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.
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