inline-min-size: 30

 -inline-max-size: 250 (user-specified)

 -inline-max-total-size: 2000

 -inline-max-per-routine: 10000

 -inline-max-per-compile: 500000


Begin optimization report for: NWCHEM

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWCHEM) [1] nwchem.F(1,15)
 -> (212,12) NWCHEM_BANNER

 -> (265,36) NW_PRINT_RESTART_INFO




   Report from: Loop nest, Vector & Auto-parallelization optimizations [loop, vec, par]



Non-optimizable loops:


LOOP BEGIN at nwchem.F(275,11)
  remark #15521: loop was not vectorized: loop control variable was not identified. Explicitly compute the iteration count before
LOOP END

Contents

===============================================================

Begin optimization report for: NWCHEM_BANNER

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWCHEM_BANNER) [2] nwchem.F(370,18)


   Report from: Loop nest, Vector & Auto-parallelization optimizations [loop, vec, par]


LOOP BEGIN at nwchem.F(460,10)
  remark #15335: loop was not vectorized: vectorization possible but seems inefficient. Use vector always directive or -vec-thres

  remark #25436: completely unrolled by 6
LOOP END

LOOP BEGIN at nwchem.F(463,11)
  remark #15335: loop was not vectorized: vectorization possible but seems inefficient. Use vector always directive or -vec-thres

  remark #25436: completely unrolled by 7
LOOP END

LOOP BEGIN at nwchem.F(465,11)
  remark #15335: loop was not vectorized: vectorization possible but seems inefficient. Use vector always directive or -vec-thres

  remark #25436: completely unrolled by 6
LOOP END
===============================================================

Begin optimization report for: NW_PRINT_RESTART_INFO

   Report from: Interprocedural optimizations [ipo]
INLINE REPORT: (NW_PRINT_RESTART_INFO) [3] nwchem.F(628,18)


   Report from: Loop nest, Vector & Auto-parallelization optimizations [loop, vec, par]


LOOP BEGIN at nwchem.F(651,15)
  remark #15301: MATERIALIZED LOOP WAS VECTORIZED
LOOP END

LOOP BEGIN at nwchem.F(651,15)
<Remainder loop for vectorization>
  remark #25436: completely unrolled by 13
LOOP END

LOOP BEGIN at nwchem.F(654,15)
<Peeled loop for vectorization>
  remark #25436: completely unrolled by 15
LOOP END

LOOP BEGIN at nwchem.F(654,15)
  remark #15301: MATERIALIZED LOOP WAS VECTORIZED
LOOP END

LOOP BEGIN at nwchem.F(661,16)
  remark #15301: MATERIALIZED LOOP WAS VECTORIZED
LOOP END

LOOP BEGIN at nwchem.F(661,16)
<Remainder loop for vectorization>
  remark #25436: completely unrolled by 12
LOOP END

LOOP BEGIN at nwchem.F(663,16)
  remark #15301: MATERIALIZED LOOP WAS VECTORIZED
LOOP END

LOOP BEGIN at nwchem.F(663,16)
<Remainder loop for vectorization>
  remark #25436: completely unrolled by 10
LOOP END

LOOP BEGIN at nwchem.F(666,13)
  remark #15335: loop was not vectorized: vectorization possible but seems inefficient. Use vector always directive or -vec-thres

  remark #25436: completely unrolled by 6
LOOP END

LOOP BEGIN at nwchem.F(666,13)
  remark #15301: MATERIALIZED LOOP WAS VECTORIZED
LOOP END

LOOP BEGIN at nwchem.F(666,13)
<Remainder loop for vectorization>
  remark #25436: completely unrolled by 7
LOOP END
===============================================================
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true
-finline-limit=250 -O2 -g -fp-model source -I.
-I/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/include
-I/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/tools/install/include
-DEXT_INT -DLINUX -DLINUX64 -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG
-DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'"
-DCOMPILATION_DIR="'/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6'"
-DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
Intel(R) Advisor can now assist with vectorization and show optimization
 report messages with your source code.
See "https://software.intel.com/en-us/intel-advisor-xe" for details.
INLINING OPTION VALUES:
 -inline-factor: 100

 -inline-min-size: 30

 -inline-max-size: 250 (user-specified)

 -inline-max-total-size: 2000

 -inline-max-per-routine: 10000

 -inline-max-per-compile: 500000


Begin optimization report for: MODULE_CENSUS

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MODULE_CENSUS) [1] stubs.F(1,18)

===============================================================

Begin optimization report for: ARGOS

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (ARGOS) [2] stubs.F(14,18)

===============================================================

Begin optimization report for: ARGOS_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (ARGOS_INPUT) [3] stubs.F(23,18)


===============================================================

Begin optimization report for: CROSSING

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (CROSSING) [4] stubs.F(32,18)

===============================================================

Begin optimization report for: DEBTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (DEBTEST) [5] stubs.F(41,18)

===============================================================

Begin optimization report for: DIA_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (DIA_INPUT) [6] stubs.F(50,18)

===============================================================

Begin optimization report for: DIANA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (DIANA) [7] stubs.F(59,18)

===============================================================
Begin optimization report for: GASDEV

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (GASDEV) [8] stubs.F(68,18)

===============================================================

Begin optimization report for: GENINTERFACE

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (GENINTERFACE) [9] stubs.F(77,18)

===============================================================

Begin optimization report for: JANTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (JANTEST) [10] stubs.F(86,18)

===============================================================

Begin optimization report for: JVLTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (JVLTEST) [11] stubs.F(95,18)

===============================================================
Begin optimization report for: JVLTEST2

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (JVLTEST2) [12] stubs.F(104,18)

===============================================================

Begin optimization report for: KGDTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (KGDTEST) [13] stubs.F(113,18)

===============================================================

Begin optimization report for: LEPS_ENERGY

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (LEPS_ENERGY) [14] stubs.F(122,18)

===============================================================

Begin optimization report for: LEPS_GRADIENT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (LEPS_GRADIENT) [15] stubs.F(131,18)

===============================================================

Begin optimization report for: LUCIA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (LUCIA) [16] stubs.F(140,18)

===============================================================

Begin optimization report for: MC_DATA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MC_DATA) [17] stubs.F(149,18)

===============================================================

Begin optimization report for: MC_DRIVER

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MC_DRIVER) [18] stubs.F(158,18)

===============================================================

Begin optimization report for: MC_MAIN

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MC_MAIN) [19] stubs.F(176,18)


Begin optimization report for: MD_DATA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MD_DATA) [20] stubs.F(185,18)

===============================================================

Begin optimization report for: MD_DRIVER

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MD_DRIVER) [21] stubs.F(194,18)

===============================================================

Begin optimization report for: MD_SET

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MD_SET) [22] stubs.F(203,18)

===============================================================

Begin optimization report for: MOINTS_SCREEN

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MOINTS_SCREEN) [23] stubs.F(212,18)

===============================================================
===============================================================

Begin optimization report for: MYMC_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MYMC_INPUT) [24] stubs.F(221,18)

===============================================================

Begin optimization report for: MYMD_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MYMD_INPUT) [25] stubs.F(230,18)

===============================================================

Begin optimization report for: NBO_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NBO_INPUT) [26] stubs.F(239,18)

===============================================================

Begin optimization report for: NWXC_EVAL_DF

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_EVAL_DF) [27] stubs.F(248,18)


===============================================================

Begin optimization report for: NWXC_EVAL_DF2

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_EVAL_DF2) [28] stubs.F(257,18)

===============================================================

Begin optimization report for: NWXC_EVAL_DF3

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_EVAL_DF3) [29] stubs.F(266,18)

===============================================================

Begin optimization report for: NWXC_GET_CAM

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_GET_CAM) [30] stubs.F(275,18)

===============================================================

Begin optimization report for: NWXC_GET_DISP

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_GET_DISP) [31] stubs.F(284,18)
===============================================================

Begin optimization report for: NWXC_GETVALS

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_GETVALS) [32] stubs.F(293,18)

===============================================================

Begin optimization report for: NWXC_GETWGHT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_GETWGHT) [33] stubs.F(302,18)

===============================================================

Begin optimization report for: NWXC_HAS_2ND

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_HAS_2ND) [34] stubs.F(311,18)

===============================================================

Begin optimization report for: NWXC_HAS_CAM

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_HAS_CAM) [35] stubs.F(320,18)

===============================================================


Begin optimization report for: NWXC_HAS_DISP

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_HAS_DISP) [36] stubs.F(329,18)

===============================================================

Begin optimization report for: NWXC_HAS_HFX

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_HAS_HFX) [37] stubs.F(338,18)

===============================================================

Begin optimization report for: NWXC_HAS_MP2C

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_HAS_MP2C) [38] stubs.F(347,18)

===============================================================

Begin optimization report for: NWXC_HAS_XC

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_HAS_XC) [39] stubs.F(356,18)

===============================================================

Begin optimization report for: NWXC_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_INPUT) [40] stubs.F(374,18)

===============================================================

Begin optimization report for: NWXC_IS_GGA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_IS_GGA) [41] stubs.F(383,18)

===============================================================

Begin optimization report for: NWXC_IS_LDA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_IS_LDA) [42] stubs.F(392,18)

===============================================================

Begin optimization report for: NWXC_IS_MGGA

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_IS_MGGA) [43] stubs.F(401,18)

===============================================================


Begin optimization report for: NWXC_IS_ON

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_IS_ON) [44] stubs.F(410,18)

===============================================================

Begin optimization report for: NWXC_PRINT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_PRINT) [45] stubs.F(419,18)

===============================================================

Begin optimization report for: NWXC_PRINT_NWPW

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_PRINT_NWPW) [46] stubs.F(428,18)

===============================================================

Begin optimization report for: NWXC_RESET_RHO_TOLERANCE

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_RESET_RHO_TOLERANCE) [47] stubs.F(437,18)

===============================================================

Begin optimization report for: NWXC_RTDB_DELETE

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_RTDB_DELETE) [48] stubs.F(446,18)

===============================================================

Begin optimization report for: NWXC_RTDB_LOAD

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_RTDB_LOAD) [49] stubs.F(455,18)

===============================================================

Begin optimization report for: NWXC_RTDB_STORE

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_RTDB_STORE) [50] stubs.F(464,18)

===============================================================

Begin optimization report for: NWXC_VDW3_DFTD3

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_VDW3_DFTD3) [51] stubs.F(473,18)

===============================================================


Begin optimization report for: NWXC_WGHT_HFX

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_WGHT_HFX) [52] stubs.F(482,18)

===============================================================

Begin optimization report for: NWXC_WGHT_MP2C

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_WGHT_MP2C) [53] stubs.F(491,18)

===============================================================

Begin optimization report for: RAKTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (RAKTEST) [54] stubs.F(500,18)

===============================================================

Begin optimization report for: RIMP2G

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (RIMP2G) [55] stubs.F(509,18)

===============================================================


Begin optimization report for: RISM_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (RISM_INPUT) [56] stubs.F(518,18)

===============================================================

Begin optimization report for: RJHTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (RJHTEST) [57] stubs.F(527,18)

===============================================================

Begin optimization report for: SMD_INPUT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (SMD_INPUT) [58] stubs.F(536,18)

===============================================================

Begin optimization report for: TASK_FRAGMENT_ENERGY

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_FRAGMENT_ENERGY) [59] stubs.F(545,18)

===============================================================


Begin optimization report for: TASK_NBO

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_NBO) [60] stubs.F(554,18)

===============================================================

Begin optimization report for: TASK_RISM

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_RISM) [61] stubs.F(563,18)

===============================================================

Begin optimization report for: TASK_SMD

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_SMD) [62] stubs.F(572,18)

===============================================================

Begin optimization report for: TASK_SMD_DYNAMICS

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_SMD_DYNAMICS) [63] stubs.F(581,18)

===============================================================

Begin optimization report for: TASK_SMD_ENERGY

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_SMD_ENERGY) [64] stubs.F(590,18)

===============================================================

Begin optimization report for: TASK_SMD_FRAGMENT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (TASK_SMD_FRAGMENT) [65] stubs.F(599,18)

===============================================================

Begin optimization report for: UCCSDT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (UCCSDT) [66] stubs.F(608,18)

===============================================================

Begin optimization report for: UCCSDTEST

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (UCCSDTEST) [67] stubs.F(617,18)

===============================================================
Begin optimization report for: URAND

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (URAND) [68] stubs.F(626,18)

===============================================================

Begin optimization report for: NWXC_INIT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (NWXC_INIT) [69] stubs.F(365,18)

===============================================================

Begin optimization report for: MC_INIT

   Report from: Interprocedural optimizations [ipo]

INLINE REPORT: (MC_INIT) [70] stubs.F(167,18)

===============================================================
make[1]: Leaving directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--expor
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
src-dir-------/Python-2.7.10/./Modules/posixmodule.c:7631: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
src-dir-------/Python-2.7.10/./Modules/posixmodule.c:7578: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_forkpty':
posixmodule.c:(.text+0x2a8f): undefined reference to `forkpty'
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_openpty':
posixmodule.c:(.text+0x4776): undefined reference to `openpty'
make: *** [link] Error 1

Clicked A Few Times
Threads 1
Posts 8
5:02:14 PM PST - Tue, Feb 2nd 2016
I see some was cut off at the end of the post, this should be complete --

make[1]: Leaving directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--export-dynamic -L/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64 -L/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/tools/install/lib -o /afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/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 /afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -l64to32 -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm -lnwcblas -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib/release -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lrt -lpthread -lnwcutil
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
src-dir-------/Python-2.7.10/./Modules/posixmodule.c:7631: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
src-dir-------/Python-2.7.10/./Modules/posixmodule.c:7578: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_forkpty':
posixmodule.c:(.text+0x2a8f): undefined reference to `forkpty'
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_openpty':
posixmodule.c:(.text+0x4776): undefined reference to `openpty'
make: *** [link] Error 1

Forum Vet
Threads 9
Posts 1570
5:40:07 PM PST - Tue, Feb 2nd 2016
Please try

make FC=ifort EXTRA_LIBS="-lnwcutil  -lpthread -ldl -lutil -lm" link

Clicked A Few Times
Threads 1
Posts 8
5:58:33 PM PST - Tue, Feb 2nd 2016
Fails here --

make[1]: Leaving directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--export-dynamic -L/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64 -L/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/tools/install/lib -o /afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/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 /afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -l64to32 -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm -lnwcblas -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib -L/afs/cad/linux/intel/parallel_studio_cluster_edition_2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib/release -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -lrt -lpthread -lnwcutil -lpthread -ldl -lutil -lm
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
src-dir-------/Python-2.7.10/./Modules/posixmodule.c:7631: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/afs/cad.njit.edu/linux/anaconda-2.1.0/anaconda/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
src-dir-------/Python-2.7.10/./Modules/posixmodule.c:7578: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwctask.a(input_parse.o): In function `input_parse':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/input/input_parse.F:176: undefined reference to `smd_input_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/input/input_parse.F:180: undefined reference to `rism_input_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwctask.a(task.o): In function `task':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task.F:289: undefined reference to `rjhtest_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task.F:296: undefined reference to `uccsdtest_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task.F:304: undefined reference to `raktest_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task.F:322: undefined reference to `task_nbo_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task.F:416: undefined reference to `task_smd_dynamics_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task.F:263: undefined reference to `task_smd_fragment_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwctask.a(task_energy.o): In function `task_energy':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task_energy.F:97: undefined reference to `task_rism_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwctask.a(task_energy.o): In function `task_energy_doit':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task_energy.F:369: undefined reference to `rimp2g_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task_energy.F:255: undefined reference to `task_smd_energy_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwctask.a(task_dynamics.o): In function `task_dynamics':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/task/task_dynamics.F:76: undefined reference to `task_smd_dynamics_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwdft.a(dft_input.o): In function `dft_input':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/nwdft/input_dft/dft_input.F:337: undefined reference to `nwxc_rtdb_store_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwdft.a(tddft_init.o): In function `tddft_init':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/nwdft/lr_tddft/tddft_init.F:572: undefined reference to `nwxc_rtdb_load_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwdft.a(dft_inpana.o): In function `dft_inpana':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/nwdft/input_dft/dft_inpana.F:213: undefined reference to `nwxc_rtdb_load_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwpw.a(nwpw_input.o): In function `nwpw_input':
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/nwpw/nwpw_input.F:641: undefined reference to `nwxc_rtdb_store_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/nwpw/nwpw_input.F:685: undefined reference to `nwxc_rtdb_delete_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwpwlib.a(control.o): In function `control_read_':
control.F:(.text+0xfc8a): undefined reference to `nwxc_rtdb_load_'
control.F:(.text+0xfcc1): undefined reference to `nwxc_rtdb_load_'
control.F:(.text+0xfcf8): undefined reference to `nwxc_rtdb_load_'
control.F:(.text+0xfd67): undefined reference to `nwxc_rtdb_load_'
control.F:(.text+0xfe8e): undefined reference to `nwxc_rtdb_load_'
/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/lib/LINUX64/libnwpwlib.a(control.o):control.F:(.text+0xff02): more undefined references to `nwxc_rtdb_load_' follow
make: *** [link] Error 1

Forum Vet
Threads 9
Posts 1570
6:20:53 PM PST - Tue, Feb 2nd 2016 
make nwchem_config NWCHEM_MODULES="all python"
make FC=ifort EXTRA_LIBS="-lnwcutil  -lpthread -ldl -lutil -lm" link

Clicked A Few Times
Threads 1
Posts 8
4:40:15 AM PST - Wed, Feb 3rd 2016
Fails here --

make[1]: Entering directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/include -I/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DIFCV8 -DIFCLINUX -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
nwchem.F(3): #error: can't find include file: errquit.fh
nwchem.F(4): #error: can't find include file: mafdecls.fh
nwchem.F(5): #error: can't find include file: global.fh
nwchem.F(6): #error: can't find include file: rtdb.fh
nwchem.F(7): #error: can't find include file: tcgmsg.fh
nwchem.F(8): #error: can't find include file: pstat.fh
nwchem.F(9): #error: can't find include file: util.fh
nwchem.F(10): #error: can't find include file: inp.fh
nwchem.F(11): #error: can't find include file: bgj_common.fh
nwchem.F(12): #error: can't find include file: stdio.fh
nwchem.F(373): #error: can't find include file: global.fh
nwchem.F(374): #error: can't find include file: inp.fh
nwchem.F(375): #error: can't find include file: mafdecls.fh
nwchem.F(376): #error: can't find include file: util.fh
nwchem.F(377): #error: can't find include file: stdio.fh
nwchem.F(630): #error: can't find include file: global.fh
nwchem.F(631): #error: can't find include file: errquit.fh
nwchem.F(632): #error: can't find include file: inp.fh
nwchem.F(633): #error: can't find include file: mafdecls.fh
nwchem.F(634): #error: can't find include file: rtdb.fh
nwchem.F(635): #error: can't find include file: stdio.fh
nwchem.F(636): #error: can't find include file: util.fh
make[1]: *** [nwchem.o] Error 22
make[1]: Leaving directory `/afs/cad.njit.edu/u/g/w/gwolosh/ftp/nwchem/nwchem-6.6/src'
make: *** [link] Error 2


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