Nwchem 6.1: Unable to open nwchem.nw --- appending .nw

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Threads 28
Posts 31
2:41:35 AM PDT - Fri, Jun 15th 2012
When I used Nchem 6.1 to carry out BLYP-D3 QM calculation, the error message is as follow. Can anybody help me to solve this problem?

 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://www.nwchem-sw.org/index.php/NWChem_Documentation




For further details see manual section:
0:0:nwchem: failed to open the input file:: 0
[k121:15041] *** Process received signal ***
[k121:15041] Signal: Segmentation fault (11)
[k121:15041] Signal code: Address not mapped (1)
[k121:15041] Failing at address: 0x8
[k121:15041] [ 0] /lib64/libc.so.6 [0x3849e302f0]
[k121:15041] [ 1] /lib64/libc.so.6(strlen+0x30) [0x3849e784a0]
[k121:15041] [ 2] /lib64/libc.so.6(_IO_vfprintf+0x425e) [0x3849e46aae]
[k121:15041] [ 3] /lib64/libc.so.6(_IO_printf+0x9a) [0x3849e4ca2a]
[k121:15041] [ 4] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(ARMCI_Error+0xbb) [0x2d09dcb]
[k121:15041] [ 5] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(pnga_error+0xfd) [0x2c17f9d]
[k121:15041] [ 6] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(ga_error_+0x2f) [0x2b8fe3f]
[k121:15041] [ 7] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(errquit_+0x4ea) [0xace5ce]
[k121:15041] [ 8] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(MAIN__+0xf5) [0x4e3f61]
[k121:15041] [ 9] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(main+0xe) [0x2e1ba0e]
[k121:15041] [10] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3849e1d994]
[k121:15041] [11] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem [0x4e2e49]
[k121:15041] *** End of error message ***
mpirun noticed that job rank 0 with PID 15041 on node k121.hn.org exited on signal 11 (Segmentation fault).
7 additional processes aborted (not shown)

The input file is:echo

start pi

memory total 6000 Mb

permanent_dir ./perm
scratch_dir ./data

set geometry:actlist 1:7 9:27

geometry noautoz units angstroms
C             1.810            -0.327             0.598

C             2.067            -0.179            -0.766

C             1.173            -0.696            -1.706

C            -0.215            -1.480             0.071

C             0.660            -0.982             1.031

N             0.016            -1.353            -1.294

H             2.502             0.075             1.331

H             2.972             0.325            -1.096

H             1.378            -0.592            -2.769

H            -1.101            -1.982             0.397

H             0.436            -1.110             2.083

C            -0.883             1.731             1.327

C            -0.678             1.987            -0.057

C            -1.553             1.525            -1.046

C            -2.641             0.770            -0.630

C            -2.860             0.495             0.736

C            -1.995             0.962             1.714

C             0.194             2.351             2.030

C             0.997             2.953             1.090

H            -1.383             1.736            -2.100

H            -3.340             0.384            -1.368

H            -3.717            -0.110             1.022

H            -2.177             0.740             2.764

H             0.351             2.368             3.101

H             1.901             3.535             1.213

N             0.466             2.740            -0.163

H             0.878             3.054            -1.031
end

basis spherical
 H  S

    34.06134100      0.60251978E-02

     5.12357460      0.45021094E-01

     1.16466260      0.20189726

 H  S

     0.32723041      1.00000000

 H  S

     0.10307241      1.00000000

 H  P

     1.40700000      1.00000000

 H  P

     0.38800000      1.00000000

 H  D

     1.05700000      1.00000000



 C  S

 13575.34968200      0.22245814E-03

  2035.23336800      0.17232738E-02

   463.22562359      0.89255715E-02

   131.20019598      0.35727985E-01

    42.85301589      0.11076260

    15.58418577      0.24295628

 C  S

     6.20671385      0.414402634

     2.57648965      0.237449687

 C  S

     0.57696339      1.000000000

 C  S

     0.22972831      1.000000000

 C  S

     0.95164440E-01  1.000000000

 C  P

    34.69723224      0.533336578E-02

     7.95826228      0.358641091E-01

     2.37808269      0.142158733

     0.81433208      0.342704718

 C  P

     0.28887547      0.464458224

 C  P

     0.10056824      0.249557899

 C  D

     1.09700000      1.000000000

 C  D

     0.31800000      1.000000000

 C  F

     0.76100000      1.000000000



 N  S

 19730.80064700      0.218879850E-03

  2957.89587450      0.169607088E-02

   673.22133595      0.879546035E-02

   190.68249494      0.353593826E-01

    62.29544190      0.110957892

    22.65416118      0.249829726

 N  S

     8.97914774      0.406238961

     3.68630024      0.243382172

 N  S

     0.84660077      1.000000000

 N  S

     0.33647134      1.000000000

 N  S

     0.13647654      1.000000000

 N  P

    49.20038051      0.555524168E-02

    11.34679054      0.380523797E-01

     3.42739724      0.149536710

     1.17855251      0.349493052

 N  P

     0.41642205      0.458431537

 N  P

     0.14260826      0.244287717

 N  D

     1.65400000      1.000000000

 N  D

     0.46900000      1.000000000

 N  F

     1.09300000      1.000000000
end

driver
 maxiter 400
end

scf
 singlet

 rhf

 maxiter 400

 direct

 print "parameters"

 print "information"

 print "convergence"
end

dft
 xc becke88 1. lyp 1.

 iterations 400

 disp vdw 3

 print "coulomb fit"

 print "intermediate energy info"

 print "intermediate evals"
end

task dft optimize

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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9:24:56 AM PDT - Fri, Jun 15th 2012
NWChem clearly cannot find your input file. What does you job script look like?

Bert


Quote:Lmyiop Jun 15th 9:41 am
When I used Nchem 6.1 to carry out BLYP-D3 QM calculation, the error message is as follow. Can anybody help me to solve this problem?

 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://www.nwchem-sw.org/index.php/NWChem_Documentation




For further details see manual section:
0:0:nwchem: failed to open the input file:: 0
[k121:15041] *** Process received signal ***
[k121:15041] Signal: Segmentation fault (11)
[k121:15041] Signal code: Address not mapped (1)
[k121:15041] Failing at address: 0x8
[k121:15041] [ 0] /lib64/libc.so.6 [0x3849e302f0]
[k121:15041] [ 1] /lib64/libc.so.6(strlen+0x30) [0x3849e784a0]
[k121:15041] [ 2] /lib64/libc.so.6(_IO_vfprintf+0x425e) [0x3849e46aae]
[k121:15041] [ 3] /lib64/libc.so.6(_IO_printf+0x9a) [0x3849e4ca2a]
[k121:15041] [ 4] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(ARMCI_Error+0xbb) [0x2d09dcb]
[k121:15041] [ 5] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(pnga_error+0xfd) [0x2c17f9d]
[k121:15041] [ 6] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(ga_error_+0x2f) [0x2b8fe3f]
[k121:15041] [ 7] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(errquit_+0x4ea) [0xace5ce]
[k121:15041] [ 8] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(MAIN__+0xf5) [0x4e3f61]
[k121:15041] [ 9] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem(main+0xe) [0x2e1ba0e]
[k121:15041] [10] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3849e1d994]
[k121:15041] [11] /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem [0x4e2e49]
[k121:15041] *** End of error message ***
mpirun noticed that job rank 0 with PID 15041 on node k121.hn.org exited on signal 11 (Segmentation fault).
7 additional processes aborted (not shown)

The input file is:echo

start pi

memory total 6000 Mb

permanent_dir ./perm
scratch_dir ./data

set geometry:actlist 1:7 9:27

geometry noautoz units angstroms
C             1.810            -0.327             0.598

C             2.067            -0.179            -0.766

C             1.173            -0.696            -1.706

C            -0.215            -1.480             0.071

C             0.660            -0.982             1.031

N             0.016            -1.353            -1.294

H             2.502             0.075             1.331

H             2.972             0.325            -1.096

H             1.378            -0.592            -2.769

H            -1.101            -1.982             0.397

H             0.436            -1.110             2.083

C            -0.883             1.731             1.327

C            -0.678             1.987            -0.057

C            -1.553             1.525            -1.046

C            -2.641             0.770            -0.630

C            -2.860             0.495             0.736

C            -1.995             0.962             1.714

C             0.194             2.351             2.030

C             0.997             2.953             1.090

H            -1.383             1.736            -2.100

H            -3.340             0.384            -1.368

H            -3.717            -0.110             1.022

H            -2.177             0.740             2.764

H             0.351             2.368             3.101

H             1.901             3.535             1.213

N             0.466             2.740            -0.163

H             0.878             3.054            -1.031
end

basis spherical
 H  S

    34.06134100      0.60251978E-02

     5.12357460      0.45021094E-01

     1.16466260      0.20189726

 H  S

     0.32723041      1.00000000

 H  S

     0.10307241      1.00000000

 H  P

     1.40700000      1.00000000

 H  P

     0.38800000      1.00000000

 H  D

     1.05700000      1.00000000



 C  S

 13575.34968200      0.22245814E-03

  2035.23336800      0.17232738E-02

   463.22562359      0.89255715E-02

   131.20019598      0.35727985E-01

    42.85301589      0.11076260

    15.58418577      0.24295628

 C  S

     6.20671385      0.414402634

     2.57648965      0.237449687

 C  S

     0.57696339      1.000000000

 C  S

     0.22972831      1.000000000

 C  S

     0.95164440E-01  1.000000000

 C  P

    34.69723224      0.533336578E-02

     7.95826228      0.358641091E-01

     2.37808269      0.142158733

     0.81433208      0.342704718

 C  P

     0.28887547      0.464458224

 C  P

     0.10056824      0.249557899

 C  D

     1.09700000      1.000000000

 C  D

     0.31800000      1.000000000

 C  F

     0.76100000      1.000000000



 N  S

 19730.80064700      0.218879850E-03

  2957.89587450      0.169607088E-02

   673.22133595      0.879546035E-02

   190.68249494      0.353593826E-01

    62.29544190      0.110957892

    22.65416118      0.249829726

 N  S

     8.97914774      0.406238961

     3.68630024      0.243382172

 N  S

     0.84660077      1.000000000

 N  S

     0.33647134      1.000000000

 N  S

     0.13647654      1.000000000

 N  P

    49.20038051      0.555524168E-02

    11.34679054      0.380523797E-01

     3.42739724      0.149536710

     1.17855251      0.349493052

 N  P

     0.41642205      0.458431537

 N  P

     0.14260826      0.244287717

 N  D

     1.65400000      1.000000000

 N  D

     0.46900000      1.000000000

 N  F

     1.09300000      1.000000000
end

driver
 maxiter 400
end

scf
 singlet

 rhf

 maxiter 400

 direct

 print "parameters"

 print "information"

 print "convergence"
end

dft
 xc becke88 1. lyp 1.

 iterations 400

 disp vdw 3

 print "coulomb fit"

 print "intermediate energy info"

 print "intermediate evals"
end

task dft optimize

Clicked A Few Times
Threads 28
Posts 31
6:58:17 PM PDT - Fri, Jun 15th 2012
My input file name is "py-tzvpp.nw" and command to run Nwchem 6.1 is as follow:

mpirun -np 8 /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem py-tzvpp.nw &> py-tzvpp.nwo

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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10:44:13 AM PDT - Mon, Jun 18th 2012
Strange. You may want to try two things in your jobscript:

1. Explicitly do a "cd" to your working directory just before the mpirun command (making sure you are in the directory you should be)

2. Slight change in the mpirun command: mpirun -np 8 /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem py-tzvpp.nw >& py-tzvpp.nwo

Bert


Quote:Lmyiop Jun 16th 1:58 am
My input file name is "py-tzvpp.nw" and command to run Nwchem 6.1 is as follow:

mpirun -np 8 /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem py-tzvpp.nw &> py-tzvpp.nwo

Clicked A Few Times
Threads 28
Posts 31
5:46:51 PM PDT - Mon, Jun 18th 2012
It still not work!
I did it as what you said, but it is still not work.

Our cluster is SGE grid system, the script is as follow

  1. !/bin/sh

  3. $ -S /bin/bash
  4. $ -cwd
  5. $ -q katyusha
  6. $ -pe katyusha 8
  7. $ -hard
  8. $ -l hostname=k129.hn.org
  9. $ -N pi-blyp-d3-tzvpp

source /etc/env/iccvars.sh
source /etc/env/ifortvars.sh
source /etc/env/openmpii.sh
export MPIRUN_PATH=/usr/local/openmpii/bin

cd /pubdata/myliu/py-indole-blyp-d3-tzvpp

mpirun -np 8 /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem py-tzvpp.nw >& py-tzvpp.nwo
Edited On 5:47:25 PM PDT - Mon, Jun 18th 2012 by Lmyiop

Clicked A Few Times
Threads 2
Posts 6
9:18:06 AM PDT - Wed, Jun 20th 2012
I have the same problem. Interestingly if you do <nwchem_executable_path> input.nw -np 4 > output.nw & , the program runs but uses only 1 processor. Does the program always expect the input file to be the second argument?

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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9:17:59 AM PDT - Fri, Jun 22nd 2012
Two suggestions:

cd /pubdata/myliu/py-indole-blyp-d3-tzvpp

mpirun -np 8 /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem /pubdata/myliu/py-indole-blyp-d3-tzvpp
/py-tzvpp.nw >& py-tzvpp.nwo

Or

cd /pubdata/myliu/py-indole-blyp-d3-tzvpp

cp /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem /pubdata/myliu/py-indole-blyp-d3-tzvpp/nwchem

mpirun -np 8 nwchem py-tzvpp.nw >& py-tzvpp.nwo


Bert



Quote:Lmyiop Jun 19th 12:46 am
I did it as what you said, but it is still not work.

Our cluster is SGE grid system, the script is as follow

  1. !/bin/sh

  3. $ -S /bin/bash
  4. $ -cwd
  5. $ -q katyusha
  6. $ -pe katyusha 8
  7. $ -hard
  8. $ -l hostname=k129.hn.org
  9. $ -N pi-blyp-d3-tzvpp

source /etc/env/iccvars.sh
source /etc/env/ifortvars.sh
source /etc/env/openmpii.sh
export MPIRUN_PATH=/usr/local/openmpii/bin

cd /pubdata/myliu/py-indole-blyp-d3-tzvpp

mpirun -np 8 /nibs/myliu/nwchem-6.1/bin/LINUX64/nwchem py-tzvpp.nw >& py-tzvpp.nwo

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Posts 597
9:19:43 AM PDT - Fri, Jun 22nd 2012
Yes, the first argument after the executable should be the input file.

-np 4 is a mpirun option, and hence should be before the executable. See the mpirun documentation.

Bert

Quote:Beulahsu Jun 20th 4:18 pm
I have the same problem. Interestingly if you do <nwchem_executable_path> input.nw -np 4 > output.nw & , the program runs but uses only 1 processor. Does the program always expect the input file to be the second argument?


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