Error Message from Task 0:: No such file or directory

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Clicked A Few Times
Threads 2
Posts 30
9:21:10 PM PDT - Wed, Sep 3rd 2014
I'm new to NWChem and facing issue to run a simple test job. the command I used to run NWChem is :
mpirun -np 2 nwchem testnw2.nw >> testnw2.out

I get the below error

mpirun -np 2 nwchem testnw2.nw >> testnw21.out
[proxy:0:0@atlas5-c01] HYDU_create_process (./utils/launch/launch.c:75): execvp error on file nwchem (No such file or directory)
[proxy:0:0@atlas5-c01] HYDU_create_process (./utils/launch/launch.c:75): execvp error on file nwchem (No such file or directory)
[root@atlas5-c01 test2]# cat testnw21.out

=======================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 255
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=======================================================================

Appreciate any help.

Srikanth

Gets Around
Threads 15
Posts 52
8:44:42 AM PDT - Thu, Sep 4th 2014
post the output of next commands
1. which nwchem
2. export | grep NWCHEM

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Threads 2
Posts 30
7:47:01 PM PDT - Thu, Sep 4th 2014
$ which nwchem
/app1/centos6.3/gnu/apps/NWChem/bin/nwchem

$ export |grep NWCHEM
declare -x NWCHEM_BASIS_LIBRARY="/app1/centos6.3/gnu/apps/NWChem/data/libraries/"
declare -x NWCHEM_TOP="/app1/centos6.3/gnu/apps/NWChem"

Forum Vet
Threads 3
Posts 889
9:07:12 PM PDT - Thu, Sep 4th 2014
Could you try the following command

mpirun -np 2 /app1/centos6.3/gnu/apps/NWChem/bin/nwchem testnw2.nw

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Threads 2
Posts 30
9:20:07 PM PDT - Thu, Sep 4th 2014
Hi Edoapra,

I still receive the error. Please see the below output.

$ mpirun -np 2 /app1/centos6.3/gnu/apps/NWChem/bin/nwchem testnw2.nw
argument  1 = testnw2.nw

hdbm_open: open of ./feco5.db failed 0
rtdb_seq_open: hdbm failed to open file ./feco5.db
------------------------------------------------------------------------

start: rtdb_open empty failed         0

------------------------------------------------------------------------

An error occured in the Runtime Database

start: rtdb_open empty failed         0

------------------------------------------------------------------------

------------------------------------------------------------------------

For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation



An error occured in the Runtime Database

------------------------------------------------------------------------



For further details see manual section:                                                                                                                                          

For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation




For further details see manual section:
0:0:start: rtdb_open empty failed:: -1
(rank:0 hostname:atlas5-c01 pid:24183):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/armci.c:ARMCI_Error():208 cond:0
(rank:1 hostname:atlas5-c01 pid:24184):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/armci.c:ARMCI_Error():208 cond:0
Last System Error Message from Task 0:: Invalid argument
Last System Error Message from Task 1:: No such file or directory
[cli_0]: aborting job:
application called MPI_Abort(comm=0x84000007, -1) - process 0
[cli_1]: aborting job:
application called MPI_Abort(comm=0x84000004, -1) - process 1

=======================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 255
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=======================================================================
Thanks
Regards
Srikanth
Edited On 9:26:04 PM PDT - Thu, Sep 4th 2014 by Sri4mailing

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Threads 2
Posts 30
9:20:39 PM PDT - Thu, Sep 4th 2014
sorry I was unable to post the full output.

Clicked A Few Times
Threads 2
Posts 30
9:31:42 PM PDT - Thu, Sep 4th 2014
Sorry, I noticed the permissions were not set properly for feco5.db, however even after I correct the issue, I'm facing segmentation violation

mpirun -np 2 /app1/centos6.3/gnu/apps/NWChem/bin/nwchem testnw2.nw
argument  1 = testnw2.nw






             Northwest Computational Chemistry Package (NWChem) 6.3

             ------------------------------------------------------




                   Environmental Molecular Sciences Laboratory

                      Pacific Northwest National Laboratory

                               Richland, WA 99352



                             Copyright (c) 1994-2012

                      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        = atlas5-c01

   program         = /app1/centos6.3/gnu/apps/NWChem/bin/nwchem

   date            = Fri Sep  5 12:30:29 2014



   compiled        = Tue_Sep_02_16:48:05_2014

   source          = /opt/ZIP/nwchem-6.3/

   nwchem branch   = 6.3

   nwchem revision = 24652

   ga revision     = 10379

   input           = testnw2.nw

   prefix          = feco5.

   data base       = ./feco5.db

   status          = startup

   nproc           =        2

   time left       =     -1s

   batch job id    = 106856



          Memory information

          ------------------



   heap     =   13107201 doubles =    100.0 Mbytes

   stack    =   13107201 doubles =    100.0 Mbytes

   global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)

   total    =   52428802 doubles =    400.0 Mbytes

   verify   = yes

   hardfail = no




          Directory information

          ---------------------



 0 permanent = .

 0 scratch   = .






                               NWChem Input Module

                               -------------------


0:Segmentation Violation error, status=: 11
(rank:0 hostname:atlas5-c01 pid:27568):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: No such file or directory
[cli_0]: aborting job:
application called MPI_Abort(comm=0x84000007, 11) - process 0

=======================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=======================================================================

Forum Vet
Threads 3
Posts 889
9:02:42 AM PDT - Fri, Sep 5th 2014
Srikanth
Could you provide details about the installation process of the NWChem executable you are using?

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Threads 2
Posts 30
12:32:13 AM PDT - Mon, Sep 8th 2014
I used the below script for compilation

  1. !/bin/bash
module load mvapich2_gnu

  1. OPTIONAL environment variables

export LARGE_FILES=TRUE
export USE_NOFSCHECK=TRUE
export LIB_DEFINES="-DDFLT_TOT_MEM=16777216"
export TCGRSH=/usr/local/bin/ssh
export USE_64TO32=yes
export MRCC_THEORY=TRUE


export HAS_BLAS=yes
export LAPACK_LIB="/app1/centos6.3/gnu/SCIlibs/lib/liblapack.a"
export BLASOPT="/app1/centos6.3/gnu/SCIlibs/lib/libatlas.a"

export USE_SCALAPACK=y
export SCALAPACK="/app1/centos6.3/gnu/SCIlibs/lib/libscalapack.a"
export SCALAPACK_SIZE=4

export NWCHEM_MODULES=all
export PYTHONHOME=/usr/
export PYTHONVERSION=2.6
export USE_PYTHON64=y
export PYTHONLIBTYPE=so
export NWCHEM_MODULES="all python"
export FOPTIMIZE=-O1


export BLASOPT="-L/app1/centos6.3/gnu/SCIlibs/lib -llapack -lf77blas -lcblas -latlas"

  1. MPICH
      export MPI_LOC=/app1/centos6.3/gnu/mvapich2-1.9  #location of mpich



      export MPI_LIB=$MPI_LOC/lib



      export MPI_INCLUDE=$MPI_LOC/include



      export LIBMPI=" -lmpichf90 -Wl,-rpath -Wl,/app1/centos6.3/gnu/mvapich2-1.9/lib -lmpich -lopa -lmpl -libmad -lrdmacm -libumad -libverbs -ldl -lrt -lm -lpthread "



      export MPI_CC=mpicc



      export MPI_CXX=mpicxx



      export USE_MPI=y



      export USE_MPIF=y



      export USE_MPIF4=y



      export MPI_F90=mpiifort



      export FC=mpif90



      export CC=mpicc


export NWCHEM_TOP=/opt/ZIP/nwchem-6.3_gnu/
cd $NWCHEM_TOP/src
export NWCHEM_TARGET=LINUX64

make clean
make 64_to_32
make nwchem_config
make |tee make.log

Clicked A Few Times
Threads 2
Posts 30
9:23:38 PM PDT - Tue, Sep 9th 2014
Got struck. Appreciate help

Forum Vet
Threads 3
Posts 889
2:25:34 PM PDT - Wed, Sep 10th 2014
Could you try to unset BLASOPT and relink, i.e.
cd $NWCHEM_TOP/src
make link

Clicked A Few Times
Threads 2
Posts 30
7:06:15 PM PDT - Wed, Sep 10th 2014
unfortunately the problem remains the same

mpirun -np 2 nwchem testnw2.nw

argument  1 = testnw2.nw






             Northwest Computational Chemistry Package (NWChem) 6.3

             ------------------------------------------------------




                   Environmental Molecular Sciences Laboratory

                      Pacific Northwest National Laboratory

                               Richland, WA 99352



                             Copyright (c) 1994-2012

                      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        = atlas5-c01

   program         = nwchem

   date            = Thu Sep 11 10:05:32 2014



   compiled        = Thu_Sep_11_09:59:58_2014

   source          = /opt/ZIP/nwchem-6.3/

   nwchem branch   = 6.3

   nwchem revision = 24652

   ga revision     = 10379

   input           = testnw2.nw

   prefix          = feco5.

   data base       = ./feco5.db

   status          = startup

   nproc           =        2

   time left       =     -1s

   batch job id    = 128467



          Memory information

          ------------------



   heap     =   13107201 doubles =    100.0 Mbytes

   stack    =   13107201 doubles =    100.0 Mbytes

   global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)

   total    =   52428802 doubles =    400.0 Mbytes

   verify   = yes

   hardfail = no




          Directory information

          ---------------------



 0 permanent = .

 0 scratch   = .






                               NWChem Input Module

                               -------------------


0:Segmentation Violation error, status=: 11
(rank:0 hostname:atlas5-c01 pid:23525):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: No such file or directory
[cli_0]: aborting job:
application called MPI_Abort(comm=0x84000007, 11) - process 0

=======================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=======================================================================

Forum Vet
Threads 3
Posts 889
10:41:25 PM PDT - Wed, Sep 10th 2014
serial execution
What happens i you try to run a single process, i.e. the command
nwchem testnw2

Could you also post the content of testnw2.nw

Clicked A Few Times
Threads 2
Posts 30
11:44:05 PM PDT - Wed, Sep 10th 2014
Same segmentation Violation error:

NWChem Input Module

                               -------------------


0:Segmentation Violation error, status=: 11
(rank:0 hostname:atlas5-c01 pid:1553):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: No such file or directory
[unset]: aborting job:
application called MPI_Abort(comm=0x84000001, 11) - process 0

Clicked A Few Times
Threads 2
Posts 30
11:44:49 PM PDT - Wed, Sep 10th 2014
$ cat testnw2.nw
start feco5

  1. Fe(CO)5 ... there are two symmetry distinct types of CO molecules

geometry units au
 symmetry group d3h



 fe 0.0 0.0 0.0



 c 0.0 0.0 3.414358

 o 0.0 0.0 5.591323



 c 2.4417087 2.4417087 0.0

 o 3.9810552 3.9810552 0.0
end

basis
 fe library 3-21g

 o  library 3-21g

 c  library 3-21g
end

basis "cd basis"
 o library "DGauss A1 DFT Coulomb Fitting"

 c library "DGauss A1 DFT Coulomb Fitting"

fe library "DGauss A1 DFT Coulomb Fitting"
end

dft
 xc becke88 lyp
end

task dft

Forum Vet
Threads 3
Posts 889
2:14:49 PM PDT - Fri, Sep 12th 2014
gdb
Could you try to run it through the gdb debugger?
Instructions

1) gdb nwchem
2) break exit
3) r testnw2
4) where

Could you please send me the output you will be getting?


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