[Smeagol-discuss] segmentation fault
Serhan Yamacli
syamacli at gmail.com
Fri Mar 27 12:35:28 GMT 2009
Hi Salvador and Ivan,
To Salvador: I tested the memory as you said but, still there seems a lot of
free memory and swap space. I attached the memfile. As it seems the maximum
RAM usage is 524 M while the total is 884 M. :(
To Ivan: Thank you also, but I made the changes you suggested. It still
gives the segmentation fault error. The new input file is attached also.
Thanks again for your help.
Cheers,
Serhan
2009/3/26 Ivan Rungger <runggeri at tcd.ie>
> Hello,
>
> I also think that you are running out of memory as Salvador says. One
> reason for that is that you use a large number of energy points. Try using
> NEnergReal 0
> NEnergImCircle 16
> NEnergImLine 16
> NPoles 16
> VInitial 0.0 eV
> VFinal 0.0 eV
> NIVPoints 0
>
> You don't need more imaginary energy points for T=300K. A note: just
> make sure that NEnergImCircle+NEnergImLine+2* NPoles is a multiple of
> the number or processors you are running on (although from your
> debugging message it seems you are running in serial). And another
> thing: I would only do the zero bias calculation, because applying a
> bias to a nanotube without contacting it to some metal surface might not
> be physically meaningful (although I have to say that I did not check in
> detail your setup, therefore maybe it might also be OK to apply a bias).
>
> Cheers,
>
> Ivan
>
>
>
> Barraza-lopez, Salvador wrote:
> >
> > Forgot to mention... you can use the output from your debug run to see
> > what's going on... What's happening on line 570 at negf.F?
> >
> > Have you tried if SZ will run?
> >
> >
> >
> > Best regards,
> >
> > -Salvador.
> >
> >
> > ----- Original Message -----
> > From: "Serhan Yamacli" <syamacli at gmail.com>
> > To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu>,
> > smeagol-discuss at lists.tchpc.tcd.ie
> > Sent: Sunday, March 22, 2009 4:44:43 AM GMT -05:00 US/Canada Eastern
> > Subject: Re: [Smeagol-discuss] segmentation fault
> >
> > Hi,
> >
> > I compiled with these options. And then googled for the error and
> > found that it's a memory error as you said. I increased the stack size
> > by the command ulimit -s unlimited. The program now does not give
> > segmentation error but instead gives the "insufficient virtual memory"
> > error. I've also attached the screenshot of the system resources at
> > their maximum when running Smeagol. Now the problem is that Smeagol
> > uses 165MB of RAM at maximum (just before it gives error) but I have
> > 2GB of RAM with 4GB of swap. It can not gather the remaining RAM which
> > is more then 1GB and gives the following error:
> >
> >
> ----------------------------------------------------------------------------------------------------------------
> > * Maximum dynamic memory allocated = 174 MB
> > gensvd: Leads decimation
> > gensvd: Dim of H1 and S1 : 468
> > gensvd: Rank of H1: 49
> > gensvd: Rank of (H1,S1): 154
> > gensvd: Decimated states: 265
> > gensvd: Decimation from the left
> > gensvd: Leads decimation
> > gensvd: Dim of H1 and S1 : 468
> > gensvd: Rank of H1: 49
> > gensvd: Rank of (H1,S1): 154
> > gensvd: Decimated states: 265
> > gensvd: Decimation from the left
> > forrtl: severe (41): insufficient virtual memory
> > Image PC Routine Line
> > Source
> > smeagol 0831F29D Unknown Unknown Unknown
> > smeagol 0831E815 Unknown Unknown Unknown
> > smeagol 082DB838 Unknown Unknown Unknown
> > smeagol 0829BB43 Unknown Unknown Unknown
> > smeagol 082C4380 Unknown Unknown Unknown
> > smeagol 081CEDAC negf_ 570 negf.F
> > smeagol 082679E3 emtg_ 280 emtg.F
> > smeagol 0826DE62 emtrans_ 208 emtrans.F
> > smeagol 08194A98 MAIN__ 1698 siesta.F
> > smeagol 0804B4D1 Unknown Unknown Unknown
> > libc.so.6 40B5A685 Unknown Unknown Unknown
> > smeagol 0804B3E1 Unknown Unknown Unknown
> >
> >
> ---------------------------------------------------------------------------------------------------------------------
> >
> > Thanks again.
> > Cheers
> > Serhan
> >
> >
> > 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>
> >
> > When you compile it, use -O0 -g -traceback. I guess you are using
> > gcc?
> >
> >
> >
> > My gut feeling is you don't have sufficient memory to run it...
> > The important number here is
> >
> > initatomlists: Number of atoms, orbitals, and projectors: 60
> > 540 960
> > the number of orbitals. You say it decreased when you changed
> > your basis size. The 540 is 1s, 3p and 5d per 60 atoms (9*60=540).
> > It went down from 13*60= 780 that you had before... In any case,
> > try running it in debug mode and use top at the same time.
> >
> >
> >
> > as an additional test, try SZ for your basis, that'll give you 4
> > orbitals per atom, matrices of size 240x240. If it crashes, try
> > compiling in debug mode.
> >
> >
> >
> > Also, investigate in google what segmentation fault means. I do
> > believe is a memory related issue.
> >
> >
> >
> > Best,
> >
> > -Salva.
> >
> >
> >
> >
> > ----- Original Message -----
> > From: "Serhan Yamacli" <syamacli at gmail.com
> > <mailto:syamacli at gmail.com>>
> > To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>
> > Sent: Saturday, March 21, 2009 1:48:02 PM GMT -05:00 US/Canada
> Eastern
> > Subject: Re: [Smeagol-discuss] segmentation fault
> >
> > I'm using Smeagol at a single machine in serial mode. The CPU is
> > 2.26GHz and memory available is 2GB. How can I run it in debug mode?
> >
> > Cheers
> > Serhan
> >
> > 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>
> >
> > can you run it in debug mode? can you share the output? how
> > much memory do you have available per processor?
> >
> >
> >
> > Best,
> >
> > -Salvador.
> >
> >
> >
> >
> > ----- Original Message -----
> > From: "Serhan Yamacli" <syamacli at gmail.com
> > <mailto:syamacli at gmail.com>>
> > To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>,
> > smeagol-discuss at lists.tchpc.tcd.ie
> > <mailto:smeagol-discuss at lists.tchpc.tcd.ie>
> > Sent: Saturday, March 21, 2009 11:59:38 AM GMT -05:00
> > US/Canada Eastern
> > Subject: Re: [Smeagol-discuss] segmentation fault
> >
> > Hi Salvador,
> >
> > I looked at the system resources as you said. Smeagol
> > executable takes 26% of memory at maximum, then it gives the
> > segmentation fault error.
> >
> > Best regards,
> > Serhan
> >
> > 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>
> >
> >
> >
> > Hi Serhan,
> >
> > Can you check the dynamic memory in your run? I believe
> > the problem is related to this but I may be wrong.
> >
> >
> >
> > you can log in to the running node, type top and get an
> > idea of the total memory as the program goes.
> >
> >
> >
> > Best regards,
> >
> > -Salvador.
> >
> >
> > ----- Original Message -----
> > From: "Serhan Yamacli" <syamacli at gmail.com
> > <mailto:syamacli at gmail.com>>
> > To: "Salvador Barraza-lopez" <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>
> > Sent: Saturday, March 21, 2009 11:19:03 AM GMT -05:00
> > US/Canada Eastern
> > Subject: Re: [Smeagol-discuss] segmentation fault
> >
> > Hi Salvador,
> >
> > Thanks for the answer but, Smeagol again gives the error
> > when changed basis to SZP:
> >
> >
> -----------------------------------------------------------------------------------------
> > initatomlists: Number of atoms, orbitals, and
> > projectors: 60 540 960
> >
> > siesta: System type = chain
> >
> > * Maximum dynamic memory allocated = 1 MB
> >
> > siesta: ===============================
> > SMEAGOL Bias step = 0, V = 0.000 Ry
> > Begin CG move = 0
> > ===============================
> >
> > InitMesh: MESH = 180 x 180 x 108 = 3499200
> > InitMesh: Mesh cutoff (required, used) = 200.000
> > 212.441 Ry
> >
> > * Maximum dynamic memory allocated = 279 MB
> > Segmentation fault
> >
> >
> -------------------------------------------------------------------------------------
> >
> > I again attached the modidied input fdf.
> >
> > Cheers,
> > Serhan
> > 2009/3/21 Barraza-lopez, Salvador <sbl3 at mail.gatech.edu
> > <mailto:sbl3 at mail.gatech.edu>>
> >
> > Hi Serhan, how about reducing the basis size to SZP?
> >
> >
> >
> > Best regards,
> >
> > -Salvador.
> >
> >
> > ----- Original Message -----
> > From: "Serhan Yamacli" <syamacli at gmail.com
> > <mailto:syamacli at gmail.com>>
> > To: smeagol-discuss at lists.tchpc.tcd.ie
> > <mailto:smeagol-discuss at lists.tchpc.tcd.ie>
> > Sent: Saturday, March 21, 2009 10:34:06 AM GMT -05:00
> > US/Canada Eastern
> > Subject: [Smeagol-discuss] segmentation fault
> >
> > Hi,
> >
> > I'm trying to simulate a (3,3) intrinsic carbon
> > nanotube. I performed the leads calculation. But when
> > I try to simulate the transport, Smeagol says:
> >
> >
> --------------------------------------------------------------------------------------------------------------
> > initatomlists: Number of atoms, orbitals, and
> > projectors: 60 780 960
> >
> > siesta: System type = chain
> >
> > * Maximum dynamic memory allocated = 1 MB
> >
> > siesta: ===============================
> > SMEAGOL Bias step = 0, V = 0.000 Ry
> > Begin CG move = 0
> > ===============================
> >
> > InitMesh: MESH = 240 x 240 x 150 = 8640000
> > InitMesh: Mesh cutoff (required, used) = 400.000
> > 409.800 Ry
> >
> > * Maximum dynamic memory allocated = 727 MB
> > Segmentation fault
> >
> >
> -------------------------------------------------------------------------------------------------------
> >
> > My fdf file is atteched. How can I solve this problem?
> > I'm using Mandriva 2008 with ifort.
> >
> > Cheers
> > Serhan
> >
> > _______________________________________________
> > Smeagol-discuss mailing list
> > Smeagol-discuss at lists.tchpc.tcd.ie
> > <mailto:Smeagol-discuss at lists.tchpc.tcd.ie>
> > http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Smeagol-discuss mailing list
> > Smeagol-discuss at lists.tchpc.tcd.ie
> > http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
>
>
> --
> =================================================
> Ivan Rungger,
>
> School of Physics and CRANN,
> Trinity College Dublin,
> Dublin 2, IRELAND
> Phone: +353-1-8968454
> Email: runggeri at tcd.ie
> =================================================
>
>
>
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