No geometry and basis in the database


Just Got Here
When I try to run nwchem in our cluster, this is the error I get in my output file:
 argument  1 = 
  Unable to open nwchem.nw --- appending .nw
 ------------------------------------------------------------------------
 nwchem: failed to open the input file                   0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line : 
     0: 
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 There is an error in the input file
 ------------------------------------------------------------------------
 For more information see the NWChem manual at http://nwchemgit.github.io/index.php/NWChem_Documentation


 For further details see manual section:                                                                                                                                                                                                                                                                
0:nwchem: failed to open the input file:Received an Error in Communication
[cli_0]: aborting job:
application called MPI_Abort(comm=0x84000004, -1) - process 0


This has been discussed somewhere else in the forum, but it didn't seem to be resolved:
http://nwchemgit.github.io/Special_AWCforum/st/id479/Nwchem_6.1%3A_Unable_to_open_...

After I change the name of the input file ti nwchem.nw, then I get the following output:
argument  1 = 
                                         
                                         


              Northwest Computational Chemistry Package (NWChem) 6.6
              ------------------------------------------------------


                    Environmental Molecular Sciences Laboratory
                       Pacific Northwest National Laboratory
                                Richland, WA 99352

                              Copyright (c) 1994-2015
                       Pacific Northwest National Laboratory
                            Battelle Memorial Institute

             NWChem is an open-source computational chemistry package
                        distributed under the terms of the
                      Educational Community License (ECL) 2.0
             A copy of the license is included with this distribution
                              in the LICENSE.TXT file

                                  ACKNOWLEDGMENT
                                  --------------

            This software and its documentation were developed at the
            EMSL at Pacific Northwest National Laboratory, a multiprogram
            national laboratory, operated for the U.S. Department of Energy
            by Battelle under Contract Number DE-AC05-76RL01830. Support
            for this work was provided by the Department of Energy Office
            of Biological and Environmental Research, Office of Basic
            Energy Sciences, and the Office of Advanced Scientific Computing.


           Job information
           ---------------

    hostname        = node24.cluster
    program         = 
    date            = Sat Feb  6 09:27:43 2016

    compiled        = Fri_Feb_05_21:36:56_2016
    source          = /home/kayahan/nwchem-6.6
    nwchem branch   = 6.6
    nwchem revision = 27746
    ga revision     = 10594
    input           = nwchem.nw
    prefix          = nwchem.
    data base       = ./nwchem.db
    status          = restart
    nproc           =       16
    time left       =     -1s



           Memory information
           ------------------

    heap     =   13107194 doubles =    100.0 Mbytes
    stack    =   13107199 doubles =    100.0 Mbytes
    global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)
    total    =   52428793 doubles =    400.0 Mbytes
    verify   = yes
    hardfail = no 
         Directory information
           ---------------------

  0 permanent = .
  0 scratch   = .



           Geometries in the database
           --------------------------

  There are no geometries in the database


           Basis sets in the database
           --------------------------

  There are no basis sets in the database



                                NWChem Input Module
                                -------------------


 Summary of allocated global arrays
-----------------------------------
  No active global arrays



                         GA Statistics for process    0
                         ------------------------------

       create   destroy   get      put      acc     scatter   gather  read&inc
calls:    0        0        0        0        0        0        0        0     
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes total:             0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes remote:            0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 0 bytes

MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:

        allocation statistics:
                                              heap           stack
                                              ----           -----
        current number of blocks                 0               0
        maximum number of blocks                 0               0
        current total bytes                      0               0
        maximum total bytes                      0               0
        maximum total K-bytes                    0               0
        maximum total M-bytes                    0               0
 
 
                                     CITATION
                                     --------


So, clearly it doesn't recognize the location of the input file and also probably the basis library. So, here is the job script I use for submitting the job:
#!/bin/sh
#PBS -l nodes=1:ppn=16
#PBS -N test

if [ -f /usr/share/Modules/init/bash ]; then
        source /usr/share/Modules/init/bash
else
        echo \"Could not source environment modules!\"
        exit 1
fi

cd $PBS_O_WORKDIR
cat $PBS_NODEFILE > nodes.out 

export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.1.117/compiler/lib/intel64:/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64

module purge
module load mvapich2-2.0/intel

source /opt/intel/composer_xe_2013.1.117/bin/compilervars.sh intel64
source /opt/intel/impi/4.1.0.024/bin64/mpivars.sh 

cd /home/kayahan/nwchem-6.6/examples/tcepolar
/opt/intel/composer_xe_2013.1.117/mpirt/bin/intel64/mpirun  -np 16 nwchem /home/kayahan/nwchem-6.6/examples/tcepolar/ccsd_polar_small.nw >& kayahan.out  

and also here are some other things that I thought would be helpful to resolve the issue
	linux-vdso.so.1 =>  (0x00007fff83bff000)
	libmkl_scalapack_ilp64.so => /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_scalapack_ilp64.so (0x00002ad02f235000)
	libmkl_cdft_core.so => /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_cdft_core.so (0x00002ad02fa3d000)
	libmkl_gf_ilp64.so => /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_gf_ilp64.so (0x00002ad02fc59000)
	libmkl_sequential.so => /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_sequential.so (0x00002ad03035b000)
	libmkl_core.so => /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_core.so (0x00002ad0309f9000)
	libmkl_blacs_intelmpi_ilp64.so => /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_blacs_intelmpi_ilp64.so (0x00002ad031c07000)
	libdl.so.2 => /lib64/libdl.so.2 (0x0000003768e00000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003769200000)
	libgfortran.so.3 => /act/gcc-4.7.2/lib64/libgfortran.so.3 (0x00002ad031e8f000)
	libm.so.6 => /lib64/libm.so.6 (0x0000003768600000)
	libmpichf90.so.10 => /act/mvapich2-2.0/intel/lib/libmpichf90.so.10 (0x00002ad0321a3000)
	libmpich.so.10 => /act/mvapich2-2.0/intel/lib/libmpich.so.10 (0x00002ad0323a5000)
	libopa.so.1 => /act/mvapich2-2.0/intel/lib/libopa.so.1 (0x00002ad0328de000)
	libmpl.so.1 => /act/mvapich2-2.0/intel/lib/libmpl.so.1 (0x00002ad032adf000)
	librt.so.1 => /lib64/librt.so.1 (0x0000003769a00000)
	libgcc_s.so.1 => /act/gcc-4.7.2/lib64/libgcc_s.so.1 (0x00002ad032ce5000)
	libc.so.6 => /lib64/libc.so.6 (0x0000003768a00000)
	libifport.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libifport.so.5 (0x00002ad032efa000)
	libifcore.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libifcore.so.5 (0x00002ad03312a000)
	libimf.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libimf.so (0x00002ad033460000)
	libintlc.so.5 => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libintlc.so.5 (0x00002ad03391c000)
	libsvml.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libsvml.so (0x00002ad033b6b000)
	/lib64/ld-linux-x86-64.so.2 (0x0000003768200000)
	libquadmath.so.0 => /act/gcc-4.7.2/lib/../lib64/libquadmath.so.0 (0x00002ad034439000)
	libibmad.so.5 => /usr/lib64/libibmad.so.5 (0x00000030f7000000)
	librdmacm.so.1 => /usr/lib64/librdmacm.so.1 (0x00002ad03466f000)
	libibumad.so.3 => /usr/lib64/libibumad.so.3 (0x00000030f6800000)
	libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x00000030f6c00000)
	libirng.so => /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libirng.so (0x00002ad034884000)

which nwchem
/home/kayahan/NWCHEM/bin/

environmental variables that I use to compile the code
export NWCHEM_TOP=$HOME/nwchem-6.6
export NWCHEM_TARGET=LINUX64
export ARMCI_NETWORK=MPI_PR
export NWCHEM_MODULES="all"
export LARGE_FILES=TRUE

export USE_NOSCFCHECK=TRUE
export USE_NOIO=TRUE

export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y

export NWCHEM_MODULES="qm"

export USE_NOFSCHECK=TRUE
export USE_NOIO=TRUE
export MKLROOT=/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64
export BLASOPT="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_cdft_core -lmkl_gf_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -ldl -lpthread -lm"

# "-L/opt/intel/composer_xe_2013.1.117/mkl/lib/ -lmkl_blacs_intelmpi_ilp64 -lmkl_core -lmkl_intel_thread -lpthread -lm"



export LIBMPI="-lmpichf90 -Wl,-rpath -Wl,/act/mvapich2-2.0/intel/lib -lmpich -lopa -lmpl"
export MPI_LIB="/act/mvapich2-2.0/intel/lib "
export MPI_INCLUDE="/act/mvapich2-2.0/intel/include"

 make nwchem_config

 make >& make.log



Thanks a lot for your help, and looking forward to hear your answers.

Clicked A Few Times
please post your input file and the command you use to submit the job

Just Got Here
Thanks Rasmus, my job submission file is attached above, but I use qsub "sub. file" to submit the job. My input file is an input file from the example directory at nwchem-6.6/examples/tcepolar/ccsd_polar_small.nw

echo

start ccsd_polar_small

#
# R = 2.068 bohr
#
geometry units au
 symmetry d2h
 N  0  0 -1.034
 N  0  0  1.034
end

basis spherical
 * library aug-cc-pVDZ
end

scf
  singlet
  rhf
  thresh 1e-8
end

tce
  scf
  ccsd
  io ga
  2eorb
end

task tce energy

Forum Regular
You need a task directive in order to run a calculation (http://nwchemgit.github.io/index.php/Release66:Top-level#TASK). In this case, add

task tce energy

to the end of your input file.

Just Got Here
Sorry, it was there actually, I made a mistake during copy-paste. I just edited the post.

Forum Regular
I was able to run the input you copied above with no problems. Additionally, based on the output you have copied above, this is not the input file that the code attempted to run. So my first suggestion is that you include the full path to the nwchem executable in your submission script.

Just Got Here
Ok, including the exact name of the executable actually worked, thanks


Forum >> NWChem's corner >> Running NWChem