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Messages - Jahangiri

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Dear Users and Developers

I got approximatly the same error:

caused collective abort of all ranks
  exit status of rank 1: killed by signal 9

but as I read whole of this article, I believe that is not because of the system of atoms which I want to do calculation for, nor the machine which I am running my jobs on.
Because I ran on of the tutorials ( Gold nano wire )  before and I got the same result as it was in the Tutorial, later on when I wanted to do almost the same calculation ( bigger molecule between two electrode ) I got the same error as I mentioned above.
in one sentence; before it was working properly but I don't know why it is giving me error( just I used another molecule with almost 40 atoms between two probes ) ?!!!
could you please let me know what can be the problem ?

Best regards

General Questions and Answers / Re: ATKError
« on: July 7, 2010, 12:20 »
Dear Anders Blom

Thank you very much.

Best regards

General Questions and Answers / Re: ATKError
« on: July 7, 2010, 09:59 »
Dear Anders Blom

We have one machine with 8 cores. But by referring to the system configuration. I think 16GB RAM would be sufficient !
Am I right?

The system Information is as following :
MemTotal:       16461608 kB
MemFree:        15317608 kB
Buffers:           19184 kB
Cached:           231664 kB
SwapCached:       106636 kB
Active:            28292 kB
Inactive:         714956 kB
Active(anon):      12044 kB
Inactive(anon):   480364 kB
Active(file):      16248 kB
Inactive(file):   234592 kB
Unevictable:           0 kB
Mlocked:               0 kB
SwapTotal:       5119992 kB
SwapFree:        4829652 kB
Dirty:                 0 kB
Writeback:             0 kB
AnonPages:        422284 kB
Mapped:            20444 kB
Slab:              56960 kB
SReclaimable:      25944 kB
SUnreclaim:        31016 kB
PageTables:        15456 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    13350796 kB
Committed_AS:     930184 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      368876 kB
VmallocChunk:   34359339227 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:        7680 kB
DirectMap2M:    16760832 kB

Thank you very much.
Best regards

General Questions and Answers / ATKError
« on: July 7, 2010, 08:26 »
Dear users and Developers

I have a question. Maximum for how many atoms for two probe system atk can work ?

I am asking because I faced an error which I think is due to memory allocation .
I am having this error:

 /opt/mpich2/bin/mpiexec -n 8 /opt/vnl-2008.10.0/atk/bin/atk > OUT1.out
Traceback (most recent call last):
  File "<string>", line 1139, in ?
ATKError: St9bad_alloc

I should mention the job gets over after one day ( by getting the error ) , and the number of atoms are 749.

Could any one give any suggestion?
Thank you.
Best regards

Dear Nordland

The version is "ATK 2008.10.0"

Thank you

Dear users and Developers

The problem was with tcl/tk. I have installed tk on system and that error is over now.
But I get another one.

File "", line 14, in ?
    trans_coeff = calculateTransmissionCoefficients(scf,energy,K)
KeyError: 'Electrode'
Traceback (most recent call last):
  File "<string>", line 14, in ?
KeyError: 'Electrode'
Traceback (most recent call last):
  File "<string>", line 14, in ?
KeyError: 'Electrode'
Traceback (most recent call last):
  File "<string>", line 14, in ?
KeyError: 'Electrode'

what can be the problem?
Thank you in advance

Best regards

Dear Anders Blom

Thank you very much. That is of course really good suggestion.

Best regards

Dear users and Developers

I am trying to do calculation according to the tutorial which is offered by Quantum wise site.
The tutorial is "Tutorial_GoldMonowire.pdf". Everything goes well till when I want to plot "the k-point dependent transmission coefficients at the Fermi level"  and I get the following error :

Traceback (most recent call last):
  File "<string>", line 19, in ?
  File "./site-packages/", line 1, in ?
  File "./site-packages/matplotlib/", line 204, in ?
  File "./site-packages/matplotlib/backends/", line 55, in ?
  File "./site-packages/matplotlib/backends/", line 24, in pylab_setup
  File "./site-packages/matplotlib/backends/", line 7, in ?
  File "./lib-tk/", line 38, in ?
ImportError: cannot open shared object file: No such file or directory

Can anyone let me know please, what is the problem ?

Best regards
Akbar Jahangiri

Dear Anders Blom

Yes ... that is right, I sometimes forget that is a program.
I have a question. I felt that I should learn Python to be able and really understand working working with VNL. Is that right ?

Thank you very much

Best regards
Akbar  :)

Dear Anders Blom

Regarding our previous discussion. I have added the line which you suggest to my script, but what I get is :

The same time is written for starting and ending job.
To be more clear I have these lines in my script :

# Generate time stamp
if processIsMaster():
    import platform, time
    print '#',time.ctime()
    print '#',platform.node(),platform.platform()+'\n'
    print "Job finished at", time.asctime()

but waht I get is >>>


# Thu Jul  1 14:49:27 2010
# Linux-

Job finished at Thu Jul  1 14:49:27 2010

this means the starting time and ending are the same !!

How can I write it in a way to have right answer?

Thank you very much
Best regards


:)Thank you ver much

 Dear Anders Blom

unfortunately I could not find the time which job was finish at in the "nc" file, since it is very huge file full of numbers.
the only line which had some information regarding time is the following....

// global attributes:
                :Generator = "2008.10.0" ;
                :ReleaseVersionString = "ATK 2008.10.0 Linux-x86_64 build 14677 2008-11-27" ;
                :TimeStamp = "Sat Jun 19 15:15:43 2010" ;

and I think that is the starting time (which is even written at the beginning of OUT3 file).

Am I right?

I should mention right now I am doing the tutorial which is placed in the QuantumWise site (Gold Nano Junction) and I can compare the result with what is given in the Tutorial itself. But if I want to run any job other than Tutorials how to know the job is over?  that is one of the reasons that i would like to have a line at the end of file that Atk tells me the job is over.

Thank you very much.

Best regards
Akbar jahangiri

Dear Anders Blom

Thank you very much fro your prompt answer.

by the way can you let me know how can I see the steps in "nc" file, since i think (if I am right ) it is not a file like text or in a format readable by human?

Best regards
Akbar Jahangiri

General Questions and Answers / When a job gets finish?
« on: July 1, 2010, 10:44 »
Dear users and developers

I don't know how can I can get information about the job which I ran before.
I would like to know when my job has been terminated!

to be more clear suppose I ran a job like :

>>>>/opt/mpich2/bin/mpiexec -n 4 /opt/vnl-2008.10.0/atk/bin/atk > OUT3

I believe I should have all information like the starting Time and ending time in my "OUT3" file,
But what I get in the last line of this file is just


# sc 47 : q =  648.83112 e  Etot = -12235.98635 Ry  dRho =  9.1524E-05  dEtot =  4.2094E-05 Ry
# sc 48 : q =  648.83122 e  Etot = -12235.98635 Ry  dRho =  1.0115E-04  dEtot =  2.5569E-06 Ry

(I should mention I have changed the "verbosity" to one"

But what I need is CPU time and in general at least I would like to know when my job got over.

Thank you very much in advance

Best regards
Akbar Jahangiri

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